Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
A
- A - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer.Base
- A - Enum constant in enum class org.broadinstitute.hellbender.utils.BaseUtils.Base
- A - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- A - Enum constant in enum class picard.analysis.artifacts.Transition.Base
- A - Enum constant in enum class picard.illumina.parser.IntensityChannel
- A_FOLLOWED_BY_INSERTION_BASE - Static variable in class org.broadinstitute.hellbender.utils.pileup.PileupElement
- aa - Enum constant in enum class picard.fingerprint.DiploidHaplotype
- Aa - Enum constant in enum class picard.fingerprint.DiploidHaplotype
- AA - Enum constant in enum class picard.arrays.illumina.IlluminaGenotype
- AA - Enum constant in enum class picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
- AA - Enum constant in enum class picard.fingerprint.DiploidGenotype
- AA - Enum constant in enum class picard.fingerprint.DiploidHaplotype
- AA_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
- AB - Enum constant in enum class picard.arrays.illumina.IlluminaGenotype
- AB - Enum constant in enum class picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
- AB_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
- AB_FILTER - Static variable in class picard.vcf.filter.AlleleBalanceFilter
-
The filter string used for sites that fail the allele balance filter.
- AbsoluteCoordinates - Class in org.broadinstitute.hellbender.utils.reference
-
Class to translate back and forth from absolute
long-typedbase positions to relative ones (the usual contig, position pairs). - AbsoluteCoordinates.Relative - Class in org.broadinstitute.hellbender.utils.reference
- AbstractAlignmentMerger - Class in org.broadinstitute.hellbender.utils.read.mergealignment
-
Abstract class that coordinates the general task of taking in a set of alignment information, possibly in SAM format, possibly in other formats, and merging that with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
- AbstractAlignmentMerger - Class in picard.sam
-
Abstract class that coordinates the general task of taking in a set of alignment information, possibly in SAM format, possibly in other formats, and merging that with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
- AbstractAlignmentMerger(File, File, File, boolean, boolean, boolean, SAMProgramRecord, List<String>, List<String>, Integer, Integer, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean) - Constructor for class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
-
Constructor
- AbstractAlignmentMerger(File, File, File, boolean, boolean, boolean, SAMProgramRecord, List<String>, List<String>, Integer, Integer, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean) - Constructor for class picard.sam.AbstractAlignmentMerger
-
constructor with a default setting for unmappingReadsStrategy.
- AbstractAlignmentMerger(File, File, File, boolean, boolean, boolean, SAMProgramRecord, List<String>, List<String>, Integer, Integer, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean, AbstractAlignmentMerger.UnmappingReadStrategy) - Constructor for class picard.sam.AbstractAlignmentMerger
-
Constructor
- AbstractAlignmentMerger.UnmappingReadStrategy - Enum Class in picard.sam
- AbstractBCICodec<F extends htsjdk.tribble.Feature> - Class in org.broadinstitute.hellbender.utils.codecs
- AbstractBCICodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.AbstractBCICodec
- AbstractConcordanceWalker - Class in org.broadinstitute.hellbender.engine
-
Base class for concordance walkers, which process one variant at a time from one or more sources of variants, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features.
- AbstractConcordanceWalker() - Constructor for class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- AbstractConcordanceWalker.TruthVersusEval - Class in org.broadinstitute.hellbender.engine
-
store a truth vc in case of a false negative, an eval vc in case of a false positive, or a concordance pair of truth and eval in case of a true positive.
- AbstractEvidenceSortMerger<F extends SVFeature> - Class in org.broadinstitute.hellbender.tools.sv
-
A FeatureSink that buffers and resolves (by merging, or by checking for redundancy) features that occur on the same interval.
- AbstractEvidenceSortMerger(SAMSequenceDictionary, FeatureSink<F>, Comparator<? super F>) - Constructor for class org.broadinstitute.hellbender.tools.sv.AbstractEvidenceSortMerger
- AbstractGtfCodec - Class in org.broadinstitute.hellbender.utils.codecs.gtf
- AbstractGtfCodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec
- AbstractIlluminaPositionFileReader - Class in picard.illumina.parser.readers
-
The position files of Illumina are nearly the same form: Pos files consist of text based tabbed x-y coordinate float pairs, locs files are binary x-y float pairs, clocs are compressed binary x-y float pairs.
- AbstractIlluminaPositionFileReader(File) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
- AbstractIlluminaPositionFileReader(File, int, int) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
Use this ctor if lane and tile are not discernible from file name.
- AbstractIlluminaPositionFileReader.PositionInfo - Class in picard.illumina.parser.readers
- AbstractInputParser - Class in picard.util
-
Class for parsing text files where each line consists of fields separated by whitespace.
- AbstractInputParser() - Constructor for class picard.util.AbstractInputParser
- AbstractLocatableCollection<METADATA extends LocatableMetadata,
RECORD extends htsjdk.samtools.util.Locatable> - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections -
Represents a sequence dictionary, an immutable, coordinate-sorted (with no overlaps allowed) collection of records that extend
Locatable(although contigs are assumed to be non-null when writing to file), a set of mandatory column headers given by aTableColumnCollection, and lambdas for reading and writing records. - AbstractMarkDuplicatesCommandLineProgram - Class in picard.sam.markduplicates.util
-
Abstract class that holds parameters and methods common to classes that perform duplicate detection and/or marking within SAM/BAM/CRAM files.
- AbstractMarkDuplicatesCommandLineProgram() - Constructor for class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator - Class in picard.sam.markduplicates.util
-
Little class used to package up a header and an iterable/iterator.
- AbstractOpticalDuplicateFinderCommandLineProgram - Class in picard.sam.markduplicates.util
-
Abstract class that holds parameters and methods common to classes that optical duplicate detection.
- AbstractOpticalDuplicateFinderCommandLineProgram() - Constructor for class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- AbstractReadThreadingGraph - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
-
Read threading graph class intended to contain duplicated code between
ReadThreadingGraphandJunctionTreeLinkedDeBruijnGraph. - AbstractReadThreadingGraph(int, boolean, byte, int, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Create a new ReadThreadingAssembler using kmerSize for matching
- AbstractReadThreadingGraph.MyEdgeFactory - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
-
Edge factory that encapsulates the numPruningSamples assembly parameter
- AbstractReadThreadingGraph.TraversalDirection - Enum Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
- AbstractRecordCollection<METADATA extends Metadata,
RECORD> - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections -
Represents
AbstractRecordCollection(which can be represented as aSAMFileHeader), an immutable collection of records, a set of mandatory column headers given by aTableColumnCollection, and lambdas for reading and writing records. - AbstractSampleLocatableCollection<RECORD extends htsjdk.samtools.util.Locatable> - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
Represents a sample name, a sequence dictionary, an immutable, coordinate-sorted (with no overlaps allowed) collection of records that extend
Locatable(although contigs are assumed to be non-null when writing to file), a set of mandatory column headers given by aTableColumnCollection, and lambdas for reading and writing records. - AbstractSampleRecordCollection<RECORD> - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
Represents a sample name, an immutable collection of records, a set of mandatory column headers given by a
TableColumnCollection, and lambdas for reading and writing records. - AbstractWgsMetricsCollector<T extends htsjdk.samtools.util.AbstractRecordAndOffset> - Class in picard.analysis
-
Class for collecting data on reference coverage, base qualities and excluded bases from one AbstractLocusInfo object for CollectWgsMetrics.
- AC - Enum constant in enum class picard.fingerprint.DiploidGenotype
- AC_ADJUSTED_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- accept(int, int) - Method in interface org.broadinstitute.hellbender.utils.functional.IntBiConsumer
- accept(int, int, int) - Method in interface org.broadinstitute.hellbender.utils.SVInterval.SVIntervalConstructorArgsValidator
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectAlignmentSummaryMetrics
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectBaseDistributionByCycle
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectGcBiasMetrics
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectInsertSizeMetrics
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectQualityYieldMetrics
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectRnaSeqMetrics
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.MeanQualityByCycle
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.QualityScoreDistribution
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.SinglePassSamProgram
-
Should be implemented by subclasses to accept SAMRecords one at a time.
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
- acceptRecord(ARGTYPE) - Method in interface org.broadinstitute.hellbender.metrics.PerUnitMetricCollector
-
Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
- acceptRecord(ARGTYPE) - Method in interface picard.metrics.PerUnitMetricCollector
-
Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
- acceptRecord(SAMRecord) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
- acceptRecord(SAMRecord) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Adds information about an individual SAMRecord to the statistics.
- acceptRecord(SAMRecord, ReferenceSequence) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelCollector
-
Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this record
- acceptRecord(SAMRecord, ReferenceSequence) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector
-
Construct an argument of ARGTYPE using the given SAMRecord and ReferenceSequence, then pass this value to all collectors that should include this record
- acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.AlignmentSummaryMetricsCollector
- acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
- acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
- acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.metrics.MultiLevelCollector
-
Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this record
- acceptRecord(InsertSizeMetricsCollectorArgs) - Method in class org.broadinstitute.hellbender.metrics.PerUnitInsertSizeMetricsCollector
- acceptRecord(PerUnitExampleMultiMetricsCollectorArgs) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.PerUnitExampleMultiMetricsCollector
- acceptRecord(InsertSizeCollectorArgs) - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
- acceptRecord(GcBiasCollectorArgs) - Method in class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
- acceptRecord(SAMRecordAndReference) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
- acceptRecord(SAMRecordAndReference) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- ACCEPTS_ALL - Static variable in interface org.broadinstitute.hellbender.utils.SVInterval.SVIntervalConstructorArgsValidator
- accessibleTruthSites - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- accessionToTaxId - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTaxonomyDatabase
- accumulate(VariantContext) - Method in class picard.vcf.CallingMetricAccumulator
-
Incorporates the provided variant's data into the metric analysis.
- accumulate(VariantContext) - Method in class picard.vcf.GvcfMetricAccumulator
- accumulate(VariantContext) - Method in interface picard.vcf.processor.VariantProcessor.Accumulator
- accumulateData(VariantContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
-
record data from a potential variant in a non-final pass of
FilterMutectCalls - accumulateDataForLearning(VariantContext, ErrorProbabilities, Mutect2FilteringEngine) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteredHaplotypeFilter
- accumulateDataForLearning(VariantContext, ErrorProbabilities, Mutect2FilteringEngine) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2Filter
- accumulateDataForLearning(VariantContext, ErrorProbabilities, Mutect2FilteringEngine) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter
- AccumulateQualityYieldMetrics - Class in picard.util
-
Combines multiple Picard QualityYieldMetrics files into a single file.
- AccumulateQualityYieldMetrics() - Constructor for class picard.util.AccumulateQualityYieldMetrics
- AccumulateVariantCallingMetrics - Class in picard.vcf
-
Combines multiple Variant Calling Metrics files into a single file.
- AccumulateVariantCallingMetrics() - Constructor for class picard.vcf.AccumulateVariantCallingMetrics
- ACCUMULATION_LEVEL - Variable in class picard.analysis.GcBiasDetailMetrics
- ACCUMULATION_LEVEL - Variable in class picard.analysis.GcBiasSummaryMetrics
- accumulationLevels - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MetricAccumulationLevelArgumentCollection
- accumulators() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
-
Returns the
VariantProcessor.Accumulators associated with this executor. - accumulators() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
- ACCURACY - Variable in class picard.sam.DownsampleSam
- ACGT_CODES - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- ACTION - Variable in class picard.util.IntervalListTools
- activateWriting() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager
-
Activates output writing for the Overhang Fixing Manager.
- ACTIVE_CLASS_PADDING_HYBRID_MODE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
- activeProbThreshold - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- activeProbThreshold - Variable in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
- ActivityProfile - Class in org.broadinstitute.hellbender.utils.activityprofile
-
Class holding information about per-base activity scores for assembly region traversal
- ActivityProfile(int, double, SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
-
Create a empty ActivityProfile, restricting output to profiles overlapping intervals, if not null
- ActivityProfileState - Class in org.broadinstitute.hellbender.utils.activityprofile
-
Captures the probability that a specific locus in the genome represents an "active" site containing real variation.
- ActivityProfileState(SimpleInterval, double) - Constructor for class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState
-
Create a new ActivityProfileState at loc with probability of being active of activeProb
- ActivityProfileState(SimpleInterval, double, ActivityProfileState.Type, Number) - Constructor for class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState
-
Create a new ActivityProfileState at loc with probability of being active of activeProb that maintains some information about the result state and value The only state value in use is HIGH_QUALITY_SOFT_CLIPS, and here the value is interpreted as the number of bp affected by the soft clips.
- ActivityProfileState.Type - Enum Class in org.broadinstitute.hellbender.utils.activityprofile
-
The type of the value returned by
ActivityProfileState.getResultValue() - ActivityProfileStateIterator - Class in org.broadinstitute.hellbender.engine
-
Given a
MultiIntervalShardofGATKRead, iterates over each locus within that shard, and calculates theActivityProfileStatethere, using the providedAssemblyRegionEvaluatorto determine if each site is active. - ActivityProfileStateIterator(MultiIntervalShard<GATKRead>, SAMFileHeader, ReferenceDataSource, FeatureManager, AssemblyRegionEvaluator) - Constructor for class org.broadinstitute.hellbender.engine.ActivityProfileStateIterator
-
Constructs an AssemblyRegionIterator over a provided read shard
- ActivityProfileStateRange - Class in org.broadinstitute.hellbender.utils.activityprofile
-
An efficient way of representing a set of
ActivityProfileStates in an interval; used by Spark. - ActivityProfileStateRange(MultiIntervalShard<?>, Iterator<ActivityProfileState>) - Constructor for class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileStateRange
- ADAM - Enum constant in enum class org.broadinstitute.hellbender.utils.read.ReadsWriteFormat
-
Write reads to a sharded set of ADAM-formatted Parquet files
- ADAMAX_BETA_1 - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- ADAMAX_BETA_1_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- ADAMAX_BETA_2 - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- ADAMAX_BETA_2_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- ADAPTER_SEQUENCE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
- ADAPTER_TRUNCATION_LENGTH - Variable in class picard.illumina.MarkIlluminaAdapters
- AdapterMarker - Class in picard.util
-
Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords.
- AdapterMarker(int, AdapterPair...) - Constructor for class picard.util.AdapterMarker
- AdapterMarker(AdapterPair...) - Constructor for class picard.util.AdapterMarker
-
Truncates adapters to DEFAULT_ADAPTER_LENGTH
- AdapterPair - Interface in org.broadinstitute.hellbender.utils.illumina
- AdapterPair - Interface in picard.util
- ADAPTERS - Variable in class picard.illumina.MarkIlluminaAdapters
- ADAPTERS_TO_CHECK - Variable in class picard.illumina.IlluminaBasecallsToFastq
- ADAPTERS_TO_CHECK - Variable in class picard.illumina.IlluminaBasecallsToSam
- adapterSequence - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord) - Method in class picard.util.AdapterMarker
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, int, double) - Method in class picard.util.AdapterMarker
-
Overrides defaults for minMatchBases and maxErrorRate
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, int, double, AdapterPair...) - Static method in class picard.util.ClippingUtility
-
Invokes adapterTrimIlluminaRead with explicit parameters for a pair of reads.
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair) - Static method in class picard.util.ClippingUtility
-
Deprecated.Use the varargs version. This no longer returns a warning string..
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair...) - Static method in class picard.util.ClippingUtility
-
Invokes adapterTrimIlluminaPairedReads with default less stringent parameters for a pair of reads.
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair, int, double) - Static method in class picard.util.ClippingUtility
-
Deprecated.Use the varargs version. This no longer returns a warning string..
- adapterTrimIlluminaSingleRead(SAMRecord) - Method in class picard.util.AdapterMarker
- adapterTrimIlluminaSingleRead(SAMRecord, int, double) - Method in class picard.util.AdapterMarker
-
Overrides defaults for minMatchBases and maxErrorRate
- adapterTrimIlluminaSingleRead(SAMRecord, int, double, AdapterPair...) - Static method in class picard.util.ClippingUtility
-
Invokes adapterTrimIlluminRead with explicit matching thresholds for a single read.
- adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair) - Static method in class picard.util.ClippingUtility
-
Deprecated.Use the varargs version. This no longer returns a warning string..
- adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair...) - Static method in class picard.util.ClippingUtility
-
Invokes adapterTrimIlluminRead with default parameters for a single read.
- adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair, int, double) - Static method in class picard.util.ClippingUtility
-
Deprecated.Use the varargs version. This no longer returns a warning string..
- AdapterTrimTransformer - Class in org.broadinstitute.hellbender.transformers
-
Trims (hard clips) adapter sequences from read ends.
- AdapterTrimTransformer(int, int, List<String>) - Constructor for class org.broadinstitute.hellbender.transformers.AdapterTrimTransformer
- AdapterUtility - Class in picard.analysis
-
A utility class for matching reads to adapters.
- AdapterUtility(List<String>) - Constructor for class picard.analysis.AdapterUtility
- ADAPTIVE_PRUNING_INITIAL_ERROR_RATE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- ADAPTIVE_PRUNING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerReadThreadingAssemblerArgumentCollection
- AdaptiveChainPruner<V extends BaseVertex,
E extends BaseEdge> - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs - AdaptiveChainPruner(double, double, double, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.AdaptiveChainPruner
- AdaptiveMetropolisSampler - Class in org.broadinstitute.hellbender.utils.mcmc
-
Metropolis MCMC sampler using an adaptive step size that increases / decreases in order to decrease / increase acceptance rate to some desired value.
- AdaptiveMetropolisSampler(double, double, double, double) - Constructor for class org.broadinstitute.hellbender.utils.mcmc.AdaptiveMetropolisSampler
- AdaptiveMetropolisSampler(double, double, double, double, double, double) - Constructor for class org.broadinstitute.hellbender.utils.mcmc.AdaptiveMetropolisSampler
- add(byte) - Method in class org.broadinstitute.hellbender.utils.Nucleotide.Counter
-
Increases the nucleotide that corresponds to the input base own count by 1.
- add(byte[], byte[]) - Method in class org.broadinstitute.hellbender.tools.validation.CompareMatrix
- add(char) - Method in class org.broadinstitute.hellbender.utils.Nucleotide.Counter
- add(double) - Method in class org.broadinstitute.hellbender.utils.MathUtils.RunningAverage
- add(int, byte) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NearbyKmerErrorCorrector.CorrectionSet
-
Add a base to this correction set at a particular offset, measured from the start of the read
- add(int, int, Genotype) - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- add(int, Genotype) - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- add(int, LocalAssembler.Contig) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigListRC
- add(long) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- add(long) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter
- add(long) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- add(long, int) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- add(E) - Method in class org.broadinstitute.hellbender.utils.collections.IndexedSet
-
Adds a new element to the set.
- add(CigarElement) - Method in class org.broadinstitute.hellbender.utils.read.CigarBuilder
- add(Locatable, String, Object) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OffRampBase
- add(Locatable, String, AssemblyResultSet, Optional<AssemblyRegion>, Optional<AssemblyRegion>, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.AssemblerOffRamp
- add(Locatable, String, AlleleLikelihoods<GATKRead, Haplotype>, AssemblyRegion, AssemblyRegion) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.PreFilterOffRamp
- add(Locatable, List<Map<Integer, AlleleLikelihoods<GATKRead, Allele>>>, List<VariantContext>, List<AssemblyResultSet>, List<SAMFileHeader>) - Method in class org.broadinstitute.hellbender.tools.walkers.variantrecalling.VariantRecallerResultWriter
- add(VariantContext) - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter
-
Add a VariantContext to this writer for emission Requires that the VC have exactly one genotype
- add(VariantContext) - Method in class org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFWriter
- add(VariantContext) - Method in class org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter
-
Adds variant to writer.
- add(VariantContext, List<List<Allele>>, List<VariantType>, List<TreeSet<String>>) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
-
Adds an element to the underlying
LabeledVariantAnnotationsData.datacollection. - add(Double) - Method in class org.broadinstitute.hellbender.utils.Histogram
-
Add a value to be stored in the histogram
- add(Double, int) - Method in class org.broadinstitute.hellbender.utils.Histogram
-
Add multiple copies of the same value into the histogram to be stored in the histogram
- add(String, List<Funcotation>) - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
-
Add the given funcotations to the given transcript ID.
- add(String, Funcotation) - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
-
Add the given funcotation to the given transcript ID.
- add(AnnotatedInterval) - Method in interface org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalWriter
-
Write one region to the file.
- add(AnnotatedInterval) - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.SimpleAnnotatedIntervalWriter
-
Write one region to the file.
- add(DragstrLocusCase) - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCases
-
Adds a case to the collection.
- add(LocalAssembler.Traversal) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.TraversalSet
- add(ReferenceSequenceTable.TableEntry) - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableRow
- add(PSPathogenTaxonScore) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- add(SVCallRecord) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine
-
Adds and clusters the given item.
- add(SVCallRecord, boolean) - Method in class org.broadinstitute.hellbender.tools.sv.concordance.ClosestSVFinder
-
Adds and clusters a new variant.
- add(CompareMatrix) - Method in class org.broadinstitute.hellbender.tools.validation.CompareMatrix
- add(BaseEdge) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge
-
Add edge to this edge, updating isRef and multiplicity as appropriate isRef is simply the or of this and edge multiplicity is the sum
- add(ActivityProfileState) - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
-
Add the next ActivityProfileState to this profile.
- add(CompressedDataList<T>) - Method in class org.broadinstitute.hellbender.utils.CompressedDataList
- add(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
Adds a GenomeLoc to the collection, inserting at the correct sorted position into the set.
- add(GenomeLoc, boolean) - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
Adds a GenomeLoc to the collection, inserting at the correct sorted position into the set.
- add(Haplotype) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Adds a haplotype to the result set without indicating a generating assembly result.
- add(Haplotype, AssemblyResult) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Adds simultaneously a haplotype and the generating assembly-result.
- add(Histogram) - Method in class org.broadinstitute.hellbender.utils.Histogram
-
Combine two histogram objects that have the same bin by adding the values to each bin
- add(Nucleotide) - Method in class org.broadinstitute.hellbender.utils.Nucleotide.Counter
-
Increases by 1 the count for a nucleotide.
- add(GATKRead) - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Add read to this region Read must have alignment start >= than the last read currently in this active region.
- add(GATKRead) - Method in class org.broadinstitute.hellbender.tools.FlagStat.FlagStatus
- add(GATKRead) - Method in class org.broadinstitute.hellbender.tools.walkers.qc.ReadPair
- add(GATKRead) - Method in class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMDestination
-
Write a read to the output specified by this destination.
- add(GATKRead) - Method in class org.broadinstitute.hellbender.utils.haplotype.SAMFileDestination
-
Write a read to the output file specified by this destination.
- add(HaplotypeProbabilities) - Method in class picard.fingerprint.Fingerprint
- add(PedFile.PedTrio) - Method in class picard.pedigree.PedFile
-
Adds a trio to the PedFile keyed by the individual id.
- add(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
Adds the end to this set, if not already added based on physical location
- add(ReadEndsForMateCigar, SamRecordTrackingBuffer, DuplicationMetrics) - Method in class picard.sam.markduplicates.util.MarkQueue
-
Add a record to the mark queue.
- add(T) - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
- add(T) - Method in class org.broadinstitute.hellbender.utils.CompressedDataList
- add(T, int) - Method in class org.broadinstitute.hellbender.utils.CompressedDataList
- ADD_MATE_CIGAR - Variable in class picard.sam.FixMateInformation
- ADD_MATE_CIGAR - Variable in class picard.sam.MergeBamAlignment
- ADD_OUTPUT_SAM_PROGRAM_RECORD - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- ADD_OUTPUT_VCF_COMMANDLINE - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- ADD_PG_TAG_TO_READS - Variable in class picard.sam.util.PGTagArgumentCollection
- ADD_TAG - Enum constant in enum class org.broadinstitute.hellbender.utils.baq.BAQ.QualityMode
- addAccession(String, long) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
- addAll(byte...) - Method in class org.broadinstitute.hellbender.utils.Nucleotide.Counter
-
Increase by one the count for a nucleotide for each occurrence of such in the input byte array base codes.
- addAll(char...) - Method in class org.broadinstitute.hellbender.utils.Nucleotide.Counter
-
Increase by one the count for a nucleotide for each occurrence of such in the input char array base codes.
- addAll(long[]) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- addAll(long[]) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter
- addAll(long[]) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- addAll(CharSequence) - Method in class org.broadinstitute.hellbender.utils.Nucleotide.Counter
-
Increase by one the count for a nucleotide for each occurrence of such in the input
CharSequence. - addAll(Iterable<CigarElement>) - Method in class org.broadinstitute.hellbender.utils.read.CigarBuilder
- addAll(Collection<? extends DragstrLocusCase>) - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCases
- addAll(Collection<Number>) - Method in class org.broadinstitute.hellbender.utils.MathUtils.RunningAverage
- addAll(Collection<GATKRead>) - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Add all readsToAdd to this region
- addAll(DragstrLocusCases) - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCases
- addAllAlignmentData(List<AlignmentAndReferenceContext>) - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Method for adding alignment data to the collection of AlignmentData associated with the ActiveRegion.
- addAlleleAndSiteFilters(VariantContext, List<Set<String>>, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.AlleleFilterUtils
-
Adds the new allele filters to the existing allele filters in the vc.
- addAlleleFilters(List<String>, List<String>) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.AlleleFilterUtils
-
Adds the new filters to the list of current filters.
- addAllLevelsToFile(MetricsFile<METRIC_TYPE, Histogram_KEY>) - Method in class picard.metrics.MultiLevelCollector
-
Add all metrics to the given file in the following MetricAccumulationLevel order ALL_READS, SAMPLE, LIBRARY, READ_GROUP.
- addAllLevelsToFile(MetricsFile<METRIC_TYPE, HISTOGRAM_KEY>) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelCollector
-
Add all metrics to the given file in the following MetricAccumulationLevel order ALL_READS, SAMPLE, LIBRARY, READ_GROUP.
- addAllLevelsToFile(MetricsFile<METRIC_TYPE, HISTOGRAM_KEY>) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector
-
Add all metrics to the given file in the following MetricAccumulationLevel order ALL_READS, SAMPLE, LIBRARY, READ_GROUP.
- addAntiSenseCount(double) - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation.Coverage
- addArgs(Object...) - Method in class org.broadinstitute.hellbender.utils.R.RScriptExecutor
-
Adds args to the end of the Rscript command line.
- addAssembledVariantsToEventMapOutput(AssemblyResultSet, Optional<PriorityQueue<VariantContext>>, int, Optional<VariantContextWriter>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- addBAQTag(GATKRead, byte[]) - Static method in class org.broadinstitute.hellbender.utils.baq.BAQ
- addBase(int) - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Adds a single point of depth at the desired offset into the coverage array.
- addBase(int, int) - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Adds some depth at the desired offset into the coverage array.
- addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in interface picard.sam.SamErrorMetric.BaseCalculator
-
The function by which new loci are "shown" to the calculator
- addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.BaseErrorAggregation
- addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.BaseErrorCalculator
-
the function by which new loci are "shown" to the calculator
- addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.IndelErrorCalculator
- addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
-
The function by which new loci are "shown" to the calculator
- addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.SimpleErrorCalculator
-
The function by which new loci are "shown" to the calculator
- addBaseQHistogram(MetricsFile<WgsMetrics, Integer>) - Method in class picard.analysis.AbstractWgsMetricsCollector
- addChild(int) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- addChromosomeCountsToHeader(Set<VCFHeaderLine>) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Add chromosome counts (AC, AN and AF) to the VCF header lines
- addColumn(String, String) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Add a column to the report and the format string used to display the data.
- addCombinedErrorProbabilites(List<Double>) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ThresholdCalculator
- AddCommentsToBam - Class in picard.sam
-
A tool to add comments to a BAM file header.
- AddCommentsToBam() - Constructor for class picard.sam.AddCommentsToBam
- addCovariate(int, int, int, int) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadCovariates
-
Update the keys for mismatch, insertion, and deletion for the current covariate at read offset NOTE: no checks are performed on the number of covariates, for performance reasons.
- addCoverageCounts(int, int, int[]) - Method in class picard.annotation.Gene.Transcript
- addCustomBindings(DocWorkUnit) - Method in class org.broadinstitute.hellbender.utils.help.GATKHelpDocWorkUnitHandler
-
Add any custom freemarker bindings discovered via custom javadoc tags.
- addCustomBindings(DocWorkUnit) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLWorkUnitHandler
-
Add any custom freemarker bindings discovered via custom javadoc tags.
- addCustomBindings(DocWorkUnit) - Method in class picard.util.help.PicardHelpDocWorkUnitHandler
-
Add any custom freemarker bindings discovered via custom javadoc tags.
- addData(ReferenceContext, VariantContext, Optional<List<VariantContext>>, AlleleLikelihoods<GATKRead, Allele>, AlleleLikelihoods<Fragment, Haplotype>, AlleleLikelihoods<Fragment, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect3DatasetEngine
- addData(ClipReads.ClippingData) - Method in class org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- addData(ClipReads.ClippingData) - Method in class org.broadinstitute.hellbender.tools.ClipReads.ReadClipperWithData
- addData(ClusterData, BarcodeData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- addData(ClusterData, PfData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- addData(ClusterData, PositionalData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- addDescendentScore(double) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- addDuplicateReadToMetrics(SAMRecord) - Method in class picard.sam.DuplicationMetrics
-
Adds duplicated read to the metrics
- addDuplicateReadToMetrics(SAMRecord) - Method in class picard.sam.FlowBasedDuplicationMetrics
- addEdge(Node, Node) - Method in class picard.util.GraphUtils.Graph
- addEdges(Supplier<E>, V, V...) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Convenience function to add multiple edges to the graph
- addEdges(V, V...) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Convenience function to add multiple edges to the graph
- addEntry(Locatable, String, byte[]) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OffRampBase
- addEntry(Locatable, String, Path) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OffRampBase
- addEvidence(Map<String, List<EVIDENCE>>, double) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Add more evidence to the collection.
- addExon(int, int) - Method in class picard.annotation.Gene.Transcript
- addExon(GencodeGtfExonFeature) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature
- addExpressions(Set<String>, List<FeatureInput<VariantContext>>, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
- addFeatureInputsAfterInitialization(String, String, Class<? extends Feature>, int) - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
A method to allow a user to inject
FeatureInputs after initialization that were not specified as command-line arguments. - addField(HtsgetRequestField) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- addFields(Collection<HtsgetRequestField>) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- addFirstOfPairOrFragment(SAMRecord) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
- addGenotypeData(ReferenceConfidenceResult, GenotypeBuilder) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
- addGenotypeData(ReferenceConfidenceResult, GenotypeBuilder) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticReferenceConfidenceModel
- addGivenAlleles(List<VariantContext>, int, SmithWatermanAligner, SWParameters, AssemblyResultSet) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- addHaplotype(HaplotypeBlock) - Method in class picard.fingerprint.HaplotypeMap
-
Adds a HaplotypeBlock to the map and updates all the relevant caches/indices.
- addHaplotypes(Locatable, String, List<Haplotype>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OffRampBase
- addHardClippedPileupReads(Collection<GATKRead>) - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
- addHomRefSite(VariantContext, Genotype) - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlockCombiner
-
Add hom-ref site from vc to this gVCF hom-ref state tracking, emitting any pending states if appropriate
- addHomRefSite(VariantContext, Genotype) - Method in class org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFBlockCombiner
-
Add hom-ref site from vc to this gVCF hom-ref state tracking, emitting any pending states if appropriate
- addInfo(AbstractLocusInfo<EdgingRecordAndOffset>, ReferenceSequence, boolean) - Method in class picard.analysis.FastWgsMetricsCollector
- addInfo(AbstractLocusInfo<SamLocusIterator.RecordAndOffset>, ReferenceSequence, boolean) - Method in class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
- addInfo(AbstractLocusInfo<T>, ReferenceSequence, boolean) - Method in class picard.analysis.AbstractWgsMetricsCollector
-
Accumulates the data from AbstractLocusInfo in inner structures
- addInfo(JSONObject, String, Object) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OffRampBase
- addInfoFieldAnnotations(VariantContext, VariantContextBuilder, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
-
Add the VCF INFO field annotations for the used alleles when subsetting
- addJunctionTree(JunctionTreeLinkedDeBruijnGraph.ThreadingTree) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JTBestHaplotype
-
Add a junction tree (corresponding to the current vertex for traversal, note that if a tree has already been visited by this path then it is ignored)
- addKmer(Kmer, int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.KMerCounter
-
Add a kmer that occurred kmerCount times
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.BciFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.BclFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.BclIndexFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.ClocsFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.FileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.FilterFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.LocsFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.PosFileFaker
- addLibrary(RScriptLibrary) - Method in class org.broadinstitute.hellbender.utils.R.RScriptExecutor
- addLocationInformation(String, PhysicalLocation) - Method in class picard.sam.util.ReadNameParser
- addLocusData(Map<DoCOutputType.Partition, Map<String, int[]>>) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoveragePartitionedDataStore
- addMetricsByLibrary(String, GATKDuplicationMetrics) - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator
- addMetricsByLibrary(String, DuplicationMetrics) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- addMetricsToFile(MetricsFile<BEAN, HKEY>) - Method in interface org.broadinstitute.hellbender.metrics.PerUnitMetricCollector
-
Any metrics collected will be added to the metric file provided.
- addMetricsToFile(MetricsFile<BEAN, HKEY>) - Method in interface picard.metrics.PerUnitMetricCollector
-
Any metrics collected will be added to the metric file provided.
- addMetricsToFile(MetricsFile<METRIC_TYPE, Integer>) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
- addMetricsToFile(MetricsFile<InsertSizeMetrics, Integer>) - Method in class org.broadinstitute.hellbender.metrics.PerUnitInsertSizeMetricsCollector
- addMetricsToFile(MetricsFile<ExampleMultiMetrics, Integer>) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.PerUnitExampleMultiMetricsCollector
- addMetricsToFile(MetricsFile<AlignmentSummaryMetrics, Integer>) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
- addMetricsToFile(MetricsFile<AlignmentSummaryMetrics, Integer>) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- addMetricsToFile(MetricsFile<CollectQualityYieldMetrics.QualityYieldMetrics, Integer>) - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
- addMetricsToFile(MetricsFile<InsertSizeMetrics, Integer>) - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
- addMetricsToFile(MetricsFile<RnaSeqMetrics, Integer>) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
- addMetricsToFile(MetricsFile<GcBiasMetrics, Integer>) - Method in class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
- addMissingAlleles(Collection<A>, double) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Add alleles that are missing in the evidence-likelihoods collection giving all evidence a default likelihood value.
- addMissingTruthAndMissingCallStates(double, long, GenotypeConcordanceCounts) - Static method in class picard.vcf.GenotypeConcordance
-
Method to add missing sites that are KNOWN to be HOM_REF in the case of the NIST truth data set.
- addNode(int, String, int, long, String) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
-
Adds a node to the tree.
- addNode(Node) - Method in class picard.util.GraphUtils.Graph
- addNonReferenceAllele(A) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Adds the non-reference allele to the evidence-likelihood collection setting each evidence likelihood to the second best found (or best one if only one allele has likelihood).
- addNonRefSymbolicAllele(VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceUtils
- addNotag(String) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- addNotags(Collection<String>) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- AddOATag - Class in picard.sam
- AddOATag() - Constructor for class picard.sam.AddOATag
- addObservation(int) - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram
- addObservation(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
- addObservations(int, long) - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram
- addObservations(IntHistogram) - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram
- addOp(ClippingOp) - Method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
-
Add clipping operation to the read.
- AddOriginalAlignmentTags - Class in org.broadinstitute.hellbender.tools
- AddOriginalAlignmentTags() - Constructor for class org.broadinstitute.hellbender.tools.AddOriginalAlignmentTags
- AddOrReplaceReadGroups - Class in picard.sam
-
Assigns all the reads in a file to a single new read-group.
- AddOrReplaceReadGroups() - Constructor for class picard.sam.AddOrReplaceReadGroups
- addOrUpdateEdge(V, V, E) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Add edge between source -> target if none exists, or add e to an already existing one if present
- addOutputSAMProgramRecord - Variable in class org.broadinstitute.hellbender.engine.GATKTool
- addOutputVCFCommandLine - Variable in class org.broadinstitute.hellbender.engine.GATKTool
- addOutputVCFCommandLine - Variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- addParameterSampler(V2, ParameterSampler<U, V2, S2, T2>, Class<U>) - Method in class org.broadinstitute.hellbender.utils.mcmc.ParameterizedModel.GibbsBuilder
-
Adds a
ParameterSamplerto the collection of parameter samplers usingParameterizedModel.GibbsBuilder. - addPileup(ReadPileup) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.AllelePileupCounter
- addPrefetcher(int, SeekableByteChannel) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Wrap a SeekableByteChannel with a prefetcher.
- addRangesToHeader(VCFHeader) - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlockCombiner
- addRead(int, int, int, boolean) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.LibraryRawStatistics
- addRead(String) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex
-
Add name information to this vertex for debugging This information will be captured as a list of strings, and displayed in DOT if this graph is written out to disk This functionality is only enabled when KEEP_TRACK_OF_READS is true
- addRead(GATKRead) - Method in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
- addRead(GATKRead) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetrics
-
Process a single read
- addRead(GATKRead) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetrics
- addRead(GATKRead) - Method in class org.broadinstitute.hellbender.tools.walkers.consensus.ReadsWithSameUMI
-
Add a read to the set.
- addRead(GATKRead) - Method in interface org.broadinstitute.hellbender.utils.read.GATKReadWriter
- addRead(GATKRead) - Method in class org.broadinstitute.hellbender.utils.read.SAMFileGATKReadWriter
- addReadData(ClusterData, int, BaseData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- addReadData(ClusterData, int, CbclData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- addReadData(ClusterData, int, QualityData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- addReadGroup(List<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager
-
Add a family of split reads to the manager
- addReadKmers(GATKRead) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NearbyKmerErrorCorrector
-
Main entry routine to add all kmers in a read to the read map counter
- addReads(Locatable, String, List<GATKRead>, List<GATKRead>, List<GATKRead>, String) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.PreFilterOffRamp
- addReadsToKmers(Collection<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NearbyKmerErrorCorrector
-
Top-level entry point that adds a collection of reads to our kmer list.
- addReadToLibraryMetrics(SAMRecord) - Method in class picard.sam.DuplicationMetrics
-
Adds a read to the metrics
- addReadToLibraryMetrics(SAMRecord) - Method in class picard.sam.FlowBasedDuplicationMetrics
- addReadToLibraryMetrics(SAMRecord, SAMFileHeader, LibraryIdGenerator, boolean) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- addRecordToHistogramGenerator(SAMRecord) - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- addReferenceFilesForSpark(JavaSparkContext, Path) - Static method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Register the reference file (and associated dictionary and index) to be downloaded to every node using Spark's copying mechanism (
SparkContext#addFile()). - addReferenceIndex(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MultiSampleEdge
- addRegion(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
Adds a GenomeLoc to the collection, merging it if it overlaps another region.
- ADDRESS_A_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- ADDRESS_B_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- addResults(MatchResults) - Method in class picard.fingerprint.FingerprintResults
- addRow(Object...) - Method in class org.broadinstitute.hellbender.utils.report.GATKReport
-
This method provides an efficient way to populate a simplified GATK report.
- addRow(GenotypeConcordanceStates.CallState, GenotypeConcordanceStates.ContingencyState[]...) - Method in class picard.vcf.GenotypeConcordanceScheme
-
Adds a row to the scheme
- addRowID(String, boolean) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Add a mapping from ID to the index of a new row added to the table.
- addRowIDMapping(Object, int, boolean) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Add a mapping from ID to row index.
- addRowIDMapping(String, int) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Add a mapping from ID to row index.
- addSample(String, URI) - Method in class org.broadinstitute.hellbender.tools.genomicsdb.SampleNameMap
-
Add a new sample mapping
- addSample(String, URI, URI) - Method in class org.broadinstitute.hellbender.tools.genomicsdb.SampleNameMap
-
Add a new sample mapping
- addSample(Sample) - Method in class org.broadinstitute.hellbender.utils.samples.SampleDB
-
Protected function to add a single sample to the database
- addSamplesFromPedigreeFiles(List<GATKPath>) - Method in class org.broadinstitute.hellbender.utils.samples.SampleDBBuilder
- addSamplesFromPedigreeStrings(List<String>) - Method in class org.broadinstitute.hellbender.utils.samples.SampleDBBuilder
- addSamplesFromSampleNames(Collection<String>) - Method in class org.broadinstitute.hellbender.utils.samples.SampleDBBuilder
-
Integrates the collection of sample names with the samples already present
- addScoreNormalized(double) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- addScript(File) - Method in class org.broadinstitute.hellbender.utils.R.RScriptExecutor
- addScript(Resource) - Method in class org.broadinstitute.hellbender.utils.R.RScriptExecutor
- addSecondOfPair(SAMRecord) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
- addSelenocysteine(GencodeGtfSelenocysteineFeature) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature
- addSelfScore(double) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- addSenseCount(double) - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation.Coverage
- addSequence(byte[], boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Add the all bases in sequence to the graph
- addSequence(String, byte[], boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Add all bases in sequence to this graph
- addSequence(String, byte[], int, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Add all bases in sequence to this graph
- addSequence(String, String, byte[], int, int, int, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Add bases in sequence to this graph
- addSingletonToCount(LibraryIdGenerator) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- addSnp(Snp) - Method in class picard.fingerprint.HaplotypeBlock
-
Adds a SNP to the haplotype.
- addSplicePosition(String, int, int) - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager
-
Add a new observed split to the list to use
- addStatus(ReferencePair.Status) - Method in class org.broadinstitute.hellbender.tools.reference.ReferencePair
-
Given a Status, add it to the ReferencePair's analysis
- addSupplementalFirstOfPairOrFragment(SAMRecord) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
- addSupplementalSecondOfPair(SAMRecord) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
- addTable(String, String, int) - Method in class org.broadinstitute.hellbender.utils.report.GATKReport
-
Add a new, empty table to the report
- addTable(String, String, int, GATKReportTable.Sorting) - Method in class org.broadinstitute.hellbender.utils.report.GATKReport
-
Add a new, empty table to the report
- addTable(GATKReportTable) - Method in class org.broadinstitute.hellbender.utils.report.GATKReport
-
Adds a table, empty or populated, to the report
- addTables(List<GATKReportTable>) - Method in class org.broadinstitute.hellbender.utils.report.GATKReport
- addTag(String) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- addTag(GATKRead) - Method in class org.broadinstitute.hellbender.utils.SATagBuilder
-
Add a read to the SATag for the encapsulated read.
- addTag(SATagBuilder) - Method in class org.broadinstitute.hellbender.utils.SATagBuilder
-
Add a read encapsulated by another SATagBuilder to this tag, if the read is set to be primary, then it will be advanced to the front of the list, otherwise it will be placed at the back of the SA string.
- addTags(Collection<String>) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- addToArrayInPlace(double[], double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Add two double arrays, modifying the first
- addToArrayInPlace(int[], int[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Add two int arrays, modifying the first
- addToIntervalStrings(String) - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
Add an extra interval string to the intervals to include.
- addToIntervalStrings(String) - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalIntervalArgumentCollection
- addToIntervalStrings(String) - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredIntervalArgumentCollection
- addToLogLikelihoods(Snp, List<Allele>, double[]) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
-
Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
- addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.AbstractWgsMetricsCollector
-
Adds collected metrics and depth histogram to file
- addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
- addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in interface picard.analysis.WgsMetricsProcessor
-
Adds result metric's data to input file
- addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.WgsMetricsProcessorImpl
- addToProbs(Snp, byte, byte) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
-
Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
- addToProbs(Snp, byte, byte) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
- addToReference(SimpleInterval, byte) - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker
- addTotalReads(int) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- addTrailingSlashIfNecessary(String) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
- addTrainingSet(TrainingSet) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- addTranscript(String, int, int, int, int, int) - Method in class picard.annotation.Gene
- addTranscript(GencodeGtfTranscriptFeature) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfGeneFeature
- addUmiObservation(String, String) - Method in class picard.sam.markduplicates.UmiMetrics
-
Add an observation of a UMI to the metrics
- addUmiObservationN() - Method in class picard.sam.markduplicates.UmiMetrics
-
Add an observation of a UMI containing at least one N to the metrics
- addUnambiguousReads(int) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- addUtr(GencodeGtfUTRFeature) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature
- addVC(VariantContext) - Method in class org.broadinstitute.hellbender.utils.haplotype.EventMap
-
Add VariantContext vc to this map, merging events with the same start sites if necessary
- addVC(VariantContext, boolean) - Method in class org.broadinstitute.hellbender.utils.haplotype.EventMap
-
Add VariantContext vc to this map
- addVCFsForSpark(JavaSparkContext, List<String>) - Static method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Register the VCF file (and associated index) to be downloaded to every node using Spark's copying mechanism (
SparkContext#addFile()). - addVertices(Collection<V>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Convenience function to add multiple vertices to the graph at once
- addVertices(V...) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Convenience function to add multiple vertices to the graph at once
- ADENINE - Static variable in enum class org.broadinstitute.hellbender.utils.Nucleotide
- adjustQualsOfOverlappingPairedFragments(Pair<GATKRead, GATKRead>, boolean, OptionalInt, OptionalInt) - Static method in class org.broadinstitute.hellbender.utils.fragments.FragmentUtils
-
Fix two overlapping reads from the same fragment by adjusting base qualities, if possible Looks at the bases and alignment, and tries its best to create adjusted base qualities so that the observations are not treated independently.
- advance() - Method in class picard.util.AbstractInputParser
- advanceBlock(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
- ADVANCED - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection.FlowMode
- ADVANCED - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection.FlowMode
- advanceFile() - Method in class picard.util.BasicInputParser
- advancePosition(SimpleInterval) - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker
- advanceToLocus(int, boolean) - Method in class org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState
-
Move this LIBS until we are over position Will return null if cannot reach position (because we run out of data in the locus)
- AF_PARAMETER_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- AF_PARAMETER_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- AFCalculationResult - Class in org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
-
Describes the results of the AFCalc Only the bare essentials are represented here, as all AFCalc models must return meaningful results for all of these fields.
- AFCalculationResult(int[], List<Allele>, double, Map<Allele, Double>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculationResult
-
Create a results object capability of storing results for calls with up to maxAltAlleles
- afDataSource - Variable in class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations
- AFFECTED - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.Affection
-
Suffers from the disease
- Affection - Enum Class in org.broadinstitute.hellbender.utils.samples
-
Categorical sample trait for association and analysis Samples can have unknown status, be affected or unaffected by the categorical trait, or they can be marked as actually having an other trait value (stored in an associated value in the Sample class)
- afterExecute(Runnable, Throwable) - Method in class picard.util.ThreadPoolExecutorWithExceptions
- afterFile - Variable in class org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates
-
File containing the recalibration tables from the second pass.
- afterFirstPass() - Method in class org.broadinstitute.hellbender.engine.TwoPassVariantWalker
-
Process the data collected during the first pass.
- afterFirstPass() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalker
- afterFirstPass() - Method in class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations
- afterFirstPass() - Method in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ArHetvarFilter
- afterFirstPass() - Method in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.TwoPassFuncotationFilter
- afterFirstPass() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MTLowHeteroplasmyFilterTool
- afterFirstPass() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants
- afterFirstPass() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.FilterVariantTranches
- afterNthPass(int) - Method in class org.broadinstitute.hellbender.engine.MultiplePassVariantWalker
-
Process the data collected during the first pass.
- afterNthPass(int) - Method in class org.broadinstitute.hellbender.engine.TwoPassVariantWalker
- afterNthPass(int) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls
- afterNthPass(int) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations
- afterNthPass(int) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- afterOnTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations
- afterOnTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
- afterOnTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- afterPipeline(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram
-
Extend this method to run code after the pipeline returns.
- afTolerance - Variable in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
-
Margin of error in allele fraction to consider a somatic variant homoplasmic, i.e.
- AG - Enum constant in enum class picard.fingerprint.DiploidGenotype
- aggregate(List<Integer>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.BaseQuality
- aggregate(List<Integer>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.FragmentLength
- aggregate(List<Integer>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.MappingQuality
- aggregate(List<Integer>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.PerAlleleAnnotation
- aggregate(List<Integer>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosition
- AGGRESSIVE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.PCRErrorModel
-
a more aggressive model will be applied that sacrifices true positives in order to remove more false positives
- ALANINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- ALGORITHM_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- ALGORITHMS_ATTRIBUTE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- aliases() - Method in enum class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistributionShape
- AliasProvider - Class in org.broadinstitute.hellbender.tools.funcotator
-
Class for managing aliases and querying
Funcotationto determine fields. - AliasProvider(LinkedHashMap<String, List<String>>) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.AliasProvider
- align(byte[], byte[], SWParameters, SWOverhangStrategy) - Method in interface org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner
-
perform a Smith-Waterman alignment of alt against ref
- align(byte[], byte[], SWParameters, SWOverhangStrategy) - Method in class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanIntelAligner
-
Aligns the alternate sequence to the reference sequence
- align(byte[], byte[], SWParameters, SWOverhangStrategy) - Method in class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner
-
Aligns the alternate sequence to the reference sequence
- align(byte[], byte[], SWParameters, SWOverhangStrategy) - Method in class org.broadinstitute.hellbender.utils.smithwaterman.SWNativeAlignerWrapper
- align(Iterable<? extends T>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SingleSequenceReferenceAligner
- align(List<? extends T>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SingleSequenceReferenceAligner
-
Aligns the input object returning a list of the outputs in the corresponding order.
- align(List<? extends T>, BiFunction<? super T, ? super U, ? extends V>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SingleSequenceReferenceAligner
-
Composes a map of the aligned sequences.
- align(JavaRDD<GATKRead>, boolean) - Method in class org.broadinstitute.hellbender.tools.spark.bwa.BwaSparkEngine
-
Performs read alignment on a RDD.
- ALIGN_LENGTHS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- Aligned - Enum constant in enum class picard.sam.ViewSam.AlignmentStatus
- ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
- ALIGNED_READS - Variable in class picard.analysis.GcBiasSummaryMetrics
-
The total number of aligned reads used to compute the gc bias metrics.
- ALIGNED_READS_ONLY - Variable in class picard.analysis.CollectBaseDistributionByCycle
- ALIGNED_READS_ONLY - Variable in class picard.analysis.MeanQualityByCycle
- ALIGNED_READS_ONLY - Variable in class picard.analysis.QualityScoreDistribution
- ALIGNED_READS_ONLY - Variable in class picard.sam.MergeBamAlignment
- AlignedAssembly - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
-
Holding necessary information about a local assembly for use in SV discovery.
- AlignedAssembly(int, List<AlignedContig>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedAssembly
- AlignedAssembly.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
- AlignedAssemblyOrExcuse - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
An assembly with its contigs aligned to reference, or a reason that there isn't an assembly.
- AlignedAssemblyOrExcuse(int, String) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse
- AlignedAssemblyOrExcuse(int, FermiLiteAssembly, int, List<List<BwaMemAlignment>>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse
- AlignedAssemblyOrExcuse.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- AlignedContig - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
-
Locally assembled contig: its name its sequence as produced by the assembler (no reverse complement like in the SAM record if it maps to '-' strand), and its stripped-down alignment information.
- AlignedContig(String, byte[], List<AlignmentInterval>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
- AlignedContig.GoodAndBadMappings - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
-
After configuration scoring and picking, the original alignments can be classified as good and bad mappings: good: the ones used the picked configuration bad: unused alignments in the chosen configuration; these likely contain more noise than information they can be turned into string representation following the format as in
AlignmentInterval.toPackedString() - AlignedContig.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
- AlignedContigGenerator - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
-
Loads various upstream assembly and alignment formats and turn into custom
AlignedContigformat in the discovery stage. - AlignedContigGenerator() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContigGenerator
- alignedContigs - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedAssembly
- alignedInput - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
-
PathSeq will rapidly filter the reads if they are aligned to a host reference, thus reducing run time.
- alignedReadsOnly - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectBaseDistributionByCycleSpark
- alignedReadsOnly - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MeanQualityByCycleSpark
- alignedReadsOnly - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityScoreDistributionSpark
- aligner - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- ALIGNER_PROPER_PAIR_FLAGS - Variable in class picard.sam.MergeBamAlignment
- alignerIndexImageFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- ALIGNMENT_ARTIFACT_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- ALIGNMENT_LOW_READ_UNIQUENESS_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
-
parameters to be passed to
AlignedContig.removeNonUniqueMappings(GoodAndBadMappings, int, int)for dropping alignments that offer either low read uniqueness. - ALIGNMENT_REGION_TAG - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- ALIGNMENT_SCORE_DIFFERENCE_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- ALIGNMENT_STATUS - Variable in class picard.sam.ViewSam
- ALIGNMENT_TO_BEST_HAPLOTYPE_SW_PARAMETERS - Static variable in class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAlignmentConstants
-
ALIGNMENT_TO_BEST_HAPLOTYPE_SW_PARAMETERSis the default for read-to-haplotype alignment and was added in https://github.com/broadinstitute/gatk/pull/4858 (superseding the use ofSmithWatermanAlignmentConstants.NEW_SW_PARAMETERSinAlignmentUtils.createReadAlignedToRef(org.broadinstitute.hellbender.utils.read.GATKRead, org.broadinstitute.hellbender.utils.haplotype.Haplotype, org.broadinstitute.hellbender.utils.haplotype.Haplotype, int, boolean, org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner, org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters)in the read-to-haplotype alignment step of that method). - alignmentAgreesWithHeader(SAMFileHeader, GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Check to ensure that the alignment makes sense based on the contents of the header.
- AlignmentAgreesWithHeaderReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads where the alignment does not match the contents of the header.
- AlignmentAgreesWithHeaderReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.AlignmentAgreesWithHeaderReadFilter
- AlignmentAgreesWithHeaderReadFilter(SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.engine.filters.AlignmentAgreesWithHeaderReadFilter
- AlignmentAndReferenceContext - Class in org.broadinstitute.hellbender.engine
-
Bundles together and AlignmentContext and a ReferenceContext
- AlignmentAndReferenceContext(AlignmentContext, ReferenceContext) - Constructor for class org.broadinstitute.hellbender.engine.AlignmentAndReferenceContext
- AlignmentContext - Class in org.broadinstitute.hellbender.engine
-
Bundles together a pileup and a location.
- AlignmentContext(Locatable, ReadPileup) - Constructor for class org.broadinstitute.hellbender.engine.AlignmentContext
- AlignmentContext(Locatable, ReadPileup, boolean) - Constructor for class org.broadinstitute.hellbender.engine.AlignmentContext
- AlignmentContext.ReadOrientation - Enum Class in org.broadinstitute.hellbender.engine
- AlignmentContextIteratorBuilder - Class in org.broadinstitute.hellbender.utils.locusiterator
-
Create an iterator for traversing alignment contexts in a specified manner.
- AlignmentContextIteratorBuilder() - Constructor for class org.broadinstitute.hellbender.utils.locusiterator.AlignmentContextIteratorBuilder
- alignmentContigsToIgnore - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
-
If using --is-host-aligned, ignores alignments to these contigs (can be specified multiple times).
- AlignmentInterval - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
-
Each assembled contig should have at least one such accompanying structure, or 0 when it is unmapped.
- AlignmentInterval(SAMRecord) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- AlignmentInterval(String) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
Compose an alignment interval instance from a SAM supplementary alignment formatted string.
- AlignmentInterval(BwaMemAlignment, List<String>, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- AlignmentInterval(GATKRead) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
Constructs an alignment interval that reflects on the mapping properties of a
GATKReadinstance. - AlignmentInterval(SimpleInterval, int, int, Cigar, boolean, int, int, int, ContigAlignmentsModifier.AlnModType) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- AlignmentInterval.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
- alignmentStartShift(Cigar, int) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
How many bases to the right does a read's alignment start shift given its cigar and the number of left soft clips
- AlignmentStateMachine - Class in org.broadinstitute.hellbender.utils.locusiterator
-
Steps a single read along its alignment to the genome The logical model for generating extended events is as follows: the "record state" implements the traversal along the reference; thus stepForwardOnGenome() returns on every and only on actual reference bases.
- AlignmentStateMachine(GATKRead) - Constructor for class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
- AlignmentSummaryMetrics - Class in picard.analysis
-
High level metrics about the alignment of reads within a SAM file, produced by the CollectAlignmentSummaryMetrics program and usually stored in a file with the extension ".alignment_summary_metrics".
- AlignmentSummaryMetrics() - Constructor for class picard.analysis.AlignmentSummaryMetrics
- AlignmentSummaryMetrics.Category - Enum Class in picard.analysis
- AlignmentSummaryMetricsCollector - Class in picard.analysis
- AlignmentSummaryMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, boolean, List<String>, int, Set<SamPairUtil.PairOrientation>, boolean) - Constructor for class picard.analysis.AlignmentSummaryMetricsCollector
- AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector - Class in picard.analysis
- AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector - Class in picard.analysis
-
Class that counts reads that match various conditions
- AlignmentUtils - Class in org.broadinstitute.hellbender.utils.read
- AlignmentUtils.MismatchCount - Class in org.broadinstitute.hellbender.utils.read
- alignPaired(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.bwa.BwaSparkEngine
-
Performs pair-end alignment on a RDD.
- alignUnpaired(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.bwa.BwaSparkEngine
-
Performs single-end alignment on a RDD.
- All - Enum constant in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
- All - Enum constant in enum class picard.sam.ViewSam.AlignmentStatus
- All - Enum constant in enum class picard.sam.ViewSam.PfStatus
- ALL - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.TranscriptSelectionMode
-
Same as CANONICAL, but indicates that no transcripts should be dropped.
- ALL - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants.ValidationType
-
Makes reference to all extra-strict tests listed below.
- ALL - Enum constant in enum class org.broadinstitute.hellbender.utils.IntervalMergingRule
- ALL - Enum constant in enum class picard.sam.markduplicates.CheckDuplicateMarking.Mode
- ALL_COVARIATES_REPORT_TABLE_TITLE - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- ALL_FAMILY_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- ALL_GTS_FILTERED - Static variable in class picard.vcf.filter.FilterApplyingVariantIterator
-
Filter string that is used to filter a Variant when all variant genotypes are filtered out.
- ALL_KMERS - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterConstants
- ALL_MRNA_VERIFIED - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.TranscriptSupportLevel
-
all splice junctions of the transcript are supported by at least one non-suspect mRNA
- ALL_POSSIBLE_HAPLOTYPES - Enum constant in enum class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter.WriterType
-
A mode that's for method developers.
- ALL_READS - Enum constant in enum class org.broadinstitute.hellbender.metrics.MetricAccumulationLevel
- ALL_READS - Enum constant in enum class org.broadinstitute.hellbender.utils.downsampling.DownsampleType
- ALL_READS - Enum constant in enum class picard.analysis.MetricAccumulationLevel
- ALL_SAMPLE_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- ALL_SITES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- ALL_SITES_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- ALL_TRANSCRIPT_DELIMITER - Static variable in class org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer
-
The delimiter to use when separating the information regarding a transcript.
- ALL_VC_NAMES - Static variable in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Variable to store the list of all valid
GencodeFuncotation.VariantClassificationtypes. - allAlleles - Variable in class picard.vcf.GenotypeConcordance.Alleles
- allele - Variable in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods.BestAllele
-
Null if there is no possible match (no allele?).
- ALLELE_A - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ALLELE_A_PROBE_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- ALLELE_B - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ALLELE_B_PROBE_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- ALLELE_BALANCE_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- ALLELE_EXTENSION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- ALLELE_FRACTION - Variable in class picard.analysis.CollectWgsMetrics
- ALLELE_FRACTION - Variable in class picard.analysis.directed.CollectTargetedMetrics
- ALLELE_FRACTION - Variable in class picard.analysis.TheoreticalSensitivityMetrics
-
The allele fraction which theoretical sensitivity is calculated for.
- ALLELE_FRACTION_DELTA_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
- ALLELE_FRACTION_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- ALLELE_FRACTION_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- ALLELE_FRACTION_LEGACY_SEGMENTS_FILE_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.ModelSegments
- ALLELE_FRACTION_MODEL_PARAMETER_FILE_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.ModelSegments
- ALLELE_FREQUENCY_DATA_SOURCE_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- ALLELE_LIKELIHOOD_MATRIX_INTERVAL - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- ALLELE_LIKELIHOOD_MATRIX_PATH - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- ALLELE_SPECIFIC_ANNOTATION_PREFIX - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- ALLELE_SPECIFIC_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- ALLELE_SPECIFIC_PREFIX - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- ALLELE_SPECIFIC_RAW_DELIM - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils
- ALLELE_SPECIFIC_REDUCED_DELIM - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils
- ALLELE_SPECIFIC_SPLIT_REGEX - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils
- AlleleAndContext - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
This class is similar to
LocationAndAllelesbut allows keeping only an allele/ref pair rather than a list of alleles. - AlleleAndContext(String, int, Allele, Allele) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleAndContext
- AlleleBalanceFilter - Class in picard.vcf.filter
-
Filters out a record if the allele balance for heterozygotes is out of a defined range across all samples.
- AlleleBalanceFilter(double) - Constructor for class picard.vcf.filter.AlleleBalanceFilter
- AlleleBiasedDownsamplingUtils - Class in org.broadinstitute.hellbender.utils.downsampling
-
The purpose of this set of utilities is to downsample a set of reads to remove contamination.
- alleleCount() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculator
-
Returns the total number of alleles for this genotype calculator.
- AlleleCount - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies the eval RODs by the allele count of the alternate allele Looks first at the MLEAC value in the INFO field, and uses that value if present.
- AlleleCount(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.AlleleCount
- alleleCountAt(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Returns the count of an allele in the genotype given is rank in the genotype (not the allele index itself).
- alleleCountFor(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Returns the count of an allele in the genotype given it index.
- alleleCountsByIndex(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Returns the allele counts for each allele index to maximum.
- alleleCountsToIndex(int...) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculator
-
Returns the likelihood index given the allele counts.
- AlleleFiltering - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Filtering haplotypes that contribute weak alleles to the genotyping.
- AlleleFilteringHC - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Filtering haplotypes that contribute weak alleles to the genotyping.
- AlleleFilteringHC(HaplotypeCallerArgumentCollection, OutputStreamWriter, HaplotypeCallerGenotypingEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleFilteringHC
- AlleleFilteringMutect - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Filtering haplotypes that contribute weak alleles to the genotyping.
- AlleleFilteringMutect(M2ArgumentCollection, OutputStreamWriter, SomaticGenotypingEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleFilteringMutect
- AlleleFilterUtils - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
-
Helps read and set allele specific filters in the INFO field.
- AlleleFilterUtils() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.AlleleFilterUtils
- AlleleFraction - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Variant allele fraction for each sample.
- AlleleFraction() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.AlleleFraction
- AlleleFractionCluster - Interface in org.broadinstitute.hellbender.tools.walkers.mutect.clustering
- AlleleFractionKernelSegmenter - Class in org.broadinstitute.hellbender.tools.copynumber.segmentation
-
Segments alternate-allele-fraction data using kernel segmentation.
- AlleleFractionKernelSegmenter(AllelicCountCollection) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.segmentation.AlleleFractionKernelSegmenter
- AlleleFractionModeller - Class in org.broadinstitute.hellbender.tools.copynumber.models
-
Given segments and counts of alt and ref reads over a list of het sites, infers the minor-allele fraction of each segment.
- AlleleFractionParameter - Enum Class in org.broadinstitute.hellbender.tools.copynumber.models
-
Enumerates the parameters for
AlleleFractionState. - AlleleFractionPrior - Class in org.broadinstitute.hellbender.tools.copynumber.models
-
Represents priors for the allele-fraction model.
- AlleleFractionPrior(double) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionPrior
- alleleFractionsPosterior(RealMatrix, double[]) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticLikelihoodsEngine
- alleleFractionsPosterior(RealMatrix, double[], double[]) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticLikelihoodsEngine
-
Given a likelihoods matrix, calculate the parameters of the Dirichlet posterior distribution on their allele fractions, which define a discrete distribution.
- AlleleFrequency - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies the eval RODs by the allele frequency of the alternate allele Either uses a constant 0.005 frequency grid, and projects the AF INFO field value or logit scale from -30 to 30.
- AlleleFrequency(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.AlleleFrequency
- alleleFrequencyCalculator - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
- AlleleFrequencyCalculator - Class in org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
- AlleleFrequencyCalculator(double, double, double, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator
- AlleleFrequencyExacUtils - Class in org.broadinstitute.hellbender.tools.funcotator.filtrationRules
-
Allele frequency calculations for the Exac dataset
- AlleleFrequencyExacUtils() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AlleleFrequencyExacUtils
- AlleleFrequencyQC - Class in org.broadinstitute.hellbender.tools.walkers.varianteval
-
This tool uses VariantEval to bin variants in Thousand Genomes by allele frequency.
- AlleleFrequencyQC() - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.AlleleFrequencyQC
- AlleleFrequencyQCMetric - Class in org.broadinstitute.hellbender.metrics.analysis
- AlleleFrequencyQCMetric() - Constructor for class org.broadinstitute.hellbender.metrics.analysis.AlleleFrequencyQCMetric
- AlleleFrequencyUtils - Class in org.broadinstitute.hellbender.tools.funcotator.filtrationRules
-
Allele frequency utilities that are dataset-agnostic
- AlleleFrequencyUtils() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AlleleFrequencyUtils
- alleleIndexAt(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Returns the index of the allele from its rank in the genotype.
- alleleIndices(List<Allele>, List<Allele>) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Find the indices in one allele list (or OptionalInt.empty() if none exists) in another list of alleles We assume that reference alleles are the first element of each list and don't assume that either list is in its minimal representation
- AlleleLengthComparator() - Constructor for class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF.AlleleLengthComparator
- alleleLikelihoodMatrixInterval - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- alleleLikelihoodMatrixPath - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- AlleleLikelihoods<EVIDENCE extends htsjdk.samtools.util.Locatable,
A extends htsjdk.variant.variantcontext.Allele> - Class in org.broadinstitute.hellbender.utils.genotyper -
Evidence-likelihoods container implementation based on integer indexed arrays.
- AlleleLikelihoods(SampleList, AlleleList<A>, Map<String, List<EVIDENCE>>) - Constructor for class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Constructs a new evidence-likelihood collection.
- AlleleLikelihoods.BestAllele - Class in org.broadinstitute.hellbender.utils.genotyper
-
Contains information about the best allele for a unit of evidence.
- alleleLikelihoodWriter - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- AlleleLikelihoodWriter - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
- AlleleLikelihoodWriter(Path, SimpleInterval) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleLikelihoodWriter
- AlleleList<A extends htsjdk.variant.variantcontext.Allele> - Interface in org.broadinstitute.hellbender.utils.genotyper
-
Minimal interface for random access to a collection of Alleles.
- AlleleList.ActualPermutation<A extends htsjdk.variant.variantcontext.Allele> - Class in org.broadinstitute.hellbender.utils.genotyper
- AlleleList.NonPermutation<A extends htsjdk.variant.variantcontext.Allele> - Class in org.broadinstitute.hellbender.utils.genotyper
-
This is the identity permutation.
- AlleleListPermutation<A extends htsjdk.variant.variantcontext.Allele> - Interface in org.broadinstitute.hellbender.utils.genotyper
-
Marks allele list permutation implementation classes.
- AlleleMapper(VariantContext) - Constructor for class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.AlleleMapper
- AlleleMapper(Map<Allele, Allele>) - Constructor for class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.AlleleMapper
- AllelePileupCounter - Class in org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
-
Useful when you know the interval and the alleles of interest ahead of the counting.
- AllelePileupCounter(Allele, List<Allele>, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.AllelePileupCounter
- AllelePileupCounter(Allele, List<Allele>, int, ReadPileup) - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.AllelePileupCounter
-
See
AllelePileupCounter(Allele, List, int), except this will immediately add the given pileup as well. - AllelePseudoDepth - Class in org.broadinstitute.hellbender.tools.walkers.annotator
- AllelePseudoDepth() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.AllelePseudoDepth
- alleleRankFor(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Returns the rank of an allele in the genotype by its index.
- alleles - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- alleles - Variable in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Allele list.
- alleles() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix
- alleles() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Returns the samples in this evidence-likelihood collection.
- alleles() - Method in interface org.broadinstitute.hellbender.utils.genotyper.LikelihoodMatrix
-
List of alleles in the matrix sorted by their index in the collection.
- Alleles(OrderedSet<String>, String, String, String, String) - Constructor for class picard.vcf.GenotypeConcordance.Alleles
- ALLELES - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants.ValidationType
-
Check whether all alternative alleles participate in a genotype call of at least on sample.
- ALLELES_ALT_PATH - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- ALLELES_REF_PATH - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- AlleleSpecificAnnotation - Interface in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
This is a marker interface used to indicate which annotations are allele-specific.
- AlleleSpecificAnnotationData<T> - Class in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
A class to encapsulate the raw data for allele-specific classes compatible with the ReducibleAnnotation interface
- AlleleSpecificAnnotationData(List<Allele>, String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AlleleSpecificAnnotationData
- allelesToIndex(int...) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculator
-
Give a list of alleles, returns the likelihood array index.
- allelesToStringList(List<Allele>) - Static method in class picard.util.LiftoverUtils
-
This is a utility method that will convert a list of alleles into a list of base strings.
- AlleleSubsettingUtils - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
-
Utilities class containing methods for restricting
VariantContextandGenotypesContextobjects to a reduced set of alleles, as well as for choosing the best set of alleles to keep and for cleaning up annotations and genotypes after subsetting. - AlleleSubsettingUtils - Class in picard.util
-
Utilities class containing methods for restricting
VariantContextandGenotypesContextobjects to a reduced set of alleles, as well as for choosing the best set of alleles to keep and for cleaning up annotations and genotypes after subsetting. - AlleleSubsettingUtils() - Constructor for class picard.util.AlleleSubsettingUtils
- alleleVcfFile - Variable in class org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeBasedVariantRecallerArgumentCollection
-
This argument specifies a VCF file with Alleles to be recalled
- ALLELIC_COUNTS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- ALLELIC_COUNTS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument
- ALLELIC_COUNTS_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- ALLELIC_PON_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- ALLELIC_PON_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- AllelicCount - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
-
Reference and alternate allele counts at a site specified by an interval.
- AllelicCount(SimpleInterval, int, int) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
- AllelicCount(SimpleInterval, int, int, Nucleotide, Nucleotide) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
-
Construct the allelic count object.
- AllelicCountCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
Simple data structure to pass and read/write a List of
AllelicCountobjects. - AllelicCountCollection(File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AllelicCountCollection
- AllelicCountCollection(SampleLocatableMetadata, List<AllelicCount>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AllelicCountCollection
- AllelicCountCollector - Class in org.broadinstitute.hellbender.tools.copynumber.datacollection
-
Collects reference/alternate allele counts at specified sites.
- AllelicCountCollector(SampleLocatableMetadata) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.datacollection.AllelicCountCollector
- AllLocusIterator - Class in org.broadinstitute.hellbender.utils.iterators
-
A super-simplified/stripped-down/faster version of
IntervalAlignmentContextIteratorthat takes a locus iterator and a *single* interval, and returns an AlignmentContext for every locus in the interval. - AllLocusIterator(SimpleInterval, Iterator<AlignmentContext>) - Constructor for class org.broadinstitute.hellbender.utils.iterators.AllLocusIterator
- allMatch(double[], DoublePredicate) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Test whether all elements of a double[] array satisfy a double -> boolean predicate
- allMatch(int[], IntPredicate) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Test whether all elements of an int[] array satisfy an int -> boolean predicate
- ALLOSOMAL_CONTIG_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- ALLOW_ALL_READS - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
-
Static, stateless read filter instances
- ALLOW_ALL_VARIANTS - Static variable in class org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary
- ALLOW_AND_IGNORE_EMPTY_LINES - Variable in class picard.sam.FastqToSam
- ALLOW_CONTIG_LENGTH_DISCORDANCE - Variable in class picard.sam.ReorderSam
- ALLOW_DUPLICATE_READS - Variable in class picard.fingerprint.CrosscheckFingerprints
- ALLOW_EMPTY_FASTQ - Variable in class picard.sam.FastqToSam
- ALLOW_INCOMPLETE_DICT_CONCORDANCE - Variable in class picard.sam.ReorderSam
- ALLOW_MISSING_FIELDS_IN_HEADER - Variable in class picard.vcf.LiftoverVcf
- ALLOW_MISSING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- ALLOW_MISSING_UMIS - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
- ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS - Variable in class picard.sam.PositionBasedDownsampleSam
- ALLOW_MULTIPLE_SORT_ORDERS_IN_INPUT_ARG - Static variable in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- ALLOW_NON_UNIQUE_KMERS_IN_REF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- AllowAllReadsReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.AllowAllReadsReadFilter
- AllowAllVariantsVariantFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary.AllowAllVariantsVariantFilter
- allowedShortFragmentOverhang - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- allowedVariance - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.AlleleFrequencyQC
- allowMissingHomRefData - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- allowMultipleSortOrders - Variable in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- allowNonUniqueKmersInRef - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
By default, the program does not allow processing of reference sections that contain non-unique kmers.
- allowOlderRawKeyValues - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
- allVisitedAlignmentsEqual() - Method in class picard.sam.SamComparisonMetric
- alnModType - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
when
alnModTypeis notContigAlignmentsModifier.AlnModType.NONE, fields "mapQual", "mismatches", "alnScore" should be viewed with care as they were either simply copied from the original alignment (e.g. - alnScore - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
Alignment score,
AlignmentInterval.NO_ASif unknown or unspecified. - alreadyBuilt - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
- ALSO_IGNORE_DUPLICATES - Variable in class picard.analysis.CollectGcBiasMetrics
- ALT_ALLELE_SUMMARY_STRATEGY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- ALT_BASE - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
-
The alternative base (or it's complement).
- ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The (upper-case) alternative base that is called as a result of DNA damage.
- ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The (upper-case) alternative base that is called as a result of DNA damage.
- ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The (upper-case) alternative base that is called as a result of DNA damage.
- ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The (upper-case) alternative base that is called as a result of DNA damage.
- ALT_COUNT - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
-
The number of alt bases observed.
- ALT_FRACTIONS_FOR_SEGMENTATION - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationSegmenter
- ALT_HIST_EXTENSION - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2CountsCollector
- ALT_NAMES - Variable in class picard.sam.CreateSequenceDictionary
- ALT_NONOXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that rules out oxidation as the cause
- ALT_ONLY - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection.Type
- ALT_OXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that is consistent with oxidative damage.
- ALT_TABLE_EXTENSION - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2CountsCollector
- altAllele - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- ALTERNATIVE_3_UTR - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
shares an identical CDS but has alternative 5' UTR with respect to a reference variant.
- ALTERNATIVE_5_UTR - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
shares an identical CDS but has alternative 3' UTR with respect to a reference variant.
- ALTERNATIVE_SINGLE_END - Enum constant in enum class org.broadinstitute.hellbender.utils.illumina.IlluminaAdapterPair
- ALTERNATIVE_SINGLE_END - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- altHaplotypeSequence - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference
- AltSiteRecord - Class in org.broadinstitute.hellbender.tools.walkers.readorientation
-
Created by tsato on 10/11/17.
- AltSiteRecord(String, int, int, int, int, Nucleotide) - Constructor for class org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord
- AltSiteRecord.AltSiteRecordTableWriter - Class in org.broadinstitute.hellbender.tools.walkers.readorientation
-
Writer
- AltSiteRecordTableWriter(Path, String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord.AltSiteRecordTableWriter
- altValues() - Static method in enum class picard.analysis.artifacts.Transition
-
Like values(), but ignores the ref:ref "transitions".
- ALWAYS_RECALCULATE - Enum constant in enum class org.broadinstitute.hellbender.tools.reference.CompareReferences.MD5CalculationMode
- AMBIGUOUS - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments.ReasonForAlignmentClassificationFailure
- AMBIGUOUS_FILTER_BASES_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- AMBIGUOUS_FILTER_FRACTION_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- AMBIGUOUS_ORF - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- AmbiguousBaseReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filters out reads that have greater than the threshold number for unknown (N) bases.
- AmbiguousBaseReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.AmbiguousBaseReadFilter
- AmbiguousBaseReadFilter(int) - Constructor for class org.broadinstitute.hellbender.engine.filters.AmbiguousBaseReadFilter
- AMINO - Static variable in enum class org.broadinstitute.hellbender.utils.Nucleotide
- AminoAcid - Enum Class in org.broadinstitute.hellbender.tools.funcotator
-
Enum to hold the amino acids and their standard codons.
- AMPLICON_INTERVALS - Variable in class picard.analysis.directed.CollectTargetedPcrMetrics
- AMPLICON_TERRITORY - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of unique bases covered by the intervals of all amplicons in the amplicon set
- AMPLIFICATION - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledCopyRatioSegment.Call
- Analysis - Annotation Interface in org.broadinstitute.hellbender.tools.walkers.varianteval.util
- ANALYSIS_DIR - Variable in class picard.fastq.BamToBfq
- ANALYSIS_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The version number of the analysis run
- ANALYSIS_VERSION_NUMBER - Variable in class picard.arrays.GtcToVcf
- ANALYSIS_VERSION_NUMBER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- AnalysisModuleScanner - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.util
- AnalysisModuleScanner(Class<?>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.util.AnalysisModuleScanner
-
create a report scanner from the passed in class
- AnalysisModuleScanner(Object) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.util.AnalysisModuleScanner
-
create a report scanner from the passed in class
- AnalyzeCovariates - Class in org.broadinstitute.hellbender.tools.walkers.bqsr
-
Evaluate and compare base quality score recalibration tables
- AnalyzeCovariates() - Constructor for class org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates
- AnalyzeSaturationMutagenesis - Class in org.broadinstitute.hellbender.tools
-
Process reads from a saturation mutagenesis experiment.
- AnalyzeSaturationMutagenesis() - Constructor for class org.broadinstitute.hellbender.tools.AnalyzeSaturationMutagenesis
- AnalyzeSaturationMutagenesis.ReportTypeCounts - Class in org.broadinstitute.hellbender.tools
- ancestralAlignmentsFile - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- ancestralTranslatorsBasePath - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- and(CountingReadFilter) - Method in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter
-
Specialization of
Predicate.and(Predicate)so that CountingReadFilter and'ed with other CountingReadFilter produce a CountingReadFilter - and(CountingVariantFilter) - Method in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter
-
Specialization of
Predicate.and(Predicate)so that CountingVariantFilter and'ed with other CountingVariantFilter produce a CountingVariantFilter - and(ReadFilter) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilter
-
Specialization of
Predicate.and(Predicate)so that ReadFilters anded with other ReadFilters produce a ReadFilter - and(VariantFilter) - Method in interface org.broadinstitute.hellbender.engine.filters.VariantFilter
- andThen(ReadTransformer) - Method in interface org.broadinstitute.hellbender.transformers.ReadTransformer
- andThen(VariantTransformer) - Method in interface org.broadinstitute.hellbender.transformers.VariantTransformer
- andThen(SVInterval.SVIntervalConstructorArgsValidator) - Method in interface org.broadinstitute.hellbender.utils.SVInterval.SVIntervalConstructorArgsValidator
- annotate(VariantContext, AlleleLikelihoods<? extends Locatable, Haplotype>, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.AssemblyComplexity
- annotate(String, String) - Method in class org.broadinstitute.hellbender.utils.dragstr.STRTableFileBuilder
-
Add an annotation that would go to the header of the summary file.
- annotate(ReferenceContext, VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.ReferenceBases
- annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.AlleleFraction
- annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.AllelePseudoDepth
-
Computes the annotation for the given genotype and the likelihoods per read.
- annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.DepthPerAlleleBySample
- annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.DepthPerSampleHC
- annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>) - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeAnnotation
-
Computes the annotation for the given genotype and the likelihoods per read.
- annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasBySample
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_InbreedingCoeff
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.AS_StrandBiasMutectAnnotation
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityHistogram
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ChromosomeCounts
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.CountNs
-
Calculate annotations for each allele based on given VariantContext and likelihoods for a given genotype's sample and add the annotations to the GenotypeBuilder.
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.Coverage
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.CycleSkipStatus
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.GcContent
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.HmerIndelLength
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.HmerMotifs
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.IndelClassify
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.VariantType
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeSummaries
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation
-
Computes the annotation for the given variant and the likelihoods per read.
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.MappingQualityZero
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.OriginalAlignment
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.PerAlleleAnnotation
-
Calculate annotations for each allele based on given VariantContext and likelihoods for a given genotype's sample and add the annotations to the GenotypeBuilder.
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.PossibleDeNovo
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.QualByDepth
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RankSumTest
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RawGtCount
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ReferenceBases
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.SampleList
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.TandemRepeat
- annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.UniqueAltReadCount
- annotate(ReferenceContext, FeatureContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>, AlleleLikelihoods<Fragment, Allele>, AlleleLikelihoods<Fragment, Haplotype>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.FeaturizedReadSets
- annotate(ReferenceContext, FeatureContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>, AlleleLikelihoods<Fragment, Allele>, AlleleLikelihoods<Fragment, Haplotype>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.FragmentDepthPerAlleleBySample
- annotate(ReferenceContext, FeatureContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>, AlleleLikelihoods<Fragment, Allele>, AlleleLikelihoods<Fragment, Haplotype>) - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.JumboGenotypeAnnotation
- annotate(ReferenceContext, FeatureContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>, AlleleLikelihoods<Fragment, Allele>, AlleleLikelihoods<Fragment, Haplotype>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.OrientationBiasReadCounts
- annotate(ReferenceContext, FeatureContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>, AlleleLikelihoods<?, Allele>, AlleleLikelihoods<?, Haplotype>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.HaplotypeFilteringAnnotation
- annotate(ReferenceContext, FeatureContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>, AlleleLikelihoods<? extends Locatable, Allele>, AlleleLikelihoods<? extends Locatable, Haplotype>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.AssemblyComplexity
- annotate(ReferenceContext, FeatureContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>, AlleleLikelihoods<? extends Locatable, Allele>, AlleleLikelihoods<? extends Locatable, Haplotype>) - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.JumboInfoAnnotation
- annotate(ClosestSVFinder.ClosestPair) - Method in class org.broadinstitute.hellbender.tools.sv.concordance.SVConcordanceAnnotator
-
Annotates the given evaluation record with genotype concordance metrics.
- ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
-
Depending on the value of the --max_alternate_alleles argument, we may genotype only a fraction of the alleles being sent on for genotyping.
- annotateAllSitesWithPLs - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection
-
Advanced, experimental argument: if SNP likelihood model is specified, and if EMIT_ALL_ACTIVE_SITES output mode is set, when we set this argument then we will also emit PLs at all sites.
- annotateBreakend(SimpleInterval, GencodeGtfTranscriptFeature) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Get consequence of breakend on transcript Shares common logic with deletions (simple consequence + TSS overlap check) but low-confidence BNDs should not be annotated as LOF, so LOF consequences are changed to BREAKEND_EXONIC
- annotateBreakpointBasedCallsWithImpreciseEvidenceLinks(List<VariantContext>, PairedStrandedIntervalTree<EvidenceTargetLink>, ReadMetadata, SAMSequenceDictionary, StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection, Logger) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.AnnotatedVariantProducer
- annotateContext(VariantContext, FeatureContext, ReferenceContext, AlleleLikelihoods<GATKRead, Allele>, Predicate<VariantAnnotation>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
-
Annotates the given variant context - adds all annotations that satisfy the predicate.
- annotateContext(VariantContext, FeatureContext, ReferenceContext, AlleleLikelihoods<GATKRead, Allele>, Optional<AlleleLikelihoods<Fragment, Allele>>, Optional<AlleleLikelihoods<Fragment, Haplotype>>, Optional<AlleleLikelihoods<GATKRead, Haplotype>>, Predicate<VariantAnnotation>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
-
Annotates the given variant context - adds all annotations that satisfy the predicate.
- annotateCopyNumberVariant(SimpleInterval, GencodeGtfTranscriptFeature, Set<String>) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Get consequence for SV of type CNV (multiallelic copy number variant).
- ANNOTATED_INTERVAL_DEFAULT_CONFIG_RESOURCE - Static variable in class org.broadinstitute.hellbender.utils.codecs.AnnotatedIntervalCodec
- ANNOTATED_INTERVALS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument
- ANNOTATED_VCF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- annotateDeletion(SimpleInterval, GencodeGtfTranscriptFeature) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Get consequence of deletion variant on transcript
- AnnotatedInterval - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
-
Represents an interval with a set of annotations.
- AnnotatedInterval - Class in org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
-
Simple class that just has an interval and sorted name-value pairs.
- AnnotatedInterval(SimpleInterval, SortedMap<String, String>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval
- AnnotatedInterval(SimpleInterval, AnnotationMap) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.AnnotatedInterval
- AnnotatedIntervalCodec - Class in org.broadinstitute.hellbender.utils.codecs
-
Read AnnotatedIntervals from a xsv file (see
XsvLocatableTableCodec. - AnnotatedIntervalCodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.AnnotatedIntervalCodec
-
Use the default config for tribble.
- AnnotatedIntervalCodec(Path) - Constructor for class org.broadinstitute.hellbender.utils.codecs.AnnotatedIntervalCodec
- AnnotatedIntervalCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
Represents a collection of intervals annotated with
CopyNumberAnnotations. - AnnotatedIntervalCollection - Class in org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
-
Represents a collection of annotated intervals.
- AnnotatedIntervalCollection(File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AnnotatedIntervalCollection
- AnnotatedIntervalCollection(LocatableMetadata, List<AnnotatedInterval>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AnnotatedIntervalCollection
- AnnotatedIntervalHeader - Class in org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
- AnnotatedIntervalHeader(String, String, String, List<String>, SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalHeader
- AnnotatedIntervalToSegmentVariantContextConverter - Class in org.broadinstitute.hellbender.tools.funcotator
-
Converts an annotated interval representing a segment to a variant context.
- AnnotatedIntervalUtils - Class in org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
- AnnotatedIntervalWriter - Interface in org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
- annotateDuplication(SimpleInterval, GencodeGtfTranscriptFeature) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Get consequence of duplication variant on transcript
- AnnotatedVariantProducer - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
-
Given identified pair of breakpoints for a simple SV and its supportive evidence, i.e.
- AnnotatedVariantProducer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.AnnotatedVariantProducer
- annotatedVcf - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- annotateGeneOverlaps(SimpleInterval, GATKSVVCFConstants.StructuralVariantAnnotationType, Map<String, Set<String>>) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Add protein-coding annotations for any transcripts overlapping the variant to the variant consequence dictionary
- annotateInsertion(SimpleInterval, GencodeGtfTranscriptFeature) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Get consequence of insertion variant on transcript
- AnnotateIntervals - Class in org.broadinstitute.hellbender.tools.copynumber
-
Annotates intervals with GC content, and optionally, mappability and segmental-duplication content.
- AnnotateIntervals() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervals
- annotateInversion(SimpleInterval, GencodeGtfTranscriptFeature) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Get consequence of inversion variant on transcript Shares common logic (simple consequence + TSS overlap -> LOF) and adds check for spanning inversions
- annotateNearestTranscriptionStartSite(SimpleInterval, Map<String, Set<String>>) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Add nearest TSS annotation to a variant's consequence dictionary To be run on intergenic variants that don't overlap promoters
- annotateOverlap(List<VariantContext>, String, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator
-
Add overlaps flag attributes to vcToAnnotate overlapTestVCs.getSource() => true if an overlapping variant context can be found in overlapTestVCs with vcToAnnotate Overlaps here means that the reference alleles are the same and at least one alt allele in vcToAnnotate is equals to one of the alt alleles in overlapTestVCs
- annotateOverlaps(FeatureContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator
-
Add overlap attributes to vcToAnnotate against all overlaps in featureContext
- annotateRawData(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth
-
Note: There is no raw annotation for AS_QualByDepth and thus this method does nothing.
- annotateRawData(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
-
Generates an annotation by calling the client implementation of getElementForRead(GATKRead read) over each read given its best assigned allele and returns the value of the allele as a double.
- annotateRawData(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality
- annotateRawData(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
-
Uses the likelihoods map to generate a 2x2 strand contingency table by counting the total read support for each allele in either the forward or reverse direction.
- annotateRawData(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation
-
Generate the raw data necessary to calculate the annotation.
- annotateRawData(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet
-
Generate the raw data necessary to calculate the annotation.
- annotateRawData(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RawGtCount
- annotateRawData(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
-
Generate the raw data necessary to calculate the annotation.
- annotateReadLikelihoodsWithRegions(AlleleLikelihoods<GATKRead, Haplotype>, Locatable) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
-
Annotates reads in AlleleLikelihoods with alignment region (the ref region spanned by the haplotype the read is aligned to) and callable region (the ref region over which a caller is using these AlleleLikelihoods to call variants)
- annotateReadLikelihoodsWithSupportedAlleles(VariantContext, AlleleLikelihoods<GATKRead, Allele>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
-
For the given variant, reads are annotated with which alleles they support, if any.
- annotateReadLikelihoodsWithSupportedAlleles(VariantContext, AlleleLikelihoods<U, Allele>, Function<U, Collection<GATKRead>>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
-
For the given variant, reads are annotated with which alleles they support, if any.
- annotateRsID(List<VariantContext>, VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator
-
Update rsID of vcToAnnotate with rsID match found in vcsAtLoc, if one exists
- annotateRsID(FeatureContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator
-
Update rsID in vcToAnnotate with rsIDs from dbSNP fetched from featureContext
- annotateStructuralVariant(VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Create a consequence -> feature name map and add all annotations for protein-coding, promoter, nearest TSS, and noncoding consequences for a variant
- annotateTranscript(SimpleInterval, GATKSVVCFConstants.StructuralVariantAnnotationType, GencodeGtfTranscriptFeature, Map<String, Set<String>>) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Add consequence of structural variant on an overlapping transcript to consequence dictionary for variant
- annotateTranslocation(SimpleInterval, GencodeGtfTranscriptFeature) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Get consequence of translocation on transcript Only called with transcripts that overlap the translocation variant, so consequence is automatically LOF because any translocation that breaks a gene is predicted to cause loss of function of that gene.
- AnnotateVcfWithBamDepth - Class in org.broadinstitute.hellbender.tools.walkers.validation
-
Annotate every variant in a VCF with the depth at that locus in a bam.
- AnnotateVcfWithBamDepth() - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithBamDepth
- AnnotateVcfWithExpectedAlleleFraction - Class in org.broadinstitute.hellbender.tools.walkers.validation
-
Given mixing weights of different samples in a pooled bam, annotate a corresponding vcf containing individual sample genotypes.
- AnnotateVcfWithExpectedAlleleFraction() - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithExpectedAlleleFraction
- annotateWithLikelihoods(VariantContext, Genotype, Set<Allele>, AlleleLikelihoods<EVIDENCE, Allele>) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.DepthPerAlleleBySample
- Annotation - Interface in org.broadinstitute.hellbender.tools.walkers.annotator
-
An annotation group is a set of annotation that have something in common and should be added at the same time.
- ANNOTATION_DEFAULTS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
-
Do not give this a static default value or the integration tests will get hosed.
- ANNOTATION_GROUP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- ANNOTATION_GROUP_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- ANNOTATION_LIST_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.CalculateAverageCombinedAnnotations
- ANNOTATION_LIST_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.CalculateAverageCombinedAnnotations
- ANNOTATION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- ANNOTATION_OVERRIDES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
-
Do not give this a static default value or the integration tests will get hosed.
- annotation_packages() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- ANNOTATION_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- ANNOTATION_SOURCE_ENA - Static variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- ANNOTATION_SOURCE_ENSEMBL - Static variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- ANNOTATION_SOURCE_HAVANA - Static variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- annotationDefaults - Variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
- annotationEngine - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
- annotationEngine - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine
- AnnotationException - Exception in picard.annotation
-
Exception thrown when loading gene annotations.
- AnnotationException(String) - Constructor for exception picard.annotation.AnnotationException
- AnnotationException(String, Throwable) - Constructor for exception picard.annotation.AnnotationException
- AnnotationKey<T> - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation
-
Represents a key for a named, typed annotation.
- AnnotationKey(String, Class<T>, Function<T, Boolean>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationKey
- annotationKeys - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- AnnotationMap - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation
-
Represents an immutable ordered collection of named, typed annotations for an interval.
- AnnotationMap(List<Pair<AnnotationKey<?>, Object>>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationMap
- annotationOrder - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator
- annotationOverrideMap - Variable in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
Map of ANNOTATION_NAME -> OVERRIDE_VALUE.
- annotationOverrides - Variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
- ANNOTATIONS - Static variable in class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.CopyNumberAnnotations
-
This defines the canonical order of these annotations.
- ANNOTATIONS_HDF5_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
- ANNOTATIONS_HDF5_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
- ANNOTATIONS_NAMES_PATH - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- ANNOTATIONS_PATH - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- ANNOTATIONS_TO_EXCLUDE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- ANNOTATIONS_TO_EXCLUDE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- ANNOTATIONS_TO_KEEP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- ANNOTATIONS_TO_MATCH - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsByAnnotation
- annotationSource - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
-
Keyword identifying the source of this feature.
- annotationType() - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeAnnotation
- annotationType() - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation
- annotationType() - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.JumboGenotypeAnnotation
- annotationType() - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.JumboInfoAnnotation
- annotationType() - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotation
- AnnotationUtils - Class in org.broadinstitute.hellbender.tools.walkers.annotator
- annotatorEngine - Variable in class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
- anonymousOptionalFields - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
-
Additional optional GTF fields.
- ANTISENSE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- ANTISENSE_RNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- ANY - Static variable in enum class org.broadinstitute.hellbender.utils.Nucleotide
- ApacheSingularValueDecomposer - Class in org.broadinstitute.hellbender.utils.svd
-
Perform singular value decomposition (and pseudoinverse calculation) in pure Java, Commons Math.
- ApacheSingularValueDecomposer() - Constructor for class org.broadinstitute.hellbender.utils.svd.ApacheSingularValueDecomposer
- api - Variable in class org.broadinstitute.hellbender.utils.dragstr.DragstrParamsBuilder
- api(int, int) - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParams
-
Returns the API for a specific period and repeat length in Phred scale.
- api(int, int) - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParamsBuilder
- API_MONO_THRESHOLD_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- API_TABLE_NAME - Static variable in class org.broadinstitute.hellbender.utils.dragstr.DragstrParamUtils
- API_VALUES_ARGUMENT_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- append(double) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the next double value in the data-line that correspond to a column.
- append(double...) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the next double values in the data-line that correspond to next few columns.
- append(int) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the next int value in the data-line that correspond to a column.
- append(int...) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the next int values in the data-line that correspond to next few columns.
- append(long) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the next long value in the data-line that correspond to a column.
- append(long...) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the next long values in the data-line that correspond to next few columns.
- append(String) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the next string value in the data-line that correspond to a column.
- append(String...) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the next string values in the data-line that correspond to next few columns.
- append(List<T>, T...) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Create a new list that contains the elements of left along with elements elts
- appendPathToDir(String, String) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Appends path to the given parent dir.
- appendSATagString(StringBuilder) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
Appends the SA string representation of this interval into a builder.
- appendSequence - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- apply(int) - Method in interface org.broadinstitute.hellbender.utils.MathUtils.IntToDoubleArrayFunction
- apply(int, int) - Method in interface org.broadinstitute.hellbender.utils.functional.IntToDoubleBiFunction
- apply(F, Object, ReadsContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker
-
Process an individual feature.
- apply(F, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.FeatureWalker
-
Process an individual feature.
- apply(Locatable, List<VariantContext>, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.VariantLocusWalker
-
Process by locus, with all variants overlapping the current locus, or by individual variant when in by-variants traversal mode.
- apply(Locatable, List<VariantContext>, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- apply(BEDFeature, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleFeatureWalker
- apply(Feature, Object, ReadsContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleMultiFeatureWalker
-
Do something with the merged stream of features.
- apply(Feature, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.sv.PrintReadCounts
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.MultiplePassVariantWalker
-
Make final to hide it from subclasses
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalker
-
Process an individual variant.
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
-
This method keeps track of all the variants it is passed and will feed all the variants that start at the same site to the reduce method.
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.VariantWalker
-
Process an individual variant.
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.CalculateAverageCombinedAnnotations
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.Funcotator
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
-
For each site of interest, annotate based on the requested annotation types
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.CountVariants
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyper
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NuMTFilterTool
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithBamDepth
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithExpectedAlleleFraction
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.CalculateMixingFractions
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.CountFalsePositives
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.RemoveNearbyIndels
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
-
Left aligns variants in repetitive regions.
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionary
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTable
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSR
- apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator
- apply(Iterator<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaFilter
- apply(Iterator<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerCounter
- apply(Iterator<GATKRead>, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaAligner
- apply(List<VariantContext>, List<ReadsContext>) - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
- apply(List<VariantContext>, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- apply(List<VariantContext>, ReferenceContext, List<ReadsContext>) - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
-
This method must be implemented by tool authors.
- apply(List<VariantContext>, ReferenceContext, List<ReadsContext>) - Method in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
- apply(List<VariantContext>, ReferenceContext, List<ReadsContext>) - Method in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- apply(List<VariantContext>, ReferenceContext, List<ReadsContext>) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- apply(List<VariantContext>, ReferenceContext, List<ReadsContext>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval
- apply(JavaPairRDD<GATKRead, Iterable<GATKVariant>>, SAMFileHeader, String, RecalibrationArgumentCollection) - Static method in class org.broadinstitute.hellbender.tools.spark.transforms.BaseRecalibratorSparkFn
-
Run the
BaseRecalibrationEngineon reads and overlapping variants. - apply(JavaRDD<GATKRead>, Broadcast<RecalibrationReport>, SAMFileHeader, ApplyBQSRArgumentCollection) - Static method in class org.broadinstitute.hellbender.tools.spark.transforms.ApplyBQSRSparkFn
- apply(AbstractConcordanceWalker.TruthVersusEval, ReadsContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- apply(AbstractConcordanceWalker.TruthVersusEval, ReadsContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVConcordance
- apply(AbstractConcordanceWalker.TruthVersusEval, ReadsContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- apply(AbstractConcordanceWalker.TruthVersusEval, ReadsContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance
- apply(AbstractConcordanceWalker.TruthVersusEval, ReadsContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3
- apply(AbstractConcordanceWalker.TruthVersusEval, ReadsContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance
- apply(AlignmentContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.LocusWalker
-
Process an individual AlignmentContext (with optional contextual information).
- apply(AlignmentContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.LocusWalkerByInterval
- apply(AlignmentContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCounts
- apply(AlignmentContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleLocusWalker
- apply(AlignmentContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- apply(AlignmentContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.MethylationTypeCaller
- apply(AlignmentContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactData
- apply(AlignmentContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.qc.CheckPileup
- apply(AlignmentContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.qc.Pileup
- apply(AlignmentContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2Counts
- apply(AlignmentContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter
- apply(AlignmentContext, ReferenceContext, FeatureContext, Set<Locatable>) - Method in class org.broadinstitute.hellbender.engine.LocusWalkerByInterval
-
Process an individual AlignmentContext (with optional contextual information).
- apply(AlignmentContext, ReferenceContext, FeatureContext, Set<Locatable>) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage
- apply(AssemblyRegion, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionWalker
-
Process an individual AssemblyRegion.
- apply(AssemblyRegion, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalker
- apply(AssemblyRegion, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
- apply(AssemblyRegion, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- apply(ReferenceContext, ReadsContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.ReferenceWalker
-
Process an individual reference locus (with optional contextual information).
- apply(ReferenceContext, ReadsContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalker
- apply(ReferenceContext, ReadsContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference
- apply(ReferenceContext, ReadsContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker
- apply(ReferenceContext, ReadsContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker
- apply(AnnotatedInterval, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotateSegments
- apply(BreakpointEvidence) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidenceClusterer
- apply(DepthEvidence, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.sv.CondenseDepthEvidence
- apply(SiteDepth, Object, ReadsContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAF
- apply(SVFeature, Object, ReadsContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.sv.PrintSVEvidence
- apply(ReadsWithSameUMI, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.DuplicateSetWalker
-
A subclass must specify how to process the duplicate sets by overriding this method.
- apply(ReadsWithSameUMI, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSet
- apply(VariantEvalContext, VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.EvaluationContext
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceWindowFunctions.FixedWindowFunction
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameFinder
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameIntervalFinder
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameKmerizer
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNamesForKmersFinder
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadClassifier
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.transformers.AdapterTrimTransformer
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.transformers.BaseQualityClipReadTransformer
-
Clip bases on the right end of the read from
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.transformers.BaseQualityReadTransformer
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.transformers.BQSRReadTransformer
-
Recalibrates the base qualities of a read
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.transformers.DRAGENMappingQualityReadTransformer
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.transformers.DUSTReadTransformer
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.transformers.IUPACReadTransformer
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.transformers.MappingQualityReadTransformer
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.transformers.MisencodedBaseQualityReadTransformer
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.transformers.NDNCigarReadTransformer
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.transformers.SimpleRepeatMaskTransformer
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.transformers.StripMateNumberTransformer
- apply(GATKRead) - Method in class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine.BQSRReferenceWindowFunction
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.DuplicateSetWalker
-
FGBio GroupByUMI returns reads sorted by molecule ID: For example, the input bam may look like read1: ...
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.MultiplePassReadWalker
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.ReadWalker
-
Process an individual read (with optional contextual information).
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.AddOriginalAlignmentTags
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.ClipReads
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.CountBases
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.CountReads
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExamplePartialReadWalker
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExamplePostTraversalPythonExecutor
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReference
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariants
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleStreamingPythonExecutor
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.FixMisencodedBaseQualityReads
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.FlagStat
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.LeftAlignIndels
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.PrintDistantMates
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.PrintReads
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.SplitReads
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.StructuralVariantDiscoverer
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator
-
For each read at this locus get the various covariate values and increment that location in the map based on whether or not the base matches the reference at this particular location
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.PairWalker
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.ReadAnonymizer
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.RevertBaseQualityScores
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- apply(GATKRead, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.UnmarkDuplicates
- apply(GATKRead, GATKRead) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler
- apply(GATKRead, GATKRead) - Method in class org.broadinstitute.hellbender.tools.walkers.PairWalker
-
This method is called once for each pair of reads.
- apply(SimpleInterval, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.IntervalWalker
-
Process an individual interval.
- apply(SimpleInterval, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalker
- apply(Tuple2<Integer, List<SVFastqUtils.FastqRead>>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FermiLiteAssemblyHandler
-
This method creates an assembly with FermiLite, and uses the graph information returned by that assembler to stitch together valid paths through the contigs.
- apply(T) - Method in interface org.broadinstitute.hellbender.utils.SerializableFunction
- apply(T, U, V) - Method in interface org.broadinstitute.hellbender.tools.spark.sv.utils.SingleSequenceReferenceAligner.TriFunction
- APPLY_BQD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- APPLY_EAMSS_FILTER - Variable in class picard.illumina.IlluminaBasecallsToFastq
- APPLY_EAMSS_FILTER - Variable in class picard.illumina.IlluminaBasecallsToSam
- APPLY_FRD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- APPLY_JEXL_FIRST_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
- APPLY_JEXL_FIRST_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
-
This flag is provided to allow the user to do JEXL filtering before subsetting the format fields, in particular the case where the filtering is done on INFO fields only, which may improve speed when working with a large cohort vcf that contains genotypes for thousands of samples (format fields).
- applyAlignment() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- applyAlignment(String, byte[], byte[], String, BwaMemAlignment, List<String>, SAMFileHeader, boolean, boolean) - Static method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignmentUtils
-
Builds a SAMRecord from unaligned read data and an alignment.
- applyBaseClipping(int, int, boolean) - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- applyBQD - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- ApplyBQSR - Class in org.broadinstitute.hellbender.tools.walkers.bqsr
-
Apply base quality score recalibration
- ApplyBQSR() - Constructor for class org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR
- applyBqsrArgs - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark
-
command-line arguments to fine tune the apply BQSR step.
- applyBqsrArgs - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
-
command-line arguments to fine tune the apply BQSR step.
- ApplyBQSRArgumentCollection - Class in org.broadinstitute.hellbender.tools
-
The collection of all arguments needed for ApplyBQSR.
- ApplyBQSRArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.ApplyBQSRArgumentCollection
- ApplyBQSRSpark - Class in org.broadinstitute.hellbender.tools.spark
-
Apply base quality score recalibration with Spark.
- ApplyBQSRSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.ApplyBQSRSpark
- ApplyBQSRSparkFn - Class in org.broadinstitute.hellbender.tools.spark.transforms
- ApplyBQSRSparkFn() - Constructor for class org.broadinstitute.hellbender.tools.spark.transforms.ApplyBQSRSparkFn
- ApplyBQSRUniqueArgumentCollection - Class in org.broadinstitute.hellbender.tools
-
The collection of those arguments for ApplyBQSR that are not already defined in RecalibrationArgumentCollection.
- ApplyBQSRUniqueArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.ApplyBQSRUniqueArgumentCollection
- applyCigarToCigar(Cigar, Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Generate a new Cigar that maps the operations of the first cigar through those in a second For example, if first is 5M and the second is 2M1I2M then the result is 2M1I2M.
- applyFilter(Iterator<GATKRead>, BiPredicate<SVReadFilter, GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter
- applyFiltersAndAccumulateOutputStats(VariantContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
-
Create a filtered variant and record statistics for the final pass of
FilterMutectCalls - applyForAllele - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- applyFRD - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- applyMapFunc(Function<I, Iterator<O>>, Iterator<? extends I>) - Static method in class org.broadinstitute.hellbender.tools.spark.utils.FlatMapGluer
- applyMapFunc(Function<I, Iterator<O>>, Iterator<? extends I>, I) - Static method in class org.broadinstitute.hellbender.tools.spark.utils.FlatMapGluer
- applyToArray(double[], DoubleUnaryOperator) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
The following method implements Arrays.stream(array).map(func).toArray(), which is concise but performs poorly due to the overhead of creating a stream, especially with small arrays.
- applyToArray(int[], IntToDoubleFunction) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
The following method implements Arrays.stream(array).map(func).toArray(), which is concise but performs poorly due to the overhead of creating a stream, especially with small arrays.
- applyToArrayInPlace(double[], DoubleUnaryOperator) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
The following method implements Arrays.stream(array).map(func).toArray(), which is concise but performs poorly due to the overhead of creating a stream, especially with small arrays.
- applyUnpaired(GATKRead) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler
- applyUnpaired(GATKRead) - Method in class org.broadinstitute.hellbender.tools.walkers.PairWalker
-
Unpaired reads, secondary and supplemental alignments, and other detritus comes through here.
- ApplyVQSR - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
-
Apply a score cutoff to filter variants based on a recalibration table
- ApplyVQSR() - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSR
- APPRIS_ALTERNATIVE_1 - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Candidate transcript(s) models that are conserved in at least three tested non-primate species.
- APPRIS_ALTERNATIVE_2 - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Candidate transcript(s) models that appear to be conserved in fewer than three tested non-primate species.
- APPRIS_CANDIDATE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
where there is no single 'appris_principal' variant the main functional isoform will be translated from one of the
- APPRIS_CANDIDATE_CCDS - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
the "appris_candidate" transcript that has an unique CCDS.
- APPRIS_CANDIDATE_HIGHEST_SCORE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
where there is no 'appris_principal' variant, the candidate with highest APPRIS score is selected as the primary
- APPRIS_CANDIDATE_LONGEST - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
where there is no 'appris_principal' variant, the longest of the 'appris_candidate' variants is selected as the primary
- APPRIS_CANDIDATE_LONGEST_CCDS - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
the "appris_candidate" transcripts where there are several CCDS, in this case APPRIS labels the longest CCDS.
- APPRIS_CANDIDATE_LONGEST_SEQ - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
where there is no "appris_candidate_ccds" or "appris_candidate_longest_ccds" variant, the longest protein of the
- APPRIS_PRINCIPAL - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Transcript expected to code for the main functional isoform based on a range of protein features (APPRIS pipeline).
- APPRIS_PRINCIPAL_1 - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
(This flag corresponds to the older flag "appris_principal") Where the transcript expected to code for the main
- APPRIS_PRINCIPAL_2 - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
(This flag corresponds to the older flag "appris_candidate_ccds") Where the APPRIS core modules are unable to choose a
- APPRIS_PRINCIPAL_3 - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Where the APPRIS core modules are unable to choose a clear principal variant and there more than one of the variants
- APPRIS_PRINCIPAL_4 - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
(This flag corresponds to the Ensembl 78 flag "appris_candidate_longest_ccds") Where the APPRIS core modules are unable
- APPRIS_PRINCIPAL_5 - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
(This flag corresponds to the Ensembl 78 flag "appris_candidate_longest_seq") Where the APPRIS core modules are unable
- approximateLog10SumLog10(double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- approximateLog10SumLog10(double[], int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- approximateLog10SumLog10(double[], int, int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Calculate the approximate log10 sum of an array range.
- approximateLog10SumLog10(double, double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- approximateLog10SumLog10(double, double, double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- AR_INFO_VALUE - Static variable in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AutosomalRecessiveConstants
- ARE_EQUAL - Variable in class picard.sam.SamComparisonMetric
-
Whether or not to consider the two input files equal.
- areAllelesArtifacts(VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MTLowHeteroplasmyFilterTool
- areAllelesArtifacts(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.BaseQualityFilter
- areAllelesArtifacts(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.DuplicatedAltReadFilter
- areAllelesArtifacts(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.HardAlleleFilter
- areAllelesArtifacts(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MappingQualityFilter
- areAllelesArtifacts(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MinAlleleFractionFilter
- areAllelesArtifacts(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadPositionFilter
- areAllelesArtifacts(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrictStrandBiasFilter
- areAnyGencodeFuncotation(List<Funcotation>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
- areClusterable(SVCallRecord, SVCallRecord) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- areClusterable(SVCallRecord, SVCallRecord) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CNVLinkage
- areClusterable(SVCallRecord, SVCallRecord) - Method in class org.broadinstitute.hellbender.tools.sv.concordance.SVConcordanceLinkage
- areClusterable(T, T) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterLinkage
-
Returns whether two given items cluster.
- areComparableForDuplicates(ReadEndsForMarkDuplicates, ReadEndsForMarkDuplicates, boolean, boolean) - Method in class picard.sam.markduplicates.MarkDuplicates
- areEqual() - Method in class picard.sam.util.SamComparison
- areHistogramsEmpty() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
- areVariantsAtSameLocusConcordant(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- areVariantsAtSameLocusConcordant(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVConcordance
- areVariantsAtSameLocusConcordant(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- areVariantsAtSameLocusConcordant(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance
- areVariantsAtSameLocusConcordant(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3
- areVariantsAtSameLocusConcordant(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance
- ARGANINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- argmax(Function<Double, Double>, double, double, double) - Static method in class org.broadinstitute.hellbender.utils.OptimizationUtils
- ARGUMENT_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- ARGUMENT_REPORT_TABLE_TITLE - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- ARGUMENT_VALUE_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- ArHetvarFilter - Class in org.broadinstitute.hellbender.tools.funcotator.filtrationRules
- ArHetvarFilter(FilterFuncotations.Reference, String[]) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ArHetvarFilter
- ArHomvarFilter - Class in org.broadinstitute.hellbender.tools.funcotator.filtrationRules
- ArHomvarFilter(FilterFuncotations.Reference) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ArHomvarFilter
- ARRAY_COLUMN_BOUNDS_END - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- ARRAY_COLUMN_BOUNDS_START - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- ARRAY_DIM - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest
- ARRAY_SIZE - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest
- ARRAY_TYPE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- arrayListCollector(int) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
-
Provides a stream collector that will collect items into an array list with a given initial capacity.
- arrayMax(double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- arrayMax(int[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- arrayMax(int[], int, int, int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Returns the maximum value within and int array interval.
- arrayMin(int[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- ArraysControlCodesSummaryMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
- ArraysControlInfo - Class in picard.arrays.illumina
-
A simple class to store names and counts for the the Control Information fields that are stored in an Illumina GTC file.
- ArraysControlInfo(String, String, int, int) - Constructor for class picard.arrays.illumina.ArraysControlInfo
- ArraysVariantCallingDetailMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
- ArraysVariantCallingSummaryMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
- ARTIFACT - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorType
- ARTIFACT - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- ARTIFACT_IN_NORMAL_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- ARTIFACT_NAME - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
A "nickname" of this artifact, if it is a known error mode.
- ARTIFACT_NAME - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
A "nickname" of this artifact, if it is a known error mode.
- ARTIFACT_PRIOR_EXTENSION - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel
- ARTIFACT_PRIOR_TABLE_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- ARTIFACT_PRIOR_TABLE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- ArtifactPrior - Class in org.broadinstitute.hellbender.tools.walkers.readorientation
-
Container for the artifact prior probabilities for the read orientation model
- ArtifactPrior(String, double[], int, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPrior
- ArtifactPrior.ArtifactPriorTableReader - Class in org.broadinstitute.hellbender.tools.walkers.readorientation
- ArtifactPrior.ArtifactPriorTableWriter - Class in org.broadinstitute.hellbender.tools.walkers.readorientation
- ArtifactPriorCollection - Class in org.broadinstitute.hellbender.tools.walkers.readorientation
-
Container class for
ArtifactPriorobjects. - ArtifactPriorCollection(String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPriorCollection
- ArtifactPriorTableReader(Path) - Constructor for class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPrior.ArtifactPriorTableReader
- ArtifactPriorTableWriter(Path, String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPrior.ArtifactPriorTableWriter
- ArtifactState - Enum Class in org.broadinstitute.hellbender.tools.walkers.readorientation
-
This enum encapsulates the domain of the discrete latent random variable z
- ArtificialBAMBuilder - Class in org.broadinstitute.hellbender.utils.read
-
Easy to use creator of artificial BAM files for testing Allows us to make a stream of reads or an index BAM file with read having the following properties - coming from n samples - of fixed read length and aligned to the genome with M operator - having N reads per alignment start - skipping N bases between each alignment start - starting at a given alignment start
- ArtificialBAMBuilder(int, int) - Constructor for class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- ArtificialBAMBuilder(SAMSequenceDictionary, int, int) - Constructor for class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- ArtificialReadIterator - Class in org.broadinstitute.hellbender.utils.read
-
this fake iterator allows us to look at how specific piles of reads are handled
- ArtificialReadQueryIterator - Class in org.broadinstitute.hellbender.utils.read
- ArtificialReadUtils - Class in org.broadinstitute.hellbender.utils.read
- ArtificialReadUtils() - Constructor for class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- AS_ALT_ALLELE_DEPTH_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_BASE_QUAL_RANK_SUM_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_BaseQualityRankSumTest - Class in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
Allele-specific rank Sum Test of REF versus ALT base quality scores
- AS_BaseQualityRankSumTest() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_BaseQualityRankSumTest
- AS_CULPRIT_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_FILTER_STATUS_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_FISHER_STRAND_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_FisherStrand - Class in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
Allele-specific strand bias estimated using Fisher's Exact Test *
- AS_FisherStrand() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_FisherStrand
- AS_INBREEDING_COEFFICIENT_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_InbreedingCoeff - Class in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
Allele-specific likelihood-based test for the inbreeding among samples
- AS_InbreedingCoeff() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_InbreedingCoeff
- AS_InbreedingCoeff(Set<String>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_InbreedingCoeff
- AS_MAP_QUAL_RANK_SUM_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_MappingQualityRankSumTest - Class in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
Allele specific Rank Sum Test for mapping qualities of REF versus ALT reads
- AS_MappingQualityRankSumTest() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_MappingQualityRankSumTest
- AS_QUAL_BY_DEPTH_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_QUAL_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_QualByDepth - Class in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
Allele-specific call confidence normalized by depth of sample reads supporting the allele
- AS_QualByDepth() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth
- AS_RankSumTest - Class in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
Allele-specific implementation of rank sum test annotations
- AS_RankSumTest() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
- AS_RAW_BASE_QUAL_RANK_SUM_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_RAW_MAP_QUAL_RANK_SUM_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_RAW_QUAL_APPROX_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_RAW_READ_POS_RANK_SUM_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_RAW_RMS_MAPPING_QUALITY_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_READ_POS_RANK_SUM_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_ReadPosRankSumTest - Class in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
Allele-specific Rank Sum Test for relative positioning of REF versus ALT allele within reads
- AS_ReadPosRankSumTest() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_ReadPosRankSumTest
- AS_RMS_MAPPING_QUALITY_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_RMSMappingQuality - Class in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
Allele-specific Root Mean Square of the mapping quality of reads across all samples.
- AS_RMSMappingQuality() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality
- AS_SB_TABLE_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_SBP_TABLE_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_StandardAnnotation - Interface in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
This is a marker interface used to indicate which annotations are "Standard" and allele-specific.
- AS_STRAND_ODDS_RATIO_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_STRAND_ODDS_RATIO_PROB_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_StrandBiasMutectAnnotation - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Adds the strand bias table annotation for use in mutect filters
- AS_StrandBiasMutectAnnotation() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.AS_StrandBiasMutectAnnotation
- AS_StrandBiasTest - Class in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
Allele-specific implementation of strand bias annotations
- AS_StrandBiasTest() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
- AS_StrandOddsRatio - Class in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
Allele-specific strand bias estimated by the Symmetric Odds Ratio test
- AS_StrandOddsRatio() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandOddsRatio
- AS_UNIQUE_ALT_READ_SET_COUNT_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_VARIANT_DEPTH_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_VQS_LOD_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- AS_Warning - Variable in class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
- asAlleleList(List<T>) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Composes a list with the alleles, possibly containing repeats i.e.
- asAttributes() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase.LocalContext
- asDoubleArray(Collection<Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection
- ASEReadCounter - Class in org.broadinstitute.hellbender.tools.walkers.rnaseq
-
Calculate read counts per allele for allele-specific expression analysis of RNAseq data
- ASEReadCounter() - Constructor for class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter
- ASEReadCounter.CountPileupType - Enum Class in org.broadinstitute.hellbender.tools.walkers.rnaseq
- ASEReadCounter.OUTPUT_FORMAT - Enum Class in org.broadinstitute.hellbender.tools.walkers.rnaseq
- asList() - Method in class org.broadinstitute.hellbender.utils.collections.IndexedSet
-
Returns a list view of the elements in the set.
- asList() - Method in class picard.vcf.GenotypeConcordance.Alleles
- asList(double...) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Returns a
List<Double>representation of an primitive double array. - asList(int...) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Returns a
List<Integer>representation of an primitive int array. - asListOfAlleles() - Method in interface org.broadinstitute.hellbender.utils.genotyper.AlleleList
-
Returns a
Listunmodifiable view of this allele-list - asListOfSamples() - Method in interface org.broadinstitute.hellbender.utils.genotyper.SampleList
-
Returns a
Listunmodifiable view of a sample-list - ASPARAGINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- ASPARTIC_ACID - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- asRealMatrix() - Method in interface org.broadinstitute.hellbender.utils.genotyper.LikelihoodMatrix
-
Returns this matrix as a
RealMatrix. - ASSEMBLED_SOME_VARIATION - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult.Status
-
Assembly succeeded, and the graph has some meaningful structure
- AssembledEvidenceResults(ReadMetadata, List<SVInterval>, List<AlignedAssemblyOrExcuse>, List<EvidenceTargetLink>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark.AssembledEvidenceResults
- assemblerArgs - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- assembleReads(AssemblyRegion, List<VariantContext>, AssemblyBasedCallerArgumentCollection, SAMFileHeader, SampleList, Logger, ReferenceSequenceFile, ReadThreadingAssembler, SmithWatermanAligner, boolean, FlowBasedArgumentCollection, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
-
High-level function that runs the assembler on the given region's reads, returning a data structure with the resulting information needed for further HC steps
- AssemblerOffRamp - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
- AssemblerOffRamp(String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.AssemblerOffRamp
- assembliesSortOrder - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- ASSEMBLY_ALIGNMENT_MQ_FILTER_DEFAULT - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- ASSEMBLY_BASED_VARIANT_ALN_LENGTH_FILTER_KEY - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- ASSEMBLY_BASED_VARIANT_MQ_FILTER_KEY - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- ASSEMBLY_NAME_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- ASSEMBLY_PADDING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- ASSEMBLY_REGION_OUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- assemblyArgs - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleFiltering
- AssemblyBasedCallerArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Set of arguments for Assembly Based Callers
- AssemblyBasedCallerArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- AssemblyBasedCallerUtils - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Created by davidben on 9/8/16.
- AssemblyBasedCallerUtils() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- AssemblyComplexity - Class in org.broadinstitute.hellbender.tools.walkers.annotator
- AssemblyComplexity() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.AssemblyComplexity
- AssemblyContigAlignmentsRDDProcessor - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
-
A simple heuristic optimizer based on extensive manual review of alignments produced by the aligner (currently "bwa mem -x intractg") with the aim for picking a configuration that provides "optimal coverage" for the input assembly contig.
- AssemblyContigAlignmentsRDDProcessor() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigAlignmentsRDDProcessor
- AssemblyContigAlignmentsRDDProcessor.SAMFormattedContigAlignmentParser - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
- AssemblyContigWithFineTunedAlignments - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
-
A wrapper around
AlignedContigto represent mapped assembly contig whose alignments went throughAssemblyContigAlignmentsRDDProcessorand may represent SV breakpoints. - AssemblyContigWithFineTunedAlignments(AlignedContig) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- AssemblyContigWithFineTunedAlignments(AlignedContig, List<String>, boolean, String) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- AssemblyContigWithFineTunedAlignments(AlignedContig, List<String>, boolean, AlignmentInterval) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- AssemblyContigWithFineTunedAlignments.AlignmentSignatureBasicType - Enum Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
- AssemblyContigWithFineTunedAlignments.ReasonForAlignmentClassificationFailure - Enum Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
- AssemblyContigWithFineTunedAlignments.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
- assemblyDebugOutStream - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- assemblyEngine - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- assemblyId - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedAssembly
- assemblyImpreciseEvidenceOverlapUncertainty - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- assemblyName - Variable in class org.broadinstitute.hellbender.tools.LocalAssembler
- AssemblyRegion - Class in org.broadinstitute.hellbender.engine
-
Region of the genome that gets assembled by the local assembly engine.
- AssemblyRegion(SimpleInterval, boolean, int, SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Create a new AssemblyRegion containing no reads
- AssemblyRegion(SimpleInterval, int, SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Simple interface to create an assembly region that isActive without any profile state
- AssemblyRegion(SimpleInterval, SimpleInterval, boolean, SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Create a new AssemblyRegion containing no reads
- assemblyRegionArgs - Variable in class org.broadinstitute.hellbender.engine.AssemblyRegionWalker
- assemblyRegionArgs - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark
- assemblyRegionArgs - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- AssemblyRegionArgumentCollection - Class in org.broadinstitute.hellbender.engine.spark
- AssemblyRegionArgumentCollection() - Constructor for class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- assemblyRegionEvaluator() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionWalker
- assemblyRegionEvaluator() - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark
- assemblyRegionEvaluator() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalker
- assemblyRegionEvaluator() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerSpark
- assemblyRegionEvaluator() - Method in class org.broadinstitute.hellbender.tools.HaplotypeCallerSpark
- assemblyRegionEvaluator() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
- assemblyRegionEvaluator() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- AssemblyRegionEvaluator - Interface in org.broadinstitute.hellbender.engine
-
Classes that implement this interface have the ability to evaluate how likely it is that a site is "active" (contains potential real variation).
- assemblyRegionEvaluatorSupplierBroadcast(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark
-
Tools that use an evaluator that is expensive to create, and/or that is not compatible with Spark broadcast, can override this method to return a broadcast of a supplier of the evaluator.
- assemblyRegionEvaluatorSupplierBroadcast(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.HaplotypeCallerSpark
- AssemblyRegionFromActivityProfileStateIterator - Class in org.broadinstitute.hellbender.engine
-
Given an iterator of
ActivityProfileState, findsAssemblyRegions. - AssemblyRegionFromActivityProfileStateIterator(Iterator<ActivityProfileState>, SAMFileHeader, int, int, int, double, int) - Constructor for class org.broadinstitute.hellbender.engine.AssemblyRegionFromActivityProfileStateIterator
-
Constructs an AssemblyRegionIterator over a provided read shard
- AssemblyRegionIterator - Class in org.broadinstitute.hellbender.engine
-
Given a
MultiIntervalShardofGATKRead, iterates over eachAssemblyRegionwithin that shard, using the providedAssemblyRegionEvaluatorto determine the boundaries between assembly regions. - AssemblyRegionIterator(MultiIntervalShard<GATKRead>, SAMFileHeader, ReferenceDataSource, FeatureManager, AssemblyRegionEvaluator, AssemblyRegionArgumentCollection, boolean) - Constructor for class org.broadinstitute.hellbender.engine.AssemblyRegionIterator
-
Constructs an AssemblyRegionIterator over a provided read shard
- assemblyRegionOut - Variable in class org.broadinstitute.hellbender.engine.AssemblyRegionWalker
-
If provided, this walker will write out its assembly regions to this file in the IGV formatted TAB-delimited output: http://www.broadinstitute.org/software/igv/IGV Intended to make debugging the active region calculations easier
- assemblyRegionPadding - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
-
Parameters that control assembly regions
- AssemblyRegionReadShardArgumentCollection - Class in org.broadinstitute.hellbender.engine.spark
- AssemblyRegionReadShardArgumentCollection() - Constructor for class org.broadinstitute.hellbender.engine.spark.AssemblyRegionReadShardArgumentCollection
- AssemblyRegionTrimmer - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Helper component to manage active region trimming
- AssemblyRegionTrimmer(AssemblyRegionArgumentCollection, SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer
-
Initializes the trimmer.
- AssemblyRegionTrimmer.Result - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Holds the result of trimming.
- AssemblyRegionWalker - Class in org.broadinstitute.hellbender.engine
-
An AssemblyRegionWalker is a tool that processes an entire region of reads at a time, each marked as either "active" (containing possible variation) or "inactive" (not likely to contain actual variation).
- AssemblyRegionWalker() - Constructor for class org.broadinstitute.hellbender.engine.AssemblyRegionWalker
- AssemblyRegionWalkerContext - Class in org.broadinstitute.hellbender.engine.spark
- AssemblyRegionWalkerContext(AssemblyRegion, ReferenceContext, FeatureContext) - Constructor for class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerContext
- AssemblyRegionWalkerSpark - Class in org.broadinstitute.hellbender.engine.spark
-
A Spark version of
AssemblyRegionWalker. - AssemblyRegionWalkerSpark() - Constructor for class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark
- AssemblyResult - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Result of assembling, with the resulting graph and status
- AssemblyResult(AssemblyResult.Status, SeqGraph, AbstractReadThreadingGraph) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult
-
Create a new assembly result
- AssemblyResult.Status - Enum Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Status of the assembly result
- AssemblyResultSet - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Collection of read assembly using several kmerSizes.
- AssemblyResultSet() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Constructs a new empty assembly result set.
- assemblyStateOutput - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- assemblyToMappedSizeRatioGuess - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- AssemblyTooComplexException() - Constructor for exception org.broadinstitute.hellbender.tools.LocalAssembler.AssemblyTooComplexException
- assertAttributeNameIsLegal(String) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Check whether the given String represents a legal attribute name according to the SAM spec, and throw an exception if it doesn't.
- assertBooleanPropertiesField(Properties, String, Path) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
-
Asserts that the given
fieldis contained in the givenpropsand is a boolean value. - assertConfigFilePropertiesAreValid(Properties, Path) - Method in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.DataSourceType
-
Asserts that the given properties and corresponding config file path are valid for this
FuncotatorArgumentDefinitions.DataSourceType. - assertConfigPropertiesContainsKey(String, Properties, Path) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
-
Asserts that the given
keyis contained in the givenconfigProperties. - assertFileIsReadable(Path) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
- assertHasCopyStateFields(Genotype) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
-
Asserts presence of
GATKSVVCFConstants.EXPECTED_COPY_NUMBER_FORMATandGATKSVVCFConstants.COPY_NUMBER_FORMATattributes. - assertIntegerPropertiesField(Properties, String, Path) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
-
Asserts that the given
fieldis contained in the givenpropsand is an integer value. - assertMinimumQualities() - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
-
Reviews the qualities observed thus far and throws an exception if any are below the minimum quality threshold.
- assertPairedMates(SAMRecord, SAMRecord) - Static method in class picard.sam.SamToFastq
- assertPathFilePropertiesField(Properties, String, Path) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
-
Asserts that the given
fieldis contained in the givenpropsand is a file path. - assertPathsAreReadable(String...) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
- assertProperFileStructure(File) - Method in class picard.illumina.parser.readers.BclReader
- assertSorted(SAMFileHeader.SortOrder) - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
-
Establishes that records returned by this iterator are expected to be in the specified sort order.
- assertValidStrand(Strand) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Asserts that the given strand is non-null and is not equal to
Strand.NONE. - assertVariantFileIsCompressedAndIndexed(Path) - Static method in class org.broadinstitute.hellbender.tools.genomicsdb.GATKGenomicsDBUtils
- assertVariantFileIsCompressedAndIndexed(Path, Path) - Static method in class org.broadinstitute.hellbender.tools.genomicsdb.GATKGenomicsDBUtils
- asSetOfSamples() - Method in interface org.broadinstitute.hellbender.utils.genotyper.SampleList
-
Returns a
Setunmodifiable view of the sample-list - assignGenotypeLikelihoods(List<Haplotype>, AlleleLikelihoods<GATKRead, Haplotype>, Map<String, List<GATKRead>>, byte[], SimpleInterval, SimpleInterval, FeatureContext, List<VariantContext>, boolean, int, SAMFileHeader, boolean, Set<Integer>, AlleleLikelihoods<GATKRead, Haplotype>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine
-
Main entry point of class - given a particular set of haplotypes, samples and reference context, compute genotype likelihoods and assemble into a list of variant contexts and genomic events ready for calling The list of samples we're working with is obtained from the readLikelihoods
- assignLocusFunctionForRange(int, LocusFunction[]) - Method in class picard.annotation.Gene.Transcript
-
Write into locusFunctions the function of each position from start to start + locusFunctions.length relative to this transcript.
- ASSUME_SORT_ORDER - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- ASSUME_SORT_ORDER_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- ASSUME_SORTED - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark
- ASSUME_SORTED - Variable in class picard.analysis.CollectMultipleMetrics
- ASSUME_SORTED - Variable in class picard.analysis.CollectRrbsMetrics
- ASSUME_SORTED - Variable in class picard.analysis.SinglePassSamProgram
- ASSUME_SORTED - Variable in class picard.sam.FixMateInformation
- ASSUME_SORTED - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
Deprecated.
- ASSUME_SORTED - Variable in class picard.sam.MergeSamFiles
- ASSUME_SORTED_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- ASSUME_SORTED_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- ASSUME_SORTED_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- assumingHW(double, double) - Static method in class org.broadinstitute.hellbender.utils.genotyper.GenotypePriorCalculator
-
Composes a calculator based on Hardy-Weinberg equilibrium so that only the het-priors are need to calculate the rest.
- assumingHW(GenotypeCalculationArgumentCollection) - Static method in class org.broadinstitute.hellbender.utils.genotyper.GenotypePriorCalculator
-
Composes a calculator based on Hardy-Weinberg equilibrium so that only the het-priors are need to calculate the rest.
- asTag(BwaMemAlignment, List<String>) - Static method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignmentUtils
-
Describes an alignment as a string for use in an SA tag, for example.
- asVcf(ReferenceSequenceFile) - Method in class picard.fingerprint.HaplotypeMap
- AsynchronousStreamWriter<T> - Class in org.broadinstitute.hellbender.utils.runtime
-
A service that can be used to write to a stream using a thread background thread and an executor service.
- AsynchronousStreamWriter(ExecutorService, OutputStream, Function<T, ByteArrayOutputStream>) - Constructor for class org.broadinstitute.hellbender.utils.runtime.AsynchronousStreamWriter
- AsyncIterator<T> - Class in picard.util
-
Wrapper around a CloseableIterator that reads in a separate thread, for cases in which that might be efficient.
- AsyncIterator(CloseableIterator<T>, int, String) - Constructor for class picard.util.AsyncIterator
- AT - Enum constant in enum class picard.fingerprint.DiploidGenotype
- AT_DROPOUT - Variable in class picard.analysis.directed.PanelMetricsBase
-
A measure of how undercovered <= 50% GC regions are relative to the mean.
- AT_DROPOUT - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Illumina-style AT dropout metric.
- atEndOfCurrentCigar() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Is the current position at the end of the current cigar? For example, if we are in element 3M, this function returns true if we are at offsetInCurrentCigar of 2, but not 0 or 1.
- AtoA - Enum constant in enum class picard.analysis.artifacts.Transition
- AtoC - Enum constant in enum class picard.analysis.artifacts.Transition
- AtoG - Enum constant in enum class picard.analysis.artifacts.Transition
- AtomicIterator<T> - Interface in picard.util
-
Describes
- atomicIteratorOf(Iterable<E>) - Static method in class picard.util.Iterators
- atomicIteratorOf(Iterator<E>) - Static method in class picard.util.Iterators
- AtoT - Enum constant in enum class picard.analysis.artifacts.Transition
- atStartOfCurrentCigar() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Is the current position at the start of the current cigar? For example, if we are in element 3M, this function returns true if we are at offsetInCurrentCigar of 0, but not 1 or 2.
- ATTEMPTED_ALLELES - Static variable in class picard.vcf.LiftoverVcf
-
Attribute used to store the position of the failed variant on the target contig prior to finding out that alleles do not match.
- ATTEMPTED_LOCUS - Static variable in class picard.vcf.LiftoverVcf
-
Attribute used to store the position of the failed variant on the target contig prior to finding out that alleles do not match.
- ATTRIBUTE_TO_CLEAR - Variable in class picard.sam.RevertSam
- ATTRIBUTE_TO_CLEAR_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- ATTRIBUTE_TO_REVERSE - Variable in class picard.sam.RevertSam
- ATTRIBUTE_TO_REVERSE_COMPLEMENT - Variable in class picard.sam.RevertSam
- attributeMap - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData
- ATTRIBUTES_TO_REMOVE - Variable in class picard.sam.MergeBamAlignment
- ATTRIBUTES_TO_RETAIN - Variable in class picard.sam.MergeBamAlignment
- ATTRIBUTES_TO_REVERSE - Variable in class picard.sam.MergeBamAlignment
- ATTRIBUTES_TO_REVERSE_COMPLEMENT - Variable in class picard.sam.MergeBamAlignment
- attributesToClear - Variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- attributeToList(Object) - Static method in class org.broadinstitute.hellbender.utils.variant.VariantContextGetters
- AUTOCALL_CALL_RATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The overall autocall call rate
- AUTOCALL_DATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The date this sample was autocalled
- AUTOCALL_DATE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- AUTOCALL_GENDER - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The sex, as determined by Autocall
- AUTOCALL_GENDER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- AUTOCALL_PF - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
Whether the sample passes QC based on call rate threshold
- AUTOCALL_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The version of autocall used for calling this sample
- AUTOCALL_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- AutoCloseableCollection<C extends Collection<? extends AutoCloseable>> - Class in org.broadinstitute.hellbender.utils.collections
-
An
AutoCloseablecollection that will automatically close all of its elements. - AutoCloseableCollection(C) - Constructor for class org.broadinstitute.hellbender.utils.collections.AutoCloseableCollection
- AutoCloseableReference<T> - Class in org.broadinstitute.hellbender.utils
-
Reference to another object that perform some action when closed.
- AutoCloseableReference(T) - Constructor for class org.broadinstitute.hellbender.utils.AutoCloseableReference
-
Extending classes need to pass the subject reference using this constructor.
- autoCloseables - Variable in class org.broadinstitute.hellbender.utils.collections.AutoCloseableCollection
- AUTOMATIC - Enum constant in enum class org.broadinstitute.hellbender.tools.GatherVcfsCloud.GatherType
- AUTOMATIC_GENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapStatus
-
Gene is from an automatic process (ENSEMBL source).
- AUTOMATIC_SMALL_NCRNA_GENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapStatus
-
Gene is from a small, automatic (ENSEMBL source) non-coding RNA.
- AUTOMATICALLY_ANNOTATED - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.LocusLevel
-
Automatically annotated locus
- AUTOSOMAL_RECESSIVE_GENES - Static variable in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AutosomalRecessiveConstants
- AUTOSOMAL_REF_COPY_NUMBER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- AutosomalRecessiveConstants - Class in org.broadinstitute.hellbender.tools.funcotator.filtrationRules
- AutosomalRecessiveConstants() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AutosomalRecessiveConstants
- AVG_POS_3PRIME_SOFTCLIP_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The average length of the soft-clipped bases at the 3' end of reads.
- avgAvgDiffs - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ThetaVariantEvaluator
- avgHet - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ThetaVariantEvaluator
- avgVarAF - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantAFEvaluator
- AVX - Enum constant in enum class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM.Implementation
-
AVX-accelerated version of PairHMM
- AVX_ENABLED - Enum constant in enum class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner.Implementation
-
use the AVX enabled Smith-Waterman aligner
- AVX_LOGLESS_CACHING - Enum constant in enum class org.broadinstitute.hellbender.utils.pairhmm.PairHMM.Implementation
- AVX_LOGLESS_CACHING_OMP - Enum constant in enum class org.broadinstitute.hellbender.utils.pairhmm.PairHMM.Implementation
- awaitCompletion() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
-
Blocks until the work is complete.
- awaitCompletion() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
- awaitThreadPoolTermination(String, ThreadPoolExecutorWithExceptions, Duration) - Static method in class picard.util.ThreadPoolExecutorUtil
- awaitTileProcessingCompletion() - Method in class picard.illumina.SortedBasecallsConverter
B
- B - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- B - Enum constant in enum class picard.illumina.parser.ReadType
- b37 - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations.Reference
- B37_MITOCHONDRIAL_CONTIG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorConstants
-
Name of the Mitochondrial contig for the B37 human reference.
- BACKWARD_SELECTION - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.utils.segmentation.KernelSegmenter.ChangepointSortOrder
- BAD_ASSAYS_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- BAD_CYCLES - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of instrument cycles in which 80% or more of base calls were no-calls.
- BAD_HAPLOTYPE_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- BadInput(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.BadInput
- BadInput(String, Throwable) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.BadInput
- badReadEditDistance - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- badReadProperPair - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- badReadSecondaryOrSupplementary - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- badReadThreshold - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
-
Arguments related to the "bad read filtering" where alleles that are supported primarily by reads that fail at least one of a number of heuristics will be filtered out
- BadTempDir(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.BadTempDir
- BadTempDir(String, Throwable) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.BadTempDir
- BadTempDir(Path, String, Throwable) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.BadTempDir
- BAF - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- BAF_EVIDENCE_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAF
- BAF_SITES_VCF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAF
- BafEvidence - Class in org.broadinstitute.hellbender.tools.sv
-
Biallelic-frequency of a sample at some locus.
- BafEvidence(String, String, int, double) - Constructor for class org.broadinstitute.hellbender.tools.sv.BafEvidence
- BafEvidence(BafEvidence, double) - Constructor for class org.broadinstitute.hellbender.tools.sv.BafEvidence
- BafEvidenceBCICodec - Class in org.broadinstitute.hellbender.utils.codecs
-
Codec to handle BafEvidence in BlockCompressedInterval files
- BafEvidenceBCICodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.BafEvidenceBCICodec
- BafEvidenceCodec - Class in org.broadinstitute.hellbender.utils.codecs
-
Codec to handle BafEvidence in tab-delimited text files
- BafEvidenceCodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.BafEvidenceCodec
- BafEvidenceSortMerger - Class in org.broadinstitute.hellbender.tools.sv
-
Imposes additional ordering of same-locus BafEvidence by sample.
- BafEvidenceSortMerger(SAMSequenceDictionary, FeatureSink<BafEvidence>) - Constructor for class org.broadinstitute.hellbender.tools.sv.BafEvidenceSortMerger
- BafRegressMetrics - Class in picard.arrays
- BafRegressMetrics() - Constructor for class picard.arrays.BafRegressMetrics
- BAFSiteIterator(Iterator<VariantContext>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence.BAFSiteIterator
- bafSitesFile - Variable in class org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAF
- BAIT_BIAS_DETAILS_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
- BAIT_BIAS_IN - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- BAIT_BIAS_SUMMARY_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
- BAIT_DESIGN_EFFICIENCY - Variable in class picard.analysis.directed.HsMetrics
-
The ratio of TARGET_TERRITORY/BAIT_TERRITORY.
- BAIT_INTERVALS - Variable in class picard.analysis.directed.CollectHsMetrics
- BAIT_OFFSET - Variable in class picard.util.BaitDesigner
- BAIT_SET - Variable in class picard.analysis.directed.HsMetrics
-
The name of the bait set used in the hybrid selection.
- BAIT_SET_NAME - Variable in class picard.analysis.directed.CollectHsMetrics
- BAIT_SIZE - Variable in class picard.util.BaitDesigner
- BAIT_TERRITORY - Variable in class picard.analysis.directed.HsMetrics
-
The number of bases which are localized to one or more baits.
- BaitBiasDetailMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
- BaitBiasSummaryMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
- BaitDesigner - Class in picard.util
-
Designs baits for hybrid selection!
- BaitDesigner() - Constructor for class picard.util.BaitDesigner
- BaitDesigner.DesignStrategy - Enum Class in picard.util
-
Set of possible design strategies for bait design.
- BAITS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- BAITS_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- BALANCING_WITHOUT_INTERVAL_SUBDIVISION - Enum constant in enum class picard.util.IntervalList.IntervalListScatterMode
-
A scatter approach that differs from
IntervalListScatterMode.INTERVAL_SUBDIVISIONin a few ways. - BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW - Enum constant in enum class picard.util.IntervalList.IntervalListScatterMode
-
A scatter approach that differs from
IntervalListScatterMode.BALANCING_WITHOUT_INTERVAL_SUBDIVISION. - bAlleleFreq - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- bam - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.RevertSamSpark.FileType
- bam - Enum constant in enum class picard.sam.RevertSam.FileType
- BAM - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetFormat
- BAM_MAGIC - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
BAM file magic value that starts every bam file
- BAM_OUTPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- BAM_OUTPUT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- BAM_PARTITION_SIZE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- BAM_PL_NAMES - Variable in enum class org.broadinstitute.hellbender.utils.NGSPlatform
-
Array of the prefix names in a BAM file for each of the platforms.
- BAM_SHARD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBam
- BAM_WITH_HEADER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBam
- BAM_WRITER_TYPE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- bamIndexCachingShouldBeEnabled() - Method in class org.broadinstitute.hellbender.engine.GATKTool
- BamIndexStats - Class in picard.sam
-
Command line program to print statistics from BAM index (.bai) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate.
- BamIndexStats() - Constructor for class picard.sam.BamIndexStats
- bamOutputPath - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
-
The assembled haplotypes and locally realigned reads will be written as BAM to this file if requested.
- bamOutputPath - Variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- bamPartitionSplitSize - Variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- BamToBfq - Class in picard.fastq
-
Converts a BAM file into a BFQ (binary fastq formatted) file.
- BamToBfq() - Constructor for class picard.fastq.BamToBfq
- BamToBfqWriter - Class in picard.fastq
-
Deprecated.
- BamToBfqWriter(File, File, String, Integer, Integer, boolean, String, boolean, boolean, Integer) - Constructor for class picard.fastq.BamToBfqWriter
-
Deprecated.
- BamToBfqWriter(File, String, boolean, String, boolean) - Constructor for class picard.fastq.BamToBfqWriter
-
Deprecated.
- bamWriterType - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
-
The type of BAM output we want to see.
- BandPassActivityProfile - Class in org.broadinstitute.hellbender.utils.activityprofile
-
A band pass filtering version of the activity profile Applies a band pass filter with a Gaussian kernel to the input state probabilities to smooth them out of an interval
- BandPassActivityProfile(int, double, int, double, boolean, SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile
-
Create an activity profile that implements a band pass filter on the states
- BandPassActivityProfile(int, double, int, double, SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile
-
sets adaptiveFilterSize to true
- BAQ - Class in org.broadinstitute.hellbender.utils.baq
- BAQ() - Constructor for class org.broadinstitute.hellbender.utils.baq.BAQ
-
Use defaults for everything
- BAQ(double) - Constructor for class org.broadinstitute.hellbender.utils.baq.BAQ
-
Use defaults for everything
- BAQ(double, double, int, byte) - Constructor for class org.broadinstitute.hellbender.utils.baq.BAQ
-
Create a new HmmGlocal object with specified parameters
- BAQ_TAG - Static variable in class org.broadinstitute.hellbender.utils.baq.BAQ
- BAQ.BAQCalculationResult - Class in org.broadinstitute.hellbender.utils.baq
- BAQ.CalculationMode - Enum Class in org.broadinstitute.hellbender.utils.baq
- BAQ.QualityMode - Enum Class in org.broadinstitute.hellbender.utils.baq
-
these are features that only the walker can override
- BAQCalculationResult(byte[], byte[], byte[]) - Constructor for class org.broadinstitute.hellbender.utils.baq.BAQ.BAQCalculationResult
- BAQCalculationResult(GATKRead, byte[]) - Constructor for class org.broadinstitute.hellbender.utils.baq.BAQ.BAQCalculationResult
- BAQGOP - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
- baqRead(GATKRead, ReferenceDataSource, BAQ.CalculationMode, BAQ.QualityMode) - Method in class org.broadinstitute.hellbender.utils.baq.BAQ
-
Modifies read in place so that the base quality scores are capped by the BAQ calculation.
- barcode - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- Barcode - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- Barcode - Static variable in enum class picard.illumina.parser.ReadType
- BARCODE - Variable in class picard.illumina.BarcodeMetric
-
The barcode (from the set of expected barcodes) for which the following metrics apply.
- BARCODE - Variable in class picard.illumina.ExtractIlluminaBarcodes
- BARCODE_BQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- BARCODE_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
-
Column header for the first barcode sequence (preferred).
- BARCODE_DELIMITER - Static variable in class picard.util.IlluminaUtil
- BARCODE_FILE - Variable in class picard.illumina.ExtractIlluminaBarcodes
- BARCODE_NAME - Variable in class picard.illumina.BarcodeMetric
-
The barcode name.
- BARCODE_NAME_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
-
Column header for the barcode name.
- BARCODE_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToSam
- BARCODE_POPULATION_STRATEGY - Variable in class picard.illumina.IlluminaBasecallsToSam
- BARCODE_PREFIXES - Static variable in class picard.illumina.ExtractBarcodesProgram
- BARCODE_SEQUENCE_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
- BARCODE_TAG - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- BARCODE_TAG - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- BARCODE_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
- BARCODE_WITHOUT_DELIMITER - Variable in class picard.illumina.BarcodeMetric
- barcodeBytes - Variable in class picard.illumina.BarcodeMetric
- barcodeBytes - Variable in class picard.util.BarcodeEditDistanceQuery
-
list of barcodes (e.g.
- BarcodeEditDistanceQuery - Class in picard.util
-
A class for finding the distance between multiple (matched) barcodes and multiple barcode reads.
- BarcodeEditDistanceQuery(byte[][], byte[][], byte[][], int, int) - Constructor for class picard.util.BarcodeEditDistanceQuery
- barcodeExtractor - Variable in class picard.illumina.BasecallsConverter
- BarcodeExtractor - Class in picard.illumina
-
BarcodeExtractor is used to match barcodes and collect barcode match metrics.
- BarcodeExtractor(Map<String, BarcodeMetric>, BarcodeMetric, ReadStructure, int, int, int, int, DistanceMetric) - Constructor for class picard.illumina.BarcodeExtractor
- BarcodeExtractor.BarcodeMatch - Class in picard.illumina
-
Utility class to hang onto data about the best match for a given barcode
- BarcodeFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- BarcodeFileFaker() - Constructor for class picard.illumina.parser.fakers.BarcodeFileFaker
- BarcodeFileReader - Class in picard.illumina.parser.readers
-
Reads a single barcode file line by line and returns the barcode if there was a match or NULL otherwise.
- BarcodeFileReader(File) - Constructor for class picard.illumina.parser.readers.BarcodeFileReader
- BarcodeMatch() - Constructor for class picard.illumina.BarcodeExtractor.BarcodeMatch
- BarcodeMetric - Class in picard.illumina
-
Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.
- BarcodeMetric() - Constructor for class picard.illumina.BarcodeMetric
-
This ctor is necessary for when reading metrics from file
- BarcodeMetric(String, String, String, String[]) - Constructor for class picard.illumina.BarcodeMetric
- barcodeRecordWriterMap - Variable in class picard.illumina.BasecallsConverter
- Barcodes - Enum constant in enum class picard.illumina.parser.IlluminaDataType
- BARCODES_DIR - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
- BARCODES_DIR - Variable in class picard.illumina.IlluminaBasecallsToFastq
- BARCODES_DIR - Variable in class picard.illumina.IlluminaBasecallsToSam
- barcodeSeqsToString(byte[][]) - Static method in class picard.util.IlluminaUtil
-
Concatenates all the barcode sequences with BARCODE_DELIMITER
- barcodeSeqsToString(String[]) - Static method in class picard.util.IlluminaUtil
-
Concatenates all the barcode sequences with BARCODE_DELIMITER
- barcodeSeqsToString(List<String>) - Static method in class picard.util.IlluminaUtil
-
Concatenates all the barcode sequences with BARCODE_DELIMITER
- barcodeToMetrics - Variable in class picard.illumina.ExtractBarcodesProgram
- base - Variable in enum class org.broadinstitute.hellbender.utils.BaseUtils.Base
- base - Variable in enum class picard.analysis.artifacts.Transition.Base
- base - Variable in class picard.illumina.parser.ParameterizedFileUtil
-
If you think of the file system as a tree, this is the deepest directory(node) on the tree that still contains all of the files for this given type (e.g.
- BASE_BREAKEND_WINDOW_DOC - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- BASE_BREAKEND_WINDOW_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- BASE_CHARS - Static variable in class org.broadinstitute.hellbender.utils.BaseUtils
- BASE_CHARS_EXTENDED - Static variable in class org.broadinstitute.hellbender.utils.BaseUtils
- BASE_DELETION - Enum constant in enum class org.broadinstitute.hellbender.utils.recalibration.EventType
- BASE_INSERTION - Enum constant in enum class org.broadinstitute.hellbender.utils.recalibration.EventType
- BASE_INTERVAL_OVERLAP_FRACTION_DOC - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- BASE_INTERVAL_OVERLAP_FRACTION_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- BASE_QUAL_HISTOGRAM_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- BASE_QUAL_RANK_SUM_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- BASE_QUALITY_SCORE_THRESHOLD - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
-
Bases with a quality below this threshold will reduced to the minimum usable qualiy score (6).
- BASE_QUALITY_SCORE_THRESHOLD - Static variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- BASE_QUALITY_SCORE_THRESHOLD_FULLNAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- BASE_SAMPLE_OVERLAP_FRACTION_DOC - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- BASE_SAMPLE_OVERLAP_FRACTION_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- BASE_SUBSTITUTION - Enum constant in enum class org.broadinstitute.hellbender.utils.recalibration.EventType
- BASE_TYPE_COUNT - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- baseArrayToKey(byte[], String) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedKeyCodec
-
Converts base space sequence to flow space
- baseArrayToKeySpace(byte[], int, byte[], byte, String) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedKeyCodec
-
Converts a numerical array into flow space by flattening per-base elements to fill empty flows based on minimum scores.
- baseAt(int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Element
- baseAt(int, int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- BaseBclReader - Class in picard.illumina.parser.readers
- BaseBclReader.CycleData - Class in picard.illumina.parser.readers
- BaseBclReader.TileData - Class in picard.illumina.parser.readers
- BaseCalculator - Interface in picard.sam.SamErrorMetric
-
An interface that can take a collection of bases (provided as
SamLocusIterator.RecordAndOffsetandSamLocusAndReferenceIterator.SAMLocusAndReference) and generates aErrorMetricfrom them. - BaseCallingProgramGroup - Class in picard.cmdline.programgroups
-
Tools that process sequencing machine data, e.g.
- BaseCallingProgramGroup() - Constructor for class picard.cmdline.programgroups.BaseCallingProgramGroup
- BaseCalls - Enum constant in enum class picard.illumina.parser.IlluminaDataType
- BASECALLS_DIR - Variable in class picard.illumina.CheckIlluminaDirectory
- BASECALLS_DIR - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
- BASECALLS_DIR - Variable in class picard.illumina.ExtractBarcodesProgram
- BASECALLS_DIR - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- BasecallsConverter<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
-
BasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
- BasecallsConverter(File, File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>, boolean, Integer, Integer, BclQualityEvaluationStrategy, boolean, boolean, boolean, AsyncWriterPool, BarcodeExtractor) - Constructor for class picard.illumina.BasecallsConverter
-
Constructs a new BasecallsConverter object.
- BasecallsConverter.ClusterDataConverter<OUTPUT_RECORD> - Interface in picard.illumina
-
Interface that defines a converter that takes ClusterData and returns OUTPUT_RECORD type objects.
- BasecallsConverter.ConvertedClusterDataWriter<OUTPUT_RECORD> - Interface in picard.illumina
-
Interface that defines a writer that will write out OUTPUT_RECORD type objects.
- BasecallsConverterBuilder<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
-
BasecallsConverterBuilder creates and configures BasecallsConverter objects.
- BasecallsConverterBuilder(File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>) - Constructor for class picard.illumina.BasecallsConverterBuilder
-
Constructs a new builder used for creating BasecallsConverter objects.
- baseCycleStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Get the one-based cycle number of the base, taking the direction of the read into account
- baseData - Variable in class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation.SingleStrandFeatureCoverage
- BaseDistributionByCycleMetrics - Class in org.broadinstitute.hellbender.metrics.analysis
- BaseDistributionByCycleMetrics - Class in picard.analysis
- BaseDistributionByCycleMetrics() - Constructor for class org.broadinstitute.hellbender.metrics.analysis.BaseDistributionByCycleMetrics
- BaseDistributionByCycleMetrics() - Constructor for class picard.analysis.BaseDistributionByCycleMetrics
- BaseEdge - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
-
Simple edge class for connecting nodes in the graph.
- BaseEdge(boolean, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge
-
Create a new BaseEdge with weight multiplicity and, if isRef == true, indicates a path through the reference
- BaseErrorAggregation<CALCULATOR extends BaseCalculator> - Class in picard.sam.SamErrorMetric
-
An interface and implementations for classes that apply a
RecordAndOffsetStratifierto put bases into various "bins" and then compute anErrorMetricon these bases using aBaseErrorCalculator. - BaseErrorAggregation(Supplier<CALCULATOR>, ReadBaseStratification.RecordAndOffsetStratifier) - Constructor for class picard.sam.SamErrorMetric.BaseErrorAggregation
- BaseErrorCalculator - Class in picard.sam.SamErrorMetric
- BaseErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.BaseErrorCalculator
- BaseErrorMetric - Class in picard.sam.SamErrorMetric
-
An error metric for the errors in bases.
- BaseErrorMetric() - Constructor for class picard.sam.SamErrorMetric.BaseErrorMetric
- BaseErrorMetric(String, long, long) - Constructor for class picard.sam.SamErrorMetric.BaseErrorMetric
- BaseFuncotatorArgumentCollection - Class in org.broadinstitute.hellbender.tools.funcotator
- BaseFuncotatorArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
- BaseGraph<V extends BaseVertex,
E extends BaseEdge> - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs -
Common code for graphs used for local assembly.
- BaseGraph(int, EdgeFactory<V, E>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Construct a TestGraph with kmerSize
- BaseIlluminaDataProvider - Class in picard.illumina.parser
-
Parse various formats and versions of Illumina Basecall files, and use them the to populate ClusterData objects.
- BaseIlluminaDataProvider(int, OutputMapping) - Constructor for class picard.illumina.parser.BaseIlluminaDataProvider
- baseIndexMap - Static variable in enum class picard.analysis.artifacts.Transition
- baseIndexToSimpleBase(int) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
-
Converts a base index to a simple base
- baseIsUsableForAssembly(byte, byte) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Determines whether a base can safely be used for assembly.
- BASELINE_COPY_NUMBER_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVNamingConstants
- BASELINE_COPY_NUMBER_TABLE_COLUMN - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVNamingConstants
- BaselineCopyNumberCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
Collection of baseline copy-number states.
- BaselineCopyNumberCollection(File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.BaselineCopyNumberCollection
- BaseQuality - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Median base quality of bases supporting each allele.
- BaseQuality() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.BaseQuality
- BaseQualityClipReadTransformer - Class in org.broadinstitute.hellbender.transformers
-
Clips reads on both ends using base quality scores
- BaseQualityClipReadTransformer(int) - Constructor for class org.broadinstitute.hellbender.transformers.BaseQualityClipReadTransformer
- BaseQualityFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- BaseQualityFilter(double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.BaseQualityFilter
- BaseQualityHistogram - Class in org.broadinstitute.hellbender.tools.walkers.annotator
- BaseQualityHistogram() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityHistogram
- BaseQualityRankSumTest - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Rank Sum Test of REF versus ALT base quality scores
- BaseQualityRankSumTest() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityRankSumTest
- BaseQualityReadTransformer - Class in org.broadinstitute.hellbender.transformers
- BaseQualityReadTransformer() - Constructor for class org.broadinstitute.hellbender.transformers.BaseQualityReadTransformer
- BaseQualityReadTransformer(int) - Constructor for class org.broadinstitute.hellbender.transformers.BaseQualityReadTransformer
- baseQualityStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into the base-quality of the base under consideration
- baseQualTieBreaker - Static variable in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
- BaseRecalibrationEngine - Class in org.broadinstitute.hellbender.utils.recalibration
- BaseRecalibrationEngine(RecalibrationArgumentCollection, SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
- BaseRecalibrationEngine.BQSRReferenceWindowFunction - Class in org.broadinstitute.hellbender.utils.recalibration
-
Reference window function for BQSR.
- BaseRecalibrator - Class in org.broadinstitute.hellbender.tools.walkers.bqsr
-
First pass of the base quality score recalibration.
- BaseRecalibrator() - Constructor for class org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator
- BaseRecalibratorSpark - Class in org.broadinstitute.hellbender.tools.spark
-
Spark version of the first pass of the base quality score recalibration.
- BaseRecalibratorSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark
- BaseRecalibratorSparkFn - Class in org.broadinstitute.hellbender.tools.spark.transforms
- BaseRecalibratorSparkFn() - Constructor for class org.broadinstitute.hellbender.tools.spark.transforms.BaseRecalibratorSparkFn
- bases - Variable in class picard.illumina.parser.BclData
- bases() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.Kmer
-
Get the bases of this kmer.
- bases() - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Insert
- BASES - Static variable in class org.broadinstitute.hellbender.tools.copynumber.datacollection.AllelicCountCollector
- BASES - Static variable in class org.broadinstitute.hellbender.utils.BaseUtils
- BASES_COMPARATOR - Static variable in class org.broadinstitute.hellbender.utils.BaseUtils
-
Lexicographical sorting of base arrays
Comparator. - BASES_EXTENDED - Static variable in class org.broadinstitute.hellbender.utils.BaseUtils
- BASES_TO_WRITE - Variable in class picard.fastq.BamToBfq
- basesAreEqual(byte, byte) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
- basesAreRepeated(String, String, String, int) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- basesMatch(Allele, Allele) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix
- basesPerLine - Variable in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker
- basesPerLine - Variable in class org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta
- basesToIUPAC(byte, byte) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
-
Converts a pair of bases to their IUPAC ambiguity code
- BaseUtils - Class in org.broadinstitute.hellbender.utils
-
BaseUtils contains some basic utilities for manipulating nucleotides.
- BaseUtils.Base - Enum Class in org.broadinstitute.hellbender.utils
- BaseUtils.BaseSubstitutionType - Enum Class in org.broadinstitute.hellbender.utils
- BaseUtils.HmerIterator - Class in org.broadinstitute.hellbender.utils
- BaseVertex - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
-
A graph vertex that holds some sequence information
- BaseVertex(byte[]) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
-
Create a new sequence vertex with sequence This code doesn't copy sequence for efficiency reasons, so sequence must absolutely not be modified in any way after passing this sequence to the BaseVertex
- BASIC - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
identifies a subset of representative transcripts for each gene; prioritises full-length protein coding transcripts
- BasicInputParser - Class in picard.util
-
TextFileParser which reads a single text file.
- BasicInputParser(boolean, int, File...) - Constructor for class picard.util.BasicInputParser
-
Constructor.
- BasicInputParser(boolean, int, InputStream...) - Constructor for class picard.util.BasicInputParser
- BasicInputParser(boolean, File...) - Constructor for class picard.util.BasicInputParser
-
Constructor.
- BasicInputParser(boolean, InputStream...) - Constructor for class picard.util.BasicInputParser
-
Constructor.
- BasicReference - Interface in org.broadinstitute.hellbender.engine
-
A source of reference base calls.
- BasicSomaticShortMutationValidator - Class in org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
- BasicValidationResult - Class in org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
- BasicValidationResult(Locatable, int, boolean, boolean, double, int, int, int, int, Allele, Allele, String, long) - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- BATCHSIZE_ARG_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- bayesianEstimateOfEmpiricalQuality(long, long, double) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- BayesianGaussianMixtureModeller - Class in org.broadinstitute.hellbender.utils.clustering
- BayesianGaussianMixtureModeller.InitMethod - Enum Class in org.broadinstitute.hellbender.utils.clustering
- BB - Enum constant in enum class picard.arrays.illumina.IlluminaGenotype
- BB - Enum constant in enum class picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
- BB_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
- BCF - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetFormat
- BCF_FILE_EXTENSION - Static variable in class org.broadinstitute.hellbender.utils.variant.VcfUtils
- bci - Variable in class picard.illumina.parser.MultiTileFileUtil
- BCI_FILE_EXTENSION - Static variable in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream
- BCI_VERSION - Static variable in class org.broadinstitute.hellbender.tools.sv.BafEvidence
- BCI_VERSION - Static variable in class org.broadinstitute.hellbender.tools.sv.DepthEvidence
- BCI_VERSION - Static variable in class org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence
- BCI_VERSION - Static variable in class org.broadinstitute.hellbender.tools.sv.SiteDepth
- BCI_VERSION - Static variable in class org.broadinstitute.hellbender.tools.sv.SplitReadEvidence
- BciFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/14/14.
- BciFileFaker() - Constructor for class picard.illumina.parser.fakers.BciFileFaker
- Bcl - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- BclData - Class in picard.illumina.parser
-
A class that implements the IlluminaData interfaces provided by this parser One BclData object is returned to IlluminaDataProvider per cluster and each first level array in bases and qualities represents a single read in that cluster
- BclData(int[]) - Constructor for class picard.illumina.parser.BclData
- BclFileFaker - Class in picard.illumina.parser.fakers
- BclFileFaker() - Constructor for class picard.illumina.parser.fakers.BclFileFaker
- BclIndexFaker - Class in picard.illumina.parser.fakers
- BclIndexFaker() - Constructor for class picard.illumina.parser.fakers.BclIndexFaker
- BclIndexReader - Class in picard.illumina.parser.readers
-
Annoyingly, there are two different files with extension .bci in NextSeq output.
- BclIndexReader(File) - Constructor for class picard.illumina.parser.readers.BclIndexReader
- bclQualityEvaluationStrategy - Variable in class picard.illumina.ExtractBarcodesProgram
- bclQualityEvaluationStrategy - Variable in class picard.illumina.parser.MultiTileBclParser
- BclQualityEvaluationStrategy - Class in picard.illumina.parser.readers
-
Describes a mechanism for revising and evaluating qualities read from a BCL file.
- BclQualityEvaluationStrategy(int) - Constructor for class picard.illumina.parser.readers.BclQualityEvaluationStrategy
- BclReader - Class in picard.illumina.parser.readers
-
BCL Files are base call and quality score binary files containing a (base,quality) pair for successive clusters.
- BclReader(File, BclQualityEvaluationStrategy, boolean) - Constructor for class picard.illumina.parser.readers.BclReader
- BclReader(List<File>, int[], BclQualityEvaluationStrategy, boolean) - Constructor for class picard.illumina.parser.readers.BclReader
- BDGAlignmentRecordToGATKReadAdapter - Class in org.broadinstitute.hellbender.utils.read
-
Implementation of the
GATKReadinterface for theAlignmentRecordclass. - BDGAlignmentRecordToGATKReadAdapter(AlignmentRecord, SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.utils.read.BDGAlignmentRecordToGATKReadAdapter
- BEAD_SET_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- BEADSET_ID - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- BedToIntervalList - Class in picard.util
- BedToIntervalList() - Constructor for class picard.util.BedToIntervalList
- beforeExecute(Thread, Runnable) - Method in class picard.util.ThreadPoolExecutorWithExceptions
- beforeFile - Variable in class org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates
-
File containing the recalibration tables from the first pass.
- BEGIN_FIT_FILE_TAG - Static variable in class org.broadinstitute.hellbender.tools.copynumber.ModelSegments
- beginOfShard(int, int) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
first offset in this shard (1-based).
- BEST_EFFECT - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.TranscriptSelectionMode
-
BEST_EFFECT Select a transcript to be reported with details with priority on effect according to the folowing list of selection criteria: Choose the transcript that is on the custom list specified by the user.
- BEST_EST_SUSPECT - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.TranscriptSupportLevel
-
the best supporting EST is flagged as suspect
- BEST_MATCH_TO_ORIGINAL - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod
-
Try to match the original GT calls, if at all possible Suppose I have 3 alleles: A/B/C and the following samples: original_GT best_match to A/B best_match to A/C S1 => A/A A/A A/A S2 => A/B A/B A/A S3 => B/B B/B A/A S4 => B/C A/B A/C S5 => C/C A/A C/C Basically, all alleles not in the subset map to ref.
- BEST_MRNA_SUSPECT - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.TranscriptSupportLevel
-
the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
- bestAllelesBreakingTies() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Default version where ties are broken in favor of the reference allele
- bestAllelesBreakingTies(String) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Default version where ties are broken in favor of the reference allele
- bestAllelesBreakingTies(String, Function<A, Double>) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Returns the collection of best allele estimates for one sample's evidence based on the evidence-likelihoods.
- bestAllelesBreakingTies(Function<A, Double>) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Returns the collection of best allele estimates for the evidence based on the evidence-likelihoods.
- BestEndMapqPrimaryAlignmentStrategy - Class in org.broadinstitute.hellbender.utils.read.mergealignment
-
For an aligner that aligns each end independently, select the alignment for each end with the best MAPQ, and make that the primary.
- BestEndMapqPrimaryAlignmentStrategy - Class in picard.sam
-
For an aligner that aligns each end independently, select the alignment for each end with the best MAPQ, and make that the primary.
- BestEndMapqPrimaryAlignmentStrategy() - Constructor for class org.broadinstitute.hellbender.utils.read.mergealignment.BestEndMapqPrimaryAlignmentStrategy
- BestEndMapqPrimaryAlignmentStrategy() - Constructor for class picard.sam.BestEndMapqPrimaryAlignmentStrategy
- BestMapqPrimaryAlignmentSelectionStrategy - Class in org.broadinstitute.hellbender.utils.read.mergealignment
-
This strategy was designed for TopHat output, but could be of general utility.
- BestMapqPrimaryAlignmentSelectionStrategy - Class in picard.sam
-
This strategy was designed for TopHat output, but could be of general utility.
- BestMapqPrimaryAlignmentSelectionStrategy() - Constructor for class org.broadinstitute.hellbender.utils.read.mergealignment.BestMapqPrimaryAlignmentSelectionStrategy
- BestMapqPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.BestMapqPrimaryAlignmentSelectionStrategy
- BETA_SHAPE_INFO_FIELD - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals
- BetaBinomialCluster - Class in org.broadinstitute.hellbender.tools.walkers.mutect.clustering
- BetaBinomialCluster(BetaDistributionShape) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BetaBinomialCluster
- BetaBinomialDistribution - Class in org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
-
Beta-binomial using the Apache Math3 Framework.
- BetaBinomialDistribution(RandomGenerator, double, double, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BetaBinomialDistribution
- BetaDistributionShape - Class in org.broadinstitute.hellbender.tools.walkers.readorientation
- BetaDistributionShape(double, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.readorientation.BetaDistributionShape
- BGMM_SCORER_SER_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.BGMMVariantAnnotationsScorer
- BGMMVariantAnnotationsModel - Class in org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling
- BGMMVariantAnnotationsModel(File) - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.BGMMVariantAnnotationsModel
- BGMMVariantAnnotationsScorer - Class in org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling
- BGMMVariantAnnotationsScorer(List<String>, BGMMVariantAnnotationsModel.Preprocesser, BayesianGaussianMixtureModeller) - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.BGMMVariantAnnotationsScorer
- BIAS_VARIANCE - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionParameter
- BICISTRONIC - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Transcript contains two confidently annotated CDSs.
- BIDIRECTIONAL_PROMOTER_LNCRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- BigQueryUtils - Class in org.broadinstitute.hellbender.utils.bigquery
-
Utility class for dealing with BigQuery connections / tables / queries /etc.
- BIN_LENGTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervals
- BINARY_TAG_NAME - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
-
The tag name for the binary tag covariate (if using it)
- binaryReader(File) - Static method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusUtils
- binaryReader(InputStream) - Static method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusUtils
- binaryReader(String, DragstrLocusUtils.BinaryTableIndex, int, int, int) - Static method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusUtils
-
Returns loci whose start base is located within an particular interval.
- binarySearchFindZero(DoubleUnaryOperator, double, double, double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- BinaryTableReader<R> - Class in org.broadinstitute.hellbender.utils
-
Abstract base class for readers of table with records stored in binary.
- BinaryTableReader(InputStream, String) - Constructor for class org.broadinstitute.hellbender.utils.BinaryTableReader
- BinaryTableWriter<R> - Class in org.broadinstitute.hellbender.utils
-
Abstract file writing class for record tables stored in binary format.
- BinaryTableWriter(OutputStream, String) - Constructor for class org.broadinstitute.hellbender.utils.BinaryTableWriter
- binaryWriter(File) - Static method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusUtils
- binaryWriter(File, File) - Static method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusUtils
- bindVariantContexts(Map<FeatureInput<VariantContext>, List<VariantContext>>, List<FeatureInput<VariantContext>>, boolean, boolean, boolean, boolean, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
-
For a list of track names, bind the variant contexts to a trackName->sampleName->VariantContext mapping.
- BinnedCNVLinkage - Class in org.broadinstitute.hellbender.tools.sv.cluster
-
CNV defragmenter for when the intervals used for coverage collection are available.
- BinnedCNVLinkage(SAMSequenceDictionary, double, double, List<GenomeLoc>) - Constructor for class org.broadinstitute.hellbender.tools.sv.cluster.BinnedCNVLinkage
- binnedHomopolymerStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies a base onto the make up (repeating base and following reference base) and length-scale of the homopolymer from whence it came.
- binnedReadCycleStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into quintiles of read cycle.
- BinnedReadCycleStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.BinnedReadCycleStratifier
- BinomialCluster - Class in org.broadinstitute.hellbender.tools.walkers.mutect.clustering
- BinomialCluster(double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BinomialCluster
- binomialCoefficient(int, int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Calculates the binomial coefficient.
- binomialProbability(int, int, double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Computes a binomial probability.
- biSiteHeterogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
the rate of heterogeneity within doubleton sets.
- biSiteHomogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
the rate of homogeneity within doubleton sets.
- BLACK_LISTED_LANES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- blackList - Variable in class org.broadinstitute.hellbender.engine.filters.ReadGroupBlackListReadFilter
- blackListedLanes - Variable in class org.broadinstitute.hellbender.engine.filters.PlatformUnitReadFilter
- Block() - Constructor for class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetResponse.Block
- BLOCK - Enum constant in enum class org.broadinstitute.hellbender.tools.GatherVcfsCloud.GatherType
- BLOCK_SIZE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
- BLOCK_SIZE - Variable in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
- BlockCompressedIntervalStream - Class in org.broadinstitute.hellbender.utils.io
- BlockCompressedIntervalStream() - Constructor for class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream
- BlockCompressedIntervalStream.IndexEntry - Class in org.broadinstitute.hellbender.utils.io
- BlockCompressedIntervalStream.Reader<T extends htsjdk.tribble.Feature> - Class in org.broadinstitute.hellbender.utils.io
- BlockCompressedIntervalStream.WriteFunc<F extends htsjdk.tribble.Feature> - Interface in org.broadinstitute.hellbender.utils.io
- BlockCompressedIntervalStream.Writer<F extends htsjdk.tribble.Feature> - Class in org.broadinstitute.hellbender.utils.io
- BLOOM_FILTER_EXTENSION - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerUtils
- BLOOM_FILTER_FALSE_POSITIVE_P_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
- BLOOM_FILTER_FALSE_POSITIVE_P_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
- bloomFpp - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
-
Note that the provided argument is used as an upper limit on the probability, and the actual false positive probability may be less.
- BND - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.StructuralVariantAnnotationType
- BND_ALLELE - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKSVVariantContextUtils
- BND_DELETION_STRANDS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- BND_DUPLICATION_STRANDS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- BND_MATEID_STR - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- body - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetClass
- Boolean - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportDataType
-
Used for boolean values.
- BOS - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.Genus
-
Cows
- BOT - Enum constant in enum class picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
- BOTH - Enum constant in enum class org.broadinstitute.hellbender.tools.LocalAssembler.ContigOrientation
- boundQual(int) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Return a quality score that bounds qual by MAX_SAM_QUAL_SCORE and 1
- boundQual(int, byte) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Return a quality score that bounds qual by maxQual and 1 WARNING -- because this function takes a byte for maxQual, you must be careful in converting integers to byte.
- BP_RES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
- BP_RESOLUTION - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceMode
-
Reference model emitted site by site.
- BpmToNormalizationManifestCsv - Class in picard.arrays.illumina
-
A simple program to convert an Illumina bpm (bead pool manifest file) into a normalization manifest (bpm.csv) file The normalization manifest (bpm.csv) is a simple text file generated by Illumina tools - it has a specific format and is used by ZCall .
- BpmToNormalizationManifestCsv() - Constructor for class picard.arrays.illumina.BpmToNormalizationManifestCsv
- bq - Variable in class org.broadinstitute.hellbender.utils.baq.BAQ.BAQCalculationResult
- BQD_HOMOPOLYMER_PHRED_ADJUSTMENT_FACTOR - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.DRAGENGenotypesModel
- BQSR_BASE_DELETION_QUALITIES - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- BQSR_BASE_INSERTION_QUALITIES - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- BQSR_RECAL_FILE - Variable in class org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates
-
Enables recalibration of base qualities, intended primarily for use with BaseRecalibrator and ApplyBQSR (see Best Practices workflow documentation).
- BQSR_RECAL_FILE - Variable in class org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR
-
This argument is required for recalibration of base qualities.
- BQSR_REFERENCE_WINDOW_FUNCTION - Static variable in class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
- BQSR_TABLE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- BQSR_TABLE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- bqsrArgs - Variable in class org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR
-
Command-line arguments to fine tune the recalibration.
- BQSRPipelineSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines
-
The full BQSR pipeline in one tool to run on Spark.
- BQSRPipelineSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark
- BQSRReadTransformer - Class in org.broadinstitute.hellbender.transformers
- BQSRReadTransformer(SAMFileHeader, File, ApplyBQSRArgumentCollection) - Constructor for class org.broadinstitute.hellbender.transformers.BQSRReadTransformer
-
Constructor using a GATK Report file
- BQSRReadTransformer(SAMFileHeader, RecalibrationReport, ApplyBQSRArgumentCollection) - Constructor for class org.broadinstitute.hellbender.transformers.BQSRReadTransformer
-
Constructor using a RecalibrationReport
- BQSRReferenceWindowFunction() - Constructor for class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine.BQSRReferenceWindowFunction
- BRACKET_REGEX - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils
- BREAK_BANDS_AT_MULTIPLES_OF - Variable in class picard.util.IntervalListTools
- BREAK_BANDS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
- BREAKEND_EXON - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- BREAKEND_STR - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- BreakEndVariantType - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- BreakEndVariantType(String, int, String, Allele, Allele, Map<String, Object>, boolean) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType
- BreakEndVariantType.InterChromosomeBreakend - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- BreakEndVariantType.IntraChromosomalStrandSwitch33BreakEnd - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- BreakEndVariantType.IntraChromosomalStrandSwitch55BreakEnd - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- BreakEndVariantType.IntraChromosomeRefOrderSwap - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- BreakEndVariantType.SupportedType - Enum Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- BREAKPOINT_SUMMARY_STRATEGY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- BreakpointComplications - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
A helper struct for annotating complications that make the locations represented by its associated
NovelAdjacencyAndAltHaplotypea little ambiguous. - BreakpointComplications() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications
- BreakpointComplications(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications
- BreakpointComplications.IntraChrStrandSwitchBreakpointComplications - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
For novel adjacency between reference locations that are on the same chromosome, and with a strand switch.
- BreakpointComplications.IntraChrStrandSwitchBreakpointComplications.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- BreakpointComplications.InvertedDuplicationBreakpointComplications - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
For this specific complication, we support a what could be defined as incomplete picture, that involves inverted duplication: two overlapping alignments to reference first alignment: --------------------> second alignment: <--------------------- |--------||----------| Seg.1 Seg.2 At least Seg.1 is invert duplicated, and Seg.2 is inverted trans-inserted between the two copies (one of which is inverted).
- BreakpointComplications.InvertedDuplicationBreakpointComplications.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
For simple deletion, insertion, and replacement (dep and ins at the same time).
- BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- BreakpointComplications.SmallDuplicationBreakpointComplications - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
For duplications small enough that we seemingly have assembled across the whole event.
- BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
This is for dealing with case when the duplicated range could NOT be inferred exactly, but only from a simple optimization scheme.
- BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- BreakpointDensityFilter - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
A class that acts as a filter for breakpoint evidence.
- BreakpointDensityFilter(Iterator<BreakpointEvidence>, ReadMetadata, double, double, PartitionCrossingChecker, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointDensityFilter
- BreakpointEvidence - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
Various types of read anomalies that provide evidence of genomic breakpoints.
- BreakpointEvidence(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
- BreakpointEvidence(SVInterval, int, boolean) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
- BreakpointEvidence.DiscordantReadPairEvidence - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.ExternalEvidence - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.ExternalEvidence.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.InterContigPair - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.InterContigPair.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.LargeIndel - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.LargeIndel.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.MateUnmapped - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.MateUnmapped.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.OutiesPair - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.OutiesPair.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.ReadEvidence - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.ReadEvidence.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.SameStrandPair - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.SameStrandPair.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.SplitRead - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.SplitRead.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.TemplateSizeAnomaly - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.TemplateSizeAnomaly.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.WeirdTemplateSize - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidence.WeirdTemplateSize.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- BreakpointEvidenceClusterer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
A class to examine a stream of BreakpointEvidence, and group it into Intervals.
- BreakpointEvidenceClusterer(int, PartitionCrossingChecker) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidenceClusterer
- BreakpointsInference - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
Based on alignment signature of the input simple chimera, and evidence contig having the chimera, infers exact position of breakpoints following the left-aligning convention, alt haplotype sequence based on given contig sequence complications such as homology, inserted sequence and duplicated ref region, if any.
- BreakpointsInference(SimpleChimera, byte[], SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference
- broadcastCNVCalls(JavaSparkContext, SAMFileHeader, String) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryPipelineSpark
- bucketPathToPublicHttpUrl(String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Convert a GCS bucket location into the equivalent public http url.
- BucketUtils - Class in org.broadinstitute.hellbender.utils.gcs
-
Utilities for dealing with google buckets.
- Buffer - Enum constant in enum class org.broadinstitute.hellbender.utils.runtime.StreamLocation
- BUFFER_SIZE - Variable in class picard.util.FifoBuffer
- BUFFER_SIZE_BYTES - Static variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- bufferSize() - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.BciFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.BclFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.BclIndexFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.ClocsFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.FileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.FilterFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.LocsFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.PosFileFaker
- bufferStream - Variable in class org.broadinstitute.hellbender.utils.runtime.CapturedStreamOutput
-
The byte stream to capture content or null if no output string content was requested.
- build() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
- build() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
-
Construct 2 tables of references: one keyed by MD5, one keyed by sequence name.
- build() - Method in class org.broadinstitute.hellbender.utils.mcmc.ParameterizedModel.GibbsBuilder
-
Builds the ParameterizedModel as specified via
ParameterizedModel.GibbsBuilder. - build() - Method in class picard.illumina.BasecallsConverterBuilder
-
Builds a basecalls converter
- build() - Method in interface picard.vcf.processor.VariantProcessor.AccumulatorGenerator
- build() - Method in class picard.vcf.processor.VariantProcessor.Builder
- build(Iterator<GATKRead>, SAMFileHeader, List<SimpleInterval>, SAMSequenceDictionary, boolean) - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentContextIteratorBuilder
-
Have this builder return an instance of the iterator as specified by the caller.
- BUILD_37 - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- Build37ExtendedIlluminaManifest - Class in picard.arrays.illumina
-
A class to represent an 'Extended' Illumina Manifest file.
- Build37ExtendedIlluminaManifest(File) - Constructor for class picard.arrays.illumina.Build37ExtendedIlluminaManifest
- Build37ExtendedIlluminaManifestRecord - Class in picard.arrays.illumina
-
A class to represent a record (line) from an Extended Illumina Manifest [Assay] entry
- Build37ExtendedIlluminaManifestRecord.Flag - Enum Class in picard.arrays.illumina
- Build37ExtendedIlluminaManifestRecordCreator - Class in picard.arrays.illumina
- buildAccessionToTaxIdMap(Map<Integer, PSPathogenReferenceTaxonProperties>, PSTree, int) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBuildReferenceTaxonomyUtils
-
Create reference_name-to-taxid map (just an inversion on taxIdToProperties)
- BuildBamIndex - Class in picard.sam
-
Command line program to generate a BAM index (.bai) file from a BAM (.bam) file
- BuildBamIndex() - Constructor for class picard.sam.BuildBamIndex
- buildContigIDToNameArray(Map<String, Integer>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- buildContigNameToIDMap(SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- buildEventMapsForHaplotypes(List<Haplotype>, byte[], Locatable, boolean, int) - Static method in class org.broadinstitute.hellbender.utils.haplotype.EventMap
-
Build event maps for each haplotype, returning the sorted set of all of the starting positions of all events across all haplotypes
- buildGraphIfNecessary() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Build the read threaded assembly graph if it hasn't already been constructed from the sequences that have been added to the graph.
- buildGroupToLibMap(SAMFileHeader) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- buildHaplotypeCallerEngine(HaplotypeCallerArgumentCollection, AssemblyRegionArgumentCollection, boolean, boolean, SAMFileHeader, CachingIndexedFastaSequenceFile, VariantAnnotatorEngine) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
- buildHaplotypeCallerEngine(HaplotypeCallerArgumentCollection, AssemblyRegionArgumentCollection, boolean, boolean, SAMFileHeader, CachingIndexedFastaSequenceFile, VariantAnnotatorEngine) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCaller
- buildIntervalTreeFromBED(FeatureDataSource<FullBEDFeature>, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate
-
Builds interval tree of noncoding elements to annotate from BED file input
- buildIntervalTreesFromGTF(FeatureDataSource<GencodeGtfGeneFeature>, SAMSequenceDictionary, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate
-
Builds transcript, TSS, and promoter interval trees from protein-coding GTF
- buildMaxMafRule(double, FilterFuncotations.AlleleFrequencyDataSource) - Static method in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AlleleFrequencyUtils
-
Build a
FuncotationFiltrationRulematching Funcotations from variants with a maximum MAF less than some threshold. - buildMetadata(StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection, SAMFileHeader, JavaRDD<GATKRead>, SVReadFilter, Logger) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark
- buildMetricsMap(List<? extends MetricBase>) - Method in class picard.analysis.CompareMetrics
- buildRamps() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerEngine
- buildReadEnds(SAMFileHeader, long, SAMRecord, boolean) - Method in class picard.sam.markduplicates.MarkDuplicates
-
Builds a read ends object that represents a single read.
- buildReadEnds(SAMFileHeader, long, SAMRecord, boolean) - Method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
-
Builds a read ends object that represents a single read - for flow based read
- buildReadEnds(SAMFileHeader, long, SAMRecord, boolean) - Method in interface picard.sam.markduplicates.MarkDuplicatesHelper
- buildTaxonomicTree(Map<Integer, PSPathogenReferenceTaxonProperties>) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBuildReferenceTaxonomyUtils
-
Returns a PSTree representing a reduced taxonomic tree containing only taxa present in the reference
- buildVariantContext(SVCallRecord) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- buildVariantContext(SVCallRecord, ReferenceSequenceFile) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- bumpCount() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.KmerAndCount
- bumpCount(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.KmerAndCount
- bumpCount(AnalyzeSaturationMutagenesis.ReportType) - Method in class org.broadinstitute.hellbender.tools.AnalyzeSaturationMutagenesis.ReportTypeCounts
- bunny - Static variable in class org.broadinstitute.hellbender.utils.logging.BunnyLog
- BunnyLog - Class in org.broadinstitute.hellbender.utils.logging
-
The "bunny" log format: =[**]= START
=[**]= STEPEND =[**]= END The functions here create an id for you and keep track of it, and format the various strings, sending it to a logger if you provided one. - BunnyLog() - Constructor for class org.broadinstitute.hellbender.utils.logging.BunnyLog
- BunnyLog(Logger) - Constructor for class org.broadinstitute.hellbender.utils.logging.BunnyLog
- BWA_MEM_INDEX_IMAGE_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.bwa.BwaArgumentCollection
- BWA_MEM_INDEX_IMAGE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.bwa.BwaArgumentCollection
- BwaAndMarkDuplicatesPipelineSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines
-
Runs BWA and MarkDuplicates on Spark.
- BwaAndMarkDuplicatesPipelineSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.BwaAndMarkDuplicatesPipelineSpark
- bwaArgs - Variable in class org.broadinstitute.hellbender.tools.spark.bwa.BwaSpark
- bwaArgs - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSpark
- bwaArgs - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark
- bwaArgs - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.BwaAndMarkDuplicatesPipelineSpark
- bwaArgs - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- BwaArgumentCollection - Class in org.broadinstitute.hellbender.tools.spark.bwa
-
A collection of the arguments that are used for BWA.
- BwaArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.spark.bwa.BwaArgumentCollection
- bwaImage - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection
- BwaMemAlignmentUtils - Class in org.broadinstitute.hellbender.utils.bwa
-
Utils to move data from a BwaMemAlignment into a GATKRead, or into a SAM tag.
- BwaMemAlignmentUtils() - Constructor for class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignmentUtils
- BwaMemIndexCache - Class in org.broadinstitute.hellbender.utils.bwa
-
Manage a global collection of
BwaMemIndexinstances. - BwaMemIndexCache() - Constructor for class org.broadinstitute.hellbender.utils.bwa.BwaMemIndexCache
- bwaMemIndexImage - Variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
-
BWA-mem index image created by
BwaMemIndexImageCreator - BwaMemIndexImageCreator - Class in org.broadinstitute.hellbender.tools
-
Create a BWA-MEM index image file for use with GATK BWA tools
- BwaMemIndexImageCreator() - Constructor for class org.broadinstitute.hellbender.tools.BwaMemIndexImageCreator
- BwaSpark - Class in org.broadinstitute.hellbender.tools.spark.bwa
- BwaSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.bwa.BwaSpark
- BwaSparkEngine - Class in org.broadinstitute.hellbender.tools.spark.bwa
-
The BwaSparkEngine provides a simple interface for transforming a JavaRDD
in which the reads are paired and unaligned, into a JavaRDD of aligned reads, and does so lazily. - BwaSparkEngine(JavaSparkContext, String, String, SAMFileHeader, SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.tools.spark.bwa.BwaSparkEngine
- bwaThreads - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection
- bwaThreads - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- BY_1KG - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.CustomMafFuncotationCreator
- BY_FREQ - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.CustomMafFuncotationCreator
- BY_SAMPLE - Enum constant in enum class org.broadinstitute.hellbender.utils.downsampling.DownsampleType
- byHundredMegabaseChunks(List<File>) - Static method in class picard.vcf.processor.VariantIteratorProducer
-
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached).
- byHundredMegabaseChunksWithOnTheFlyFilteringByInterval(List<File>, IntervalList) - Static method in class picard.vcf.processor.VariantIteratorProducer
-
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached), that also performs on-the-fly filtering of
VariantContext - byHundredMegabasePathChunks(List<PicardHtsPath>) - Static method in class picard.vcf.processor.VariantIteratorProducer
-
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached).
- byHundredMegabasePathChunksWithOnTheFlyFilteringByInterval(List<PicardHtsPath>, IntervalList) - Static method in class picard.vcf.processor.VariantIteratorProducer
-
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached), that also performs on-the-fly filtering of
VariantContext - ByIntervalListVariantContextIterator - Class in picard.vcf
-
Takes a VCFFileReader and an IntervalList and provides a single iterator over all variants in all the intervals.
- ByIntervalListVariantContextIterator(VCFFileReader, IntervalList) - Constructor for class picard.vcf.ByIntervalListVariantContextIterator
- BYPASS_FEATURE_READER - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- ByteArrayIterator - Class in org.broadinstitute.hellbender.utils.iterators
-
Trivial adapter class allowing a primitive byte[] array to be accessed using the java.util.Iterator interface
- ByteArrayIterator(byte[]) - Constructor for class org.broadinstitute.hellbender.utils.iterators.ByteArrayIterator
- ByteArrayIterator(byte[], int, int) - Constructor for class org.broadinstitute.hellbender.utils.iterators.ByteArrayIterator
-
Iterates through this array, starting at index 'firstIndex' and going until (but not including) index 'stopIndex'.
- byteArrayToCharArray(byte[]) - Static method in class picard.arrays.illumina.InfiniumDataFile
- byteArrayToFloat(byte[]) - Static method in class picard.arrays.illumina.InfiniumDataFile
-
Utility method to convert a byte array to a float value.
- byteArrayToInt(byte[]) - Static method in class picard.arrays.illumina.InfiniumDataFile
-
Utility method to convert an unsigned short to an int.
- byteArrayToString(byte[][], String) - Static method in class picard.util.IlluminaUtil
-
Concatenates all the barcode sequences with BARCODE_DELIMITER
- BYTEWISE_REVERSE_COMPLEMENT - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer
- byWholeContigSubdividingWithWidth(long) - Static method in class picard.vcf.processor.VcfFileSegmentGenerator
-
Deprecated.
- byWholeContigSubdividingWithWidth(long) - Static method in class picard.vcf.processor.VcfPathSegmentGenerator
C
- C - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer.Base
- C - Enum constant in enum class org.broadinstitute.hellbender.utils.BaseUtils.Base
- C - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- C - Enum constant in enum class picard.analysis.artifacts.Transition.Base
- C - Enum constant in enum class picard.illumina.parser.IntensityChannel
- C_CSS_CS - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- C_CSS_NS - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- C_CSS_PCS - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- C_DELETE - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- C_FOLLOWED_BY_INSERTION_BASE - Static variable in class org.broadinstitute.hellbender.utils.pileup.PileupElement
- C_H_MER - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- C_INSERT - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- C_NA - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- C_NON_H_MER - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- C_QUALITY_THRESHOLD - Variable in class picard.analysis.CollectRrbsMetrics
- C_REF_ALT_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of alt (A/T) basecalls observed at sites where the genome reference == C.
- C_REF_OXO_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The rate at which C>A and G>T substitutions are observed at C reference sites above the expected rate if there were no bias between sites with a C reference base vs.
- C_REF_OXO_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
C_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
- C_REF_REF_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of ref basecalls observed at sites where the genome reference == C.
- C_SNP - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- CACHE_LOOKAHEAD - Static variable in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- CachingIndexedFastaSequenceFile - Class in org.broadinstitute.hellbender.utils.fasta
-
A caching version of the IndexedFastaSequenceFile that avoids going to disk as often as the raw indexer.
- CachingIndexedFastaSequenceFile(Path) - Constructor for class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
-
Open the given indexed fasta sequence file.
- CachingIndexedFastaSequenceFile(Path, boolean) - Constructor for class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
-
Open the given indexed fasta sequence file.
- CachingIndexedFastaSequenceFile(Path, long, boolean, boolean) - Constructor for class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
-
Open the given indexed fasta sequence file.
- CachingIndexedFastaSequenceFile(GATKPath) - Constructor for class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
-
Open the given indexed fasta sequence file.
- CAGE_SUPPORTED_TSS - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Transcript 5' end overlaps ENCODE or Fantom CAGE cluster.
- calcAlignmentByteArrayOffset(Cigar, int, boolean, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Calculate the index into the read's bases of the beginning of the encompassing cigar element for a given cigar and offset
- calcAlignmentByteArrayOffset(Cigar, PileupElement, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
- calcBAQFromHMM(byte[], byte[], byte[], int, int) - Method in class org.broadinstitute.hellbender.utils.baq.BAQ
- calcBAQFromHMM(GATKRead, byte[], int) - Method in class org.broadinstitute.hellbender.utils.baq.BAQ
- calcBAQFromHMM(GATKRead, ReferenceDataSource) - Method in class org.broadinstitute.hellbender.utils.baq.BAQ
- calcBAQFromTag(GATKRead, boolean, boolean) - Static method in class org.broadinstitute.hellbender.utils.baq.BAQ
-
Returns a new qual array for read that includes the BAQ adjustment.
- calcBAQFromTag(GATKRead, int, boolean) - Static method in class org.broadinstitute.hellbender.utils.baq.BAQ
-
Returns the BAQ adjusted quality score for this read at this offset.
- calcEfficiency() - Method in class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
-
Returns the efficiency (% of hits of all queries) of this object
- calcEpsilon(byte, byte, byte) - Method in class org.broadinstitute.hellbender.utils.baq.BAQ
- calcGenotypeLikelihoodsOfRefVsAny(int, ReadPileup, byte, byte, MathUtils.RunningAverage, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
-
Calculate the genotype likelihoods for the sample in pileup for being hom-ref contrasted with being ref vs.
- calcGenotypeLikelihoodsOfRefVsAny(int, ReadPileup, byte, byte, MathUtils.RunningAverage, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticReferenceConfidenceModel
-
Calculate the genotype likelihoods for the sample in pileup for being hom-ref contrasted with being ref vs.
- calcMD5(byte[]) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Calculate the md5 for bytes, and return the result as a 32 character string
- calcMD5(String) - Static method in class org.broadinstitute.hellbender.utils.Utils
- CalcMetadataSpark - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
(Internal) Collects read metrics relevant to structural variant discovery
- CalcMetadataSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.CalcMetadataSpark
- calculate(VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator
- calculate(VariantContext, int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator
-
Compute the probability of the alleles segregating given the genotype likelihoods of the samples in vc
- CALCULATE_AS_NECESSARY - Enum constant in enum class org.broadinstitute.hellbender.utils.baq.BAQ.CalculationMode
- CALCULATE_BY - Variable in class picard.fingerprint.CalculateFingerprintMetrics
- CALCULATE_TUMOR_AWARE_RESULTS - Variable in class picard.fingerprint.CrosscheckFingerprints
- calculateAllGcs(byte[], int, int) - Static method in class picard.analysis.GcBiasUtils
- calculateAnnotationFromGTfield(GenotypesContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
- calculateAnnotationFromGTfield(GenotypesContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.FisherStrand
- calculateAnnotationFromGTfield(GenotypesContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest
- calculateAnnotationFromGTfield(GenotypesContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandOddsRatio
- calculateAnnotationFromLikelihoods(AlleleLikelihoods<GATKRead, Allele>, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_FisherStrand
- calculateAnnotationFromLikelihoods(AlleleLikelihoods<GATKRead, Allele>, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandOddsRatio
- calculateAnnotationFromLikelihoods(AlleleLikelihoods<GATKRead, Allele>, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.FisherStrand
- calculateAnnotationFromLikelihoods(AlleleLikelihoods<GATKRead, Allele>, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest
- calculateAnnotationFromLikelihoods(AlleleLikelihoods<GATKRead, Allele>, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandOddsRatio
- calculateArtifactProbabilities(VariantContext, Mutect2FilteringEngine) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter
- CalculateAverageCombinedAnnotations - Class in org.broadinstitute.hellbender.tools
- CalculateAverageCombinedAnnotations() - Constructor for class org.broadinstitute.hellbender.tools.CalculateAverageCombinedAnnotations
- calculateBaseDistributionByCycle(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectBaseDistributionByCycleSpark
-
Computes the MeanQualityByCycle.
- calculateBasicValidationResult(Genotype, Allele, ReadPileup, int, int, int, SimpleInterval, String) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicSomaticShortMutationValidator
-
Perform basic somatic pileup validation and return a result instance.
- calculateBQDLikelihoods(LikelihoodMatrix<GATKRead, A>, List<DRAGENGenotypesModel.DragenReadContainer>, List<DRAGENGenotypesModel.DragenReadContainer>, byte[], int, GenotypeLikelihoodCalculators) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculatorDRAGEN
-
Calculate the BQD model outputs to the likelihoods array.
- calculateChecksumFromMessageDigest() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- calculateChecksumOnInputStream(InputStream) - Method in interface org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter.ChecksumCalculator
- calculateCigar(byte[], byte[], SmithWatermanAligner, SWParameters, SWOverhangStrategy) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
Calculate the cigar elements for this path against the reference sequence.
- calculateCigar(byte[], SmithWatermanAligner, SWParameters) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
-
Calculate the cigar elements for this path against the reference sequence
- CalculateContamination - Class in org.broadinstitute.hellbender.tools.walkers.contamination
-
Calculates the fraction of reads coming from cross-sample contamination, given results from
GetPileupSummaries. - CalculateContamination() - Constructor for class org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination
- calculateContaminationFromHoms(List<PileupSummary>) - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel
-
Calculate the contamination in a tumor sample using the hom alt and hom ref sites inferred from this model, which could be derived from the tumor itself or a matched normal.
- calculateDerivedFields() - Method in class picard.analysis.artifacts.ErrorSummaryMetrics
- calculateDerivedFields() - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
- calculateDerivedFields() - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- calculateDerivedFields() - Method in class picard.analysis.MergeableMetricBase
-
Placeholder method that will calculate the derived fields from the other ones.
- calculateDerivedFields() - Method in class picard.analysis.replicates.IndependentReplicateMetric
- calculateDerivedFields() - Method in class picard.analysis.WgsMetrics
- calculateDerivedFields() - Method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
- calculateDerivedFields() - Method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
- calculateDerivedFields() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
- calculateDerivedFields() - Method in class picard.sam.DuplicationMetrics
-
Fills in the ESTIMATED_LIBRARY_SIZE based on the paired read data examined where possible and the PERCENT_DUPLICATION.
- calculateDerivedFields() - Method in class picard.sam.FlowBasedDuplicationMetrics
- calculateDerivedFields() - Method in class picard.sam.markduplicates.UmiMetrics
- calculateDerivedFields() - Method in class picard.sam.SamErrorMetric.BaseErrorMetric
- calculateDerivedFields() - Method in class picard.sam.SamErrorMetric.IndelErrorMetric
- calculateDerivedFields() - Method in class picard.sam.SamErrorMetric.OverlappingErrorMetric
- calculateDerivedFields() - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
- calculateDerivedFields() - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
- calculateDerivedFields() - Method in class picard.vcf.MendelianViolations.MendelianViolationMetrics
- calculateDerivedMetrics() - Method in class picard.sam.DuplicationMetrics
-
Deprecated.
- calculateDerivedStatistics() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
Calculate the error rate given the raw counts.
- calculateDerivedStatistics() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
Calculate the error rate given the raw counts.
- calculateEH(GenotypeCounts, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet
- calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteredHaplotypeFilter
- calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.GermlineFilter
- calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.HardFilter
- calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2VariantFilter
- calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NormalArtifactFilter
- calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.PolymeraseSlippageFilter
- calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadOrientationFilter
- calculateErrorProbabilityForAlleles(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ContaminationFilter
- calculateErrorProbabilityForAlleles(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.HardAlleleFilter
- calculateErrorProbabilityForAlleles(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2AlleleFilter
- calculateErrorProbabilityForAlleles(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter
- calculateErrorProbabilityForAlleles(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.TumorEvidenceFilter
- calculateFileMD5(File) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Calculates the MD5 for the specified file and returns it as a String
- CalculateFingerprintMetrics - Class in picard.fingerprint
-
Calculates various metrics on a sample fingerprint, indicating whether the fingerprint satisfies the assumptions we have.
- CalculateFingerprintMetrics() - Constructor for class picard.fingerprint.CalculateFingerprintMetrics
- calculateFractionalErrorArray(int[], byte[]) - Static method in class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
- calculateFRDLikelihoods(LikelihoodMatrix<GATKRead, A>, double[], List<DRAGENGenotypesModel.DragenReadContainer>, double, double, int, GenotypeLikelihoodCalculators) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculatorDRAGEN
-
Calculate the BQD model outputs to the likelihoods array.
- calculateFromDerivedFields() - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
- calculateFromDerivedFields(long) - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
- calculateGc(byte[], int, int, GcBiasUtils.CalculateGcState) - Static method in class picard.analysis.GcBiasUtils
- calculateGcContent(Allele, Allele, ReferenceContext, int) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
Calculates the fraction of Guanine and Cytosine bases in a window of a given size around a variant.
- calculateGenotypeConcordance(GenotypeConcordanceScheme, boolean) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Genotype Concordance is the number of times the truth and call states match exactly / all truth and call combinations made If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
- CalculateGenotypePosteriors - Class in org.broadinstitute.hellbender.tools.walkers.variantutils
-
Calculate genotype posterior probabilities given family and/or known population genotypes
- CalculateGenotypePosteriors() - Constructor for class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
- calculateGenotypes(VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
- calculateGenotypes(VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine
- calculateGenotypes(VariantContext, GenotypePriorCalculator, List<VariantContext>) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
-
Main entry function to calculate genotypes of a given VC with corresponding GLs that is shared across genotypers (namely GGVCFs and HC).
- calculateGLsForThisEvent(AlleleLikelihoods<GATKRead, Allele>, VariantContext, List<Allele>, byte[], int, DragstrReferenceAnalyzer) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine
-
For a particular event described in inputVC, form PL vector for each sample by looking into allele read map and filling likelihood matrix for each allele
- calculateGQFromPLs(int[]) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Calculate the Genotype Quality (GQ) by subtracting the smallest Phred-scaled likelihoods (PL) from the second smallest.
- calculateIC(VariantContext, Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_InbreedingCoeff
- calculateIsSNPOrIndel(GATKRead, ReferenceDataSource, int[], int[], int[]) - Static method in class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
-
Locates all SNP and indel events, storing them in the provided snp, isIns, and isDel arrays, and returns the total number of SNP/indel events.
- calculateKnownSites(GATKRead, Iterable<? extends Locatable>) - Static method in class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
- calculateLikelihoods(AlleleList<A>, GenotypingData<A>, byte[], int, DragstrReferenceAnalyzer) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.DRAGENGenotypesModel
- calculateLikelihoods(AlleleList<A>, GenotypingData<A>, byte[], int, DragstrReferenceAnalyzer) - Method in interface org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingModel
- calculateLikelihoods(AlleleList<A>, GenotypingData<A>, byte[], int, DragstrReferenceAnalyzer) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.IndependentSampleGenotypesModel
- calculateLog10DynamicReadQualThreshold(GATKRead, double) - Static method in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
-
Dynamic likelihood DRAGEN-GATK threshold.
- calculateMatchResults(Fingerprint, Fingerprint) - Static method in class picard.fingerprint.FingerprintChecker
-
Compares two fingerprints and calculates a MatchResults object which contains detailed information about the match (or mismatch) between fingerprints including the LOD score for whether or not the two are likely from the same sample.
- calculateMatchResults(Fingerprint, Fingerprint, double, double) - Static method in class picard.fingerprint.FingerprintChecker
- calculateMatchResults(Fingerprint, Fingerprint, double, double, boolean, boolean) - Static method in class picard.fingerprint.FingerprintChecker
-
Compares two fingerprints and calculates a MatchResults object which contains detailed information about the match (or mismatch) between fingerprints including the LOD score for whether or not the two are likely from the same sample.
- calculateMaxAltRatio(ReadPileup, Allele, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.PowerCalculationUtils
-
Calculate the fraction of non-ref reads in the given pileup.
- calculateMD5(GATKPath, SimpleInterval) - Static method in class org.broadinstitute.hellbender.utils.reference.ReferenceUtils
-
Given a reference path and a sequence interval, calculates the MD5 for the given sequence.
- calculateMeanQualityByCycle(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MeanQualityByCycleSpark
-
Computes the MeanQualityByCycle.
- calculateMinCountForSignal(int, double) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.PowerCalculationUtils
- CalculateMixingFractions - Class in org.broadinstitute.hellbender.tools.walkers.validation
-
Given a VCF of known variants from multiple samples, calculate how much each sample contributes to a pooled BAM.
- CalculateMixingFractions() - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.CalculateMixingFractions
- calculateMostLikelyAlleles(VariantContext, int, int, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
-
Returns the new set of alleles to use based on a likelihood score: alleles' scores are the sum of their counts in sample genotypes, weighted by the confidence in the genotype calls.
- calculateNonRefGenotypeConcordance(GenotypeConcordanceScheme, boolean) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Non Ref Genotype Concordance is the number of times the truth and call states match exactly for *vars only* / all truth and call *var* combinations made If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
- calculateNumReadsSupportingAllele(ReadPileup, Allele, Allele, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.PowerCalculationUtils
-
Get a count of the number of reads supporting an allele in a given pileup.
- calculateOneSidedU(double[], double[], MannWhitneyU.TestType) - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU
-
Calculates the rank-sum test statisic U (sometimes W) from two sets of input data for a one-sided test with an int indicating which group is the dominator.
- calculatePathMD5(Path) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Calculates the MD5 for the specified file and returns it as a String
- calculatePosteriorGLs(VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.FamilyLikelihoods
-
Computes phred-scaled genotype posteriors given the data in the given variant context and family priors given by this object.
- calculatePosteriorProbs(VariantContext, List<VariantContext>, int, PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions) - Static method in class org.broadinstitute.hellbender.tools.walkers.variantutils.PosteriorProbabilitiesUtils
-
Calculates phred-scaled posterior probabilities for genotypes given the data and allele frequency priors.
- calculatePosteriorProbs(List<double[]>, double[], int, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.variantutils.PosteriorProbabilitiesUtils
-
Given genotype likelihoods and known allele counts, calculate the posterior probabilities over the genotype states
- calculatePower(int, int, int, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.PowerCalculationUtils
-
Calculate the power to validate the mutation with given alt and total counts.
- calculateRank(double[], double[]) - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU
- calculateRankSum(Map<Allele, CompressedDataList<Integer>>, Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
- calculateRawData(VariantContext, AlleleLikelihoods<GATKRead, Allele>, ReducibleAnnotationData) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality
- CalculateReadGroupChecksum - Class in picard.sam
- CalculateReadGroupChecksum() - Constructor for class picard.sam.CalculateReadGroupChecksum
- calculateReducedData(Map<Allele, Histogram>, Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
- calculateReducedData(AlleleSpecificAnnotationData<List<Integer>>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_FisherStrand
- calculateReducedData(AlleleSpecificAnnotationData<List<Integer>>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
-
Method which determines how the Strand Bias read direction allele data must be combined into a final annotation Must be overridden by client methods.
- calculateReducedData(AlleleSpecificAnnotationData<List<Integer>>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandOddsRatio
- calculateRefConfidence(Haplotype, Collection<Haplotype>, SimpleInterval, AssemblyRegion, AlleleLikelihoods<GATKRead, Haplotype>, PloidyModel, List<VariantContext>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
- calculateRefConfidence(Haplotype, Collection<Haplotype>, SimpleInterval, AssemblyRegion, AlleleLikelihoods<GATKRead, Haplotype>, PloidyModel, List<VariantContext>, boolean, List<VariantContext>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
-
Calculate the reference confidence for a single sample given the its read data Returns a list of variant contexts, one for each position in the
activeRegion.getLoc(), each containing detailed information about the certainty that the sample is hom-ref for each base in the region. - calculateRefWindowsByGc(int, File, int) - Static method in class picard.analysis.GcBiasUtils
- calculateRoiHistogram() - Method in class picard.sam.DuplicationMetrics
-
Calculates a histogram using the estimateRoi method to estimate the effective yield doing x sequencing for x=1..10.
- calculateRunningMetric(List<VariantDatum>) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager.SelectionMetric
- calculateRunningMetric(List<VariantDatum>) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager.TruthSensitivityMetric
- calculateSensitivities(int, Histogram<Integer>, Histogram<Integer>, List<Double>) - Static method in class picard.analysis.TheoreticalSensitivity
-
This is a utility function to calculate the metrics specific to running theoretical sensitivity over several different allele fractions.
- calculateSingleSampleBiallelicNonRefPosterior(double[], boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator
-
Calculate the posterior probability that a single biallelic genotype is non-ref The nth genotype (n runs from 0 to the sample ploidy, inclusive) contains n copies of the alt allele
- calculateSingleSampleRefVsAnyActiveStateProfileValue(double[]) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
-
Calculates the active state profile value for a single sample.
- calculateSOR(int[][]) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandOddsRatio
-
Computes the SOR value of a table after augmentation.
- calculateSortOrder(double[]) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
-
Get a list of indices which give the ascending sort order of the data array
- calculateThresholdBasedOnFalseDiscoveryRate(List<Double>, double) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ThresholdCalculator
-
Compute the filtering threshold that ensures that the false positive rate among the resulting pass variants will not exceed the requested false positive rate
- calculateTwoSidedU(double[], double[]) - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU
-
Calculates the two-sided rank-sum test statisic U (sometimes W) from two sets of input data.
- calculateU1andU2(double[], double[]) - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU
-
Rank both groups together and return a TestStatistic object that includes U1, U2 and number of ties for sigma
- calculateVCDepth(VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
-
lookup the depth from the VC DP field or calculate by summing the depths of the genotypes
- calculateWordCount(byte[]) - Method in class picard.util.AbstractInputParser
-
Calculates the number of delimiter-separated "words" in a line and sets the value of
wordCount - calculateWorstPerformingAnnotation(List<VariantDatum>, GaussianMixtureModel, GaussianMixtureModel) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorEngine
- calculateZ(double, int, int, double, MannWhitneyU.TestType) - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU
-
Calculates the Z score (i.e.
- CalibrateDragstrModel - Class in org.broadinstitute.hellbender.tools.dragstr
-
Estimates the parameters for the DRAGstr model for an input sample.
- CalibrateDragstrModel() - Constructor for class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- CALIBRATION_LABEL - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- CALIBRATION_SCORES_HDF5_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
- CALIBRATION_SENSITIVITY_KEY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- CALIBRATION_SENSITIVITY_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
- call() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase.OutputCapture
-
Runs the capture.
- call() - Method in enum class picard.analysis.artifacts.Transition
-
Gets the call for the transition.
- call(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.ContainsKmerReadFilterSpark
- call(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.utils.ReadFilterSparkifier
- call(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.utils.ReadTransformerSparkifier
- CALL_CONFIDENCE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- CALL_CONFIDENCE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- CALL_GENOTYPES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection
- CALL_RATE - Variable in class picard.arrays.BafRegressMetrics
-
The call rate of the sample (number of non-missing genotypes)
- CALL_RATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The overall call rate
- CALL_RATE_PF_THRESHOLD - Static variable in class picard.arrays.CollectArraysVariantCallingMetrics
- CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordance
- CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The name of the 'call' sample
- CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The name of the 'call' sample
- CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The name of the 'call' sample
- CALL_STATE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The state of the 'call' sample (i.e.
- CALL_VCF - Variable in class picard.vcf.GenotypeConcordance
- CALLABLE_DEPTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- CALLABLE_REGION_TAG - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- CALLABLE_SITES_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- callableDepth - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- callAllele1 - Variable in class picard.vcf.GenotypeConcordance.Alleles
- callAllele2 - Variable in class picard.vcf.GenotypeConcordance.Alleles
- callAlleles() - Method in class picard.vcf.GenotypeConcordance.Alleles
- CallCopyRatioSegments - Class in org.broadinstitute.hellbender.tools.copynumber
-
Calls copy-ratio segments as amplified, deleted, or copy-number neutral.
- CallCopyRatioSegments() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegments
- CALLED_HAPLOTYPES - Enum constant in enum class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter.WriterType
-
A mode for users.
- CALLED_HAPLOTYPES_NO_READS - Enum constant in enum class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter.WriterType
-
Same as CALLED_HAPLOTYPES, but without reads
- CalledCopyRatioSegment - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
- CalledCopyRatioSegment(CopyRatioSegment, CalledCopyRatioSegment.Call) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledCopyRatioSegment
- CalledCopyRatioSegment.Call - Enum Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
- CalledCopyRatioSegmentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
- CalledCopyRatioSegmentCollection(File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.CalledCopyRatioSegmentCollection
- CalledCopyRatioSegmentCollection(SampleLocatableMetadata, List<CalledCopyRatioSegment>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.CalledCopyRatioSegmentCollection
- CalledHaplotypes - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Carries the result of a call to #assignGenotypeLikelihoods
- CalledHaplotypes(List<VariantContext>, Set<Haplotype>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.CalledHaplotypes
- CalledLegacySegment - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
- CalledLegacySegment(String, SimpleInterval, int, double, CalledCopyRatioSegment.Call) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledLegacySegment
- CalledLegacySegmentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
Represents a CBS-style segmentation to enable IGV-compatible plotting.
- CalledLegacySegmentCollection(File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.CalledLegacySegmentCollection
- CalledLegacySegmentCollection(SampleLocatableMetadata, List<CalledLegacySegment>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.CalledLegacySegmentCollection
- CALLER_EXTERNAL_ADMIXING_RATE - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- CALLER_EXTERNAL_ADMIXING_RATE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- CALLER_INTERNAL_ADMIXING_RATE - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- CALLER_INTERNAL_ADMIXING_RATE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- CALLER_UPDATE_CONVERGENCE_THRESHOLD - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- CALLER_UPDATE_CONVERGENCE_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- callGenotypes - Variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection
-
Output called genotypes in the final VCF (otherwise no-call)
- callGTAlleles - Variable in class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
- callImpreciseDeletionFromEvidenceLinks(PairedStrandedIntervalTree<EvidenceTargetLink>, ReadMetadata, ReferenceMultiSparkSource, int, int, Logger) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.ImpreciseVariantDetector
- CALLING_COPY_RATIO_Z_SCORE_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegments
- CallingMetricAccumulator - Class in picard.vcf
-
Collects variants and generates metrics about them.
- CallingMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets) - Constructor for class picard.vcf.CallingMetricAccumulator
- CallingMetricAccumulator.Result - Class in picard.vcf
- callMutations(AlleleLikelihoods<GATKRead, Haplotype>, AssemblyResultSet, ReferenceContext, SimpleInterval, FeatureContext, List<VariantContext>, SAMFileHeader, boolean, boolean, Set<Integer>) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine
-
Main entry point of class - given a particular set of haplotypes, samples and reference context, compute genotype likelihoods and assemble into a list of variant contexts and genomic events ready for calling The list of samples we're working with is obtained from the readLikelihoods
- callRegion(Locatable, List<VariantContext>, ReferenceContext, FeatureContext, ReferenceConfidenceVariantContextMerger, boolean, double, double, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine
- callRegion(AssemblyRegion, FeatureContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
-
Generate variant calls for an assembly region
- callRegion(AssemblyRegion, FeatureContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerEngine
-
Generate variant calls for an assembly region
- callRegion(AssemblyRegion, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- CALLS_PATH_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy
- CALLS_PATH_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller
- CALLS_SHARD_PATH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- callsAtTruthSites - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- callSourceString() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
-
What string to use as source of variant-context generated by this genotyper-engine.
- callSourceString() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine
- callSourceString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine
- callState - Variable in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
- callVariantsWithHaplotypeCallerAndWriteOutput(JavaSparkContext, JavaRDD<GATKRead>, SAMFileHeader, SAMSequenceDictionary, String, List<ShardBoundary>, HaplotypeCallerArgumentCollection, AssemblyRegionReadShardArgumentCollection, AssemblyRegionArgumentCollection, String, Collection<Annotation>, Logger, boolean, boolean) - Static method in class org.broadinstitute.hellbender.tools.HaplotypeCallerSpark
-
Call Variants using HaplotypeCaller on Spark and write out a VCF file.
- callVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
- CAN_SKIP - Enum constant in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.AnnotatedIntervalCodec
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceBCICodec
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceCodec
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.copynumber.SimpleCountCodec
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceBCICodec
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceCodec
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceBCICodec
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceCodec
- canDecode(String) - Method in interface org.broadinstitute.hellbender.utils.codecs.FeatureOutputCodec
-
File formats are typically recognized by their extensions.
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.EnsemblGtfCodec
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
-
Can the file be decoded?
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupCodec
-
Only files with
SAMPileupCodec.SAM_PILEUP_FILE_EXTENSIONScould be parsed - canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.SiteDepthBCICodec
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.SiteDepthCodec
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceBCICodec
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceCodec
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.table.TableCodec
- canDecode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
- canDecodeFileChecks(String) - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
-
Checks the content of the given config file to see if it can be decoded.
- canDecodeFileChecks(String, String) - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
-
Checks the content of the given config file and backing data file to see if they can be decoded.
- canMakeInstances(Class<?>) - Static method in class org.broadinstitute.hellbender.utils.ClassUtils
-
Returns true iff we can make instances of this class.
- canMerge(MergeableMetricBase) - Method in class picard.analysis.MergeableMetricBase
-
Checks if this instance can be merged with another Other must have all the fields that this instance has, and the fields that are annotated as MergeByAssertEquals must contain the same value
- CANNOT_COMPUTE_ADAPTOR_BOUNDARY - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- CANNOT_SKIP_FOUND_NO_MC - Enum constant in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
- CANNOT_SKIP_FOUND_OQ - Enum constant in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
- cannotBeGenotyped(VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
-
Checks whether the variant context has too many alternative alleles for progress to genotyping the site.
- CannotExecuteScript(String, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CannotExecuteScript
- CannotHandleGzippedRef() - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CannotHandleGzippedRef
- canonical() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- canonical() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- canonical() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- canonical() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- canonical() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- canonical() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- canonical(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer
- canonical(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
-
Returns a SVKmerLong that is a canonical representation of this one.
- canonical(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
-
Returns a SVKmerShort that is a canonical representation of this one.
- CANONICAL - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.TranscriptSelectionMode
-
CANONICAL Select a transcript to be reported with details with priority on canonical order according to the folowing list of selection criteria: Choose the transcript that is on the custom list specified by the user.
- canonicalizeAndMask(SVKmerShort, int, SVKmerShort) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerCollection
-
Definition for the order of canonicalization and masking
- canonicalStream(byte[], int, int, SVKmer) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVDUSTFilteredKmerizer
- canonicalStream(byte[], int, SVKmer) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- canonicalStream(CharSequence, int, int, SVKmer) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVDUSTFilteredKmerizer
- CanonicalSVCollapser - Class in org.broadinstitute.hellbender.tools.sv.cluster
-
Class for collapsing a collection of similar
SVCallRecordobjects, such as clusters produced byCanonicalSVLinkage, into a single representative call. - CanonicalSVCollapser(ReferenceSequenceFile, CanonicalSVCollapser.AltAlleleSummaryStrategy, CanonicalSVCollapser.BreakpointSummaryStrategy) - Constructor for class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
- CanonicalSVCollapser.AltAlleleSummaryStrategy - Enum Class in org.broadinstitute.hellbender.tools.sv.cluster
-
Define strategies for collapsing alt alleles with different subtypes.
- CanonicalSVCollapser.BreakpointSummaryStrategy - Enum Class in org.broadinstitute.hellbender.tools.sv.cluster
-
Define strategies for collapsing variant intervals.
- CanonicalSVLinkage<T extends SVCallRecord> - Class in org.broadinstitute.hellbender.tools.sv.cluster
-
Main class for SV clustering.
- CanonicalSVLinkage(SAMSequenceDictionary, boolean) - Constructor for class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
-
Create a new engine
- canReadFile(File...) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Checks that one or more user provided files are in fact regular (i.e.
- canSkip() - Method in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
- canSkipSAMFile(File, int, boolean, File) - Static method in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
-
Checks if we can skip the SAM/BAM/CRAM file when reverting origin base qualities and adding mate cigars.
- capacity() - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- capacity() - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
-
maximum number of elements that can be held without resizing.
- capacity() - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
-
maximum number of elements that can be held without resizing.
- CAPACITY - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect3DatasetEngine
- capBaseByBAQ(byte, byte, int, int) - Method in class org.broadinstitute.hellbender.utils.baq.BAQ
- capFromAbove(double[], double) - Static method in class picard.util.MathUtil
-
Returns the array capped (from above) by the value of top
- capFromBelow(double[], double) - Static method in class picard.util.MathUtil
-
Returns the array capped (from below) by the value of floor
- CAPILLARY - Enum constant in enum class org.broadinstitute.hellbender.utils.NGSPlatform
- CappedHaplotypeProbabilities - Class in picard.fingerprint
- CappedHaplotypeProbabilities(HaplotypeProbabilities, double) - Constructor for class picard.fingerprint.CappedHaplotypeProbabilities
- CAPTURE_ASSEMBLY_FAILURE_BAM_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- captureAssemblyFailureBAM - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- CapturedStreamOutput - Class in org.broadinstitute.hellbender.utils.runtime
-
Stream output captured from a stream.
- CapturedStreamOutput(OutputStreamSettings, InputStream, PrintStream) - Constructor for class org.broadinstitute.hellbender.utils.runtime.CapturedStreamOutput
- CapturedStreamOutputSnapshot - Class in org.broadinstitute.hellbender.utils.runtime
-
Stream output captured from a streaming stream.
- CapturedStreamOutputSnapshot(OutputStreamSettings, InputStream, PrintStream) - Constructor for class org.broadinstitute.hellbender.utils.runtime.CapturedStreamOutputSnapshot
- CASAVA_1_8 - Enum constant in enum class picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
- Casava18ReadNameEncoder - Class in picard.fastq
-
A read name encoder conforming to the standard described by Illumina Casava 1.8.
- Casava18ReadNameEncoder(String, String, String) - Constructor for class picard.fastq.Casava18ReadNameEncoder
- CASE - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.RunMode
- CASE - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.RunMode
- CASE_DETERMINE_PLOIDY_AND_DEPTH_PYTHON_SCRIPT - Static variable in class org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy
- CASE_SAMPLE_CALLING_PYTHON_SCRIPT - Static variable in class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller
- CATEGORY - Variable in class picard.analysis.AlignmentSummaryMetrics
-
One of either UNPAIRED (for a fragment run), FIRST_OF_PAIR when metrics are for only the first read in a paired run, SECOND_OF_PAIR when the metrics are for only the second read in a paired run or PAIR when the metrics are aggregated for both first and second reads in a pair.
- CATEGORY - Variable in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
-
One of either WHOLE_GENOME or NON_ZERO_REGIONS
- CATEGORY - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
-
Grouping categories for controls.
- Cbcl - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- CbclData - Class in picard.illumina.parser
-
This class provides that data structure for cbcls.
- CbclData(int[], int) - Constructor for class picard.illumina.parser.CbclData
- CbclReader - Class in picard.illumina.parser.readers
-
------------------------------------- CBCL Header ----------------------------------- Bytes 0 - 1 Version number, current version is 1 unsigned 16 bits little endian integer Bytes 2 - 5 Header size unsigned 32 bits little endian integer Byte 6 Number of bits per basecall unsigned Byte 7 Number of bits per q-score unsigned
- CbclReader(List<File>, Map<Integer, File>, int[], int, List<AbstractIlluminaPositionFileReader.PositionInfo>, int[]) - Constructor for class picard.illumina.parser.readers.CbclReader
- CC - Enum constant in enum class picard.fingerprint.DiploidGenotype
- CCDS - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
member of the consensus CDS gene set, confirming coding regions between ENSEMBL, UCSC, NCBI and HAVANA.
- cd - Variable in class org.broadinstitute.hellbender.utils.baq.BAQ
- CDF(float[], long) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.CDF
- CDF(IntHistogram) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.CDF
- CDF_PREFIX - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- CDS - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- CDS - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureType
- CDS_END - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- CDS_END_NF - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
The coding region end could not be confirmed.
- CDS_START - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- CDS_START_NF - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
The coding region start could not be confirmed.
- center - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Partition
- CenteredConstrained - Enum constant in enum class picard.util.BaitDesigner.DesignStrategy
-
Implementation that "constrains" baits to be within the target region when possible.
- CENTERS_KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3
- CF1R2Args - Variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2Counts
- CG - Enum constant in enum class picard.fingerprint.DiploidGenotype
- CHAIN - Variable in class picard.fingerprint.LiftOverHaplotypeMap
- CHAIN - Variable in class picard.util.LiftOverIntervalList
- CHAIN - Variable in class picard.vcf.LiftoverVcf
- chainHeads() - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
- ChainPruner<V extends BaseVertex,
E extends BaseEdge> - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs - ChainPruner() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.ChainPruner
- chainsToRemove(List<Path<V, E>>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.AdaptiveChainPruner
- chainsToRemove(List<Path<V, E>>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.ChainPruner
- chainsToRemove(List<Path<V, E>>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.LowWeightChainPruner
- changeAlleles(List<A>) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Replaces the alleles in the readLikelihood matrix.
- changeCallToHomRefVersusNonRef(VariantContext, Map<String, Object>) - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
-
Produce a GenotypeBuilder for a hom-ref call suitable to be merged into a reference block, i.e.
- changeEvidence(Map<EVIDENCE, EVIDENCE>) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
- changeTraversalModeToByVariant() - Method in class org.broadinstitute.hellbender.engine.VariantLocusWalker
-
Traverse by variant instead of by grouped by locus.
- Character - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportDataType
-
Used for char values.
- charAt(int) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.SequenceRC
- charAt(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer.ASCIICharSequence
- CHART_OUTPUT - Variable in class picard.analysis.CollectBaseDistributionByCycle
- CHART_OUTPUT - Variable in class picard.analysis.CollectGcBiasMetrics
- CHART_OUTPUT - Variable in class picard.analysis.CollectRnaSeqMetrics
- CHART_OUTPUT - Variable in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
- CHART_OUTPUT - Variable in class picard.analysis.MeanQualityByCycle
- CHART_OUTPUT - Variable in class picard.analysis.QualityScoreDistribution
- chartOutput - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectBaseDistributionByCycleSpark
- chartOutput - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MeanQualityByCycleSpark
- chartOutput - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityScoreDistributionSpark
- CHECK_FIRST_N_RECORDS - Variable in class picard.vcf.FixVcfHeader
- CHECK_MD5_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.HtsgetReader
- checkAndClearHeaderSequences(SAMFileHeader, PSFilterArgumentCollection, Logger) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSUtils
-
Returns a deep copy of the input header with an empty sequence dictionary, and logs warnings if the input may be aligned but --is-host-aligned was not set to true (or vice versa).
- checkCommand(String[]) - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- CheckDuplicateMarking - Class in picard.sam.markduplicates
- CheckDuplicateMarking() - Constructor for class picard.sam.markduplicates.CheckDuplicateMarking
- CheckDuplicateMarking.Mode - Enum Class in picard.sam.markduplicates
- checkError() - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter
- checkError() - Method in class org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter
- checkFilter(Set<Map.Entry<String, String>>, VariantContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.FuncotationFilter
-
Check all of this filter's rules against a set of Funcotations.
- CheckFingerprint - Class in picard.fingerprint
-
Checks the sample identity of the sequence/genotype data in the provided file (SAM/BAM or VCF) against a set of known genotypes in the supplied genotype file (in VCF format).
- CheckFingerprint() - Constructor for class picard.fingerprint.CheckFingerprint
- checkFingerprints(List<Path>, List<Path>, String, boolean) - Method in class picard.fingerprint.FingerprintChecker
-
Top level method to take a set of one or more SAM files and one or more Genotype files and compare each read group in each SAM file to each set of fingerprint genotypes.
- checkFingerprintsFromPaths(List<Path>, List<Path>, String, String) - Method in class picard.fingerprint.FingerprintChecker
-
Top level method to take a set of one or more observed genotype (VCF) files and one or more expected genotype (VCF) files and compare one or more sample in the observed genotype file with one or more in the expected file and generate results for each set.
- checkForDuplicatesAndReturnSet(Collection<E>, String) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Checks that the collection does not contain a duplicate value (throws an
IllegalArgumentExceptionif it does). - checkHasTrainingSet() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- checkHasTruthSet() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- checkHistograms(List<BreakpointEvidence>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
-
Used in production to gather evidence derived from K-S calculation on windows.
- CheckIlluminaDirectory - Class in picard.illumina
-
Program to check a lane of an Illumina output directory.
- CheckIlluminaDirectory() - Constructor for class picard.illumina.CheckIlluminaDirectory
- checkIndexVersionAndModificationTime(Path, Path, Index) - Static method in class org.broadinstitute.hellbender.utils.IndexUtils
- checkMandatoryColumns(TableColumnCollection, TableColumnCollection, Function<String, RuntimeException>) - Static method in class org.broadinstitute.hellbender.utils.tsv.TableUtils
-
Checks if all mandatory columns are present in a
TableColumnCollection. - checkNames(Object[], Function<String, RuntimeException>) - Static method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Checks that a column name, as objects, array is valid.
- checkNames(String[], Function<String, RuntimeException>) - Static method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Checks that a column name array is valid.
- checkOutOfBounds(int) - Method in class picard.analysis.CounterManager
-
Method checks that new locus position is not out of bounds of Counter arrays and there is enough space in them to hold information on at least one more read of length
CounterManager.readLength. - CheckPileup - Class in org.broadinstitute.hellbender.tools.walkers.qc
-
Compare GATK's internal pileup to a reference Samtools pileup
- CheckPileup() - Constructor for class org.broadinstitute.hellbender.tools.walkers.qc.CheckPileup
- checkPythonEnvironmentForPackage(String) - Static method in class org.broadinstitute.hellbender.utils.python.PythonScriptExecutor
- CheckReferenceCompatibility - Class in org.broadinstitute.hellbender.tools.reference
-
Check a BAM/VCF for compatibility against specified references.
- CheckReferenceCompatibility() - Constructor for class org.broadinstitute.hellbender.tools.reference.CheckReferenceCompatibility
- CheckReferenceCompatibility.CheckReferenceCompatibilityTableWriter - Class in org.broadinstitute.hellbender.tools.reference
-
TableWriter to format and write the table output.
- CheckReferenceCompatibilityTableWriter(Writer, TableColumnCollection) - Constructor for class org.broadinstitute.hellbender.tools.reference.CheckReferenceCompatibility.CheckReferenceCompatibilityTableWriter
- CheckReferenceCompatibilityTableWriter(Path, TableColumnCollection) - Constructor for class org.broadinstitute.hellbender.tools.reference.CheckReferenceCompatibility.CheckReferenceCompatibilityTableWriter
- checkRInstallation(boolean) - Static method in class picard.cmdline.CommandLineProgram
-
Check if R is installed
- checkSettings(InputStreamSettings) - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- checkSettings(OutputStreamSettings) - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- checkStructure() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
-
Because of the piecemeal way we allow the tree to be constructed, we can end up with invalid tree structures.
- checksum - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- CheckTerminatorBlock - Class in picard.sam
-
Simple class to check the terminator block of a SAM file.
- CheckTerminatorBlock() - Constructor for class picard.sam.CheckTerminatorBlock
- checkTileCount() - Method in class picard.illumina.parser.ParameterizedFileUtil
- checkTileCount() - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
- checkVariantType(VariantContext, VariantContext) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.VariantType
-
Returns true if both
vcandresourceVCare the same variant type, following our definitions. - checkVariationClass(VariantContext, Allele, VariantRecalibratorArgumentCollection.Mode) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- checkVariationClass(VariantContext, VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- checkVariationClass(VariantContext, VariantRecalibratorArgumentCollection.Mode) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- CHI_SQ_VALUE - Variable in class org.broadinstitute.hellbender.metrics.analysis.AlleleFrequencyQCMetric
- CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
-
The Chi-squared pvalue of the observed counts vector relative to the expected counts, (3x2 table)
- CHIMERA_KB_MIN - Variable in class picard.analysis.CollectJumpingLibraryMetrics
- ChimeraUtil - Class in picard.analysis
- ChimeraUtil() - Constructor for class picard.analysis.ChimeraUtil
- CHIMERIC - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
- CHIMERIC_ALIGNMENTS_HIGHMQ_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- CHIMERIC_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of pairs where either (a) the ends fall on different chromosomes or (b) the insert size is greater than the maximum of 100000 or 2 times the mode of the insert size for outward-facing pairs.
- CHIP_TYPE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The chip type name
- CHIP_WELL_BARCODE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The chip well barcode of the Illumina array being assayed
- CHIP_WELL_BARCODE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- chiSqDist - Static variable in class org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAF
- chooseAlleleForRead(PileupElement, Allele, List<Allele>, int) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Given a set of alleles (reference and alternate), choose the allele that is the best match for the given read (and offset) TODO: This method cannot recognize equivalent alleles (See https://github.com/broadinstitute/gatk/issues/5061)
- CHR_COUNTS - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants.ValidationType
-
Check that the AN and AC annotations are consistent with the number of calls, alleles and then number these are called across samples.
- CHR1_B36 - Static variable in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
- CHR1_B37 - Static variable in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
- CHR1_HG18 - Static variable in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
- CHR1_HG19 - Static variable in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
- CHR10_B36 - Static variable in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
- CHR10_B37 - Static variable in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
- CHR10_HG18 - Static variable in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
- CHR10_HG19 - Static variable in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
- CHR2_B36 - Static variable in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
- CHR2_B37 - Static variable in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
- CHR2_HG18 - Static variable in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
- CHR2_HG19 - Static variable in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
- CHROM - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The chromosome on which the SNP resides.
- CHROMOSOME - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- CHROMOSOME - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- CHROMOSOME_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- ChromosomeCounts - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Counts and frequency of alleles in called genotypes
- ChromosomeCounts() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.ChromosomeCounts
- CHUNK_INDEX_PATH_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils
- CIEND - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- CIGAR - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestField
- CIGAR_CONTAINS_NO_N_OPERATOR - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- cigarAlong5to3DirectionOfContig - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- cigarAlongReference() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
Returns the cigar of this alignment interval along the reference.
- CigarBuilder - Class in org.broadinstitute.hellbender.utils.read
-
This class allows code that manipulates cigars to do so naively by handling complications such as merging consecutive identical operators within the builder.
- CigarBuilder() - Constructor for class org.broadinstitute.hellbender.utils.read.CigarBuilder
- CigarBuilder(boolean) - Constructor for class org.broadinstitute.hellbender.utils.read.CigarBuilder
- CigarBuilder.Result - Class in org.broadinstitute.hellbender.utils.read
- CigarContainsNoNOperator() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.CigarContainsNoNOperator
- CigarOperatorsInReadStratifier(CigarOperator) - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.CigarOperatorsInReadStratifier
- CigarUtils - Class in org.broadinstitute.hellbender.utils.read
- CIPOS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- CircularByteBuffer - Class in picard.util
-
Implementation of a circular byte buffer that uses a large byte[] internally and supports basic read/write operations from/to other byte[]s passed as arguments.
- CircularByteBuffer(int) - Constructor for class picard.util.CircularByteBuffer
-
Constructs a buffer capable of holding the given number of bytes.
- CLASS_COHERENCE_LENGTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCallingArgumentCollection
- CLASS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.HtsgetReader
- CLASSIFICATION - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
The classification of this read: {EMPTY, POLYCLONAL, MISALIGNED, UNKNOWN} (See PFFailSummaryMetric for explanation regarding the possible classification.)
- classifyVariants(Optional<VariantContext>, String, Optional<VariantContext>, String, int, int, boolean) - Static method in class picard.vcf.GenotypeConcordance
- classifyVariants(Optional<VariantContext>, String, Optional<VariantContext>, String, Optional<GenotypeConcordanceCounts>, Optional<GenotypeConcordanceCounts>, int, int, boolean) - Static method in class picard.vcf.GenotypeConcordance
-
Attempts to determine the concordance state given the truth and all variant context and optionally increments the genotype concordance count for the given variant type (SNP or INDEL).
- ClassUtils - Class in org.broadinstitute.hellbender.utils
-
Utilities for dealing with reflection.
- cleanerMaxCopyNumber - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- cleanerMaxIntervals - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- cleanerMinKmerCount - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- cleanNonRefPaths() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Remove edges that are connected before the reference source and after the reference sink Also removes all vertices that are orphaned by this process
- cleanOverlappingReadPairs(List<GATKRead>, SampleList, SAMFileHeader, boolean, OptionalInt, OptionalInt) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
-
Modify base qualities when paired reads overlap to account for the possibility of PCR error.
- CleanSam - Class in picard.sam
- CleanSam() - Constructor for class picard.sam.CleanSam
- cleanUp() - Method in class picard.util.ThreadPoolExecutorWithExceptions
-
Calls `shutdownNow, adjusts the core size to 0 and low timeout to ensure threads get killed and garbage collected.
- clear() - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram
- clear() - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter
- clear() - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- clear() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.KMerCounter
-
Remove all current counts, resetting the counter to an empty state
- clear() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteringOutputStats
- clear() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ThresholdCalculator
- clear() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- clear() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- clear() - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
- clear() - Method in class org.broadinstitute.hellbender.utils.collections.IndexedSet
-
Removes all elements in the set.
- clear() - Method in class org.broadinstitute.hellbender.utils.Nucleotide.Counter
-
Reset all the counts to 0.
- clear() - Method in class org.broadinstitute.hellbender.utils.SATagBuilder
-
Clears all SA tag units from the SATagBuilder as they exist.
- clear() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Remove all entries.
- clear() - Method in class picard.analysis.CounterManager
-
Clears all inner Counter arrays
- clear() - Method in class picard.illumina.parser.readers.CbclReader
- CLEAR_DT - Variable in class picard.sam.markduplicates.MarkDuplicates
- clearAccumulatedData() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteredHaplotypeFilter
- clearAccumulatedData() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2Filter
- clearAccumulatedData() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter
- clearAttribute(String) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Clear an individual attribute on the read.
- clearAttribute(String) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- clearAttributes() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Clear all attributes on the read.
- clearAttributes() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- clearContig() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- clearContig() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- clearContig() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- clearHaplotypes() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
- clearItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.Downsampler
-
Empty the downsampler of all finalized/pending items
- clearItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.FractionalDownsampler
- clearItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.LevelingDownsampler
- clearItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.MutectDownsampler
- clearItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.PassThroughDownsampler
- clearItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.PositionalDownsampler
- clearItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.ReservoirDownsampler
-
Clear the data structures used to hold information
- clearReads() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Clear all of the reads currently in this region
- clearTransientAttribute(String) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Clear an individual transient attribute on the read.
- clearTransientAttribute(String) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- CLINSIG_INFO_KEY - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsConstants
-
Key for the INFO field added to all variants by
FilterFuncotations, indicating the clinical significance (if any) of the Funcotations on that variant. - CLINSIG_INFO_KEY_DESCRIPTION - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsConstants
-
Description for "CLINSIG" to include in VCF headers.
- CLINSIG_INFO_NOT_SIGNIFICANT - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsConstants
-
Value to assign to "CLINSIG" for variants that have no clinically-significant Funcotations.
- CLINSIG_INFO_VALUE - Static variable in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ClinVarFilter
-
Value to include in the "CLINSIG" INFO annotation of variants matching this rule.
- CLINSIG_INFO_VALUE - Static variable in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.LmmFilter
-
Value to include in the "CLINSIG" INFO annotation of variants matching this rule.
- CLINSIG_INFO_VALUE - Static variable in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.LofFilter
-
Value to include in the "CLINSIG" INFO annotation of variants matching this rule.
- ClinVarFilter - Class in org.broadinstitute.hellbender.tools.funcotator.filtrationRules
-
FuncotationFiltermatching variants which: Occur on a gene in the American College of Medical Genomics (ACMG)'s list of clinically-significant variants Have been labeled by ClinVar as pathogenic or likely pathogenic Have a max MAF of 5% across sub-populations of ExAC or gnomAD - ClinVarFilter(FilterFuncotations.AlleleFrequencyDataSource) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ClinVarFilter
-
Build a new ClinVar filter using the ExAC or gnomAD datasoure
- CLIP - Enum constant in enum class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner.State
- CLIP_ADAPTER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- CLIP_ADAPTER_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- CLIP_ADAPTERS - Variable in class picard.fastq.BamToBfq
- CLIP_ADAPTERS - Variable in class picard.sam.MergeBamAlignment
- CLIP_OVERLAPPING_READS - Variable in class picard.analysis.directed.CollectTargetedMetrics
- CLIP_OVERLAPPING_READS - Variable in class picard.sam.MergeBamAlignment
- CLIP_REPRESENTATION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- CLIP_REPRESENTATION_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- CLIP_SEQUENCE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- CLIP_SEQUENCE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- CLIP_SEQUENCES_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- CLIP_SEQUENCES_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- clipAlignmentInterval(AlignmentInterval, int, boolean) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier
-
Given
clipLengthOnReadto be clipped from an aligned contig'sAlignmentIntervalinput, return a modifiedAlignmentIntervalwith the requested number of bases clipped away and ref span recomputed. - clipByReferenceCoordinates(int, int, ClippingRepresentation) - Method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
-
Generic functionality to clip a read, used internally by hardClipByReferenceCoordinatesLeftTail and hardClipByReferenceCoordinatesRightTail.
- clipCigar(Cigar, int, int, CigarOperator) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
Given a cigar string, soft clip up to leftClipEnd and soft clip starting at rightClipBegin
- clipForOverlappingReads(SAMRecord, SAMRecord) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
-
Checks to see whether the ends of the reads overlap and soft clips reads them if necessary.
- clipForOverlappingReads(SAMRecord, SAMRecord, boolean) - Static method in class picard.sam.AbstractAlignmentMerger
-
Checks to see whether the ends of the reads overlap and clips reads if necessary.
- clipLowQualEnds(GATKRead, byte, ClippingRepresentation) - Static method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
- CLIPPING_ACTION - Variable in class picard.sam.SamToFastq
- CLIPPING_ATTRIBUTE - Variable in class picard.sam.SamToFastq
- CLIPPING_MIN_LENGTH - Variable in class picard.sam.SamToFastq
- CLIPPING_RANK_SUM_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- CLIPPING_TAG_CONTAINS_A - Static variable in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- CLIPPING_TAG_CONTAINS_AQ - Static variable in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- CLIPPING_TAG_CONTAINS_QZ - Static variable in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- CLIPPING_TAG_NAME - Static variable in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- CLIPPING_TAG_NAME - Static variable in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- ClippingData(List<ClipReads.SeqToClip>) - Constructor for class org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- ClippingOp - Class in org.broadinstitute.hellbender.utils.clipping
-
Represents a clip on a read.
- ClippingOp(int, int) - Constructor for class org.broadinstitute.hellbender.utils.clipping.ClippingOp
- ClippingRankSumTest - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Rank Sum Test for hard-clipped bases on REF versus ALT reads
- ClippingRankSumTest() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.ClippingRankSumTest
- ClippingRepresentation - Enum Class in org.broadinstitute.hellbender.utils.clipping
-
How should we represent a clipped bases in a read?
- ClippingUtility - Class in picard.util
-
Utilities to clip the adapter sequence from a SAMRecord read
- ClippingUtility() - Constructor for class picard.util.ClippingUtility
- clipRead(ClippingRepresentation) - Method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
-
Clips a read according to ops and the chosen algorithm.
- ClipReads - Class in org.broadinstitute.hellbender.tools
-
Read clipping based on quality, position or sequence matching.
- ClipReads() - Constructor for class org.broadinstitute.hellbender.tools.ClipReads
- ClipReads.ClippingData - Class in org.broadinstitute.hellbender.tools
- ClipReads.ReadClipperWithData - Class in org.broadinstitute.hellbender.tools
- Clocs - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- ClocsFileFaker - Class in picard.illumina.parser.fakers
- ClocsFileFaker() - Constructor for class picard.illumina.parser.fakers.ClocsFileFaker
- ClocsFileReader - Class in picard.illumina.parser.readers
-
The clocs file format is one of 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
- ClocsFileReader(File) - Constructor for class picard.illumina.parser.readers.ClocsFileReader
- clone() - Method in class htsjdk.samtools.SAMRecordSparkCodec
- clone() - Method in class org.broadinstitute.hellbender.testutils.TestingReadThreadingGraph
- clone() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
-
Creates a new GenotypeCalculationArgumentCollection with the values from other instance.
- clone() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
- clone() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqGraph
- clone() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
- clone() - Method in class org.broadinstitute.hellbender.utils.MathUtils.RunningAverage
- clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
- clone() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- cloneSAMFileHeader(SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
HACK: This is used to make a copy of a header.
- cloneSAMRecord(SAMRecord) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
HACK: This is used to make a copy of a read.
- close() - Method in interface org.broadinstitute.hellbender.cmdline.CommandLineProgram.AutoCloseableNoCheckedExceptions
- close() - Method in class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Permanently close this data source, invalidating any open iteration over it, and making it invalid for future iterations and queries.
- close() - Method in class org.broadinstitute.hellbender.engine.FeatureManager
-
Permanently closes this manager by closing all backing data sources
- close() - Method in class org.broadinstitute.hellbender.engine.MultiVariantDataSource
-
Permanently close this data source, invalidating any open iteration over it, and making it invalid for future iterations and queries.
- close() - Method in interface org.broadinstitute.hellbender.engine.ReadsDataSource
-
Shut down this data source permanently, closing all iterations and readers.
- close() - Method in class org.broadinstitute.hellbender.engine.ReadsPathDataSource
-
Shut down this data source permanently, closing all iterations and readers.
- close() - Method in interface org.broadinstitute.hellbender.engine.ReferenceDataSource
-
Permanently close this data source.
- close() - Method in class org.broadinstitute.hellbender.engine.ReferenceFileSource
-
Permanently close this data source
- close() - Method in class org.broadinstitute.hellbender.engine.ReferenceMemorySource
-
no-op (nothing's open)
- close() - Method in interface org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalWriter
-
attempt to close the file
- close() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.SimpleAnnotatedIntervalWriter
-
attempt to close the file
- close() - Method in class org.broadinstitute.hellbender.tools.funcotator.compositeoutput.CompositeOutputRenderer
-
Close the
OutputRenderer. - close() - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
Perform cleanup tasks for this
DataSourceFuncotationFactory. - close() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory
- close() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
- close() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory
- close() - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine
-
Shutdown the engine.
- close() - Method in class org.broadinstitute.hellbender.tools.funcotator.genelistoutput.GeneListOutputRenderer
-
Since we have to wait until all segments are processed, the output renderer will do nothing until closed.
- close() - Method in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRenderer
- close() - Method in class org.broadinstitute.hellbender.tools.funcotator.OutputRenderer
-
Close the
OutputRenderer. - close() - Method in class org.broadinstitute.hellbender.tools.funcotator.simpletsvoutput.SimpleTsvOutputRenderer
- close() - Method in class org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer
- close() - Method in class org.broadinstitute.hellbender.tools.spark.bwa.BwaSparkEngine
- close() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterEmptyLogger
- close() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterFileLogger
- close() - Method in interface org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterLogger
- close() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreFileLogger
- close() - Method in interface org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreLogger
- close() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaAlignerSpark
- close() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilter
-
After doFilter(), this should be run after a Spark action (e.g.
- close() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPairedUnpairedSplitterSpark
-
Call only after Spark is done with all closures involving the paired/unpaired RDDs, i.e.
- close() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SingleSequenceReferenceAligner
- close() - Method in class org.broadinstitute.hellbender.tools.sv.AbstractEvidenceSortMerger
- close() - Method in class org.broadinstitute.hellbender.tools.sv.DepthEvidenceSortMerger
- close() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter
- close() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleLikelihoodWriter
- close() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
- close() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedHMMEngine
- close() - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingDebugger
- close() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine
- close() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.AssemblerOffRamp
- close() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OffRampBase
- close() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OnRampBase
- close() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.PostAssemblerOnRamp
- close() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase
- close() - Method in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
-
This method must be called when the client is done with likelihood calculations.
- close() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- close() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect3DatasetEngine
- close() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine
-
This method must be called when the client is done with genotyping.
- close() - Method in class org.broadinstitute.hellbender.tools.walkers.variantrecalling.VariantRecallerResultWriter
- close() - Method in class org.broadinstitute.hellbender.utils.AutoCloseableReference
- close() - Method in class org.broadinstitute.hellbender.utils.bigquery.StorageAPIAvroReader
- close() - Method in class org.broadinstitute.hellbender.utils.BinaryTableReader
- close() - Method in class org.broadinstitute.hellbender.utils.BinaryTableWriter
- close() - Method in interface org.broadinstitute.hellbender.utils.codecs.FeatureSink
- close() - Method in class org.broadinstitute.hellbender.utils.codecs.LineIteratorReader
- close() - Method in class org.broadinstitute.hellbender.utils.collections.AutoCloseableCollection
- close() - Method in class org.broadinstitute.hellbender.utils.dragstr.STRTableFile
- close() - Method in class org.broadinstitute.hellbender.utils.dragstr.STRTableFileBuilder
- close() - Method in class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
-
Close the backing
ReferenceSequenceFile - close() - Method in class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter
-
Close any output resource associated with this writer.
- close() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- close() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Writer
- close() - Method in class org.broadinstitute.hellbender.utils.io.FeatureOutputStream
-
Closes the underlying stream and indexer
- close() - Method in class org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator
- close() - Method in class org.broadinstitute.hellbender.utils.nio.PathLineIterator
- close() - Method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
-
Called at the end of the program to close files, print profiling information etc
- close() - Method in class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM
- close() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- close() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
- close() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.MultiHitAlignedReadIterator
- close() - Method in class org.broadinstitute.hellbender.utils.read.SAMFileGATKReadWriter
- close() - Method in interface org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner
-
Implementations may optionally implement close in order to release any resources that they are holding.
- close() - Method in class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanIntelAligner
-
Close the aligner
- close() - Method in class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner
- close() - Method in class org.broadinstitute.hellbender.utils.smithwaterman.SWNativeAlignerWrapper
-
Report total compute time and close aligner
- close() - Method in class org.broadinstitute.hellbender.utils.text.XReadLines
- close() - Method in class org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter
- close() - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
- close() - Method in class org.broadinstitute.hellbender.utils.tsv.TableWriter
- close() - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter
-
Close this GVCF writer.
- close() - Method in class org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter
- close() - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter
- close() - Method in class picard.arrays.illumina.IlluminaBPMFile
- close() - Method in class picard.arrays.illumina.InfiniumEGTFile
- close() - Method in class picard.arrays.illumina.InfiniumGTCFile
- close() - Method in interface picard.illumina.BasecallsConverter.ConvertedClusterDataWriter
-
Closes the writer.
- close() - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- close() - Method in class picard.illumina.parser.MultiTileParser
- close() - Method in class picard.illumina.parser.MultiTileFilterParser
- close() - Method in class picard.illumina.parser.MultiTileLocsParser
- close() - Method in class picard.illumina.parser.MultiTileBclParser
- close() - Method in class picard.illumina.parser.PerTileParser
- close() - Method in class picard.illumina.parser.readers.BarcodeFileReader
- close() - Method in class picard.illumina.parser.readers.BclReader
- close() - Method in class picard.illumina.parser.readers.CbclReader
- close() - Method in class picard.illumina.parser.readers.ClocsFileReader
- close() - Method in class picard.illumina.parser.readers.LocsFileReader
- close() - Method in class picard.illumina.parser.readers.PosFileReader
- close() - Method in class picard.sam.AbstractAlignmentMerger
- close() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- close() - Method in class picard.util.AbstractInputParser
-
Closes this stream and releases any system resources associated with it.
- close() - Method in class picard.util.AsyncIterator
-
Stops the thread and then calls synchronouslyClose() to allow implementation to do any one time clean up.
- close() - Method in class picard.util.BasicInputParser
-
Closes the underlying stream
- close() - Method in class picard.util.CircularByteBuffer
-
Signals that the buffer is closed and no further writes will occur.
- close() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- close() - Method in class picard.util.TabbedTextFileWithHeaderParser
-
Release all resources associated with the parser.
- close() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
- close() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
- close() - Method in class picard.vcf.processor.VariantIteratorProducer
-
Closes any latent file handles that may have been opened by calls to
VariantIteratorProducer.iterators(). - close(B) - Method in class org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec
- close(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec
- close(BlockCompressedIntervalStream.Reader<F>) - Method in class org.broadinstitute.hellbender.utils.codecs.AbstractBCICodec
- close(T) - Method in class org.broadinstitute.hellbender.utils.AutoCloseableReference
-
Method that performs additional closing actions given this wrapper subject.
- closeAllDistributedInstances(JavaSparkContext) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.ContainsKmerReadFilterSpark
-
Closes kmer library on all executors
- closeAllDistributedInstances(JavaSparkContext) - Static method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndexCache
-
Closes all instances in all the VMs involved in the spark context provided.
- closeAndArchiveFiles() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2CountsCollector
- CloseAtEndIterator<E> - Class in org.broadinstitute.hellbender.utils.iterators
-
An
Iteratorthat automatically closes a resource when the end of the iteration is reached. - CloseAtEndIterator(Iterator<E>, AutoCloseable) - Constructor for class org.broadinstitute.hellbender.utils.iterators.CloseAtEndIterator
- closeInstance(String) - Static method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndexCache
-
Closes an index instance in the cache given its index file name.
- closeInstance(BwaMemIndex) - Static method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndexCache
-
Closes an index instance.
- closeInstances() - Static method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndexCache
-
Closes all instances in the VM.
- closeKmerLib() - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.ContainsKmerReadFilter
- ClosestPair(SVCallRecord, SVCallRecord) - Constructor for class org.broadinstitute.hellbender.tools.sv.concordance.ClosestSVFinder.ClosestPair
- ClosestSVFinder - Class in org.broadinstitute.hellbender.tools.sv.concordance
-
Efficiently clusters a set of evaluation ("eval") SVs with their closest truth SVs.
- ClosestSVFinder(SVConcordanceLinkage, Function<ClosestSVFinder.ClosestPair, SVCallRecord>, SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.tools.sv.concordance.ClosestSVFinder
- ClosestSVFinder.ClosestPair - Class in org.broadinstitute.hellbender.tools.sv.concordance
-
Output container for an evaluation record and its closest truth record.
- closeTool() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
This method is called by the GATK framework at the end of the
GATKTool.doWork()template method. - closeTool() - Method in class org.broadinstitute.hellbender.tools.AddOriginalAlignmentTags
- closeTool() - Method in class org.broadinstitute.hellbender.tools.CalculateAverageCombinedAnnotations
- closeTool() - Method in class org.broadinstitute.hellbender.tools.ClipReads
- closeTool() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalker
- closeTool() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleFeatureWalker
- closeTool() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalker
- closeTool() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleLocusWalker
- closeTool() - Method in class org.broadinstitute.hellbender.tools.examples.ExamplePartialReadWalker
- closeTool() - Method in class org.broadinstitute.hellbender.tools.examples.ExamplePostTraversalPythonExecutor
- closeTool() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReference
- closeTool() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariants
- closeTool() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleStreamingPythonExecutor
- closeTool() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalker
- closeTool() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker
- closeTool() - Method in class org.broadinstitute.hellbender.tools.FixMisencodedBaseQualityReads
- closeTool() - Method in class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations
- closeTool() - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotateSegments
- closeTool() - Method in class org.broadinstitute.hellbender.tools.funcotator.Funcotator
- closeTool() - Method in class org.broadinstitute.hellbender.tools.LeftAlignIndels
- closeTool() - Method in class org.broadinstitute.hellbender.tools.PrintDistantMates
- closeTool() - Method in class org.broadinstitute.hellbender.tools.PrintReads
- closeTool() - Method in class org.broadinstitute.hellbender.tools.reference.CompareReferences
- closeTool() - Method in class org.broadinstitute.hellbender.tools.SplitReads
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
-
Make sure that the writer is closed upon completing the tool.
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSet
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyper
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.MethylationTypeCaller
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MTLowHeteroplasmyFilterTool
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NuMTFilterTool
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.CheckPileup
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.Pileup
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.PostProcessReadsForRSEM
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.ReadAnonymizer
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2Counts
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.RevertBaseQualityScores
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVConcordance
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.UnmarkDuplicates
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithBamDepth
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithExpectedAlleleFraction
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.RemoveNearbyIndels
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
-
Close out the new variants file.
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
-
Close out the new variants file.
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionary
-
Close out the new variants file.
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSR
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.FilterVariantTranches
- closeTool() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator
- closeWriter() - Method in class picard.sam.FixMateInformation
- closeWriters() - Method in class picard.illumina.BasecallsConverter
-
Closes all writers.
- CLOUD_INDEX_PREFETCH_BUFFER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- CLOUD_INDEX_PREFETCH_BUFFER_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- CLOUD_PREFETCH_BUFFER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- CLOUD_PREFETCH_BUFFER_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- cloudIndexPrefetchBuffer - Variable in class org.broadinstitute.hellbender.engine.GATKTool
- cloudIndexPrefetchBuffer() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- cloudPrefetchBuffer - Variable in class org.broadinstitute.hellbender.engine.GATKTool
- cloudPrefetchBuffer - Variable in class org.broadinstitute.hellbender.tools.GatherVcfsCloud
- cloudPrefetchBuffer() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- cluster() - Method in class picard.util.GraphUtils.Graph
-
returns the cluster map of connected components
- cluster(Iterator<BreakpointEvidence>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLinkClusterer
- CLUSTER - Variable in class picard.fingerprint.ClusteredCrosscheckMetric
-
The cluster identifier to which the two groups within this metric (
CrosscheckMetric.LEFT_GROUP_VALUEandCrosscheckMetric.RIGHT_GROUP_VALUE) belong. - CLUSTER_DENSITY - Variable in class picard.illumina.IlluminaLaneMetrics
-
The number of clusters per unit area on the this lane expressed in units of [cluster / mm^2].
- CLUSTER_FILE - Variable in class picard.arrays.GtcToVcf
- CLUSTER_FILE - Variable in class picard.arrays.illumina.BpmToNormalizationManifestCsv
- CLUSTER_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- CLUSTER_FILE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- CLUSTER_FILE_NAME - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The name of the cluster file used
- CLUSTER_ID - Enum constant in enum class picard.illumina.parser.IlluminaMetricsCode
- CLUSTER_MEMBER_IDS_KEY - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- CLUSTER_SIZE - Variable in class picard.fingerprint.ClusteredCrosscheckMetric
-
The number of different groups that are assigned to this cluster.
- CLUSTER_SIZE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- CLUSTER_WINDOW_SIZE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- ClusterCrosscheckMetrics - Class in picard.fingerprint
-
Summary
- ClusterCrosscheckMetrics() - Constructor for class picard.fingerprint.ClusterCrosscheckMetrics
- ClusterData - Class in picard.illumina.parser
-
Store the information from Illumina files for a single cluster with one or more reads.
- ClusterData(ReadData...) - Constructor for class picard.illumina.parser.ClusterData
-
Used for testing, reads is set directly with no copying to the input array
- ClusterData(ReadType[]) - Constructor for class picard.illumina.parser.ClusterData
-
Creates a ClusterData with one read for each type provided
- ClusterDataToSamConverter - Class in picard.illumina
-
Takes ClusterData provided by an IlluminaDataProvider into one or two SAMRecords, as appropriate, and optionally marking adapter sequence.
- ClusterDataToSamConverter(String, Map<Integer, String>, ReadStructure, List<AdapterPair>, ClusterDataToSamConverter.PopulateBarcode, boolean) - Constructor for class picard.illumina.ClusterDataToSamConverter
-
Constructor
- clusterDelWithDup - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- CLUSTERED_EVENTS_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- CLUSTERED_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- CLUSTERED_SNP_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- ClusteredCrosscheckMetric - Class in picard.fingerprint
-
A metric class to hold the result of
ClusterCrosscheckMetricsfingerprints. - ClusteredCrosscheckMetric() - Constructor for class picard.fingerprint.ClusteredCrosscheckMetric
- ClusteredCrosscheckMetric(CrosscheckMetric) - Constructor for class picard.fingerprint.ClusteredCrosscheckMetric
- ClusteredEventsFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- ClusteredEventsFilter(int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ClusteredEventsFilter
- CLUSTERING_BREAKEND_WINDOW_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- CLUSTERING_INTERVAL_OVERLAP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- clusteringMetadata() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel
- ClusteringParameters - Class in org.broadinstitute.hellbender.tools.sv.cluster
-
Stores clustering parameters for different combinations of supporting algorithm types (depth-only/depth-only, depth-only/PESR, and PESR/PESR)
- ClusteringParameters(double, int, double, boolean, BiPredicate<SVCallRecord, SVCallRecord>) - Constructor for class org.broadinstitute.hellbender.tools.sv.cluster.ClusteringParameters
- clusteringType - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine
- clusterIntervalOverlap - Variable in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- clusterSize - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
-
Works together with the --cluster-window-size argument.
- clusterVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
- clusterWindow - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
-
Works together with the --cluster-size argument.
- clusterWindow - Variable in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- CNN_1D_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- CNN_2D_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- CNNScoreVariants - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
-
Annotate a VCF with scores from a Convolutional Neural Network (CNN).
- CNNScoreVariants() - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants
- CNNVariantTrain - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
-
Train a Convolutional Neural Network (CNN) for filtering variants.
- CNNVariantTrain() - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNVariantTrain
- CNNVariantWriteTensors - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
-
Write variant tensors for training a Convolutional Neural Network (CNN) for filtering variants.
- CNNVariantWriteTensors() - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNVariantWriteTensors
- CNV - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.StructuralVariantAnnotationType
- CNV - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary.Type
- CNV_COHERENCE_LENGTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCallingArgumentCollection
- cnvCallsFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- cnvGenotypesMatch(String, SVCallRecord, SVCallRecord) - Method in class org.broadinstitute.hellbender.tools.sv.concordance.SVConcordanceAnnotator
-
Returns whether the copy state of the given sample's genotype matches.
- CNVInputReader - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- CNVInputReader() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.CNVInputReader
- CNVLinkage - Class in org.broadinstitute.hellbender.tools.sv.cluster
-
Clustering engine class for defragmenting depth-based DEL/DUP calls, such as those produced by
GermlineCNVCaller. - CNVLinkage(SAMSequenceDictionary, double, double) - Constructor for class org.broadinstitute.hellbender.tools.sv.cluster.CNVLinkage
- code() - Method in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateType
- codec_packages() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- CODING - Enum constant in enum class picard.annotation.LocusFunction
- CODING_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Number of bases in primary alignments that align to a non-UTR coding base for some gene, and not ribosomal sequence.
- CODING_REGION - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.SnpEffPositionModifier.PositionModifier
- CODING_START_INDEX - Static variable in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- CODING_STOP_INDEX - Static variable in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- codingEnd - Variable in class picard.annotation.Gene.Transcript
- codingStart - Variable in class picard.annotation.Gene.Transcript
- CODON_CHANGE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- CODON_CHANGE_PLUS_CODON_DELETION - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- CODON_CHANGE_PLUS_CODON_INSERTION - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- CODON_DELETION - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- CODON_INSERTION - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- CODON_LENGTH - Static variable in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
-
The length of a codon in bases.
- COHORT - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.RunMode
- COHORT - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.RunMode
- COHORT_DENOISING_CALLING_PYTHON_SCRIPT - Static variable in class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller
- COHORT_DETERMINE_PLOIDY_AND_DEPTH_PYTHON_SCRIPT - Static variable in class org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy
- COL_DELIMITER - Static variable in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceCodec
- COL_DELIMITER - Static variable in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceCodec
- COL_DELIMITER - Static variable in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceCodec
- COL_DELIMITER - Static variable in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceCodec
- collapse(SVClusterEngine.OutputCluster) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
- collapseAlgorithms(Collection<SVCallRecord>) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
- collapseAlleles(List<Allele>, Allele) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
- collapseAltAlleles(Collection<SVCallRecord>) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
-
Collapses alternate alleles into a list of representative alleles.
- collapseAttributes(SVCallRecord, Collection<SVCallRecord>) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
- collapseInterval(Collection<SVCallRecord>) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
- collapseLength(SVCallRecord, GATKSVVCFConstants.StructuralVariantAnnotationType, int, int) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
-
Calculates new SVLEN value.
- collapseRefAlleles(String, int) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
-
Returns the ref allele at the given locus.
- collapseSampleGenotypes(Collection<Genotype>, Allele) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
-
Collapses collection of genotypes belonging to a single sample.
- collapseTypes(Collection<SVCallRecord>) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
- COLLECT_ALIGNMENT_INFORMATION - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
- CollectAlignmentRefArgCollection() - Constructor for class picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
- CollectAlignmentSummaryMetrics - Class in picard.analysis
-
A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment.
- CollectAlignmentSummaryMetrics - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- CollectAlignmentSummaryMetrics() - Constructor for class picard.analysis.CollectAlignmentSummaryMetrics
- CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection - Class in picard.analysis
- CollectAllelicCounts - Class in org.broadinstitute.hellbender.tools.copynumber
-
Collects reference and alternate allele counts at specified sites.
- CollectAllelicCounts() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCounts
- CollectAllelicCountsSpark - Class in org.broadinstitute.hellbender.tools.copynumber
-
See
CollectAllelicCounts. - CollectAllelicCountsSpark() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSpark
- CollectArraysVariantCallingMetrics - Class in picard.arrays
-
Collects summary and per-sample metrics about variant calls in a VCF file.
- CollectArraysVariantCallingMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics
- CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics - Class in picard.arrays
- CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics - Class in picard.arrays
- CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics - Class in picard.arrays
- collectAtLocus(Nucleotide, ReadPileup, Locatable, int) - Method in class org.broadinstitute.hellbender.tools.copynumber.datacollection.AllelicCountCollector
-
Add counts to this class for a specific locus.
- CollectBaseDistributionByCycle - Class in picard.analysis
- CollectBaseDistributionByCycle - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- CollectBaseDistributionByCycle() - Constructor for class picard.analysis.CollectBaseDistributionByCycle
- CollectBaseDistributionByCycleSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines.metrics
-
Collects base distribution per cycle in SAM/BAM/CRAM file(s).
- CollectBaseDistributionByCycleSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectBaseDistributionByCycleSpark
- CollectDuplicateMetrics - Class in picard.sam.markduplicates
-
Collect DuplicateMark'ing metrics from an input file that was already Duplicate-Marked.
- CollectDuplicateMetrics() - Constructor for class picard.sam.markduplicates.CollectDuplicateMetrics
- collectErrorMessages(List<String>, String[]) - Method in class picard.illumina.ExtractBarcodesProgram
- CollectF1R2Counts - Class in org.broadinstitute.hellbender.tools.walkers.readorientation
-
At each genomic locus, count the number of F1R2/F2R1 alt reads.
- CollectF1R2Counts() - Constructor for class org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2Counts
- CollectF1R2CountsArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.readorientation
- CollectF1R2CountsArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsArgumentCollection
- collectFromCollector(AllelicCountCollector) - Method in class org.broadinstitute.hellbender.tools.copynumber.datacollection.AllelicCountCollector
-
Reminder that any additional information used through this method will not be able to enforce the minBaseQuality.
- CollectGcBiasMetrics - Class in picard.analysis
-
Tool to collect information about GC bias in the reads in a given BAM file.
- CollectGcBiasMetrics - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- CollectGcBiasMetrics() - Constructor for class picard.analysis.CollectGcBiasMetrics
- CollectHiSeqXPfFailMetrics - Class in picard.illumina.quality
-
Collect metrics regarding the reason for reads (sequenced by HiSeqX) not passing the Illumina PF Filter.
- CollectHiSeqXPfFailMetrics() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- CollectHiSeqXPfFailMetrics.PFFailDetailedMetric - Class in picard.illumina.quality
-
a metric class for describing FP failing reads from an Illumina HiSeqX lane *
- CollectHiSeqXPfFailMetrics.PFFailSummaryMetric - Class in picard.illumina.quality
-
Metrics produced by the GetHiSeqXPFFailMetrics program.
- CollectHiSeqXPfFailMetrics.ReadClassifier - Class in picard.illumina.quality
- CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason - Enum Class in picard.illumina.quality
- CollectHsMetrics - Class in picard.analysis.directed
-
This tool takes a SAM/BAM file input and collects metrics that are specific for sequence datasets generated through hybrid-selection.
- CollectHsMetrics() - Constructor for class picard.analysis.directed.CollectHsMetrics
- CollectIlluminaBasecallingMetrics - Class in picard.illumina
-
A Command line tool to collect Illumina Basecalling metrics for a sequencing run Requires a Lane and an input file of Barcodes to expect.
- CollectIlluminaBasecallingMetrics() - Constructor for class picard.illumina.CollectIlluminaBasecallingMetrics
- CollectIlluminaLaneMetrics - Class in picard.illumina
-
Command-line wrapper around
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector. - CollectIlluminaLaneMetrics() - Constructor for class picard.illumina.CollectIlluminaLaneMetrics
- CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector - Class in picard.illumina
-
Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
- CollectIndependentReplicateMetrics - Class in picard.analysis.replicates
-
A CLP that, given a BAM and a VCF with genotypes of the same sample, estimates the rate of independent replication of reads within the bam.
- CollectIndependentReplicateMetrics() - Constructor for class picard.analysis.replicates.CollectIndependentReplicateMetrics
- CollectInsertSizeMetrics - Class in picard.analysis
-
Command line program to read non-duplicate insert sizes, create a Histogram and report distribution statistics.
- CollectInsertSizeMetrics - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark.SparkCollectors
- CollectInsertSizeMetrics - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- CollectInsertSizeMetrics() - Constructor for class picard.analysis.CollectInsertSizeMetrics
- CollectInsertSizeMetricsSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines.metrics
-
Collects insert size distribution information in alignment data.
- CollectInsertSizeMetricsSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectInsertSizeMetricsSpark
- CollectionStratifier(Collection<ReadBaseStratification.RecordAndOffsetStratifier<?>>) - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.CollectionStratifier
- CollectJumpingLibraryMetrics - Class in picard.analysis
-
Command-line program to compute metrics about outward-facing pairs, inward-facing pairs, and chimeras in a jumping library.
- CollectJumpingLibraryMetrics() - Constructor for class picard.analysis.CollectJumpingLibraryMetrics
- collectLaneMetrics(File, File, String, MetricsFile<MetricBase, Comparable<?>>, MetricsFile<MetricBase, Comparable<?>>, ReadStructure, String, ValidationStringency) - Static method in class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
-
Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files
- collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleCollectMultiMetricsSpark
-
Execute the actual metrics collection.
- collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollectorSpark
-
Do he actual Metrics collection.
- collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleCollectSingleMetricsSpark
-
Execute the actual metrics collection.
- collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetricsCollectorSpark
-
Do the actual metrics collection on the provided RDD.
- collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectInsertSizeMetricsSpark
- collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark
- collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.InsertSizeMetricsCollectorSpark
- collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) - Method in interface org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSpark
-
Do the actual metrics collection on the provided RDD.
- collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSparkTool
- collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityYieldMetricsCollectorSpark
-
Do the actual metrics collection on the provided RDD.
- CollectMultipleMetrics - Class in picard.analysis
-
Class that is designed to instantiate and execute multiple metrics programs that extend SinglePassSamProgram while making only a single pass through the SAM file and supplying each program with the records as it goes.
- CollectMultipleMetrics() - Constructor for class picard.analysis.CollectMultipleMetrics
- CollectMultipleMetrics.Program - Enum Class in picard.analysis
- CollectMultipleMetrics.ProgramInterface - Interface in picard.analysis
- CollectMultipleMetricsSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines.metrics
-
Runs multiple metrics collection modules for a given alignment file.
- CollectMultipleMetricsSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark
- CollectMultipleMetricsSpark.SparkCollectorProvider - Interface in org.broadinstitute.hellbender.tools.spark.pipelines.metrics
- CollectMultipleMetricsSpark.SparkCollectors - Enum Class in org.broadinstitute.hellbender.tools.spark.pipelines.metrics
- CollectOxoGMetrics - Class in picard.analysis
-
Class for trying to quantify the CpCG->CpCA error rate.
- CollectOxoGMetrics() - Constructor for class picard.analysis.CollectOxoGMetrics
- CollectOxoGMetrics.CpcgMetrics - Class in picard.analysis
-
Metrics class for outputs.
- CollectQualityYieldMetrics - Class in picard.analysis
-
Command line program to calculate quality yield metrics
- CollectQualityYieldMetrics - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark.SparkCollectors
- CollectQualityYieldMetrics - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- CollectQualityYieldMetrics() - Constructor for class picard.analysis.CollectQualityYieldMetrics
- CollectQualityYieldMetrics.QualityYieldMetrics - Class in picard.analysis
-
A set of metrics used to describe the general quality of a BAM file
- CollectQualityYieldMetrics.QualityYieldMetricsCollector - Class in picard.analysis
- CollectQualityYieldMetrics.QualityYieldMetricsFlow - Class in picard.analysis
- CollectQualityYieldMetricsSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines.metrics
-
Collects quality yield metrics in SAM/BAM/CRAM file(s).
- CollectQualityYieldMetricsSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark
- CollectRawWgsMetrics - Class in picard.analysis
-
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments, same implementation as
CollectWgsMetrics, with different defaults: lacks baseQ and mappingQ filters and has much higher coverage cap. - CollectRawWgsMetrics() - Constructor for class picard.analysis.CollectRawWgsMetrics
- CollectRawWgsMetrics.RawWgsMetrics - Class in picard.analysis
- CollectReadCounts - Class in org.broadinstitute.hellbender.tools.copynumber
-
Collects read counts at specified intervals.
- CollectReadCounts() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts
- CollectReadCounts.Format - Enum Class in org.broadinstitute.hellbender.tools.copynumber
- CollectRnaSeqMetrics - Class in picard.analysis
- CollectRnaSeqMetrics() - Constructor for class picard.analysis.CollectRnaSeqMetrics
- CollectRrbsMetrics - Class in picard.analysis
-
Calculates and reports QC metrics for RRBS data based on the methylation status at individual C/G bases as well as CpG sites across all reads in the input BAM/SAM file.
- CollectRrbsMetrics() - Constructor for class picard.analysis.CollectRrbsMetrics
- CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection - Class in picard.analysis
- CollectRrbsMetricsReferenceArgumentCollection() - Constructor for class picard.analysis.CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
- CollectSamErrorMetrics - Class in picard.sam.SamErrorMetric
-
Program to collect error metrics on bases stratified in various ways.
- CollectSamErrorMetrics() - Constructor for class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- CollectSequencingArtifactMetrics - Class in picard.analysis.artifacts
-
Quantify substitution errors caused by mismatched base pairings during various stages of sample / library prep.
- CollectSequencingArtifactMetrics - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- CollectSequencingArtifactMetrics() - Constructor for class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- CollectSVEvidence - Class in org.broadinstitute.hellbender.tools.walkers.sv
-
Creates discordant read pair, split read evidence, site depth, and read depth files for use in the GATK-SV pipeline.
- CollectSVEvidence() - Constructor for class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- CollectSVEvidence.BAFSiteIterator - Class in org.broadinstitute.hellbender.tools.walkers.sv
- CollectTargetedMetrics<METRIC extends MultilevelMetrics,
COLLECTOR extends TargetMetricsCollector<METRIC>> - Class in picard.analysis.directed -
Both CollectTargetedPCRMetrics and CollectHsSelection share virtually identical program structures except for the name of their targeting mechanisms (e.g.
- CollectTargetedMetrics() - Constructor for class picard.analysis.directed.CollectTargetedMetrics
- CollectTargetedPcrMetrics - Class in picard.analysis.directed
-
This tool calculates a set of PCR-related metrics from an aligned SAM or BAM file containing targeted sequencing data.
- CollectTargetedPcrMetrics() - Constructor for class picard.analysis.directed.CollectTargetedPcrMetrics
- CollectVariantCallingMetrics - Class in picard.vcf
-
Collects summary and per-sample metrics about variant calls in a VCF file.
- CollectVariantCallingMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics
- CollectVariantCallingMetrics.VariantCallingDetailMetrics - Class in picard.vcf
-
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
- CollectVariantCallingMetrics.VariantCallingSummaryMetrics - Class in picard.vcf
-
A collection of metrics relating to snps and indels within a variant-calling file (VCF).
- CollectWgsMetrics - Class in picard.analysis
-
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
- CollectWgsMetrics() - Constructor for class picard.analysis.CollectWgsMetrics
- CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection - Class in picard.analysis
- CollectWgsMetrics.WgsMetricsCollector - Class in picard.analysis
- CollectWgsMetricsIntervalArgumentCollection() - Constructor for class picard.analysis.CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
- CollectWgsMetricsWithNonZeroCoverage - Class in picard.analysis
- CollectWgsMetricsWithNonZeroCoverage() - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
- CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage - Class in picard.analysis
-
Metrics for evaluating the performance of whole genome sequencing experiments.
- CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category - Enum Class in picard.analysis
- CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector - Class in picard.analysis
- COLOR_STATUS - Static variable in class picard.cmdline.CommandLineDefaults
-
Implementation note, this is duplicate code stolen from HTSJDK's Default.java /** Decides if we want to write colors to the terminal.
- COLS - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.TableDataHeaderFields
- column() - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Insert
- COLUMN_SEPARATOR - Static variable in class org.broadinstitute.hellbender.utils.tsv.TableUtils
-
Column separator .
- COLUMN_SEPARATOR_STRING - Static variable in class org.broadinstitute.hellbender.utils.tsv.TableUtils
-
Column separator as an string.
- columnCount() - Method in class org.broadinstitute.hellbender.utils.codecs.table.TableFeature
-
Gets the number of columns in the feature.
- columnCount() - Method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Returns the number of columns.
- columnLabels() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- columnLabels() - Method in class picard.util.TabbedTextFileWithHeaderParser
- columnLabelsList() - Method in class picard.util.TabbedTextFileWithHeaderParser
- columns() - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the column collection for this data-line instance.
- columns() - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Returns the column collection for this reader.
- COLUMNS - Static variable in enum class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection.SimpleCountTableColumn
- COLUMNS - Static variable in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
- COLUMNS_OF_INTEREST_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.CombineSegmentBreakpoints
- combine(InsertSizeMetricsCollector, InsertSizeMetricsCollector) - Method in class org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollector
-
Combine two InsertSizeMetricsCollector objects and return a single InsertSizeMetricsCollector object representing the combined results.
- combine(MultiLevelReducibleCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE, UNIT_COLLECTOR>) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector
-
Combine a source MultiLevelReducibleCollector object into this MultiLevelReducibleCollector.
- combine(PerUnitInsertSizeMetricsCollector) - Method in class org.broadinstitute.hellbender.metrics.PerUnitInsertSizeMetricsCollector
-
Combine this PerUnitInsertSizeMetricsCollector with sourceCollector and return a combined PerUnitInsertSizeMetricsCollector.
- combine(QualityYieldMetrics) - Method in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
- combine(AllelicCountCollector, AllelicCountCollector, SampleLocatableMetadata) - Static method in class org.broadinstitute.hellbender.tools.copynumber.datacollection.AllelicCountCollector
-
TODO: Docs and input parameter checking
- combine(ExampleMultiMetrics) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetrics
-
Combines two ExampleMultiMetrics objects
- combine(ExampleMultiMetricsCollector, ExampleMultiMetricsCollector) - Static method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollector
-
Combine two ExampleMultiMetricsCollector objects and return a single ExampleMultiMetricsCollector object representing the combined results.
- combine(PerUnitExampleMultiMetricsCollector) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.PerUnitExampleMultiMetricsCollector
-
Combine this PerUnitExampleMultiMetricsCollector with sourceCollector and return a combined PerUnitExampleMultiMetricsCollector.
- combine(ExampleSingleMetrics) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetrics
- combine(LocalAssembler.Traversal, LocalAssembler.Traversal) - Static method in class org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- combine(VariantEvaluator) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
-
Evaluation modules that override this function to indicate that they support combining the results of two independent collections of eval data into a single meaningful result.
- combine(EvaluationContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.EvaluationContext
- combine(RecalDatum) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
-
Add in all of the data from other into this object, updating the reported quality from the expected error rate implied by the two reported qualities
- combine(RecalibrationReport) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport
-
Combines two recalibration reports by adding all observations and errors Note: This method DOES NOT recalculate the empirical qualities and quantized qualities.
- combine(RecalibrationTables) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
-
Merge all of the tables from toMerge into into this set of tables
- combine(V, V) - Method in interface org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager.Combiner
-
take two values of type V and return a combined value of type V
- COMBINE_VARIANTS_DISTANCE - Static variable in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
- combineAltDepthOneHistogramWithRC(List<Histogram<Integer>>, List<Histogram<Integer>>, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel
- combineAndSortBreakpoints(List<T>, List<T>, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Combine the breakpoints of multiple intervals and return a list of locatables based on the updated breakpoints.
- combineAnnotations(List<Allele>, Map<String, List<?>>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
-
Combine (raw) data for reducible annotations (those that use raw data in gVCFs) according to their primary raw key Mutates annotationMap by removing the annotations that were combined Additionally, will combine other annotations by parsing them as numbers and reducing them down to the
- combineAttributeMap(ReducibleAnnotationData<Double>, ReducibleAnnotationData<Double>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality
- combineAttributeMap(ReducibleAnnotationData<List<Integer>>, ReducibleAnnotationData<List<Integer>>) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils
-
Combine allele-specific data from two ReducibleAnnotationData data structures
- combineAttributeMap(ReducibleAnnotationData<Histogram>, ReducibleAnnotationData<Histogram>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
- combinedLikelihoodMatrix(List<LikelihoodMatrix<EVIDENCE, Allele>>, AlleleList<Allele>) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine
- CombineGenotypingArrayVcfs - Class in picard.arrays
-
A simple program to combine multiple genotyping array VCFs into one VCF The input VCFs must have the same sequence dictionary and same list of variant loci.
- CombineGenotypingArrayVcfs() - Constructor for class picard.arrays.CombineGenotypingArrayVcfs
- CombineGVCFs - Class in org.broadinstitute.hellbender.tools.walkers
-
Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file
- CombineGVCFs() - Constructor for class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
- combineOverlappers(LocalAssembler.Traversal, LocalAssembler.Traversal, int) - Static method in class org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- combinePositiveAndNegativeScorer(VariantAnnotationsScorer, VariantAnnotationsScorer) - Static method in interface org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsScorer
-
Yields a VQSR-style positive-negative scorer that returns the difference of the positive score and the negative score.
- COMBINER - Static variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.EvaluationContext
- combineRawData(List<Allele>, List<ReducibleAnnotationData<?>>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth
-
Note there is no raw annotation data for AS_QualByDepth and thus data cannot be combined
- combineRawData(List<Allele>, List<ReducibleAnnotationData<?>>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
-
Parses expected raw data strings per-allele, which are in the form of run length encoded histograms and combines them by summing the counts for each histogram bin, producing a new set histograms for each output allele.
- combineRawData(List<Allele>, List<ReducibleAnnotationData<?>>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality
-
For AS_RMSMappingQuality annotations, the annotations will simply consist of a list of the total value for every allele computed by parsing all of the individual AS_RMSMappingQuality Raw Key values as doubles and totaling them.
- combineRawData(List<Allele>, List<ReducibleAnnotationData<?>>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
-
Method which combines the per allele contingency tables from the underlying variant contexts by totaling supported values for both forward and reverse data and outputting it as a new contingency table.
- combineRawData(List<Allele>, List<ReducibleAnnotationData<?>>) - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation
-
Combine raw data, typically during the merging of raw data contained in multiple gVCFs as in CombineGVCFs and the preliminary merge for GenotypeGVCFs
- combineRawData(List<Allele>, List<ReducibleAnnotationData<?>>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet
-
Combine raw data, typically during the merging of raw data contained in multiple gVCFs as in CombineGVCFs and the preliminary merge for GenotypeGVCFs
- combineRawData(List<Allele>, List<ReducibleAnnotationData<?>>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RawGtCount
- combineRawData(List<Allele>, List<ReducibleAnnotationData<?>>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
- combineRefHistogramWithRC(String, Histogram<Integer>, Histogram<Integer>, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel
- CombineSegmentBreakpoints - Class in org.broadinstitute.hellbender.tools.copynumber.utils
- CombineSegmentBreakpoints() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.utils.CombineSegmentBreakpoints
- combineStates(List<Object>, List<Object>) - Static method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- combineStrats(K, K, StratificationManager.Combiner<V>, Map<Object, Object>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
-
Remaps the stratifications from one stratification set to another, combining the values in V according to the combiner function.
- combineTables(NestedIntegerArray<RecalDatum>, NestedIntegerArray<RecalDatum>) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
-
Combines the recalibration data for table1 and table2 into table1 Note that table1 is the destination, so it is modified
- combineUnit(PerUnitInsertSizeMetricsCollector, PerUnitInsertSizeMetricsCollector) - Method in class org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollector
-
Combine two PerUnitInsertSizeMetricsCollector objects and return a single PerUnitInsertSizeMetricsCollector object representing the combined results.
- combineUnit(PerUnitExampleMultiMetricsCollector, PerUnitExampleMultiMetricsCollector) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollector
-
Combine two PerUnitExampleMultiMetricsCollector objects and return a single PerUnitExampleMultiMetricsCollector object representing the combined results.
- combineUnit(UNIT_COLLECTOR, UNIT_COLLECTOR) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector
-
Combined two UNIT_COLLECTOR objects into a single object representing the combined collectors.
- combiningResultsBy(VariantProcessor.ResultMerger<R>) - Method in class picard.vcf.processor.VariantProcessor.Builder
- CommandLineArgumentValidator - Class in org.broadinstitute.hellbender.cmdline
-
Adapter shim/alternate GATK entry point for use by GATK tests to run tools in command line argument validation mode.
- CommandLineArgumentValidator(CommandLineProgram) - Constructor for class org.broadinstitute.hellbender.cmdline.CommandLineArgumentValidator
- CommandLineArgumentValidatorMain - Class in org.broadinstitute.hellbender
-
Main class to be used as an alternative entry point to
org.broadinstitute.hellbender.Mainfor performing command line validation only rather than executing the tool. - CommandLineArgumentValidatorMain() - Constructor for class org.broadinstitute.hellbender.CommandLineArgumentValidatorMain
- CommandLineDefaults - Class in picard.cmdline
-
Embodies defaults for global values that affect how the Picard Command Line operates.
- CommandLineDefaults() - Constructor for class picard.cmdline.CommandLineDefaults
- CommandLineProgram - Class in org.broadinstitute.hellbender.cmdline
-
Abstract class to facilitate writing command-line programs.
- CommandLineProgram - Class in picard.cmdline
-
Abstract class to facilitate writing command-line programs.
- CommandLineProgram() - Constructor for class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- CommandLineProgram() - Constructor for class picard.cmdline.CommandLineProgram
- CommandLineProgram.AutoCloseableNoCheckedExceptions - Interface in org.broadinstitute.hellbender.cmdline
-
A shim to make use of try-with-resources for tool shutdown
- CommandLineSyntaxTranslater - Class in picard.cmdline
-
Class for handling translation of Picard-style command line argument syntax to POSIX-style argument syntax; used for running tests written with Picard style syntax against the Barclay command line parser.
- CommandLineSyntaxTranslater() - Constructor for class picard.cmdline.CommandLineSyntaxTranslater
- COMMENT - Variable in class picard.sam.AddCommentsToBam
- COMMENT - Variable in class picard.sam.FastqToSam
- COMMENT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- COMMENT - Variable in class picard.sam.MergeSamFiles
- COMMENT - Variable in class picard.util.IntervalListTools
- COMMENT - Variable in class picard.vcf.GatherVcfs
- COMMENT - Variable in class picard.vcf.MergeVcfs
- COMMENT_DELIMITER - Static variable in class org.broadinstitute.hellbender.utils.codecs.table.TableCodec
- COMMENT_LINE_CHARACTER - Static variable in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- COMMENT_PREFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.formats.CopyNumberFormatsUtils
- COMMENT_PREFIX - Static variable in class org.broadinstitute.hellbender.utils.tsv.TableUtils
-
Comment line prefix string "#".
- COMMENT_STRING - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- COMMON_PROB_VALUE_1 - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
- COMMON_PROB_VALUE_1_LOG10 - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
- COMMON_PROB_VALUE_2 - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
- COMMON_PROB_VALUE_2_LOG10 - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
- COMMON_SUBSET - Enum constant in enum class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.SequenceDictionaryCompatibility
- COMMON_SUBTYPE - Enum constant in enum class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser.AltAlleleSummaryStrategy
-
Use subtypes in common among all alleles.
- commonMaximumPrefixLength(List<byte[]>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.GraphUtils
-
Compute the maximum shared prefix length of list of bytes.
- commonMaximumSuffixLength(List<byte[]>, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.GraphUtils
-
Compute the maximum shared suffix length of list of bytes.
- CommonSuffixSplitter - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
-
Split a collection of middle nodes in a graph into their shared prefix and suffix values This code performs the following transformation.
- commonToString() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
A human-digestable representation of the read.
- compare(int, int) - Static method in class picard.util.MathUtil
- compare(SAMRecord, SAMRecord) - Method in class org.broadinstitute.hellbender.utils.read.HeaderlessSAMRecordCoordinateComparator
- compare(Allele, Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF.AlleleLengthComparator
- compare(LocalAssembler.Traversal, LocalAssembler.Traversal) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.TraversalEndpointComparator
- compare(PileupSummary, PileupSummary) - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary.PileupSummaryComparator
- compare(DRAGENGenotypesModel.DragenReadContainer, DRAGENGenotypesModel.DragenReadContainer) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.DRAGENGenotypesModel.ReadFeatherEndForwardComparator
-
Evaluate first the number of bases to the end of the read and follow that by the base quality
- compare(DRAGENGenotypesModel.DragenReadContainer, DRAGENGenotypesModel.DragenReadContainer) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.DRAGENGenotypesModel.ReadFeatherEndReverseComparator
-
Evaluate first the number of bases to the end of the read and follow that by the base quality
- compare(TruthSensitivityTranche, TruthSensitivityTranche) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche.TrancheTruthSensitivityComparator
- compare(Haplotype, Haplotype) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampUtils.HaplotypeComparator
- compare(GATKRead, GATKRead) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampUtils.GATKReadComparator
- compare(GATKRead, GATKRead) - Method in class org.broadinstitute.hellbender.utils.read.ReadCoordinateComparator
- compare(GATKRead, GATKRead) - Method in class org.broadinstitute.hellbender.utils.read.ReadQueryNameComparator
- compare(TransientFieldPhysicalLocation, TransientFieldPhysicalLocation) - Method in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils.TransientFieldPhysicalLocationComparator
- compare(T, T) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche.TrancheComparator
- COMPARE_MQ - Variable in class picard.sam.util.SAMComparisonArgumentCollection
- COMPARE_STRINGS_NULLS_FIRST - Static variable in class org.broadinstitute.hellbender.utils.Utils
-
Comparator for strings that sorts null first;
- compareAgainstKeyReference(GATKPath) - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
-
Create list ReferencePair for comparison of references in the table against a key dictionary and analyze each pair.
- compareAllReferences() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
-
Create list of ReferencePair for pairwise comparison of references in the table and analyze each pair.
- CompareBaseQualities - Class in org.broadinstitute.hellbender.tools.validation
-
Compares the base qualities of two SAM/BAM/CRAM files.
- CompareBaseQualities() - Constructor for class org.broadinstitute.hellbender.tools.validation.CompareBaseQualities
- compareCalls(SVCallRecord, SVCallRecord, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
-
Compare two records based by performing comparisons in the following order: start position, end position, start strand, end strand, length, SV type.
- compareContigs(Locatable, Locatable, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Determines the relative contig ordering of first and second using the provided sequence dictionary
- compareContigs(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
conpare this genomeLoc's contig to another genome loc
- compareCoordinates(GATKRead, GATKRead, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.ReadCoordinateComparator
- compareDictionaries(SAMSequenceDictionary, SAMSequenceDictionary, boolean) - Static method in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
-
Workhorse routine that takes two dictionaries and returns their compatibility.
- compareDoubles(double, double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Compares double values for equality (within 1e-6), or inequality.
- compareDoubles(double, double, double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Compares double values for equality (within epsilon), or inequality.
- CompareDuplicatesSpark - Class in org.broadinstitute.hellbender.tools.spark.validation
-
Determine if two potentially identical BAMs have the same duplicate reads.
- CompareDuplicatesSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark
- CompareGtcFiles - Class in picard.arrays.illumina
-
A simple tool to compare two Illumina GTC files.
- CompareGtcFiles() - Constructor for class picard.arrays.illumina.CompareGtcFiles
- compareHaplotypes(Collection<Haplotype>, Collection<Haplotype>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampUtils
- CompareIntervalLists - Class in org.broadinstitute.hellbender.tools
- CompareIntervalLists() - Constructor for class org.broadinstitute.hellbender.tools.CompareIntervalLists
- compareLocatables(Locatable, Locatable, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Compare two locations using a
SAMSequenceDictionarysequence ordering - CompareMatrix - Class in org.broadinstitute.hellbender.tools.validation
-
CompareMatrix contains a square matrix of linear dimension QualityUtils.MAX_SAM_QUAL_SCORE.
- CompareMatrix(byte[]) - Constructor for class org.broadinstitute.hellbender.tools.validation.CompareMatrix
- CompareMetrics - Class in picard.analysis
-
Compare two metrics files.
- CompareMetrics() - Constructor for class picard.analysis.CompareMetrics
- CompareMetrics.MetricComparisonDifferences - Class in picard.analysis
- compareMetricsForEntry(MetricBase, MetricBase, Field[], Set<String>, String) - Method in class picard.analysis.CompareMetrics
- compareMetricValues(Object, Object, String) - Method in class picard.analysis.CompareMetrics
- compareReadNames(GATKRead, GATKRead) - Method in class org.broadinstitute.hellbender.utils.read.ReadQueryNameComparator
-
compare read names lexicographically without any additional tie breakers
- compareReads(Collection<GATKRead>, Collection<GATKRead>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampUtils
- CompareReferences - Class in org.broadinstitute.hellbender.tools.reference
-
Display reference comparison as a tab-delimited table and summarize reference differences.
- CompareReferences() - Constructor for class org.broadinstitute.hellbender.tools.reference.CompareReferences
- CompareReferences.BaseComparisonMode - Enum Class in org.broadinstitute.hellbender.tools.reference
- CompareReferences.CompareReferencesOutputTableWriter - Class in org.broadinstitute.hellbender.tools.reference
-
TableWriter to format and write the table output.
- CompareReferences.FindSNPsOnlyTableWriter - Class in org.broadinstitute.hellbender.tools.reference
-
TableWriter to format and write SNP table output.
- CompareReferences.MD5CalculationMode - Enum Class in org.broadinstitute.hellbender.tools.reference
- CompareReferencesOutputTableWriter(Writer, TableColumnCollection) - Constructor for class org.broadinstitute.hellbender.tools.reference.CompareReferences.CompareReferencesOutputTableWriter
- CompareReferencesOutputTableWriter(Path, TableColumnCollection) - Constructor for class org.broadinstitute.hellbender.tools.reference.CompareReferences.CompareReferencesOutputTableWriter
- compareReportArguments(RecalibrationArgumentCollection, String, String) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
-
Returns a map with the arguments that differ between this an another
RecalibrationArgumentCollectioninstance. - CompareSAMs - Class in picard.sam
-
Rudimentary SAM comparer.
- CompareSAMs() - Constructor for class picard.sam.CompareSAMs
- compareSVLocatables(SVLocatable, SVLocatable, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
-
Compares two objects based on start and end positions.
- compareTo(CharSequence) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.SequenceRC
- compareTo(DocWorkUnit) - Method in class org.broadinstitute.hellbender.utils.help.GATKDocWorkUnit
-
Sort in order of the name of this WorkUnit
- compareTo(MultiFeatureWalker.PQEntry<F>) - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker.PQEntry
- compareTo(IntegerCopyNumberState) - Method in class org.broadinstitute.hellbender.tools.copynumber.gcnv.IntegerCopyNumberState
- compareTo(DragstrLocus) - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocus
- compareTo(SVKmerLong) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
-
SVKmerLong comparison is consistent with equals.
- compareTo(SVKmerShort) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
-
SVKmerShort comparison is consistent with equals.
- compareTo(SVLocation) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVLocation
- compareTo(FlowFeatureMapper.MappedFeature) - Method in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper.MappedFeature
- compareTo(FlowFeatureMapper.ReadContext) - Method in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper.ReadContext
- compareTo(GenotypeAlleleCounts) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Compares to genotypes.
- compareTo(VariantEvaluator) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
- compareTo(VariantStratifier) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier
- compareTo(SortableJexlVCMatchExp) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SortableJexlVCMatchExp
- compareTo(VQSLODTranche) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VQSLODTranche
- compareTo(GencodeGtfFeature) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
-
Comparable interface implementation for
GencodeGtfFeature. - compareTo(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- compareTo(PrimaryAlignmentKey) - Method in class org.broadinstitute.hellbender.utils.read.PrimaryAlignmentKey
- compareTo(QualQuantizer.QualInterval) - Method in class org.broadinstitute.hellbender.utils.recalibration.QualQuantizer.QualInterval
- compareTo(Sample) - Method in class org.broadinstitute.hellbender.utils.samples.Sample
- compareTo(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVInterval
- compareTo(SequencingArtifactMetrics.BaitBiasDetailMetrics) - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
- compareTo(SequencingArtifactMetrics.PreAdapterDetailMetrics) - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
- compareTo(Gene) - Method in class picard.annotation.Gene
- compareTo(HaplotypeBlock) - Method in class picard.fingerprint.HaplotypeBlock
- compareTo(MatchResults) - Method in class picard.fingerprint.MatchResults
-
Provides a natural sort so that better matches (by LOD) sort earlier.
- compareTo(Snp) - Method in class picard.fingerprint.Snp
- compareTo(Pair<X, Y>) - Method in class picard.sam.util.Pair
- compareTo(PrimaryAlignmentKey) - Method in class picard.sam.util.PrimaryAlignmentKey
- compareTo(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
- CompareVariantContextToLocus(SAMSequenceDictionary, VariantContext, Locus) - Static method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
-
Compares a VariantContext to a Locus providing information regarding possible overlap, or relative location
- COMPARISON_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- COMPARISON_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- CompFeatureInput - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Required stratification grouping output by each comp
- CompFeatureInput(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.CompFeatureInput
- CompFiltered - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- complain(F) - Method in class org.broadinstitute.hellbender.tools.sv.AbstractEvidenceSortMerger
- complain(BafEvidence) - Method in class org.broadinstitute.hellbender.tools.sv.BafEvidenceSortMerger
- complain(SiteDepth) - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepthSortMerger
- complain(SplitReadEvidence) - Method in class org.broadinstitute.hellbender.tools.sv.SplitReadEvidenceSortMerger
- complement() - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns the complement nucleotide code for this one.
- complement() - Method in enum class picard.analysis.artifacts.Transition
-
Return the complementary transition.
- complement(byte) - Static method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns the complement for a base code.
- complement(byte, boolean) - Static method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns the complement for a base code.
- COMPLETE - Enum constant in enum class org.broadinstitute.hellbender.engine.AlignmentContext.ReadOrientation
- COMPLETE_GENOMICS - Enum constant in enum class org.broadinstitute.hellbender.utils.NGSPlatform
- COMPLEX - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments.AlignmentSignatureBasicType
- COMPLEX_CHIMERA_VCF_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark
- ComplexityPartitioner - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
-
A Spark Partitioner that puts tasks with greater complexities into earlier partitions.
- ComplexityPartitioner(int[]) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.ComplexityPartitioner
- CompMonoEvalFiltered - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- CompMonoEvalMono - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- CompMonoEvalNoCall - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- CompMonoEvalPoly - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- compose(ReadTransformer) - Method in interface org.broadinstitute.hellbender.transformers.ReadTransformer
- compose(VariantTransformer) - Method in interface org.broadinstitute.hellbender.transformers.VariantTransformer
- composeCallAttributes(VariantContext, List<Integer>, AFCalculationResult, List<Allele>, GenotypesContext) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
- composeHaplotypeBasedOnReference(int, int, ReferenceMultiSparkSource) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVContext
-
Composes the haplotype that corresponds to an allele based on the reference sequence.
- composeLine(CheckReferenceCompatibility.CompatibilityRecord, DataLine) - Method in class org.broadinstitute.hellbender.tools.reference.CheckReferenceCompatibility.CheckReferenceCompatibilityTableWriter
- composeLine(CompareReferences.SNPRecord, DataLine) - Method in class org.broadinstitute.hellbender.tools.reference.CompareReferences.FindSNPsOnlyTableWriter
- composeLine(ReferenceSequenceTable.TableRow, DataLine) - Method in class org.broadinstitute.hellbender.tools.reference.CompareReferences.CompareReferencesOutputTableWriter
- composeLine(PileupSummary, DataLine) - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary.PileupSummaryTableWriter
- composeLine(NormalArtifactRecord, DataLine) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.NormalArtifactRecord.NormalArtifactWriter
- composeLine(AltSiteRecord, DataLine) - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord.AltSiteRecordTableWriter
- composeLine(ArtifactPrior, DataLine) - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPrior.ArtifactPriorTableWriter
- composeLine(GeneExpressionEvaluation.SingleStrandFeatureCoverage, DataLine) - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation.FragmentCountWriter
- composeLine(ConcordanceSummaryRecord, DataLine) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceSummaryRecord.Writer
- composeLine(InfoConcordanceRecord, DataLine) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.InfoConcordanceRecord.InfoConcordanceWriter
- composeLine(R, DataLine) - Method in class org.broadinstitute.hellbender.utils.tsv.TableWriter
-
Composes the data-line to write into the output to represent a given record
- ComposeSTRTableFile - Class in org.broadinstitute.hellbender.tools.dragstr
-
This tool looks for low-complexity STR sequences along the reference that are later used to estimate the Dragstr model during single sample auto calibration
CalibrateDragstrModel. - ComposeSTRTableFile() - Constructor for class org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFile
- composeVariantContextHeader(SAMSequenceDictionary, Set<VCFHeaderLine>) - Method in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVIntervalVariantComposer
- composeVariantContextHeader(SAMSequenceDictionary, Set<VCFHeaderLine>) - Method in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVSegmentVariantComposer
- CompositeOutputRenderer - Class in org.broadinstitute.hellbender.tools.funcotator.compositeoutput
-
Class to make multiple funcotator output at the same time.
- CompositeOutputRenderer(List<OutputRenderer>, String) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.compositeoutput.CompositeOutputRenderer
- CompOverlap - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
- CompOverlap(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap
- CompPolyEvalFiltered - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- CompPolyEvalMono - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- CompPolyEvalNoCall - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- CompPolyEvalPoly - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- compRate - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap
- compRate() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap
- COMPRESS_OUTPUTS - Variable in class picard.illumina.ExtractBarcodesProgram
- COMPRESS_OUTPUTS_PER_RG - Variable in class picard.sam.SamToFastq
- COMPRESS_OUTPUTS_PER_TAG_GROUP - Variable in class picard.sam.SamToFastqWithTags
- CompressedDataList<T> - Class in org.broadinstitute.hellbender.utils
-
A class to represent data as a list of <value,count> pairs.
- CompressedDataList() - Constructor for class org.broadinstitute.hellbender.utils.CompressedDataList
- COMPRESSION_LEVEL - Variable in class org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram
- COMPRESSION_LEVEL - Variable in class picard.cmdline.CommandLineProgram
- COMPRESSION_LEVEL_ARGNAME - Static variable in class org.broadinstitute.hellbender.tools.sv.CondenseDepthEvidence
- COMPRESSION_LEVEL_ARGUMENT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- COMPRESSION_LEVEL_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.PrintSVEvidence
- COMPRESSION_LEVEL_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAF
- comps - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
-
If a call overlaps with a record from the provided comp track, the INFO field will be annotated as such in the output with the track name (e.g.
- comps - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
-
If a call overlaps with a record from the provided comp track, the INFO field will be annotated as such in the output with the track name (e.g.
- comps - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- compsProvided - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
-
The variant file(s) to compare against.
- compute(int) - Method in class org.broadinstitute.hellbender.utils.DigammaCache
- compute(int) - Method in class org.broadinstitute.hellbender.utils.IntToDoubleFunctionCache
- compute(int) - Method in class org.broadinstitute.hellbender.utils.Log10Cache
- compute(int) - Method in class org.broadinstitute.hellbender.utils.Log10FactorialCache
- computeAssociatedDistOnRead(Cigar, int, int, boolean) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
Computes the corresponding distance needs to be walked on the read, given the Cigar and distance walked on the reference.
- computeCovariates(GATKRead, SAMFileHeader, StandardCovariateList, boolean, CovariateKeyCache) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
-
Computes all requested covariates for every offset in the given read by calling covariate.getValues(..).
- computeCovariates(GATKRead, SAMFileHeader, StandardCovariateList, ReadCovariates, boolean) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
-
Computes all requested covariates for every offset in the given read by calling covariate.getValues(..).
- computeDerivedMetrics() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterMetrics
-
Computes number of reads filtered at each step and total final reads.
- computeDiploidGenotypeCounts(VariantContext, GenotypesContext, boolean) - Static method in class org.broadinstitute.hellbender.utils.GenotypeUtils
-
Returns a triple of ref/het/hom genotype "counts".
- computeIndelBQSRTables - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
- computeLikelihoodLocal(FlowBasedRead, FlowBasedHaplotype, int, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper
- computeLog10Likelihoods(LikelihoodMatrix<GATKRead, Haplotype>, List<GATKRead>, PairHMMInputScoreImputator) - Method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
-
Given a list of reads and haplotypes, for every read compute the total probability of said read arising from each haplotype given base substitution, insertion, and deletion probabilities.
- computeLog10Likelihoods(LikelihoodMatrix<GATKRead, Haplotype>, List<GATKRead>, PairHMMInputScoreImputator) - Method in class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM
-
Given a list of reads and haplotypes, for every read compute the total probability of said read arising from each haplotype given base substitution, insertion, and deletion probabilities.
- computeLog10LikelihoodsFlowBased(LikelihoodMatrix<GATKRead, Haplotype>, List<FlowBasedRead>, List<FlowBasedHaplotype>) - Method in class org.broadinstitute.hellbender.utils.pairhmm.FlowBasedPairHMM
-
Given a list of reads and haplotypes, for every read compute the total probability of said read arising from each haplotype given base substitution, insertion, and deletion probabilities.
- computeLogPenaltyScore(int, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotype
- computeMaxAcceptableAlleleCount(int, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculators
-
Compute the maximally acceptable allele count (ref allele included) given the maximally acceptable genotype count.
- computeQScore(long) - Method in class picard.sam.SamErrorMetric.ErrorMetric
-
compute a qscore given the number of errors and the total number of bases.
- computeQScore(long, long) - Method in class picard.sam.SamErrorMetric.ErrorMetric
-
compute a qscore given the number of errors and the total number of bases.
- computeReadLikelihoods(List<Haplotype>, SAMFileHeader, SampleList, Map<String, List<GATKRead>>, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
-
Read/haplotype likelihood calculation for all samples
- computeReadLikelihoods(List<Haplotype>, SAMFileHeader, SampleList, Map<String, List<GATKRead>>, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedHMMEngine
- computeReadLikelihoods(List<Haplotype>, SAMFileHeader, SampleList, Map<String, List<GATKRead>>, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine
- computeReadLikelihoods(List<Haplotype>, SAMFileHeader, SampleList, Map<String, List<GATKRead>>, boolean) - Method in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
-
Implementation of computeReadLikelihoods that is intended to be implemented by implementers.
- computeReadLikelihoods(AssemblyResultSet, SampleList, Map<String, List<GATKRead>>, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine
- computeReadLikelihoods(AssemblyResultSet, SampleList, Map<String, List<GATKRead>>, boolean) - Method in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
-
Calculates the likelihood of reads across many samples evaluated against haplotypes resulting from the active region assembly process.
- computeReadLikelihoods(LikelihoodMatrix<GATKRead, Haplotype>, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
-
Compute read likelihoods for a single sample
- computeResponsibilities(Nucleotide, Nucleotide, int, int, int, double[], boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelEngine
-
Return normalized probabilities
- computeSBAnnotation(VariantContext, AlleleLikelihoods<GATKRead, Allele>, String) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils
- computeTaxScores(Iterator<PSPathogenAlignmentHit>, PSTaxonomyDatabase, boolean) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScorer
-
Computes abundance scores and returns key-values of taxonomic id and scores
- CON_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that refutes the presence of this artifact.
- CON_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The number of REF_BASE:REF_BASE alignments having a read number and orientation that refutes the presence of this artifact.
- concat(byte[]...) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Concatenates byte arrays
- concat(byte[], byte[]) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Concats two byte arrays.
- concat(GATKReport) - Method in class org.broadinstitute.hellbender.utils.report.GATKReport
-
This is the main function is charge of gathering the reports.
- concat(GATKReportTable) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Concatenates the rows from the table to this one
- concat(T[], T[], IntFunction<T[]>) - Static method in class org.broadinstitute.hellbender.utils.Utils
- CONCAT - Enum constant in enum class picard.util.IntervalListTools.Action
- CONCAT_ALL - Enum constant in enum class picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
- concatenateLists(List<T>, List<T>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
-
Concatenate two lists.
- concatIterators(Iterator<? extends Iterable<T>>) - Static method in class org.broadinstitute.hellbender.utils.Utils
- concatIterators(Iterator<Iterator<T>>) - Static method in class org.broadinstitute.hellbender.tools.spark.utils.FlatMapGluer
- concatMerge - Enum constant in enum class org.broadinstitute.hellbender.engine.spark.GATKSparkTool.ReadInputMergingPolicy
- Concordance - Class in org.broadinstitute.hellbender.tools.walkers.validation
-
Evaluate site-level concordance of an input VCF against a truth VCF.
- Concordance() - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- concordanceRate() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap
- ConcordanceState - Enum Class in org.broadinstitute.hellbender.tools.walkers.validation
-
Created by davidben on 3/2/17.
- ConcordanceSummaryRecord - Class in org.broadinstitute.hellbender.tools.walkers.validation
-
Created by tsato on 2/8/17.
- ConcordanceSummaryRecord(VariantContext.Type, long, long, long) - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceSummaryRecord
- ConcordanceSummaryRecord.Reader - Class in org.broadinstitute.hellbender.tools.walkers.validation
- ConcordanceSummaryRecord.Writer - Class in org.broadinstitute.hellbender.tools.walkers.validation
- concordantRate - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap
- concordantRate - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MetricsCollection
- CONCRETE_TYPES - Static variable in enum class org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants.ValidationType
-
Unmodifiable set of concrete validation types.
- CondenseDepthEvidence - Class in org.broadinstitute.hellbender.tools.sv
-
Combines adjacent intervals in DepthEvidence files.
- CondenseDepthEvidence() - Constructor for class org.broadinstitute.hellbender.tools.sv.CondenseDepthEvidence
- confidence - Variable in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods.BestAllele
-
Confidence that the evidence actually was generated under that likelihood.
- CONFIDENCE_CONCORDANCE_HISTOGRAM_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance
- CONFIDENCE_CONCORDANCE_HISTOGRAM_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance
- CONFIDENCE_REGION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- CONFIDENCE_REGION_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- confidenceConcordanceHistogramFile - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance
- CONFIG_FILE_EXTENSION - Static variable in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
- CONFIG_FILE_FIELD_NAME_CONTIG_COLUMN - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_END_COLUMN - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_GENCODE_FASTA_PATH - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_IS_B37_DATA_SOURCE - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_LOOKAHEAD_CACHE_BP - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_NCBI_BUILD_VERSION - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_ORIGIN_LOCATION - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_PREPROCESSING_SCRIPT - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_SRC_FILE - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_START_COLUMN - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_TYPE - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_VERSION - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_XSV_DELIMITER - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_XSV_KEY - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_XSV_KEY_COLUMN - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_FIELD_NAME_XSV_PERMISSIVE_COLS - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- CONFIG_FILE_VARIABLE_CLASS_PATH - Static variable in interface org.broadinstitute.hellbender.utils.config.GATKConfig
-
Name of the configuration file variable to be used in the
Config.Sourcesannotation forGATKConfigas a place to find the configuration file corresponding to this interface. - CONFIG_FILE_VARIABLE_FILE_NAME - Static variable in interface org.broadinstitute.hellbender.utils.config.GATKConfig
-
Name of the configuration file variable to be used in the
Config.Sourcesannotation forGATKConfigas a place to find the configuration file corresponding to this interface. - CONFIG_RESOURCE - Static variable in class org.broadinstitute.hellbender.tools.funcotator.genelistoutput.GeneListOutputRenderer
- ConfigFactory - Class in org.broadinstitute.hellbender.utils.config
-
A singleton class to act as a user interface for loading configuration files from
org.aeonbits.owner. - configuration - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
- cons(T, List<T>) - Static method in class org.broadinstitute.hellbender.utils.Utils
- consensusStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratify by tags used during duplex and single index consensus calling.
- ConsensusStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.ConsensusStratifier
- CONSERVATIVE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.PCRErrorModel
-
a less aggressive model will be applied that tries to maintain a high true positive rate at the expense of allowing more false positives
- CONSOLIDATE_ARG_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- CONSTANT - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ThresholdCalculator.Strategy
- constantsAreInitialized - Variable in class org.broadinstitute.hellbender.utils.pairhmm.FlowBasedPairHMM
- constantsAreInitialized - Variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- constructLibraryIndex(SAMFileHeader) - Static method in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils
-
Method which generates a map of the libraries found tagged in readgroups from the header so they can be serialized as indexes to save space
- constructStaticQuantizedMapping(List<Integer>, boolean) - Static method in class org.broadinstitute.hellbender.transformers.BQSRReadTransformer
-
Constructs an array that maps particular quantized values to a rounded value in staticQuantizedQuals Rounding is done in probability space.
- consume(GATKRead, ReferenceContext, FeatureContext) - Method in interface org.broadinstitute.hellbender.engine.MultiplePassReadWalker.GATKReadConsumer
- consumeCachedReads() - Method in class org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator
- consumeFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.Downsampler
-
Return (and *remove*) all items that have survived downsampling and are waiting to be retrieved.
- consumeFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.FractionalDownsampler
- consumeFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.LevelingDownsampler
- consumeFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.MutectDownsampler
- consumeFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.PassThroughDownsampler
-
Note that this list is a linked list and so doesn't support fast random access
- consumeFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.PositionalDownsampler
- consumeFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.ReservoirDownsampler
- consumeFinalizedItems() - Method in interface org.broadinstitute.hellbender.utils.iterators.PushPullTransformer
-
Return (and *remove*) all items that have survived transformation and are waiting to be retrieved.
- consumeFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlockCombiner
- containedInRegionToIgnore(SVInterval, SVIntervalTree<SVInterval>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter
- contains(long) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- contains(long) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter
- contains(long) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- contains(long, int) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- contains(Locatable) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
-
Checks if
otheris contained within thisGencodeGtfFeature. - contains(Locatable) - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
-
Returns true if the specified interval 'that' overlaps with any of the exons actually spliced into this transcript.
- contains(Locatable) - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
-
Determines whether this interval contains the entire region represented by other (in other words, whether it covers it).
- contains(Object) - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
- contains(Object) - Method in class org.broadinstitute.hellbender.utils.collections.IndexedSet
- contains(String) - Method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Check whether there is such a column by name.
- contains(PairedStrandedIntervals) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree
- contains(SVKmerShort) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerBloomFilter
-
Input should not be canonicalized/masked
- contains(SVKmerShort) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet
-
Input should not be canonicalized/masked
- contains(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVInterval
- contains(Snp) - Method in class picard.fingerprint.HaplotypeBlock
-
Returns true if the SNP is contained within the haplotype block, false otherwise.
- containsAll(long[]) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- containsAll(long[]) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter
- containsAll(long[]) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- containsAll(Iterable<String>) - Method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Checks whether columns contain all the names in an array.
- containsAll(String...) - Method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Checks whether columns contain all the names in an array.
- containsAllele(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Checks whether this genotype contain at least one call on a particular allele index.
- containsAllele(Allele) - Method in interface org.broadinstitute.hellbender.utils.genotyper.AlleleList
-
Returns
trueif this AlleleList contains the specified allele andfalseotherwise. - containsAllVertices(Collection<? extends V>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Checks whether the graph contains all the vertices in a collection.
- containsAltAllele(Genotype) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
- containsCalls(CalledHaplotypes) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- containsExactly(String...) - Method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Checks whether columns contain all the names in an array and no other.
- containsGapOfEqualOrLargerSize(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- containsIndelLargerOrSmallerThan(VariantContext, int, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
- containsInlineIndel(VariantContext) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- containsKey(Object) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- containsKey(List<Object>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- containsKey(Set<Map.Entry<String, String>>, String) - Method in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.FuncotationFilter
-
Does the set of funcotations contain the key supplied
- ContainsKmerReadFilter - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Keep reads that do NOT contain one or more kmers from a set of SVKmerShorts
- ContainsKmerReadFilter(String, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.ContainsKmerReadFilter
- ContainsKmerReadFilterSpark - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Wrapper for ContainsKmerReadFilter to avoid serializing the kmer filter in Spark
- ContainsKmerReadFilterSpark(String, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.ContainsKmerReadFilterSpark
- containsNoNull(Collection<?>, String) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Checks that the collection does not contain a
nullvalue (throws anIllegalArgumentExceptionif it does). - containsNOperator(List<CigarElement>) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
Returns whether the list has any N operators.
- containsOnRead(AlignmentInterval) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- containsOnRef(AlignmentInterval) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- containsP(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- containsSuspectHaplotypes() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult
- containsValue(Object) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- containsVertex(V) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
-
Does this path contain the given vertex?
- contamination - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
- CONTAMINATION - Variable in class picard.fingerprint.ExtractFingerprint
- CONTAMINATION - Variable in class picard.fingerprint.IdentifyContaminant
- CONTAMINATION_ESTIMATE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- CONTAMINATION_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- CONTAMINATION_FRACTION - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection
-
If this fraction is greater is than zero, the caller will aggressively attempt to remove contamination through biased down-sampling of reads.
- CONTAMINATION_FRACTION_FILE - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection
-
This argument specifies a file with two columns "sample" and "contamination" specifying the contamination level for those samples.
- CONTAMINATION_QUAL_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- CONTAMINATION_TABLE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
-
Input files and values to use if inputs are missing
- contaminationDownsampling(Map<String, Double>) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Downsamples reads based on contamination fractions making sure that all alleles are affected proportionally.
- contaminationEstimate - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- ContaminationFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- ContaminationFilter(List<File>, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ContaminationFilter
- ContaminationModel - Class in org.broadinstitute.hellbender.tools.walkers.contamination
-
This is the probabilistic contamination model that we use to distinguish homs from hets The model is similar to that of ContEst, in that it assumes that each contaminant read is independently drawn from the population.
- ContaminationModel(List<PileupSummary>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel
- ContaminationRecord - Class in org.broadinstitute.hellbender.tools.walkers.contamination
-
Created by David Benjamin on 2/13/17.
- ContaminationRecord(String, double, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationRecord
- ContaminationSegmenter - Class in org.broadinstitute.hellbender.tools.walkers.contamination
- contaminationTables - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- CONTEXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The sequence context to which the analysis is constrained.
- CONTEXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The sequence context to which the analysis is constrained.
- CONTEXT - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The sequence context being reported on.
- CONTEXT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- CONTEXT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
- ContextCovariate - Class in org.broadinstitute.hellbender.utils.recalibration.covariates
- ContextCovariate(RecalibrationArgumentCollection) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.covariates.ContextCovariate
- contextFromKey(int) - Static method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ContextCovariate
-
Converts a key into the dna string representation.
- contextMatchesLoc(VariantContext, Locatable) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- CONTEXTS - Variable in class picard.analysis.CollectOxoGMetrics
- CONTEXTS_TO_PRINT - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- contig - Variable in class org.broadinstitute.hellbender.utils.reference.AbsoluteCoordinates.Relative
- contig() - Method in class picard.vcf.processor.VcfFileSegment
-
Deprecated.
- contig() - Method in class picard.vcf.processor.VcfPathSegment
- Contig - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies the evaluation by each contig in the reference sequence.
- Contig(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Contig
- CONTIG - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection.SimpleCountTableColumn
- CONTIG_COL_COMMENT - Static variable in class org.broadinstitute.hellbender.utils.codecs.AnnotatedIntervalCodec
- CONTIG_ID_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- CONTIG_INDEX - Static variable in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- CONTIG_LENGTH_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- CONTIG_NAMES - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- CONTIG_PLOIDY_CALLS_DIRECTORY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller
- CONTIG_PLOIDY_CALLS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- CONTIG_PLOIDY_PRIORS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy
- CONTIG_SEPARATOR - Static variable in class org.broadinstitute.hellbender.utils.SimpleInterval
- CONTIG2_ATTRIBUTE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- ContigAlignmentsModifier - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
- ContigAlignmentsModifier() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier
- ContigAlignmentsModifier.AlnModType - Enum Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
- ContigAlignmentsModifier.AlnModType.ModTypeString - Enum Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
- ContigChimericAlignmentIterativeInterpreter - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
This class scans the chimeric alignments of input
AlignedContig, filters out the alignments that offers weak evidence for a breakpoint and, makes interpretation based on theSimpleChimeraextracted. - ContigChimericAlignmentIterativeInterpreter() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.ContigChimericAlignmentIterativeInterpreter
- ContigEndKmer(long, LocalAssembler.Contig, LocalAssembler.ContigOrientation) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.ContigEndKmer
- ContigImpl(int, LocalAssembler.Contig, LocalAssembler.Contig) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- ContigImpl(int, LocalAssembler.KmerAdjacency) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- contigIndex - Variable in class org.broadinstitute.hellbender.utils.GenomeLoc
-
the basic components of a genome loc, its contig index, start and stop position, and (optionally) the contig name
- contigIndex - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator
- contigIndex - Variable in class org.broadinstitute.hellbender.utils.reference.AbsoluteCoordinates.Relative
- contigIsInDictionary(String) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Determines whether the given contig is valid with respect to the sequence dictionary already installed in the GenomeLoc.
- contigLength - Variable in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
-
A cached value of the regionStartLoc contig length, to make calls to getCurrentContigLength efficient
- ContigListRC(List<LocalAssembler.Contig>) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.ContigListRC
- contigName - Variable in class org.broadinstitute.hellbender.utils.GenomeLoc
- ContigRCImpl(LocalAssembler.ContigImpl) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- contigsAligner(String, byte[], Function<? super T, String>, Function<? super T, byte[]>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SingleSequenceReferenceAligner
-
Composes a contig aligner from an arbitrary input type given contig name and base sequence generation functions.
- contiguousP(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- CONTINGENCY_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
- CONTINGENCY_STATE_HEADER_LINE - Static variable in class picard.vcf.GenotypeConcordance
- CONTINGENCY_STATE_TAG - Static variable in class picard.vcf.GenotypeConcordance
- CONTINGENCY_VALUES - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The list of contingency table values (TP, TN, FP, FN) that are deduced from the truth/call state comparison, given the reference.
- continueAfterAnError - Variable in class org.broadinstitute.hellbender.tools.walkers.qc.CheckPileup
-
By default the program will quit if it encounters an error (such as missing truth data for a given position).
- CONTROL - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
-
Various control intensities that are present on the infinium chips.
- CONTROL_INFO - Static variable in class picard.arrays.illumina.ArraysControlInfo
- controllerId - Variable in class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase
- CONVENTIONAL - Enum constant in enum class org.broadinstitute.hellbender.tools.GatherVcfsCloud.GatherType
- CONVERGENCE_SNR_AVERAGING_WINDOW - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- CONVERGENCE_SNR_AVERAGING_WINDOW_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- CONVERGENCE_SNR_COUNTDOWN_WINDOW - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- CONVERGENCE_SNR_COUNTDOWN_WINDOW_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- CONVERGENCE_SNR_TRIGGER_THRESHOLD - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- CONVERGENCE_SNR_TRIGGER_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- CONVERGENCE_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticLikelihoodsEngine
- convert(SAMRecord, SequenceDictionary, ReadGroupDictionary) - Static method in class org.broadinstitute.hellbender.utils.read.GATKReadToBDGAlignmentRecordConverter
- convert(File, File, File, Boolean) - Static method in class picard.sam.SamFormatConverter
-
Convert a file from one of sam/bam/cram format to another based on the extension of output.
- convert(Method, String) - Method in class org.broadinstitute.hellbender.utils.config.CustomBooleanConverter
- convert(AnnotatedInterval, ReferenceContext) - Static method in class org.broadinstitute.hellbender.tools.funcotator.AnnotatedIntervalToSegmentVariantContextConverter
-
Convert a segment (as annotated interval) to a
VariantContext. - convert(GATKRead, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.GATKReadToBDGAlignmentRecordConverter
- convert(GATKRead, SAMFileHeader, SequenceDictionary, ReadGroupDictionary) - Static method in class org.broadinstitute.hellbender.utils.read.GATKReadToBDGAlignmentRecordConverter
- CONVERT_INV_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- convertB37ContigToHg19Contig(String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Converts a given B37 style contig name to the equivalent in hg19.
- convertClusterToOutputRecord(ClusterData) - Method in interface picard.illumina.BasecallsConverter.ClusterDataConverter
-
Creates the OUTPUT_RECORDs from the cluster
- convertClusterToOutputRecord(ClusterData) - Method in class picard.illumina.ClusterDataToSamConverter
-
Creates the SAMRecord for each read in the cluster
- CONVERTED_BASE_COVERAGE_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- CONVERTED_SITES - Variable in class picard.analysis.RrbsCpgDetailMetrics
-
Number of times this CpG site was converted (TG for + strand, CA for - strand)
- converter - Variable in class picard.illumina.BasecallsConverter
- convertGenomeLocsToSimpleIntervals(List<GenomeLoc>) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Convert a List of intervals in GenomeLoc format into a List of intervals in SimpleInterval format.
- ConvertHaplotypeDatabaseToVcf - Class in picard.fingerprint
- ConvertHaplotypeDatabaseToVcf() - Constructor for class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
- convertHeaderlessHadoopBamShardToBam(File, SAMFileHeader, File) - Static method in class org.broadinstitute.hellbender.utils.spark.SparkUtils
-
Converts a headerless Hadoop bam shard (eg., a part0000, part0001, etc.
- ConvertHeaderlessHadoopBamShardToBam - Class in org.broadinstitute.hellbender.tools
-
This is a troubleshooting utility that converts a headerless BAM shard (e.g., a part-r-00000.bam, part-r-00001.bam, etc.), produced by a Spark tool with --sharded-output set to true, into a readable BAM file by adding a header and a BGZF terminator.
- ConvertHeaderlessHadoopBamShardToBam() - Constructor for class org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBam
- convertHG19ContigToB37Contig(String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Converts a given HG19 style contig name to the equivalent in B37.
- convertInversionsToBreakends(SVCallRecord, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
-
Converts the given record into a pair of BND records with "++" and "--" strandedness.
- convertIUPACtoN(byte[], boolean, boolean) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
- convertJavaTypeToWDLType(WorkflowOutput, Class<?>, String, String) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLWorkUnitHandler
-
Given a Java class representing the underlying field type of an argument, and a human readable doc type, convert the docType to a WDL type.
- convertLODtoInt(double) - Method in class org.broadinstitute.hellbender.utils.variant.writers.SomaticGVCFWriter
- convertLODtoInt(double, int) - Static method in class org.broadinstitute.hellbender.utils.variant.writers.SomaticGVCFBlockCombiner
- convertMetric(TargetMetrics) - Method in class picard.analysis.directed.HsMetricCollector
- convertMetric(TargetMetrics) - Method in class picard.analysis.directed.TargetedPcrMetricsCollector
- convertMetric(TargetMetrics) - Method in class picard.analysis.directed.TargetMetricsCollector
- convertPicardStyleToPosixStyle(String[]) - Static method in class picard.cmdline.CommandLineSyntaxTranslater
- convertRealMatrixToSparkRowMatrix(JavaSparkContext, RealMatrix, int) - Static method in class org.broadinstitute.hellbender.utils.spark.SparkConverter
-
Create a distributed matrix given an Apache Commons RealMatrix.
- ConvertSequencingArtifactToOxoG - Class in picard.analysis.artifacts
- ConvertSequencingArtifactToOxoG() - Constructor for class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- convertSimpleIntervalToQueryInterval(SimpleInterval, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Converts an interval in SimpleInterval format into an htsjdk QueryInterval.
- convertSolexaQualityAscii_1_1_ToPhredBinary(byte[]) - Static method in class picard.util.IlluminaUtil
-
Converts from Solexa ASCII to Phred binary in place.
- convertSparkMatrixToRealMatrix(Matrix) - Static method in class org.broadinstitute.hellbender.utils.spark.SparkConverter
-
Convert a local (not distributed) Spark Matrix to an Apache Commons matrix.
- convertSparkRowMatrixToRealMatrix(RowMatrix, int) - Static method in class org.broadinstitute.hellbender.utils.spark.SparkConverter
-
Create an Apache Commons RealMatrix from a Spark RowMatrix.
- convertTerminalInsertionToSoftClip(Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
Convert the 'I' CigarElement, if it is at either end (terminal) of the input cigar, to a corresponding 'S' operator.
- convertToBDGAlignmentRecord() - Method in class org.broadinstitute.hellbender.utils.read.BDGAlignmentRecordToGATKReadAdapter
- convertToFlowBasedRead(GATKRead, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
-
create a FlowBasedRead from a proper SAMRecord
- convertToSAMRecord(SAMFileHeader) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Convert this read into a SAMRecord.
- convertToSAMRecord(SAMFileHeader) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- coordinateByHitIndex() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
-
Some alignment strategies expect to receive alignments for ends that are coordinated by hit index (HI) tag.
- copy() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- copy() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge
-
Create a new copy of this BaseEdge
- copy() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MultiSampleEdge
- copy() - Method in class org.broadinstitute.hellbender.utils.mcmc.ParameterizedState
- copy() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Return a copy of this read.
- copy() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.GATKDuplicationMetrics
- copy() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- copy() - Method in class picard.illumina.BarcodeMetric
-
Creates a copy of metric initialized with only non-accumulated and non-calculated values set
- COPY_GAIN - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- COPY_NEUTRAL_ALLELE - Static variable in class org.broadinstitute.hellbender.tools.funcotator.AnnotatedIntervalToSegmentVariantContextConverter
- COPY_NEUTRAL_ALLELE_STRING - Static variable in class org.broadinstitute.hellbender.tools.funcotator.AnnotatedIntervalToSegmentVariantContextConverter
- COPY_NUMBER_CONCORDANCE_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- COPY_NUMBER_FORMAT - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- COPY_NUMBER_POSTERIOR_EXPECTATION_MODE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
- COPY_NUMBER_POSTERIOR_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVNamingConstants
- COPY_NUMBER_QUALITY_FORMAT - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- COPY_NUMBER_SEGMENTS_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVNamingConstants
- COPY_NUMBER_TABLE_COLUMN_PREFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVNamingConstants
- COPY_OF_QD_KEY_NAME - Static variable in class org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalker
- COPY_RATIO_LEGACY_SEGMENTS_FILE_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.ModelSegments
- COPY_RATIO_MODEL_PARAMETER_FILE_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.ModelSegments
- COPY_RATIO_SEGMENTS_FOR_CALLER_FILE_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.ModelSegments
- COPY_SPEED_HISTORY_SIZE - Static variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- COPY_TO_TAG - Enum constant in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- copyAlleleCounts(int[], int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Copies the sorted allele counts into an array.
- copyAlleleLikelihoods(int, double[], int) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix
- copyAlleleLikelihoods(int, double[], int) - Method in interface org.broadinstitute.hellbender.utils.genotyper.LikelihoodMatrix
-
Copies the likelihood of all the evidence for a given allele into an array from a particular offset.
- copyAttr - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
attributes to copy from bam
- copyAttrPrefix - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
prefix to add to attributes to copy from bam
- copyBaseQualities(int, byte[], int, int) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Copy base qualities into an existent byte array.
- copyBases(byte[]) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Insert
- copyBases(int, byte[], int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Insert
- copyBases(int, byte[], int, int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Insert
- copyBases(int, byte[], int, int) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Copy the base into an existent byte array.
- copyBuffer - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- copyCallWithNewAttributes(SVCallRecord, Map<String, Object>) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
- copyCallWithNewGenotypes(SVCallRecord, GenotypesContext) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
-
Creates shallow copy of the given record with genotypes replaced.
- copyComplete - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- copyFile(String, String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Copies a file.
- copyFromBaseClass(T, S) - Static method in class picard.util.ReflectionUtil
- copyInsertBases(int, byte[], int, int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Element
- copyInsertQuals(int, byte[], int, int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Element
- CopyNumberAnnotations - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation
- CopyNumberAnnotations() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.CopyNumberAnnotations
- CopyNumberArgumentValidationUtils - Class in org.broadinstitute.hellbender.tools.copynumber.arguments
- CopyNumberFormatsUtils - Class in org.broadinstitute.hellbender.tools.copynumber.formats
- CopyNumberPosteriorDistribution - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
-
A record containing the integer copy-number posterior distribution for a single interval.
- CopyNumberPosteriorDistribution(Map<IntegerCopyNumberState, Double>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyNumberPosteriorDistribution
-
Constructor for storing copy number posterior distribution given a mapping between copy number states and their respective probabilities in log scale
- CopyNumberPosteriorDistributionCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
Collection of integer copy-number posteriors.
- CopyNumberPosteriorDistributionCollection(File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.CopyNumberPosteriorDistributionCollection
- CopyNumberProgramGroup - Class in org.broadinstitute.hellbender.cmdline.programgroups
-
Tools that analyze read coverage to detect copy number variants
- CopyNumberProgramGroup() - Constructor for class org.broadinstitute.hellbender.cmdline.programgroups.CopyNumberProgramGroup
- CopyNumberStandardArgument - Class in org.broadinstitute.hellbender.tools.copynumber.arguments
- CopyNumberStandardArgument() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument
- copyQuals(byte[]) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Insert
- copyQuals(int, byte[], int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Insert
- copyQuals(int, byte[], int, int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Insert
- CopyRatio - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
- CopyRatio(SimpleInterval, double) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatio
- CopyRatioCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
- CopyRatioCollection(File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.CopyRatioCollection
- CopyRatioCollection(SampleLocatableMetadata, List<CopyRatio>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.CopyRatioCollection
- CopyRatioKernelSegmenter - Class in org.broadinstitute.hellbender.tools.copynumber.segmentation
-
Segments copy-ratio data using kernel segmentation.
- CopyRatioKernelSegmenter(CopyRatioCollection) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.segmentation.CopyRatioKernelSegmenter
- CopyRatioModeller - Class in org.broadinstitute.hellbender.tools.copynumber.models
-
Represents a segmented model for copy ratio fit to denoised log2 copy-ratio data.
- CopyRatioParameter - Enum Class in org.broadinstitute.hellbender.tools.copynumber.models
-
Enumerates the parameters for
CopyRatioState. - CopyRatioSegment - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
- CopyRatioSegment(SimpleInterval, int, double) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatioSegment
- CopyRatioSegment(SimpleInterval, List<CopyRatio>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatioSegment
- CopyRatioSegmentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
- CopyRatioSegmentCollection(File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.CopyRatioSegmentCollection
- CopyRatioSegmentCollection(SampleLocatableMetadata, List<CopyRatioSegment>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.CopyRatioSegmentCollection
- copyStandardCallerArgsFrom(StandardCallerArgumentCollection) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection
-
Copies the values from other into this StandardCallerArgumentCollection
- copyStreamToPath(InputStream, Path) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase
- CORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
Number of aligned reads that are mapped to the correct strand.
- correctedLogLikelihood(Datum) - Method in interface org.broadinstitute.hellbender.tools.walkers.mutect.clustering.AlleleFractionCluster
-
The log likelihood of real variation relative to a sequencing error log likelihood of zero obtained by correcting the TLOD of Mutect2's somatic likelihoods model, which has a flat prior on allele fraction, to account for a clustered allele fraction.
- correctedLogLikelihood(Datum) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BetaBinomialCluster
- correctedLogLikelihood(Datum) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BinomialCluster
- correctedLogLikelihood(Datum, BetaDistributionShape) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BetaBinomialCluster
- correctGCBias(RealMatrix, double[]) - Static method in class org.broadinstitute.hellbender.tools.copynumber.denoising.GCBiasCorrector
-
Corrects GC bias of read counts in place.
- CorrectionSet(int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NearbyKmerErrorCorrector.CorrectionSet
-
Main class constructor.
- correctReads(Collection<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NearbyKmerErrorCorrector
-
Correct a collection of reads based on stored k-mer counts
- correctReads(Collection<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupReadErrorCorrector
- correctReads(Collection<GATKRead>) - Method in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadErrorCorrector
- correspondingInterval() - Method in class picard.vcf.processor.VcfFileSegment
-
Deprecated.
- correspondingInterval() - Method in class picard.vcf.processor.VcfPathSegment
- CORTURNIX - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.Genus
-
Pheasant
- COSMIC - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.DataSourceType
-
This value indicates a pre-processed COSMIC database file.
- CosmicFuncotationFactory - Class in org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic
-
Factory for creating
Funcotations by handling a SQLite database containing information from COSMIC. - CosmicFuncotationFactory(Path) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory
- CosmicFuncotationFactory(Path, LinkedHashMap<String, String>, String) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory
- CosmicFuncotationFactory(Path, LinkedHashMap<String, String>, String, boolean) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory
- CosmicFuncotationFactory(Path, LinkedHashMap<String, String>, String, boolean, int) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory
- COULD_NOT_DETERMINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Variant classification could not be determined.
- CouldNotCreateOutputFile(File, Exception) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotCreateOutputFile
- CouldNotCreateOutputFile(File, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotCreateOutputFile
- CouldNotCreateOutputFile(String, Exception) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotCreateOutputFile
- CouldNotCreateOutputFile(String, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotCreateOutputFile
- CouldNotCreateOutputFile(String, String, Exception) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotCreateOutputFile
- CouldNotCreateOutputFile(GATKPath, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotCreateOutputFile
- CouldNotCreateOutputFile(GATKPath, String, Exception) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotCreateOutputFile
- CouldNotIndexFile(Path, Exception) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotIndexFile
- CouldNotReadInputFile(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotReadInputFile
- CouldNotReadInputFile(String, Exception) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotReadInputFile
- CouldNotReadInputFile(String, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotReadInputFile
- CouldNotReadInputFile(String, String, Throwable) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotReadInputFile
- CouldNotReadInputFile(Path) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotReadInputFile
- CouldNotReadInputFile(Path, Exception) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotReadInputFile
- CouldNotReadInputFile(Path, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotReadInputFile
- CouldNotReadInputFile(Path, String, Throwable) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotReadInputFile
- CouldNotReadInputFile(GATKPath, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotReadInputFile
- CouldNotReadInputFile(GATKPath, String, Throwable) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.CouldNotReadInputFile
- count - Variable in class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation.SingleStrandFeatureCoverage
- COUNT - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection.SimpleCountTableColumn
- COUNT - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The number of events of type TRUTH_STATE and CALL_STATE for the EVENT_TYPE and SAMPLEs
- COUNT_FIELD_NAMES - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.CustomMafFuncotationCreator
- COUNT_FRAGMENTS - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter.CountPileupType
-
Count all fragments (even if the reads that compose the fragment are not consistent at that base).
- COUNT_FRAGMENTS_REQUIRE_SAME_BASE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter.CountPileupType
-
Count all fragments (but only if the reads that compose the fragment are consistent at that base).
- COUNT_OUTPUT - Variable in class picard.util.IntervalListTools
- COUNT_PANEL_OF_NORMALS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument
- COUNT_READS - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter.CountPileupType
-
Count all reads independently (even if from the same fragment).
- COUNT_UNPAIRED - Variable in class picard.analysis.CollectWgsMetrics
- countAlignedBases(Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
- CountBases - Class in org.broadinstitute.hellbender.tools
-
Count and print to standard output (and optionally to a file) the total number of bases in a SAM/BAM/CRAM file
- CountBases() - Constructor for class org.broadinstitute.hellbender.tools.CountBases
- CountBasesInReference - Class in org.broadinstitute.hellbender.tools.walkers.fasta
-
Counts the number of times each base occurs in a reference, and prints the counts to standard output (and optionally to a file).
- CountBasesInReference() - Constructor for class org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference
- CountBasesSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines
-
Calculate the overall number of bases SAM/BAM/CRAM file
- CountBasesSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.CountBasesSpark
- countBooleanOccurrences(boolean, boolean[]) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Returns the number of occurrences of a boolean element in a boolean array.
- countBreakendsInsideFeature(SimpleInterval, SimpleInterval) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Counts variant endpoints (breakends) inside feature interval
- countCallsAtTruth(List<VariantDatum>, double) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager
- countClippedBases(Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
Count the number of clipped bases (both soft and hard) over both ends of a cigar
- countClippedBases(Cigar, CigarOperator) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
Count the number of soft- and hard-clipped bases over both ends of a cigar
- countClippedBases(Cigar, Tail) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
Count the number clipped bases (both soft and hard) from either the left or right end of a cigar
- countClippedBases(Cigar, Tail, CigarOperator) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
Count the number of soft- or hard- clipped bases from either the left or right end of a cigar
- counter - Variable in class picard.analysis.AbstractWgsMetricsCollector
-
The number of processed genomic bases
- Counter() - Constructor for class org.broadinstitute.hellbender.utils.Nucleotide.Counter
-
Creates a new counter with all counts set to 0.
- CounterManager - Class in picard.analysis
-
Class for managing a list of Counters of integer, provides methods to access data from Counters with respect to an offset.
- CounterManager(int, int) - Constructor for class picard.analysis.CounterManager
-
Constructor creates new CounterManager without any Counters, counters are added to CounterManager via newCounter() method
- CounterManager.Counter - Class in picard.analysis
-
Class represents an integer array with methods to increment and get the values from it with respect to offset of outer
CounterManager. - CountFalsePositives - Class in org.broadinstitute.hellbender.tools.walkers.validation
-
Count variants which were not filtered in a VCF.
- CountFalsePositives() - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.CountFalsePositives
- countFamilyViolations(SampleDB, Set<String>, VariantContext) - Method in class org.broadinstitute.hellbender.utils.samples.MendelianViolation
-
Counts the number of mendelian violations in the provided sample DB.
- countHighQualitySoftClips(GATKRead, byte) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Calculate the number of bases that are soft clipped in read with quality score greater than threshold Handles the case where the cigar is null (i.e., the read is unmapped), returning 0
- CountingAdapterFilter - Class in picard.filter
-
Counting filter that discards reads are unaligned or aligned with MQ==0 and whose 5' ends look like adapter Sequence
- CountingAdapterFilter() - Constructor for class picard.filter.CountingAdapterFilter
- CountingDuplicateFilter - Class in picard.filter
-
Counting filter that discards reads that have been marked as duplicates.
- CountingDuplicateFilter() - Constructor for class picard.filter.CountingDuplicateFilter
- CountingFilter - Class in picard.filter
-
A SamRecordFilter that counts the number of bases in the reads which it filters out.
- CountingFilter() - Constructor for class picard.filter.CountingFilter
- CountingMapQFilter - Class in picard.filter
-
Counting filter that discards reads below a configurable mapping quality threshold.
- CountingMapQFilter(int) - Constructor for class picard.filter.CountingMapQFilter
- CountingPairedFilter - Class in picard.filter
-
Counting filter that discards reads that are unpaired in sequencing and paired reads whose mates are not mapped.
- CountingPairedFilter() - Constructor for class picard.filter.CountingPairedFilter
- CountingReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Wrapper/adapter for
ReadFilterthat counts the number of reads filtered, and provides a filter count summary. - CountingReadFilter(ReadFilter) - Constructor for class org.broadinstitute.hellbender.engine.filters.CountingReadFilter
- CountingReadFilter.CountingAndReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Private class for Counting AND filters
- CountingVariantFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Wrapper/adapter for
VariantFilterthat counts the number of variants filtered, and provides a filter count summary. - CountingVariantFilter(VariantFilter) - Constructor for class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter
- CountingVariantFilter.CountingAndVariantFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Private class for Counting AND filters
- CountNs - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Apply a read-based annotation that reports the number of Ns seen at a given site.
- CountNs() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.CountNs
- CountReads - Class in org.broadinstitute.hellbender.tools
-
Count and print to standard output (and optionally to a file) the total number of reads in a SAM/BAM/CRAM file.
- CountReads() - Constructor for class org.broadinstitute.hellbender.tools.CountReads
- CountReadsSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines
-
Calculate the overall number of reads in a SAM/BAM file
- CountReadsSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark
- countRefBasesAndClips(List<CigarElement>, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
Compute the number of reference bases between the start (inclusive) and end (exclusive) cigar elements.
- countRefBasesAndSoftClips(List<CigarElement>, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
- countSplitRead(GATKRead, PriorityQueue<CollectSVEvidence.SplitPos>, FeatureSink<SplitReadEvidence>) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
-
Adds split read information about the current read to the counts in splitCounts.
- countStrands(List<GATKRead>) - Static method in class org.broadinstitute.hellbender.tools.walkers.consensus.MoleculeID
-
Assumes that the input reads have the same molecule number in the
SAMTag.MItag - countType - Variable in class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter
-
These options modify how the tool deals with overlapping read pairs.
- countUnclippedReadBases(Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
Returns the length of the original read considering all clippings based on this cigar.
- CountVariants - Class in org.broadinstitute.hellbender.tools.walkers
-
Count variant records in a VCF file, regardless of filter status.
- CountVariants - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
- CountVariants() - Constructor for class org.broadinstitute.hellbender.tools.walkers.CountVariants
- CountVariants(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- CountVariantsSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines
- CountVariantsSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.CountVariantsSpark
- Covariate - Interface in org.broadinstitute.hellbender.utils.recalibration.covariates
-
The Covariate interface.
- COVARIATE - Variable in class picard.sam.SamErrorMetric.ErrorMetric
-
The value of the covariate define the bases included in this metric
- COVARIATE_NAME_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- COVARIATE_VALUE_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- CovariateKeyCache - Class in org.broadinstitute.hellbender.utils.recalibration.covariates
- CovariateKeyCache() - Constructor for class org.broadinstitute.hellbender.utils.recalibration.covariates.CovariateKeyCache
- covariateNames() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList
-
Return a human-readable string representing the used covariates
- Coverage - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Total depth of coverage per sample and over all samples.
- Coverage() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.Coverage
- Coverage(double, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation.Coverage
- Coverage(Interval, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Constructs a new coverage object for the provided mapping with the desired padding either side.
- COVERAGE_CAP - Variable in class picard.analysis.CollectWgsMetrics
- COVERAGE_CAP - Variable in class picard.analysis.directed.CollectTargetedMetrics
- coverage_counts - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.FileType
- coverage_proportions - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.FileType
- CoverageAnalysisProgramGroup - Class in org.broadinstitute.hellbender.cmdline.programgroups
-
Tools that count coverage, e.g.
- CoverageAnalysisProgramGroup() - Constructor for class org.broadinstitute.hellbender.cmdline.programgroups.CoverageAnalysisProgramGroup
- coverageCap - Variable in class picard.analysis.AbstractWgsMetricsCollector
-
Positions with coverage exceeding this value are treated as if they had coverage at this value
- coverageCap - Variable in class picard.analysis.WgsMetrics
-
The maximum depth/coverage to consider.
- coverageIntervals - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.BinnedCNVLinkage
- CoverageOutputWriter - Class in org.broadinstitute.hellbender.tools.walkers.coverage
-
This is a class for managing the output formatting/files for DepthOfCoverage.
- CoverageOutputWriter(CoverageOutputWriter.DEPTH_OF_COVERAGE_OUTPUT_FORMAT, EnumSet<DoCOutputType.Partition>, String, boolean, boolean, boolean, boolean, boolean, boolean, List<Integer>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter
-
Creates a CoverageOutputWriter for managing all of the output files for DepthOfCoverage.
- CoverageOutputWriter.DEPTH_OF_COVERAGE_OUTPUT_FORMAT - Enum Class in org.broadinstitute.hellbender.tools.walkers.coverage
- CoveragePerContig - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
-
Represents total coverage over each contig in an ordered set associated with a named sample.
- CoveragePerContig(String, LinkedHashMap<String, Integer>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.CoveragePerContig
- CoveragePerContigCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
Represents a sequence dictionary and total coverage over each contig in an ordered set associated with a cohort of named samples.
- CoveragePerContigCollection(LocatableMetadata, List<CoveragePerContig>, List<String>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.CoveragePerContigCollection
- coveredSize() - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
Return the size, in bp, of the genomic regions by all of the regions in this set
- CpcgMetrics() - Constructor for class picard.analysis.CollectOxoGMetrics.CpcgMetrics
- CpG - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
CpG is a stratification module for VariantEval that divides the input data by within/not within a CpG site
- CpG(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.CpG
- CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of CpG sites that were converted (TG for +, CA for -)
- CPG_BASES_SEEN - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of CpG sites encountered
- CPX - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.StructuralVariantAnnotationType
- CPX_ALLELE - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKSVVariantContextUtils
- CPX_EVENT_ALT_ARRANGEMENTS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- CPX_EVENT_KEY - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- CPX_INTERVALS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- CPX_SV_REF_SEGMENTS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- CPX_SV_SYB_ALT_ALLELE_STR - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- CPX_TYPE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- CpxVariantCanonicalRepresentation - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
This struct contains two key pieces of information that provides interpretation of the event:
- CpxVariantCanonicalRepresentation.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- CpxVariantInducingAssemblyContig - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
One of the two fundamental classes (the other is
CpxVariantCanonicalRepresentation) for complex variant interpretation and alt haplotype extraction. - CpxVariantInducingAssemblyContig.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- CpxVariantInterpreter - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
This deals with the special case where a contig has multiple (> 2) alignments and seemingly has the complete alt haplotype assembled.
- CpxVariantInterpreter() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInterpreter
- CpxVariantReInterpreterSpark - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
(Internal) Tries to extract simple variants from a provided GATK-SV CPX.vcf
- CpxVariantReInterpreterSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantReInterpreterSpark
- cram - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.RevertSamSpark.FileType
- cram - Enum constant in enum class picard.sam.RevertSam.FileType
- CRAM - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetFormat
- create() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.WalkDataFactory
- create(int, int, String, String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo
-
Create a
ProteinChangeInfoobject containing given information about a protein change. - create(Locatable, Allele, String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.LocatableFuncotationCreator
-
Create a funcotation with only the locatable inforamtion (CONTIG, START, and END) from a locatable.
- create(Allele, Allele, int, int, String, Strand, boolean) - Static method in class org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo
-
Create a
ProteinChangeInfoobject which will represent the change in the protein sequence which would be caused by a variant. - create(VariantContext) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
-
Creates a new
SVCallRecordfrom the givenVariantContext, keeping any variant fields. - create(VariantContext, boolean) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
-
Creates a new
SVCallRecordfrom the givenVariantContext. - create(File, String, SAMSequenceDictionary, RealMatrix, List<String>, List<SimpleInterval>, double[], double, double, double, double, boolean, double, int, int, JavaSparkContext) - Static method in class org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals
-
Create the panel of normals and write it to an HDF5 file.
- create(Class<? extends T>, Map<?, ?>...) - Method in class org.broadinstitute.hellbender.utils.config.ConfigFactory
-
Wrapper around
ConfigFactory.create(Class, Map[])which will ensure that path variables specified inConfig.Sourcesannotations are resolved prior to creation. - create(String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedAllele
-
Create a new
StrandCorrectedAlleleobject with the given bases. - create(String[], String) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfCDSFeature
- create(String[], String) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfExonFeature
- create(String[], String) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
-
Create a
GencodeGtfFeaturebased on a line from a Gencode GTF File. - create(String[], String) - Method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureType
-
Create a
GencodeGtfFeatureof this type givengtfFields - create(String[], String) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfGeneFeature
- create(String[], String) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfSelenocysteineFeature
- create(String[], String) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfStartCodonFeature
- create(String[], String) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfStopCodonFeature
- create(String[], String) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature
- create(String[], String) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfUTRFeature
- create(String, boolean) - Static method in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedAllele
-
Create a new
StrandCorrectedAlleleobject with the given bases. - create(String, boolean, Strand) - Static method in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedAllele
-
Create a new
StrandCorrectedAlleleobject with the given bases. - create(String, Strand) - Static method in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedAllele
-
Create a new
StrandCorrectedAlleleobject with the given bases. - create(String, String) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
-
Create a
GencodeGtfFeaturebased on a line from a Gencode GTF File. - create(Path, Path) - Static method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
-
Create an
NioFileCopierWithProgressMeter. - create(Path, Path, boolean) - Static method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
-
Create an
NioFileCopierWithProgressMeter. - create(Path, Path, boolean, NioFileCopierWithProgressMeter.Verbosity) - Static method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
-
Create an
NioFileCopierWithProgressMeter. - create(Path, Path, Set<String>) - Static method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection
-
Create a collection based on the contents of an input file and a given config file.
- create(Path, Set<String>) - Static method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection
-
Same as
AnnotatedIntervalCollection.create(Path, Path, Set), but uses the default annotated interval config file in the GATK. - create(LinkedHashMap<String, String>, Allele, String, FuncotationMetadata) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
- create(LinkedHashSet<String>, List<String>, Allele, String, FuncotationMetadata) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
-
Convenience method to create a table funcotation from a
LinkedHashSet, which preserves order. - create(List<VCFInfoHeaderLine>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.metadata.VcfFuncotationMetadata
- create(List<String>, List<String>, Allele, String, FuncotationMetadata) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
-
Create a TableFuncotation with given name value pairs.
- create(List<AnnotatedInterval>, SAMFileHeader, List<String>) - Static method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection
-
Create a collection from components.
- create(List<GATKRead>) - Static method in class org.broadinstitute.hellbender.utils.fragments.FragmentCollection
-
Create a FragmentCollection containing SAMRecords from a list of reads
- create(List<GATKRead>) - Static method in class org.broadinstitute.hellbender.utils.read.Fragment
- create(DragstrLocus, int, int, int, int) - Static method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCase
- create(FuncotationMap) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
-
Copy creation.
- create(GencodeGtfFeatureBaseData) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfCDSFeature
- create(GencodeGtfFeatureBaseData) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfExonFeature
- create(GencodeGtfFeatureBaseData) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
-
Create the appropriate
GencodeGtfFeatureobject based on the givenbaseData - create(GencodeGtfFeatureBaseData) - Method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureType
-
Create a
GencodeGtfFeatureof this type givenbaseData - create(GencodeGtfFeatureBaseData) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfGeneFeature
- create(GencodeGtfFeatureBaseData) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfSelenocysteineFeature
- create(GencodeGtfFeatureBaseData) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfStartCodonFeature
- create(GencodeGtfFeatureBaseData) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfStopCodonFeature
- create(GencodeGtfFeatureBaseData) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature
- create(GencodeGtfFeatureBaseData) - Static method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfUTRFeature
- create(XsvTableFeature, Allele, String, FuncotationMetadata) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
- create(ReadPileup) - Static method in class org.broadinstitute.hellbender.utils.fragments.FragmentCollection
-
Create a FragmentCollection containing PileupElements from the ReadBackedPileup rbp
- CREATE_BAI_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndex
- CREATE_INDEX - Variable in class org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram
- CREATE_INDEX - Variable in class picard.cmdline.CommandLineProgram
- CREATE_MD5_FILE - Variable in class org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram
- CREATE_MD5_FILE - Variable in class picard.cmdline.CommandLineProgram
- CREATE_OUTPUT_BAM_INDEX_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- CREATE_OUTPUT_BAM_INDEX_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- CREATE_OUTPUT_BAM_MD5_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- CREATE_OUTPUT_BAM_MD5_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- CREATE_OUTPUT_BAM_SPLITTING_INDEX_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- CREATE_OUTPUT_VARIANT_INDEX_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- CREATE_OUTPUT_VARIANT_INDEX_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- CREATE_OUTPUT_VARIANT_MD5_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- CREATE_OUTPUT_VARIANT_MD5_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- createAlleleLikelihoods(AlleleList, SampleList, List<List<EVIDENCE>>, List<List<EVIDENCE>>, double[][][]) - Static method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
- createAlleleLikelihoodWriter(AssemblyBasedCallerArgumentCollection) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- createAlleleMapper(VariantContext, int, List<Haplotype>, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
-
Returns a mapping from Allele in the mergedVC, which represents all of the alleles being genotyped at loc, to a list of Haplotypes that support that allele.
- createAlleleMapping(Allele, Allele, List<Allele>) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Create an allele mapping for the given context where its reference allele must (potentially) be extended to the given allele The refAllele is the longest reference allele seen at this start site.
- createAlleleMapping(Allele, VariantContext) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- createAlleleToFuncotationMapFromFuncotationVcfAttribute(String[], VariantContext, String, String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Create a mapping for a single variant.
- createAndAvoidFailure(List<GATKRead>) - Static method in class org.broadinstitute.hellbender.utils.read.Fragment
- createAndSetHeader(int) - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- createAnnotatedStructuralVariantContext(VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Create VariantContext for input variant with added functional annotation INFO keys
- createAnnotationEngine() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- createArtificialRead(byte[], byte[], String) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createArtificialRead(Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createArtificialRead(Cigar, String) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createArtificialRead(SAMFileHeader, byte[], byte[], String) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Create an artificial GATKRead with the following default parameters : header: numberOfChromosomes = 1 startingChromosome = 1 chromosomeSize = 1000000 read: name = "default_read" refIndex = 0 alignmentStart = 10000
- createArtificialRead(SAMFileHeader, Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createArtificialRead(SAMFileHeader, String) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createArtificialRead(SAMFileHeader, String, int, int, byte[], byte[]) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Create an artificial GATKRead based on the parameters.
- createArtificialRead(SAMFileHeader, String, int, int, byte[], byte[], String) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Create an artificial GATKRead based on the parameters
- createArtificialRead(SAMFileHeader, String, int, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Create an artificial GATKRead based on the parameters.
- createArtificialRead(SAMFileHeader, String, String, int, byte[], byte[]) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Create an artificial GATKRead based on the parameters.
- createArtificialRead(SAMFileHeader, String, String, int, byte[], byte[], String) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Create an artificial GATKRead based on the parameters
- createArtificialRead(String) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createArtificialSamHeader() - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Creates an artificial SAM header with standard test parameters
- createArtificialSamHeader(int, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Creates an artificial SAM header, matching the parameters, chromosomes which will be labeled chr1, chr2, etc
- createArtificialSamHeader(SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Creates an artificial SAM header based on the sequence dictionary dict
- createArtificialSamHeaderWithGroups(int, int, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Creates an artificial SAM header, matching the parameters, chromosomes which will be labeled chr1, chr2, etc It also adds read groups.
- createArtificialSamHeaderWithPrograms(int, int, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Creates an artificial SAM header, matching the parameters, chromosomes which will be labeled chr1, chr2, etc It also adds program records.
- createArtificialSamHeaderWithReadGroup(SAMReadGroupRecord) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Creates an artificial SAM header with standard test parameters and a Read Group
- createArtificialSAMRecord(byte[], byte[], String) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createArtificialSAMRecord(Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createArtificialSAMRecord(SAMFileHeader, byte[], byte[], String) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Create an artificial SAMRecord with the following default parameters : header: numberOfChromosomes = 1 startingChromosome = 1 chromosomeSize = 1000000 read: name = "default_read" refIndex = 0 alignmentStart = 10000
- createArtificialSAMRecord(SAMFileHeader, Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createArtificialSAMRecord(SAMFileHeader, Cigar, String) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createArtificialSAMRecord(SAMFileHeader, String, int, int, byte[], byte[]) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Create an artificial SAMRecord based on the parameters.
- createArtificialSAMRecord(SAMFileHeader, String, int, int, byte[], byte[], String) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Create an artificial SAMRecord based on the parameters
- createArtificialSAMRecord(SAMFileHeader, String, int, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Create an artificial SAMRecord based on the parameters.
- createArtificialUnmappedRead(SAMFileHeader, byte[], byte[]) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createArtificialUnmappedReadWithAssignedPosition(SAMFileHeader, String, int, byte[], byte[]) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createAsAllTableFuncotationsFromVcf(String, String[], String, Allele, String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
-
Create a FuncotationMap where all Funcotations will be TableFuncotations.
- CreateBafRegressMetricsFile - Class in picard.arrays
-
A simple program to create a standard picard metrics file from the output of bafRegress
- CreateBafRegressMetricsFile() - Constructor for class picard.arrays.CreateBafRegressMetricsFile
- createBai - Variable in class org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndex
- createBamWriter(AssemblyBasedCallerArgumentCollection, boolean, boolean, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- createBarcodeExtractor() - Method in class picard.illumina.ExtractBarcodesProgram
- createBinnedCNVDefragmenter(SAMSequenceDictionary, CanonicalSVCollapser.AltAlleleSummaryStrategy, ReferenceSequenceFile, double, double, List<GenomeLoc>) - Static method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineFactory
- createBracketedSymbAlleleString(String) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType
- createCanonical(SVClusterEngine.CLUSTERING_TYPE, CanonicalSVCollapser.BreakpointSummaryStrategy, CanonicalSVCollapser.AltAlleleSummaryStrategy, SAMSequenceDictionary, ReferenceSequenceFile, boolean, ClusteringParameters, ClusteringParameters, ClusteringParameters) - Static method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineFactory
- createCNVDefragmenter(SAMSequenceDictionary, CanonicalSVCollapser.AltAlleleSummaryStrategy, ReferenceSequenceFile, double, double) - Static method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineFactory
- createCollector(String, Set<MetricAccumulationLevel>, List<Header>, SAMFileHeader) - Method in interface org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark.SparkCollectorProvider
-
For each collector type, provide a type-safe, collector-specific method that creates and populates an instance of the collector's input argument class; creates an instance of the collector; initializes the collector with the arguments, and returns the initialized collector.
- createColumnNameToAliasesMap(Path) - Static method in class org.broadinstitute.hellbender.tools.funcotator.simpletsvoutput.SimpleTsvOutputRenderer
-
Create key value pairs where the key is the output column name and the value is a list of possible field names, in order of priority.
- createColumnNameToFieldNameMap(FuncotationMap, String) - Method in class org.broadinstitute.hellbender.tools.funcotator.AliasProvider
-
Create a mapping that links the fields of this alias provider to the funcotation fields in the given
FuncotationMap. - createCommonSAMWriter(File, File, SAMFileHeader, boolean, boolean, boolean) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Create a common SAMFileWriter for use with GATK tools.
- createCommonSAMWriter(Path, Path, SAMFileHeader, boolean, boolean, boolean) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Create a common SAMFileWriter for use with GATK tools.
- createCommonSAMWriterFromFactory(SAMFileWriterFactory, File, File, SAMFileHeader, boolean) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Create a common SAMFileWriter from a factory for use with GATK tools.
- createCommonSAMWriterFromFactory(SAMFileWriterFactory, Path, Path, SAMFileHeader, boolean, OpenOption...) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Create a common SAMFileWriter from a factory for use with GATK tools.
- createCustomMafCountFields(VariantContext, List<TumorNormalPair>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.CustomMafFuncotationCreator
-
Create the fields in
CustomMafFuncotationCreator.COUNT_FIELD_NAMESfor the pair given in the variant. - createCustomMafDbSnpFields(List<Funcotation>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.CustomMafFuncotationCreator
-
Creates a list of funcotations for each input dbSNP funcotation.
- createDataFIFO() - Method in class org.broadinstitute.hellbender.utils.runtime.StreamingProcessController
-
Create a temporary FIFO suitable for sending output to the remote process.
- createDataSourceFuncotationFactoriesForDataSources(Map<Path, Properties>, LinkedHashMap<String, String>, TranscriptSelectionMode, Set<String>, GATKTool, int, FlankSettings, boolean, int) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
-
Create a
ListofDataSourceFuncotationFactorybased on meta data on the data sources, overrides, and transcript reporting priority information. - createDefaultFuncotationsOnVariant(VariantContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
- createDefaultFuncotationsOnVariant(VariantContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory
- createDefaultFuncotationsOnVariant(VariantContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
- createDefaultFuncotationsOnVariant(VariantContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory
- createDefaultFuncotationsOnVariant(VariantContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.LocatableXsvFuncotationFactory
- createDefaultFuncotationsOnVariant(VariantContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory
- createDepthOnlyFromGCNVWithOriginalGenotypes(VariantContext, double, Set<String>, int, SampleDB) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
-
Attempts to create a new record from the given variant produced by
GermlineCNVCaller. - createDepthParameters(double, int, double) - Static method in class org.broadinstitute.hellbender.tools.sv.cluster.ClusteringParameters
- createDirectory(String) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Creates a directory, in local FS, HDFS, or Google buckets to write individual files in.
- createDownsampler() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionWalker
- createDownsampler() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- createDummyStratifiedReadMap(Haplotype, SampleList, SAMFileHeader, AssemblyRegion) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- createEdge(MultiDeBruijnVertex, MultiDeBruijnVertex) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph.MyEdgeFactory
- createEmpty() - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
- createEmptyHistogram() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics
- createEmptyHistogram() - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.CDF
- createEvaluationContext(Set<Class<? extends VariantEvaluator>>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
-
Create the EvaluationContext (new instance) for the provided set of VariantEvaluators.
- createExportConfiguration(String, String, String, String) - Static method in class org.broadinstitute.hellbender.tools.genomicsdb.GATKGenomicsDBUtils
- createExportConfiguration(String, String, String, String, GenomicsDBOptions) - Static method in class org.broadinstitute.hellbender.tools.genomicsdb.GATKGenomicsDBUtils
- CreateExtendedIlluminaManifest - Class in picard.arrays.illumina
-
Create an Extended Illumina Manifest by performing a liftover to Build 37.
- CreateExtendedIlluminaManifest() - Constructor for class picard.arrays.illumina.CreateExtendedIlluminaManifest
- createFeatureContextForTesting(Map<FeatureInput<? extends Feature>, Class<? extends Feature>>, String, SimpleInterval, int, int, int, Path) - Static method in class org.broadinstitute.hellbender.engine.FeatureContext
-
Convenience method to create a new instance for test methods.
- createFifoFile(Path) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Create a Unix FIFO file with the given path string.
- createFifoFile(Path, boolean) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Create a Unix FIFO file with the given path string.
- createFile(String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Open a binary file for writing regardless of whether it's on GCS, HDFS or local disk.
- createFilterListWithAppend(VariantContext, String) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Create a string with existing filters plus the one to append
- createFromFile(Path, LinkedHashMap<String, String>, LinkedHashMap<String, String>, Set<String>, Path, String, boolean) - Static method in class org.broadinstitute.hellbender.tools.funcotator.simpletsvoutput.SimpleTsvOutputRenderer
- createFromGencodeFuncotations(List<GencodeFuncotation>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
-
This method checks for transcript duplications in the list of GencodeFuncotations.
- createFromResource(Path, LinkedHashMap<String, String>, LinkedHashMap<String, String>, Set<String>, Path, String, boolean) - Static method in class org.broadinstitute.hellbender.tools.funcotator.simpletsvoutput.SimpleTsvOutputRenderer
-
Use when loading the config file from the jar.
- createFuncotationFromLinkedHashMap(LinkedHashMap<String, String>, Allele, String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.OutputRenderer
-
Utility for output renderers.
- createFuncotationMapForVariant(VariantContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine
-
Creates a
FuncotationMapfor the givenvariantContext. - createFuncotations(VariantContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
- createFuncotations(VariantContext, ReferenceContext, FeatureContext, List<GencodeFuncotation>) - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
Creates a
ListofFuncotationfor the givenvariant,referenceContext,featureContext, andgencodeFuncotations. - createFuncotations(VariantContext, FuncotationMetadata, String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Create funcotations (one for each alt allele) corresponding to the given variant context.
- createFuncotationsOnSegment(VariantContext, ReferenceContext, List<Feature>) - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
Sublclasses that support annotating segments should override this method to create funcotations for segments.
- createFuncotationsOnSegment(VariantContext, ReferenceContext, List<Feature>) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
Create Funcotations for a given segment variant context.
- createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>) - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
- createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory
- createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
Attempts to treat the given features as
GencodeGtfFeatureobjects in order to create funcotations for the given variant and reference. - createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory
- createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.LocatableXsvFuncotationFactory
- createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory
- createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>, List<GencodeFuncotation>) - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
Creates a
ListofFuncotationfor the givenvariant,referenceContext,featureContext, andgencodeFuncotations. - createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>, List<GencodeFuncotation>) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory
- createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>, List<GencodeFuncotation>) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
Creates a
ListofFuncotationfor the givenvariant,referenceContext,featureContext, andgencodeFuncotations. - createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>, List<GencodeFuncotation>) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory
- createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>, List<GencodeFuncotation>) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.LocatableXsvFuncotationFactory
- createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>, List<GencodeFuncotation>) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory
- createGATKReport() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport
-
Creates the recalibration report.
- createGenomeLoc(Locatable) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Creates a GenomeLoc from a
Locatable. - createGenomeLoc(Feature) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Creates a GenomeLoc from a Tribble feature
- createGenomeLoc(Feature, boolean) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Creates a GenomeLoc from a Tribble feature
- createGenomeLoc(String, int) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Create a new GenomeLoc, on contig, including the single position pos.
- createGenomeLoc(String, int, int) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
- createGenomeLoc(String, int, int, boolean) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
- createGenomeLoc(String, int, int, int) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
- createGenomeLoc(String, int, int, int, boolean) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Create a GenomeLoc on contig, starting at start and ending (inclusive) at stop.
- createGenomeLoc(GATKRead) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
- createGenomeLocAtStart(GenomeLoc, int) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Creates a loc to the left (starting at the loc start + 1) of maxBasePairs size.
- createGenomeLocAtStop(GenomeLoc, int) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Creates a loc to the right (starting at the loc stop + 1) of maxBasePairs size.
- createGenomeLocOnContig(String, int, int) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
- createGenomeLocOnContig(String, int, int, int) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Create a new genome loc, bounding start and stop by the start and end of contig This function will return null if start and stop cannot be adjusted in any reasonable way to be on the contig.
- createGSONWorkUnit(DocWorkUnit, List<Map<String, String>>, List<Map<String, String>>) - Method in class org.broadinstitute.hellbender.utils.help.GATKHelpDoclet
-
Create a GSONWorkUnit-derived object that holds our custom data.
- CreateHadoopBamSplittingIndex - Class in org.broadinstitute.hellbender.tools.spark
-
Create a Hadoop BAM splitting index and optionally a BAM index from a BAM file.
- CreateHadoopBamSplittingIndex() - Constructor for class org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndex
- createHeaderForWriter(Path, List<String>, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.codecs.AnnotatedIntervalCodec
-
Create an annotated interval header based on a config file (for locatable field names only) and a list of annotations (the rest of the fields).
- createHeaderForWriter(List<String>, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.codecs.AnnotatedIntervalCodec
-
See
AnnotatedIntervalCodec.createHeaderForWriter(Path, List, SAMFileHeader)This will use the default headers for annotated regions. - createHeaderlessSamBackedRead(String, String, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Creates an artificial GATKRead backed by a SAMRecord with no header.
- createIdenticalArtificialReads(int, SAMFileHeader, String, int, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Create a collection of identical artificial reads based on the parameters.
- createIndex - Variable in class org.broadinstitute.hellbender.tools.GatherVcfsCloud
- createInstanceForPlugin(Class<?>) - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
-
Return an instance of the specified pluggable class.
- createInstanceForPlugin(Class<?>) - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
- createIntronicCDnaString(int, List<? extends Locatable>, String, String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Create a cDNA string for an intronic variant.
- createLibraryStatistics(long) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.LibraryRawStatistics
- createLikelihoodCalculationEngine(LikelihoodEngineArgumentCollection, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
-
Instantiates the appropriate likelihood calculation engine.
- createLikelihoodCalculationEngine(LikelihoodEngineArgumentCollection, FlowBasedAlignmentArgumentCollection, boolean, ReadLikelihoodCalculationEngine.Implementation) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- createLinkedHashMapFromLists(List<T>, List<U>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Create a linked hash map from two lists with corresponding values.
- createMetrics() - Static method in class picard.sam.DuplicationMetricsFactory
-
Create non-flow duplication metrics
- createMetrics(boolean) - Static method in class picard.sam.DuplicationMetricsFactory
-
Create empty regular of flow duplication metrics
- createMixedParameters(double, int, double) - Static method in class org.broadinstitute.hellbender.tools.sv.cluster.ClusteringParameters
- createNewCigarsIfMapsOffEndOfReference(SAMRecord) - Static method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
-
Soft-clip an alignment that hangs off the end of its reference sequence.
- createNewCigarsIfMapsOffEndOfReference(SAMRecord) - Static method in class picard.sam.AbstractAlignmentMerger
-
Soft-clip an alignment that hangs off the end of its reference sequence.
- createNewWriter() - Method in class org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter
-
Creates a writer for a new shard
- createNextRead() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- createNextShard() - Method in class org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter
-
Initializes a new sharded file.
- createNonIndelPileupElement(int, Allele, int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
See
ArtificialReadUtils.createSplicedInsertionPileupElement(int, htsjdk.variant.variantcontext.Allele, int), except that this method returns a pileup element containing base-by-base replacement. - createNoTranscriptInfo(List<Funcotation>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
- createOptimalCoverageAlignmentSetsForContigs(JavaRDD<GATKRead>, SAMFileHeader, Set<String>, double, Logger) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigAlignmentsRDDProcessor
-
Filters input alignments of single-ended long reads, e.g.
- createOutputBamIndex - Variable in class org.broadinstitute.hellbender.engine.GATKTool
- createOutputBamIndex - Variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- createOutputBamIndex() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- createOutputBamMD5 - Variable in class org.broadinstitute.hellbender.engine.GATKTool
- createOutputBamSplittingIndex - Variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- createOutputVariantIndex - Variable in class org.broadinstitute.hellbender.engine.GATKTool
- createOutputVariantIndex - Variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- createOutputVariantMD5 - Variable in class org.broadinstitute.hellbender.engine.GATKTool
- createOverEntireContig(String) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Creates a GenomeLoc than spans the entire contig.
- createOverlapMap(List<T>, List<U>, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Creates a map of which locatables (keys) overlap the other list of locatables (vals) Input lists will be sorted sorted by the input dictionary.
- createPaddedGenomeLoc(GenomeLoc, int) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Creates a loc padded in both directions by maxBasePairs size (if possible).
- createPair(SAMFileHeader, String, int, int, int, boolean, boolean) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createPair(SAMFileHeader, String, int, int, int, int, boolean, boolean) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createPesrParameters(double, int, double) - Static method in class org.broadinstitute.hellbender.tools.sv.cluster.ClusteringParameters
- createPileupForReadAndOffset(GATKRead, int) - Static method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Create a pileup element for read at offset.
- createRandomRead(int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createRandomRead(int, boolean) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createRandomRead(SAMFileHeader, int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createRandomRead(SAMFileHeader, int, boolean) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- createRandomReadBases(int, boolean) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Create random read qualities
- createRandomReadQuals(int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Create random read qualities
- createReadAlignedToRef(GATKRead, Haplotype, Haplotype, int, boolean, SmithWatermanAligner, SWParameters) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Aligns reads the haplotype, and then projects this alignment of read -> hap onto the reference via the alignment of haplotype (via its getCigar) method.
- CreateReadCountPanelOfNormals - Class in org.broadinstitute.hellbender.tools.copynumber
-
Creates a panel of normals (PoN) for read-count denoising given the read counts for samples in the panel.
- CreateReadCountPanelOfNormals() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormals
- createReadThreadingAssembler() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- createReadThreadingAssembler() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- createRecalibrationGATKReport(GATKReportTable, QuantizationInfo, RecalibrationTables, StandardCovariateList) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
-
Creates a consolidated GATK report, first generating report tables.
- createRecalibrationGATKReport(GATKReportTable, GATKReportTable, List<GATKReportTable>) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
-
Creates a consolidated GATK report from the tables.
- createRecalibrationReport(GATKReportTable, GATKReportTable, List<GATKReportTable>) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
-
Creates a consolidated RecalibrationReport report from the tables.
- createRecord(DataLine) - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.MinorAlleleFractionRecord.MinorAlleleFractionTableReader
- createRecord(DataLine) - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPrior.ArtifactPriorTableReader
- createRecord(DataLine) - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation.FragmentCountReader
- createRecord(DataLine) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceSummaryRecord.Reader
- createRecord(DataLine) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.InfoConcordanceRecord.InfoConcordanceReader
- createRecord(DataLine) - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Transforms a data-line column values into a record.
- createRecord(IlluminaManifestRecord) - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- createReferenceHaplotype(AssemblyRegion, byte[], SimpleInterval) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
-
Create a reference haplotype for an active region
- createReferenceHaplotype(AssemblyRegion, SimpleInterval, ReferenceSequenceFile) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
-
Helper function to create the reference haplotype out of the active region and a padded loc
- createReferenceReader(GATKPath) - Static method in class org.broadinstitute.hellbender.utils.reference.ReferenceUtils
- createReferenceSnippet(Allele, Allele, ReferenceContext, Strand, int) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Get the bases around the given ref allele in the correct direction of the strand for this variant.
- createSamBackedRead(String, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Creates an artificial GATKRead backed by a SAMRecord.
- createSamBackedRead(String, String, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Creates an artificial GATKRead backed by a SAMRecord.
- createSamFileHeader() - Method in class picard.sam.FastqToSam
-
Creates a simple header with the values provided on the command line.
- createSamFileWriter(SAMFileHeader) - Method in class picard.sam.FixMateInformation
- createSampleDBFromPedigree(GATKPath) - Static method in class org.broadinstitute.hellbender.utils.samples.SampleDB
- createSampleDBFromPedigree(GATKPath, PedigreeValidationType) - Static method in class org.broadinstitute.hellbender.utils.samples.SampleDB
- createSampleDBFromPedigreeAndDataSources(GATKPath, Collection<String>, PedigreeValidationType) - Static method in class org.broadinstitute.hellbender.utils.samples.SampleDB
- createSAMWriter(File, File, SAMFileHeader, boolean) - Method in class org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram
-
Create a common SAMFileWriter for use with Picard tools.
- createSAMWriter(GATKPath, boolean) - Method in class org.broadinstitute.hellbender.engine.GATKTool
- createSATags(List<BwaMemAlignment>, List<String>) - Static method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignmentUtils
-
Produces an SA tag for each primary line and supplemental alignment as a map from alignment to tag value.
- createScoreToCalibrationSensitivityConverter(double[]) - Static method in interface org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsScorer
-
Given scores for a calibration set, returns a function for converting a subsequent score to a sensitivity with respect to that calibration set.
- CreateSeqDictReferenceArgumentCollection() - Constructor for class picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
- CreateSequenceDictionary - Class in picard.sam
-
Create a SAM/BAM file from a fasta containing reference sequence.
- CreateSequenceDictionary() - Constructor for class picard.sam.CreateSequenceDictionary
- CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection - Class in picard.sam
- createSequenceDictionaryFromFeatureIndex(Path) - Static method in class org.broadinstitute.hellbender.utils.IndexUtils
-
get the sequence dictionary contig list that is in the index or null if there is no index or no contigs Note: the dictionary returned will not have the contig lengths filled in
SAMSequenceRecord.UNKNOWN_SEQUENCE_LENGTHis used. - createSetFromList(GenomeLocParser, List<GenomeLoc>) - Static method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
Create a sorted genome location set from a list of GenomeLocs.
- createSetFromSequenceDictionary(SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
create a list of genomic locations, given a reference sequence
- createShard(Iterable<T>) - Method in class org.broadinstitute.hellbender.engine.ShardBoundary
- createSignedUrlToGcsObject(String, long) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Take a GCS path and return a signed url to the same resource which allows unauthenticated users to access the file.
- createSnpAndIndelBitSets(File, SAMSequenceDictionary) - Static method in class picard.util.DbSnpBitSetUtil
-
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
- createSnpAndIndelBitSets(File, SAMSequenceDictionary, IntervalList) - Static method in class picard.util.DbSnpBitSetUtil
-
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
- createSnpAndIndelBitSets(File, SAMSequenceDictionary, IntervalList, Optional<Log>) - Static method in class picard.util.DbSnpBitSetUtil
-
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
- createSnpAndIndelBitSets(PicardHtsPath, SAMSequenceDictionary, IntervalList) - Static method in class picard.util.DbSnpBitSetUtil
-
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
- createSnpAndIndelBitSets(PicardHtsPath, SAMSequenceDictionary, IntervalList, Optional<Log>) - Static method in class picard.util.DbSnpBitSetUtil
-
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
- CreateSomaticPanelOfNormals - Class in org.broadinstitute.hellbender.tools.walkers.mutect
-
Create a panel of normals (PoN) containing germline and artifactual sites for use with Mutect2.
- CreateSomaticPanelOfNormals() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals
- createSplicedDeletionPileupElement(int, Allele, int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
See
ArtificialReadUtils.createSplicedInsertionPileupElement(int, htsjdk.variant.variantcontext.Allele, int), except that this method returns a pileup element containing the specified deletion. - createSplicedInsertionPileupElement(int, Allele, int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Create a pileupElement with the given insertion added to the bases.
- createSpliceSiteCodonChange(int, int, int, int, Strand, int) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Gets a codon change string for a splice site.
- createStratificationStates(List<VariantStratifier>, Set<Class<? extends VariantEvaluator>>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- createSVD(RealMatrix) - Method in class org.broadinstitute.hellbender.utils.svd.ApacheSingularValueDecomposer
-
Create a SVD instance using Apache Commons Math.
- createSVD(RealMatrix) - Method in class org.broadinstitute.hellbender.utils.svd.OjAlgoSingularValueDecomposer
-
Create a SVD instance using ojAlgo.
- createSVD(RealMatrix) - Method in interface org.broadinstitute.hellbender.utils.svd.SingularValueDecomposer
- createSVD(RealMatrix) - Method in class org.broadinstitute.hellbender.utils.svd.SparkSingularValueDecomposer
-
Create a SVD of the given matrix using the given Java Spark Context.
- createSVD(RealMatrix) - Static method in class org.broadinstitute.hellbender.utils.svd.SVDFactory
-
Create a SVD instance using Apache Commons Math.
- createSVD(RealMatrix, JavaSparkContext) - Static method in class org.broadinstitute.hellbender.utils.svd.SVDFactory
-
Create a SVD instance using a spark context.
- createTempDir(String) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Creates a temp directory with the given prefix.
- createTempFile(String, String) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Creates a temp file that will be deleted on exit This will also mark the corresponding Tribble/Tabix/BAM indices matching the temp file for deletion.
- createTempFileInDirectory(String, String, File) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Creates a temp file in a target directory that will be deleted on exit This will also mark the corresponding Tribble/Tabix/BAM indices matching the temp file for deletion.
- createTempPath(String, String) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Creates a temp path that will be deleted on exit.
- createTransitionMatrix(int) - Static method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Creates a transition probability matrix large enough to work with sequences of a particular length.
- createUniqueArtificialRead(Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Makes a new read with a name that is unique (so that it will return false to equals(otherRead)
- createUniqueArtificialRead(String) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Makes a new read with a name that is unique (so that it will return false to equals(otherRead)
- createUniqueArtificialSAMRecord(Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
Makes a new read with a name that is unique (so that it will return false to equals(otherRead)
- createVariantEvaluator(Class<? extends VariantEvaluator>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- createVariantStratifier(Class<? extends VariantStratifier>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- createVcfWriter(Set<VCFHeaderLine>) - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- createVCFWriter(File) - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Creates a VariantContextWriter whose outputFile type is determined by the vcfOutput's extension, using the best available sequence dictionary for this tool, and default index, leniency and md5 generation settings.
- createVCFWriter(Path) - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Creates a VariantContextWriter whose outputFile type is determined by vcfOutput's extension, using the best available sequence dictionary for this tool, and default index, leniency and md5 generation settings.
- createVCFWriter(Path, SAMSequenceDictionary, boolean, Options...) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Creates a VariantContextWriter whose outputFile type is based on the extension of the output file name.
- createVCFWriter(GATKPath) - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Creates a VariantContextWriter whose outputFile type is determined by the vcfOutput's extension, using the best available sequence dictionary for this tool, and default index, leniency and md5 generation settings.
- createVCSetFromFingerprint(Fingerprint, ReferenceSequenceFile, String) - Static method in class picard.fingerprint.FingerprintUtils
-
A utility function that takes a fingerprint and returns a VariantContextSet with variants representing the haplotypes in the fingerprint
- CreateVerifyIDIntensityContaminationMetricsFile - Class in picard.arrays
-
A simple program to create a standard picard metrics file from the output of VerifyIDIntensity
- CreateVerifyIDIntensityContaminationMetricsFile() - Constructor for class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
- createWithUnknownAttributes(List<String>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.metadata.FuncotationMetadataUtils
- createWorkUnit(Element, Class<?>, DocumentedFeature) - Method in class org.broadinstitute.hellbender.utils.help.GATKHelpDoclet
- createWorkUnit(Element, Class<?>, DocumentedFeature) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLDoclet
- createWorkUnit(Element, Class<?>, DocumentedFeature) - Method in class picard.util.help.PicardHelpDoclet
- CROSS_ENTROPY_LOD - Variable in class picard.fingerprint.FingerprintMetrics
-
The categorical cross entropy of the counts of genotypes relative to expected (big is bad)
- CROSSCHECK_BY - Variable in class picard.fingerprint.CrosscheckFingerprints
- CROSSCHECK_LIBRARIES - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
Deprecated.
- CROSSCHECK_MODE - Variable in class picard.fingerprint.CrosscheckFingerprints
- CROSSCHECK_SAMPLES - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
Deprecated.
- CrosscheckFingerprints - Class in picard.fingerprint
-
Checks that all data in the set of input files appear to come from the same individual.
- CrosscheckFingerprints() - Constructor for class picard.fingerprint.CrosscheckFingerprints
- CrosscheckMetric - Class in picard.fingerprint
-
A class to hold the result of crosschecking fingerprints.
- CrosscheckMetric() - Constructor for class picard.fingerprint.CrosscheckMetric
- CrosscheckMetric.DataType - Enum Class in picard.fingerprint
-
The data type.
- CrosscheckMetric.FingerprintResult - Enum Class in picard.fingerprint
- CrosscheckReadGroupFingerprints - Class in picard.fingerprint
-
Deprecated.6/6/2017 Use
CrosscheckFingerprintsinstead. - CrosscheckReadGroupFingerprints() - Constructor for class picard.fingerprint.CrosscheckReadGroupFingerprints
-
Deprecated.
- crossContigsToIgnoreFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
-
This is a path to a text file of contig names (one per line) that will be ignored when looking for inter-contig pairs.
- CSV - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter.DEPTH_OF_COVERAGE_OUTPUT_FORMAT
- CSV - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter.OUTPUT_FORMAT
- csvFile - Variable in class org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates
-
Output csv file name.
- CsvInputParser - Class in picard.util
- CsvInputParser(boolean, File...) - Constructor for class picard.util.CsvInputParser
-
Constructor
- CsvInputParser(boolean, InputStream...) - Constructor for class picard.util.CsvInputParser
-
Constructor
- csvPrinter(File, StandardCovariateList) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
-
Returns a csv output printer.
- CT - Enum constant in enum class picard.fingerprint.DiploidGenotype
- CTG_GOOD_NONCANONICAL_MAPPING - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- CtoA - Enum constant in enum class picard.analysis.artifacts.Transition
- CtoC - Enum constant in enum class picard.analysis.artifacts.Transition
- CtoG - Enum constant in enum class picard.analysis.artifacts.Transition
- CtoT - Enum constant in enum class picard.analysis.artifacts.Transition
- CTX - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.StructuralVariantAnnotationType
- CULPRIT_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- cumulative - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Aggregation
- cumulativeProbability(int) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BetaBinomialDistribution
- curContig - Variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
- curEnd - Variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
- CURRENT_MAXIMUM_DATA_SOURCE_VERSION - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
-
The maximum supported version of the data sources for funcotator to run.
- CURRENT_MINIMUM_DATA_SOURCE_VERSION - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
-
The minimum version of the data sources required for funcotator to run.
- CURRENT_SCHEMA_VERSION - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVSegmentVariantComposer
- currentChromo - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- currentInterval - Variable in class org.broadinstitute.hellbender.utils.iterators.IntervalLocusIterator
- currentLocus - Variable in class org.broadinstitute.hellbender.tools.sv.AbstractEvidenceSortMerger
- currentRead - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- currentReadBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies bases into the current (uppercase) base as it was read from the sequencer (i.e.
- currentReadsWithSameUMI - Variable in class org.broadinstitute.hellbender.engine.DuplicateSetWalker
- currentTile - Variable in class picard.illumina.parser.MultiTileBclParser
-
The current tile number
- CUSHION_FOR_INDELS - Static variable in class org.broadinstitute.hellbender.utils.recalibration.covariates.CycleCovariate
- CUSTOM - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- CUSTOM_AMPLICON_SET - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The name of the amplicon set used in this metrics collection run
- CUSTOM_AMPLICON_SET_NAME - Variable in class picard.analysis.directed.CollectTargetedPcrMetrics
- CUSTOM_VARIANT_CLASS_ORDER_FILE - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- CustomBooleanConverter - Class in org.broadinstitute.hellbender.utils.config
-
Converts a given string into a Boolean after trimming whitespace from that string.
- CustomBooleanConverter() - Constructor for class org.broadinstitute.hellbender.utils.config.CustomBooleanConverter
- customCommandLineValidation() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
-
Enforce that output ordering is queryname when sanitization is turned on since it requires a queryname sort.
- customCommandLineValidation() - Method in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
-
mode adjustments
- customCommandLineValidation() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
-
This is being used to set the mapping quality filter when in dragen and/or flow mode.
- customCommandLineValidation() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
-
mode adjustments
- customCommandLineValidation() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants
- customCommandLineValidation() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- customCommandLineValidation() - Method in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- customCommandLineValidation() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
- customCommandLineValidation() - Method in class picard.analysis.CollectBaseDistributionByCycle
- customCommandLineValidation() - Method in class picard.analysis.CollectGcBiasMetrics
- customCommandLineValidation() - Method in class picard.analysis.CollectInsertSizeMetrics
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class picard.analysis.CollectMultipleMetrics
- customCommandLineValidation() - Method in class picard.analysis.CollectOxoGMetrics
- customCommandLineValidation() - Method in class picard.analysis.CollectRnaSeqMetrics
- customCommandLineValidation() - Method in class picard.analysis.CollectRrbsMetrics
- customCommandLineValidation() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
- customCommandLineValidation() - Method in class picard.analysis.CompareMetrics
- customCommandLineValidation() - Method in class picard.analysis.directed.CollectTargetedMetrics
- customCommandLineValidation() - Method in class picard.analysis.MeanQualityByCycle
- customCommandLineValidation() - Method in class picard.analysis.QualityScoreDistribution
- customCommandLineValidation() - Method in class picard.arrays.CollectArraysVariantCallingMetrics
- customCommandLineValidation() - Method in class picard.arrays.GtcToVcf
- customCommandLineValidation() - Method in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- customCommandLineValidation() - Method in class picard.cmdline.CommandLineProgram
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class picard.fastq.BamToBfq
- customCommandLineValidation() - Method in class picard.fingerprint.CheckFingerprint
- customCommandLineValidation() - Method in class picard.fingerprint.CrosscheckFingerprints
- customCommandLineValidation() - Method in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
Deprecated.
- customCommandLineValidation() - Method in class picard.illumina.CheckIlluminaDirectory
- customCommandLineValidation() - Method in class picard.illumina.ExtractBarcodesProgram
-
Parses all barcodes from input files and validates all barcodes are the same length and unique
- customCommandLineValidation() - Method in class picard.illumina.ExtractIlluminaBarcodes
- customCommandLineValidation() - Method in class picard.illumina.IlluminaBasecallsToFastq
- customCommandLineValidation() - Method in class picard.illumina.IlluminaBasecallsToSam
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class picard.illumina.MarkIlluminaAdapters
- customCommandLineValidation() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- customCommandLineValidation() - Method in class picard.sam.AddOrReplaceReadGroups
- customCommandLineValidation() - Method in class picard.sam.CreateSequenceDictionary
-
Use reference filename to create URI to go into header if URI was not passed on cmd line.
- customCommandLineValidation() - Method in class picard.sam.DownsampleSam
- customCommandLineValidation() - Method in class picard.sam.FastqToSam
- customCommandLineValidation() - Method in class picard.sam.FilterSamReads
- customCommandLineValidation() - Method in class picard.sam.markduplicates.EstimateLibraryComplexity
- customCommandLineValidation() - Method in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- customCommandLineValidation() - Method in class picard.sam.MergeBamAlignment
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class picard.sam.MergeSamFiles
- customCommandLineValidation() - Method in class picard.sam.PositionBasedDownsampleSam
- customCommandLineValidation() - Method in class picard.sam.RevertSam
-
Enforce that output ordering is queryname when sanitization is turned on since it requires a queryname sort.
- customCommandLineValidation() - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- customCommandLineValidation() - Method in class picard.sam.SamToFastq
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class picard.sam.SamToFastqWithTags
- customCommandLineValidation() - Method in class picard.sam.SplitSamByNumberOfReads
- customCommandLineValidation() - Method in class picard.sam.ValidateSamFile
- customCommandLineValidation() - Method in class picard.sam.ViewSam
- customCommandLineValidation() - Method in class picard.util.BaitDesigner
- customCommandLineValidation() - Method in class picard.util.IntervalListTools
- customCommandLineValidation() - Method in class picard.vcf.FixVcfHeader
- customCommandLineValidation() - Method in class picard.vcf.GenotypeConcordance
- customCommandLineValidation() - Method in class picard.vcf.MendelianViolations.FindMendelianViolations
-
Validates that the sex chromosomes don't overlap and parses the pseudo-autosomal regions into usable objects to ensure their parsability
- CustomMafFuncotationCreator - Class in org.broadinstitute.hellbender.tools.funcotator.mafOutput
-
Produces custom MAF fields (e.g.
- CustomMafFuncotationCreator() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.mafOutput.CustomMafFuncotationCreator
- customVariantClassificationOrderFile - Variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
- CUTOFF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- cutToShards(Iterable<SimpleInterval>, int) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Splits the given input intervals into shards of at most the requested size.
- cycle - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
- CYCLE - Variable in class org.broadinstitute.hellbender.metrics.analysis.BaseDistributionByCycleMetrics
- CYCLE - Variable in class picard.analysis.BaseDistributionByCycleMetrics
- CYCLE_SUBDIRECTORY_PATTERN - Static variable in class picard.illumina.parser.IlluminaFileUtil
- CycleCovariate - Class in org.broadinstitute.hellbender.utils.recalibration.covariates
-
The Cycle covariate.
- CycleCovariate(RecalibrationArgumentCollection) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.covariates.CycleCovariate
- cycleFromKey(int) - Static method in class org.broadinstitute.hellbender.utils.recalibration.covariates.CycleCovariate
-
Decodes the cycle number from the key.
- cycleKey(int, GATKRead, boolean, int) - Static method in class org.broadinstitute.hellbender.utils.recalibration.covariates.CycleCovariate
-
Computes the encoded value of CycleCovariate's key for the given position at the read.
- CYCLES_TO_TRIM_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- CYCLES_TO_TRIM_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- cycleSkip(VariantContext, FlowAnnotatorBase.LocalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- CycleSkipStatus - Class in org.broadinstitute.hellbender.tools.walkers.annotator.flow
-
Flow Annotation: cycle skip status: cycle-skip, possible-cycle-skip, non-skip
- CycleSkipStatus() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.flow.CycleSkipStatus
- CYSTEINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- CYTOSINE - Static variable in enum class org.broadinstitute.hellbender.utils.Nucleotide
D
- D - Enum constant in enum class org.broadinstitute.hellbender.utils.BaseUtils.Base
- D - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- data - Variable in class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray
- DATA_SOURCES_BUCKET_PATH - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- DATA_SOURCES_FTP_PATH - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- DATA_SOURCES_NAME_PREFIX - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- DATA_SOURCES_PATH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- DATA_TYPE - Variable in class picard.fingerprint.CrosscheckMetric
-
The data type that was being compared.
- DATA_TYPES - Variable in class picard.illumina.CheckIlluminaDirectory
- DATA_TYPES_WITH_BARCODE - Static variable in class picard.illumina.BasecallsConverter
- DATA_TYPES_WITHOUT_BARCODE - Static variable in class picard.illumina.BasecallsConverter
- DataCollection - Interface in org.broadinstitute.hellbender.utils.mcmc
-
Interface for tagging any class that represents a collection of datasets required to update posterior samples for Markov-Chain Monte Carlo sampling using samplers implementing the
ParameterSamplerinterface. - dataFile - Variable in class picard.illumina.parser.MultiTileFileUtil
- DataLine - Class in org.broadinstitute.hellbender.utils.tsv
-
Table data-line string array wrapper.
- DataLine(long, TableColumnCollection, Function<String, RuntimeException>) - Constructor for class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Creates a new data-line instance.
- DataLine(TableColumnCollection, Function<String, RuntimeException>) - Constructor for class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Creates a new data-line instance with no line-number.
- dataOut - Variable in class org.broadinstitute.hellbender.utils.BinaryTableWriter
- DataPoint - Annotation Interface in org.broadinstitute.hellbender.tools.walkers.varianteval.util
- DATASOURCE_NAME_FOR_INPUT_VCFS - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorConstants
-
Datasource name to use for Funcotations created from input variants from a VCF.
- datasourceComparator(DataSourceFuncotationFactory, DataSourceFuncotationFactory) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
-
Sort by putting gencode datasources first and then non-gencode in alphabetical order.
- dataSourceDirectories - Variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
- dataSourceFactories - Variable in class org.broadinstitute.hellbender.tools.funcotator.OutputRenderer
- DataSourceFuncotationFactory - Class in org.broadinstitute.hellbender.tools.funcotator
-
An abstract class to allow for the creation of a
Funcotationfor a given data source. - DataSourceFuncotationFactory(int) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
Constructor to initialize final fields in this class with defaults.
- DataSourceFuncotationFactory(FeatureInput<? extends Feature>, int) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
Constructor to initialize final fields in this class.
- dataSourceIsB37 - Variable in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
Enables b37 data sources to be combined with hg19 data sources and work with the same input variants.
- DataSourceUtils - Class in org.broadinstitute.hellbender.tools.funcotator.dataSources
-
Utilities for reading / working with / manipulating Data Sources.
- dateCreated - Variable in class picard.arrays.illumina.InfiniumEGTFile
- Datum - Class in org.broadinstitute.hellbender.tools.walkers.mutect.clustering
- Datum(double, double, double, int, int, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.Datum
- datumValue(VariantDatum) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager.SelectionMetric
- datumValue(VariantDatum) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager.TruthSensitivityMetric
- DAY_IN_MS - Static variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- daynamicLog10MinLiklihoodModel(double, ToDoubleFunction<GATKRead>) - Static method in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
- DB_SNP - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- DB_SNP - Variable in class picard.analysis.CollectMultipleMetrics
- DB_SNP - Variable in class picard.analysis.CollectOxoGMetrics
- dbsnp - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.DbsnpArgumentCollection
-
A dbSNP VCF file.
- dbsnp - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
-
The rsIDs from this file are used to populate the ID column of the output.
- dbsnp - Variable in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
-
The rsIDs from this file are used to populate the ID column of the output.
- dbsnp - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
-
rsIDs from this file are used to populate the ID column of the output.
- dbsnp - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
-
dbSNP comparison VCF.
- dbsnp - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
-
The rsIDs from this file are used to populate the ID column of the output.
- DBSNP - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
- DBSNP - Variable in class picard.vcf.CollectVariantCallingMetrics
- DBSNP_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- DBSNP_INS_DEL_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The Insertion/Deletion ratio of the indel calls made at dbSNP sites
- DBSNP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.DbsnpArgumentCollection
- DBSNP_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.DbsnpArgumentCollection
- DBSNP_TITV - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The Transition/Transversion ratio of the passing bi-allelic SNP calls made at dbSNP sites
- DBSNP_VALIDATION_VALUE_MAP - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.CustomMafFuncotationCreator
- DbsnpArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
- DbsnpArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.DbsnpArgumentCollection
- DbSnpBitSets() - Constructor for class org.broadinstitute.hellbender.utils.variant.DbSnpBitSetUtil.DbSnpBitSets
- DbSnpBitSets() - Constructor for class picard.util.DbSnpBitSetUtil.DbSnpBitSets
- DbSnpBitSetUtil - Class in org.broadinstitute.hellbender.utils.variant
-
Utility class to use with DbSnp files to determine is a locus is a dbSnp site.
- DbSnpBitSetUtil - Class in picard.util
-
Utility class to use with DbSnp files to determine is a locus is a dbSnp site.
- DbSnpBitSetUtil(File, SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.utils.variant.DbSnpBitSetUtil
-
Constructor that creates a bit set with bits set to true for all variant types.
- DbSnpBitSetUtil(File, SAMSequenceDictionary) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor that creates a bit set with bits set to true for all variant types.
- DbSnpBitSetUtil(File, SAMSequenceDictionary, Collection<DbSnpVariantType>) - Constructor for class org.broadinstitute.hellbender.utils.variant.DbSnpBitSetUtil
-
Constructor.
- DbSnpBitSetUtil(File, SAMSequenceDictionary, Collection<VariantType>) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor that creates a bit set with bits set to true for the given variant types.
- DbSnpBitSetUtil(File, SAMSequenceDictionary, Collection<VariantType>, IntervalList) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor that creates a bit set with bits set to true for the given variant types over the given regions.
- DbSnpBitSetUtil(File, SAMSequenceDictionary, Collection<VariantType>, IntervalList, Optional<Log>) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor.
- DbSnpBitSetUtil(Path, SAMSequenceDictionary) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor that creates a bit set with bits set to true for all variant types.
- DbSnpBitSetUtil(Path, SAMSequenceDictionary, Collection<VariantType>) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor that creates a bit set with bits set to true for the given variant types.
- DbSnpBitSetUtil(Path, SAMSequenceDictionary, Collection<VariantType>, IntervalList) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor that creates a bit set with bits set to true for the given variant types over the given regions.
- DbSnpBitSetUtil(Path, SAMSequenceDictionary, Collection<VariantType>, IntervalList, Optional<Log>) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor.
- DbSnpBitSetUtil.DbSnpBitSets - Class in org.broadinstitute.hellbender.utils.variant
-
Little tuple class to contain one bitset for SNPs and another for Indels.
- DbSnpBitSetUtil.DbSnpBitSets - Class in picard.util
-
Little tuple class to contain one bitset for SNPs and another for Indels.
- DbSnpVariantType - Enum Class in org.broadinstitute.hellbender.utils.variant
-
Enum to hold the possible types of dbSnps.
- dDUP - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.ComplexVariantSubtype
- dDUP_iDEL - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.ComplexVariantSubtype
- DE_NOVO_START_IN_FRAME - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
New start codon is created by the given variant using the chosen transcript.
- DE_NOVO_START_OUT_FRAME - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
New start codon is created by the given variant using the chosen transcript.
- DEBUG_ASSEMBLY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- DEBUG_ASSEMBLY_REGION_STATE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- DEBUG_ASSEMBLY_VARIANTS_OUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- DEBUG_FREQUENCY - Variable in class picard.util.FifoBuffer
- DEBUG_GENOTYPER_OUTPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- DEBUG_GRAPH_TRANSFORMATIONS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- DEBUG_SITES_OUTPUT_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- debugAssembly - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- debugAssemblyVariantsOut - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- debugDump(Logger) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Dumps debugging information into a logger.
- debugFile - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.AlleleFrequencyQC
- debugGraphTransformations - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
- debugGraphTransformations - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- debugMode - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- debugNegatives - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
debug negatives?
- debugOutputStream - Variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- debugReadName - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
debug read names?
- Decile - Enum Class in org.broadinstitute.hellbender.utils.mcmc
-
Enumerates individual deciles.
- DECILE_10 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.Decile
- DECILE_20 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.Decile
- DECILE_30 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.Decile
- DECILE_40 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.Decile
- DECILE_50 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.Decile
- DECILE_60 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.Decile
- DECILE_70 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.Decile
- DECILE_80 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.Decile
- DECILE_90 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.Decile
- DecileCollection - Class in org.broadinstitute.hellbender.utils.mcmc
-
Represents a set of deciles.
- DecileCollection(List<Double>) - Constructor for class org.broadinstitute.hellbender.utils.mcmc.DecileCollection
-
Constructs a DecileCollection from a list of samples using Apache Commons
Percentile. - Decimal - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportDataType
-
Used for float and double values.
- decimate(int, int) - Method in class org.broadinstitute.hellbender.utils.dragstr.STRTableFileBuilder
-
Note that a site with a period and repeat-length has been decimated.
- decimate(long, int, long) - Method in class org.broadinstitute.hellbender.tools.dragstr.STRDecimationTable
- DECIMATION_TABLE_FILE_NAME - Static variable in class org.broadinstitute.hellbender.utils.dragstr.STRTableFile
- decimationBit(int, int) - Method in class org.broadinstitute.hellbender.tools.dragstr.STRDecimationTable
- decimationTable() - Method in class org.broadinstitute.hellbender.utils.dragstr.STRTableFile
-
Returns a copy of the decimation table in this STR table file.
- decode() - Method in class htsjdk.samtools.SAMRecordSparkCodec
-
Read the next record from the input stream and convert into a java object.
- decode() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- decode() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
- decode() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- decode(byte) - Static method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns the nucleotide that corresponds to a particular
bytetyped base code. - decode(char) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.Strand
- decode(char) - Static method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns the nucleotide that corresponds to a particular
chartyped base code. - decode(B) - Method in class org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec
- decode(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec
- decode(CharSequence) - Static method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Transform a single-letter character string into the corresponding nucleotide.
- decode(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistributionShape
- decode(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.Strand
- decode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.AnnotatedIntervalCodec
- decode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceCodec
- decode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.copynumber.SimpleCountCodec
- decode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceCodec
- decode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceCodec
- decode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
-
Fills this object from a text line in RefSeq (UCSC) text dump file
- decode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupCodec
- decode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.SiteDepthCodec
- decode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceCodec
- decode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.table.TableCodec
- decode(String) - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
- decode(BlockCompressedIntervalStream.Reader<BafEvidence>) - Method in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceBCICodec
- decode(BlockCompressedIntervalStream.Reader<DepthEvidence>) - Method in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceBCICodec
- decode(BlockCompressedIntervalStream.Reader<DiscordantPairEvidence>) - Method in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceBCICodec
- decode(BlockCompressedIntervalStream.Reader<SiteDepth>) - Method in class org.broadinstitute.hellbender.utils.codecs.SiteDepthBCICodec
- decode(BlockCompressedIntervalStream.Reader<SplitReadEvidence>) - Method in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceBCICodec
- decodeAnnotations(VariantDatum, VariantContext, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- decodeAnyASList(String) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils
-
Helper function to convert a comma-separated String (such as a vc.getAttrbute().toString() output) to a List of Strings
- decodeAnyASListWithRawDelim(String) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils
-
Helper method to split a "raw" annotation string delimited with "|"
- decodeASFilters(VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.AlleleFilterUtils
-
Decode the AS_FilterStatus INFO attribute.
- decodeLoc(B) - Method in class org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec
- decodeLoc(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- decodeLoc(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupCodec
-
For fast indexing
- decodeLoc(BlockCompressedIntervalStream.Reader<F>) - Method in class org.broadinstitute.hellbender.utils.codecs.AbstractBCICodec
- decodeSBBS(int[]) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest
-
Helper function to turn the SB annotation array into a contingency table
- deduceIdealSplitWeight(IntervalList, int) - Method in interface picard.util.IntervalList.IntervalListScatterer
-
A method that determines the ideal target "weight" of the output IntervalList.
- deduceIdealSplitWeight(IntervalList, int) - Method in class picard.util.IntervalList.IntervalListScattererByBaseCount
- deduceIdealSplitWeight(IntervalList, int) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
- deduceIdealSplitWeight(IntervalList, int) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
- deepCopy() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Return a deep copy of this read.
- deepCopy() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- deepCopy() - Method in class picard.fingerprint.CappedHaplotypeProbabilities
- deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilities
- deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
- deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
- deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
- deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- DEFAULT - Static variable in class org.broadinstitute.hellbender.tools.dragstr.STRDecimationTable
-
The default decimation table.
- DEFAULT - Static variable in class org.broadinstitute.hellbender.utils.dragstr.DragstrParams
-
Default parameters when there is not enough data for estimation.
- DEFAULT_ACTIVE_PROB_THRESHOLD - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- DEFAULT_ADAPTER_LENGTH - Static variable in class picard.util.AdapterMarker
- DEFAULT_ADAPTER_SEQUENCE - Static variable in class picard.analysis.AdapterUtility
- DEFAULT_AF_FOR_MITO_CALLING - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_AF_FOR_TUMOR_NORMAL_CALLING - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_AF_FOR_TUMOR_ONLY_CALLING - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_AF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_AF_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_ANNOTATION_PACKAGES - Static variable in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- DEFAULT_API_MONO_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- DEFAULT_ARRAY_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBConstants
- DEFAULT_ASSEMBLED_IMPRECISE_EVIDENCE_OVERLAP_UNCERTAINTY - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- DEFAULT_ASSEMBLY_REGION_PADDING - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- DEFAULT_ATTRIBUTES_TO_CLEAR - Static variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- DEFAULT_BANDWIDTH - Static variable in class org.broadinstitute.hellbender.utils.baq.BAQ
- DEFAULT_BASE_QUALITY - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.FeaturizedReadSets
- DEFAULT_BIG_DUPLICATE_SET_SIZE - Static variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
- DEFAULT_CACHE_SIZE - Static variable in class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
-
The default cache size in bp
- DEFAULT_CALIBRATION_SENSITIVITY_KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- DEFAULT_CALLABLE_DEPTH - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_CALLSETMAP_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBConstants
- DEFAULT_CIGAR_STRINGS_FOR_DUP_SEQ_ON_CTG - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications
- DEFAULT_COMPRESSION_LEVEL - Static variable in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Writer
- DEFAULT_CONTAMINATION_FRACTION - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection
- DEFAULT_CONVERGENCE_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel
- DEFAULT_DECIMATION_STR - Static variable in class org.broadinstitute.hellbender.tools.dragstr.STRDecimationTable
-
Strings that represents the default decimation table.
- DEFAULT_DEPTH_ONLY_PARAMS - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- DEFAULT_DISTANCE_TO_GROUP_VARIANTS - Static variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- DEFAULT_DOUBLE_FORMAT - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- DEFAULT_DOWN_SAMPLE_SIZE - Static variable in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- DEFAULT_DOWNSAMPLING_TYPE - Static variable in class org.broadinstitute.hellbender.utils.downsampling.DownsamplingMethod
-
Default type to use if no type is specified
- DEFAULT_DRIVING_VARIANTS_LOOKAHEAD_BASES - Static variable in class org.broadinstitute.hellbender.engine.VariantWalkerBase
-
Default value to control the size of the cache for our driving variants input(s) (specifically, the number of additional bases worth of overlapping records to cache for queries on the driving variants).
- DEFAULT_DROP_RATIO - Static variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
- DEFAULT_DYNAMIC_DISQUALIFICATION_SCALE_FACTOR - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine
- DEFAULT_EMISSION_LOG_10_ODDS - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_EXPECTED_ERROR_RATE_PER_BASE - Static variable in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
-
The expected rate of random sequencing errors for a read originating from its true haplotype.
- DEFAULT_EXPECTED_ORIENTATIONS - Static variable in class picard.analysis.ChimeraUtil
- DEFAULT_EXTENSION - Static variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- DEFAULT_FILL_VALUE - Static variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- DEFAULT_FLOW_BASED_ARGUMENT_COLLECTION - Static variable in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- DEFAULT_FLOW_ORDER - Static variable in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- DEFAULT_GATK3_HAPLOTYPE_READ_GROUP_ID - Static variable in class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter
- DEFAULT_GCNV_OUTPUT_COLUMN_PREFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVNamingConstants
- DEFAULT_GENOTYPING_ERROR_RATE - Static variable in class picard.fingerprint.FingerprintChecker
- DEFAULT_GERMLINE_TAG_PADDING_IN_BP - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEvents
- DEFAULT_GOP - Static variable in class org.broadinstitute.hellbender.utils.baq.BAQ
- DEFAULT_GVCF_INDEX_PARAMETER - Static variable in class org.broadinstitute.hellbender.utils.variant.VcfUtils
- DEFAULT_GVCF_INDEX_TYPE - Static variable in class org.broadinstitute.hellbender.utils.variant.VcfUtils
- DEFAULT_GVCF_LOG_10_ODDS - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_HAPLOTYPE_READ_GROUP_ID - Static variable in class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter
- DEFAULT_HEADER_DELIMITER - Static variable in class org.broadinstitute.hellbender.utils.codecs.table.TableCodec
- DEFAULT_HET_TO_HOM_RATIO - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- DEFAULT_IMPRECISE_VARIANT_EVIDENCE_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- DEFAULT_INDEL_START_TOLERANCE - Static variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- DEFAULT_INITIAL_LOG_10_ODDS - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_INSERT_SIZE_LIMIT - Static variable in class picard.analysis.ChimeraUtil
- DEFAULT_INSERTION_DELETION_QUAL - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
The default quality score for an insertion or deletion, if none are provided for this read.
- DEFAULT_KMER_SIZE - Static variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- DEFAULT_LOW_SCORE_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- DEFAULT_MATE_TOO_DISTANT_THRESHOLD - Static variable in class org.broadinstitute.hellbender.engine.filters.MateDistantReadFilter
- DEFAULT_MAX_ACCEPTABLE_DECISION_EDGES_WITHOUT_JT_GUIDANCE - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
- DEFAULT_MAX_ACCEPTABLE_REPETITIONS_OF_A_KMER_IN_A_PATH - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
- DEFAULT_MAX_ALTERNATE_ALLELES - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- DEFAULT_MAX_ASSEMBLY_REGION_SIZE - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- DEFAULT_MAX_CALLABLE_IMPRECISE_DELETION_SIZE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- DEFAULT_MAX_DUPLICATE_SET_SIZE - Static variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
- DEFAULT_MAX_EVAL - Static variable in class org.broadinstitute.hellbender.utils.OptimizationUtils
- DEFAULT_MAX_GENOTYPE_COUNT - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- DEFAULT_MAX_GERMLINE_PROBABILITY - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals
- DEFAULT_MAX_GROUPED_SPAN - Static variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- DEFAULT_MAX_ITERATIONS - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel
- DEFAULT_MAX_LEADING_BASES - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
- DEFAULT_MAX_PATHS_TO_CONSIDER_WITHOUT_RESULT - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
- DEFAULT_MAX_PATHS_TO_EVER_CONSIDER - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
- DEFAULT_MAX_PERIOD - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- DEFAULT_MAX_PROB_PROPAGATION_DISTANCE - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- DEFAULT_MAX_READS_PER_ALIGNMENT - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- DEFAULT_MAX_REASONABLE_FRAGMENT_LENGTH - Static variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
- DEFAULT_MAX_REPEAT_LENGTH - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- DEFAULT_MAX_UPSTREAM_REFERENCE_JUMP_TO_ALLOW - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
- DEFAULT_MIN_ALIGNER_SCORE_DIFFERENCE_PER_BASE - Static variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
- DEFAULT_MIN_ALIGNMENT_LENGTH - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- DEFAULT_MIN_ASSEMBLY_REGION_SIZE - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- DEFAULT_MIN_BQ_CUTOFF - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- DEFAULT_MIN_DEPTH - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- DEFAULT_MIN_GENOTYPE_QUALITY_P - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.PossibleDeNovo
- DEFAULT_MIN_LOCI_COUNT - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- DEFAULT_MIN_MISMATCH_DIFFERENCE_PER_BASE - Static variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
- DEFAULT_MIN_NUM_BASES_FOR_VALID_SEGMENT - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
- DEFAULT_MIN_SAMPLE_COUNT - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals
- DEFAULT_MIN_SEED_LENGTH - Static variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
- DEFAULT_MINIMUM_BASE_QUALITY - Static variable in class picard.fingerprint.FingerprintChecker
- DEFAULT_MINIMUM_MAPPING_QUALITY - Static variable in class picard.fingerprint.FingerprintChecker
- DEFAULT_MINIMUM_WEIGHT_FOR_JT_BRANCH_TO_NOT_BE_PRUNED - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
- DEFAULT_MITO_EMISSION_LOD - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_MITO_INITIAL_LOG_10_ODDS - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_MITO_PRUNING_LOG_ODDS_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_MIXED_PARAMS - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- DEFAULT_MUTECT3_ALT_DOWNSAMPLE - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_MUTECT3_NON_ARTIFACT_RATIO - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_MUTECT3_REF_DOWNSAMPLE - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
Default name for this data source.
- DEFAULT_NO_CALL_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- DEFAULT_NORMAL_LOG_10_ODDS - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DEFAULT_NUM_ADAPTERS_TO_KEEP - Static variable in class picard.util.AdapterMarker
- DEFAULT_NUM_REGULAR_CONTIGS - Static variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
- DEFAULT_NUM_UPSTREAM_REFERENCE_EDGES_TO_TOLERATE - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
- DEFAULT_NUMBER_OF_DIGITS - Static variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- DEFAULT_OPTICAL_DUPLICATE_DISTANCE - Static variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
- DEFAULT_OPTIMIZER - Static variable in class org.broadinstitute.hellbender.utils.OptimizationUtils
- DEFAULT_OUTGOING_JT_EVIDENCE_THRESHOLD_TO_BELEIVE - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
- DEFAULT_PADDING_FRACTION - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CNVLinkage
- DEFAULT_PCR_SNV_ERROR_QUAL - Static variable in class org.broadinstitute.hellbender.utils.fragments.FragmentUtils
- DEFAULT_PCR_SNV_ERROR_RATE - Static variable in class org.broadinstitute.hellbender.utils.fragments.FragmentUtils
- DEFAULT_PESR_PARAMS - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- DEFAULT_PHRED_API_VALUES - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- DEFAULT_PHRED_GOP_VALUES - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- DEFAULT_PHRED_GP_VALUES - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- DEFAULT_PLATFORM - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
- DEFAULT_PLOIDY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- DEFAULT_PLOIDY - Static variable in class org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants
-
Standard ploidy for autosomal chromosomes.
- DEFAULT_PREFIX - Static variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- DEFAULT_PROGRESS_DISPLAY_PERCENT_INCREMENT - Static variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- DEFAULT_PROPERTIES - Static variable in class org.broadinstitute.hellbender.engine.spark.SparkContextFactory
-
Default properties, GATK may not run if these are set to bad values.
- DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN - Static variable in class picard.util.AdapterMarker
- DEFAULT_PRUNING_LOG_ODDS_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- DEFAULT_PRUNING_SEEDING_LOG_ODDS_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- DEFAULT_QUERY_LOOKAHEAD_BASES - Static variable in class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Default value for queryLookaheadBases, if none is specified.
- DEFAULT_QUEUE_SIZE - Static variable in class picard.util.AsyncIterator
- DEFAULT_READ_LENGTH - Static variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- DEFAULT_READ_NAME_REGEX - Static variable in class picard.sam.util.ReadNameParser
-
The read name regular expression (regex) is used to extract three pieces of information from the read name: tile, x location, and y location.
- DEFAULT_READ_QUALITY_FILTER_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
-
Reads with mapping quality lower than this number won't be considered for genotyping, even if they have passed earlier filters (e.g.
- DEFAULT_READ_VALIDATION_STRINGENCY - Static variable in class org.broadinstitute.hellbender.utils.read.ReadConstants
-
Value used as the default validation stringency for all read input
- DEFAULT_READSHARD_PADDING_SIZE - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionReadShardArgumentCollection
- DEFAULT_READSHARD_SIZE - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionReadShardArgumentCollection
- DEFAULT_READSHARD_SIZE - Static variable in class org.broadinstitute.hellbender.tools.HaplotypeCallerSpark
- DEFAULT_RECIPROCAL_OVERLAP_DEPTH_ONLY - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- DEFAULT_RECIPROCAL_OVERLAP_MIXED - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- DEFAULT_RECIPROCAL_OVERLAP_PESR - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- DEFAULT_RECORD_LABEL - Static variable in class org.broadinstitute.hellbender.engine.ProgressMeter
-
Default label for records in logger messages.
- DEFAULT_RECORDS_BETWEEN_TIME_CHECKS - Static variable in class org.broadinstitute.hellbender.engine.ProgressMeter
-
We check the current time every time we process this many records, by default (to cut down on the number of system calls)
- DEFAULT_REF_PADDING - Static variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- DEFAULT_REFERENCE_SEQUENCE_BUFFER_SIZE - Static variable in class org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFile
- DEFAULT_SAMPLE_OVERLAP - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CNVLinkage
- DEFAULT_SAMPLE_OVERLAP_DEPTH_ONLY - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- DEFAULT_SAMPLE_OVERLAP_MIXED - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- DEFAULT_SAMPLE_OVERLAP_PESR - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- DEFAULT_SAMPLING_MIN_MQ - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- DEFAULT_SAMPLING_PADDING - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- DEFAULT_SCORE_KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- DEFAULT_SECONDS_BETWEEN_UPDATES - Static variable in class org.broadinstitute.hellbender.engine.ProgressMeter
-
By default, we output a line to the logger after this many seconds have elapsed
- DEFAULT_SEED_SPLIT_FACTOR - Static variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
- DEFAULT_SHARD_RECORDS - Static variable in class org.broadinstitute.hellbender.tools.SplitCRAM
- DEFAULT_SHARD_SIZE - Static variable in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- DEFAULT_SIGMA - Static variable in class org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile
- DEFAULT_SNP_KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- DEFAULT_SPARK_MASTER - Static variable in class org.broadinstitute.hellbender.engine.spark.SparkContextFactory
- DEFAULT_STANDARD_CONFIDENCE_FOR_CALLING - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- DEFAULT_STATS_EXTENSION - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- DEFAULT_TAGS_TO_DROP - Static variable in class picard.util.LiftoverUtils
- DEFAULT_TAGS_TO_REVERSE - Static variable in class picard.util.LiftoverUtils
-
Default list of attributes that need to be reversed or dropped from the INFO field when alleles have been swapped.
- DEFAULT_TIME_FUNCTION - Static variable in class org.broadinstitute.hellbender.engine.ProgressMeter
-
By default, we use this function to get the current time
- DEFAULT_TRANCHE_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- DEFAULT_TRUTH_INTERVAL_PADDING - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- DEFAULT_VCFHEADER_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBConstants
- DEFAULT_VERSION_STRING - Static variable in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
Default version string for this
DataSourceFuncotationFactory. - DEFAULT_VIDMAP_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBConstants
- DEFAULT_WINDOW_DEPTH_ONLY - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- DEFAULT_WINDOW_MIXED - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- DEFAULT_WINDOW_PESR - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- defaultActiveProbThreshold() - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- defaultAssemblyRegionPadding() - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- defaultBaseQualities - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
-
If reads are missing some or all base quality scores, this value will be used for all base quality scores.
- defaultDistanceToGroupVariants() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
- defaultDistanceToGroupVariants() - Method in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- defaultEndBiasBases - Static variable in class picard.analysis.directed.RnaSeqMetricsCollector
- DefaultGATKReadFilterArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.GATKPlugin
-
Default
GATKReadFilterArgumentCollectionapplied in GATK for optional read filters in the command line. - DefaultGATKReadFilterArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKReadFilterArgumentCollection
- DefaultGATKVariantAnnotationArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.GATKPlugin
-
Arguments for requesting VariantContext annotations to be processed by
VariantAnnotatorEnginefor tools that process variants objects. - DefaultGATKVariantAnnotationArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKVariantAnnotationArgumentCollection
- defaultMaxAssemblyRegionSize() - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- defaultMaxDepthPerSample() - Method in class org.broadinstitute.hellbender.engine.LocusWalker
-
Returns default value for the
LocusWalker.maxDepthPerSampleparameter, if none is provided on the command line. - defaultMaxDepthPerSample() - Method in class org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark
-
Returns default value for the
LocusWalkerSpark.maxDepthPerSampleparameter, if none is provided on the command line. - defaultMaxGroupedSpan() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
- defaultMaxGroupedSpan() - Method in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- defaultMaxProbPropagationDistance() - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- defaultMaxReadsPerAlignmentStart() - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- defaultMinAssemblyRegionSize() - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- DefaultMultiVariantInputArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.MultiVariantInputArgumentCollection.DefaultMultiVariantInputArgumentCollection
- defaultReferenceWindowPadding() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
- defaultReferenceWindowPadding() - Method in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- DefaultSkipEmptyFiles - Static variable in class picard.illumina.parser.ParameterizedFileUtil
- defaultToAC - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
-
By default the tool looks for MLEAC first, and then falls back to AC if MLEAC is not found.
- DEFINITE_GENOTYPES - Variable in class picard.fingerprint.FingerprintMetrics
-
Number of haplotypes that had enough evidence to make a definite genotype call (genotype LOD > Threshold
- DEFRAG_PADDING_FRACTION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- DEFRAG_SAMPLE_OVERLAP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- DEFRAGMENTATION_PADDING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- Degeneracy - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Experimental stratification by the degeneracy of an amino acid, according to VCF annotation.
- Degeneracy(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Degeneracy
- DEL - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantType
- DEL - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.SupportedType
- DEL - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.StructuralVariantAnnotationType
- DEL_ALLELE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- DEL_DUP_CONTRACTION - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera
- delegateFilter - Variable in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter
- delegateFilter - Variable in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter
- DELETED - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapStatus
-
Gene or transcript did not map to the target genome.
- deleteFile(String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Deletes a file: local, GCS or HDFS.
- deleteOnExit(Path) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Schedule a file or directory to be deleted on JVM shutdown.
- deleteRecursively(Path) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Delete rootPath recursively
- deletion - Enum constant in enum class org.broadinstitute.hellbender.utils.variant.DbSnpVariantType
- deletion - Enum constant in enum class picard.util.VariantType
- Deletion(String, int, int, String, Allele, Allele, int, Map<String, Object>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.Deletion
- Deletion(NovelAdjacencyAndAltHaplotype, BasicReference) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.Deletion
- DELETION - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledCopyRatioSegment.Call
- DELETION - Enum constant in enum class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner.State
- DELETION_BASE - Static variable in class org.broadinstitute.hellbender.utils.pileup.PileupElement
- DELETION_QUAL - Static variable in class org.broadinstitute.hellbender.utils.pileup.PileupElement
- deletionMatrix - Variable in class org.broadinstitute.hellbender.utils.pairhmm.FlowBasedPairHMM
- deletionMatrix - Variable in class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM
- DeletionMDElement(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.DeletionMDElement
- DELETIONS_DEFAULT_QUALITY - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
-
A default base qualities to use as a prior (reported quality) in the mismatch covariate model.
- DELETIONS_Q - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
-
The (phred) rate of deletions.
- deletionsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratify by Deletions in the read cigars.
- deletionToDeletion - Static variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Position in the transition probability array for the Deletion-to-Deletion transition.
- DelimitedTextFileWithHeaderIterator - Class in picard.util
-
Iterate through a delimited text file in which columns are found by looking at a header line rather than by position.
- DelimitedTextFileWithHeaderIterator(BasicInputParser) - Constructor for class picard.util.DelimitedTextFileWithHeaderIterator
- DelimitedTextFileWithHeaderIterator.Row - Class in picard.util
- delimiter_regex - Variable in class org.broadinstitute.hellbender.utils.codecs.table.TableCodec
- delINV - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.ComplexVariantSubtype
- delINVdel - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.ComplexVariantSubtype
- delINVdup - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.ComplexVariantSubtype
- delOpenPenalties() - Method in interface org.broadinstitute.hellbender.utils.pairhmm.PairHMMInputScoreImputation
- demultiplex - Variable in class picard.illumina.BasecallsConverter
- denoise(SimpleCountCollection, int) - Method in interface org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals
-
Standardizes and denoises
readCountsusingnumEigensamplesof the eigensamples. - DENOISED_COPY_RATIO_MEAN_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVNamingConstants
- DENOISED_COPY_RATIOS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument
- DenoiseReadCounts - Class in org.broadinstitute.hellbender.tools.copynumber
-
Denoises read counts to produce denoised copy ratios.
- DenoiseReadCounts() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts
- denormalizeDatum(double, int) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
-
Convert a normalized point to it's original annotation value norm = (orig - mu) / sigma orig = norm * sigma + mu
- deNovoPrior - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
-
The de novo mutation prior -- i.e.
- DENSITY_ID - Enum constant in enum class picard.illumina.parser.IlluminaMetricsCode
- DEPRECATED_RecoverDanglingHeads - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerReadThreadingAssemblerArgumentCollection
-
As of version 3.3, this argument is no longer needed because dangling end recovery is now the default behavior.
- DeprecatedToolsRegistry - Class in org.broadinstitute.hellbender.cmdline
-
When a tool is removed from GATK (after having been tagged with @DeprecatedFeature for a suitable period), an entry should be added to this list to issue a message when the user tries to run that tool.
- DeprecatedToolsRegistry() - Constructor for class org.broadinstitute.hellbender.cmdline.DeprecatedToolsRegistry
- DEPTH_ALGORITHM - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- DEPTH_BREAKEND_WINDOW_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- DEPTH_CORRECTION_TAU_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
- DEPTH_EVIDENCE_INTERVALS_INPUT_FILE_ARGUMENT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- DEPTH_EVIDENCE_INTERVALS_INPUT_FILE_ARGUMENT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- DEPTH_EVIDENCE_OUTPUT_FILE_ARGUMENT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- DEPTH_EVIDENCE_OUTPUT_FILE_ARGUMENT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- DEPTH_EVIDENCE_SUMMARY_FILE_ARGUMENT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- DEPTH_EVIDENCE_SUMMARY_FILE_ARGUMENT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- DEPTH_HEADER_LINE - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.AllelePseudoDepth
- DEPTH_INTERVAL_OVERLAP_FRACTION_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- DEPTH_SAMPLE_OVERLAP_FRACTION_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- DEPTH_WINDOW_SIZE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark
- depthBreakendWindow - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
-
Maximum allowed distance between endpoints (in bp) to cluster depth-only/depth-only variant pairs.
- DepthEvidence - Class in org.broadinstitute.hellbender.tools.sv
-
Read counts for an indefinite number of samples on some interval.
- DepthEvidence(Locatable, int[]) - Constructor for class org.broadinstitute.hellbender.tools.sv.DepthEvidence
- DepthEvidence(String, int, int, int[]) - Constructor for class org.broadinstitute.hellbender.tools.sv.DepthEvidence
- DepthEvidenceBCICodec - Class in org.broadinstitute.hellbender.utils.codecs
-
Codec to handle DepthEvidence in BlockCompressedInterval files
- DepthEvidenceBCICodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceBCICodec
- DepthEvidenceCodec - Class in org.broadinstitute.hellbender.utils.codecs
-
Codec to handle DepthEvidence in tab-delimited text files
- DepthEvidenceCodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceCodec
- depthEvidenceInputFilename - Variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- depthEvidenceOutputFilename - Variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- DepthEvidenceSortMerger - Class in org.broadinstitute.hellbender.tools.sv
-
Merges records for the same interval into a single record, when possible, throws if not possible.
- DepthEvidenceSortMerger(SAMSequenceDictionary, FeatureSink<DepthEvidence>) - Constructor for class org.broadinstitute.hellbender.tools.sv.DepthEvidenceSortMerger
- depthEvidenceSummaryFilename - Variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- DepthFilter - Class in picard.vcf.filter
-
Filters out a record if all variant samples have depth lower than the given value.
- DepthFilter(int) - Constructor for class picard.vcf.filter.DepthFilter
- DepthOfCoverage - Class in org.broadinstitute.hellbender.tools.walkers.coverage
-
Assess sequence coverage by a wide array of metrics, partitioned by sample, read group, or library
- DepthOfCoverage() - Constructor for class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage
- DepthOfCoveragePartitionedDataStore - Class in org.broadinstitute.hellbender.tools.walkers.coverage
-
A class helper for storing running intervalPartition data.
- DepthOfCoveragePartitionedDataStore(Collection<DoCOutputType.Partition>, int, int, int, boolean, boolean, Map<DoCOutputType.Partition, List<String>>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoveragePartitionedDataStore
- DepthOfCoverageStats - Class in org.broadinstitute.hellbender.tools.walkers.coverage
-
A class for storing summarized coverage statistics for DepthOfCoverage.
- DepthOfCoverageStats(int[], boolean, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
- DepthOneHistograms - Class in org.broadinstitute.hellbender.tools.walkers.readorientation
-
Holds histograms of alt depth=1 sites for reference contexts.
- DepthOneHistograms(int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.readorientation.DepthOneHistograms
- depthOnlyParams - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- depthOverlapFraction - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
-
Minimum interval reciprocal overlap fraction to cluster depth-only/depth-only variant pairs.
- DepthPerAlleleBySample - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Depth of coverage of each allele per sample
- DepthPerAlleleBySample() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.DepthPerAlleleBySample
- DepthPerSampleHC - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Depth of informative coverage for each sample.
- DepthPerSampleHC() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.DepthPerSampleHC
- depthSampleOverlapFraction - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
-
Minimum carrier sample reciprocal overlap fraction to cluster depth-only/depth-only variant pairs.
- description() - Element in annotation interface org.broadinstitute.hellbender.tools.walkers.varianteval.util.Analysis
- description() - Element in annotation interface org.broadinstitute.hellbender.tools.walkers.varianteval.util.DataPoint
- description() - Element in annotation interface org.broadinstitute.hellbender.tools.walkers.varianteval.util.Molten
- DESCRIPTION - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.TableNameHeaderFields
- DESCRIPTION - Variable in class picard.sam.FastqToSam
- DESCRIPTION_PREAMBLE_DELIMITER - Static variable in class org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer
-
The delimiter used between the preamble and the actual fields in the description of the
VcfOutputRenderer.FUNCOTATOR_VCF_FIELD_NAMEattribute i the header. - descriptors - Variable in class picard.illumina.parser.ReadStructure
- deserialize(File) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.BGMMVariantAnnotationsScorer
- DESIGN_NAME - Variable in class picard.util.BaitDesigner
- DESIGN_ON_TARGET_STRAND - Variable in class picard.util.BaitDesigner
- DESIGN_STRATEGY - Variable in class picard.util.BaitDesigner
- dest - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- destroyBroadcast(Broadcast<T>, String) - Static method in class org.broadinstitute.hellbender.utils.spark.SparkUtils
-
Sometimes Spark has trouble destroying a broadcast variable, but we'd like the app to continue anyway.
- destroyed - Variable in class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase
- DETAIL_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
- DETAIL_OUTPUT - Variable in class picard.fingerprint.CheckFingerprint
- DETAILED_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
- detailedMetricsExtension - Static variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- DETAILS - Variable in class picard.metrics.GcBiasMetrics
- detectIndels - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
-
Enables detection of indels from the pileups in.
- DETERMINE_COLLAPSE_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- determineFilterSize(double[], double) - Static method in class org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile
- determineFormats(Set<IlluminaDataType>, IlluminaFileUtil) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
-
For all requestedDataTypes return a map of file format to set of provided data types that covers as many requestedDataTypes as possible and chooses the most preferred available formats possible
- DetermineGermlineContigPloidy - Class in org.broadinstitute.hellbender.tools.copynumber
-
Determines the integer ploidy state of all contigs for germline samples given counts data.
- DetermineGermlineContigPloidy() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy
- DetermineGermlineContigPloidy.RunMode - Enum Class in org.broadinstitute.hellbender.tools.copynumber
- determineProgessDisplayIncrement(long) - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- determineQualityFormat(FastqReader, FastqReader, FastqQualityFormat) - Static method in class picard.sam.FastqToSam
-
Looks at fastq input(s) and attempts to determine the proper quality format Closes the reader(s) by side effect
- determineReferenceAllele(Allele, Allele) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- determineReferenceAllele(List<VariantContext>, Locatable) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Determines the common reference allele
- determineSegmentExonPosition(GencodeGtfTranscriptFeature, Locatable) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment.SegmentExonUtils
- determineState(VariantContext, String, VariantContext, String, int, int, Boolean) - Static method in class picard.vcf.GenotypeConcordance
-
A method to determine the truth and call states for a pair of variant contexts representing truth and call.
- DEV_R - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- DEV_THETA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- DEV_X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- DEV_Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- DEVIATIONS - Variable in class picard.analysis.CollectInsertSizeMetrics
- devR - Variable in class picard.arrays.illumina.InfiniumEGTFile
- devTheta - Variable in class picard.arrays.illumina.InfiniumEGTFile
- DiagnosticsAndQCProgramGroup - Class in picard.cmdline.programgroups
-
Tools that collect sequencing quality-related and comparative metrics
- DiagnosticsAndQCProgramGroup() - Constructor for class picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup
- dict - Variable in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- dictionary - Variable in class org.broadinstitute.hellbender.tools.sv.AbstractEvidenceSortMerger
- dictionary - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- dictionary - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.CNVLinkage
- dictionary() - Method in class org.broadinstitute.hellbender.utils.dragstr.STRTableFile
-
Returns the dictionary of the reference this str-table is based on.
- DICTIONARY_ARGUMENT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionary
- DictSource(SAMSequenceDictionary, String) - Constructor for class org.broadinstitute.hellbender.engine.MultiFeatureWalker.DictSource
- DIFFER_IN_SEQUENCE - Enum constant in enum class org.broadinstitute.hellbender.tools.reference.ReferencePair.Status
- DIFFER_IN_SEQUENCE_NAMES - Enum constant in enum class org.broadinstitute.hellbender.tools.reference.ReferencePair.Status
- DIFFER_IN_SEQUENCES_PRESENT - Enum constant in enum class org.broadinstitute.hellbender.tools.reference.ReferencePair.Status
- DIFFERENT_INDICES - Enum constant in enum class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.SequenceDictionaryCompatibility
- digamma(int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- DigammaCache - Class in org.broadinstitute.hellbender.utils
- DigammaCache() - Constructor for class org.broadinstitute.hellbender.utils.DigammaCache
- dimension - Static variable in class org.broadinstitute.hellbender.tools.validation.CompareMatrix
- dimensions - Variable in class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray
- DiploidGenotype - Enum Class in picard.fingerprint
-
A genotype produced by one of the concrete implementations of AbstractAlleleCaller.
- DiploidHaplotype - Enum Class in picard.fingerprint
-
Simple enum to represent the three possible combinations of major/major, major/minor and minor/minor haplotypes for a diploid individual.
- DIRECTION_LEFT - Static variable in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceCodec
- DIRECTION_RIGHT - Static variable in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceCodec
- directlyAccessEngineFeatureManager() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Get the
FeatureManagerfor thisGATKTool. - directlyAccessEngineFeatureManager() - Method in class org.broadinstitute.hellbender.engine.WalkerBase
-
Get the
FeatureManagerfor thisGATKTool. - directlyAccessEngineReadsDataSource() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Get the
ReadsDataSourcefor thisGATKTool. - directlyAccessEngineReadsDataSource() - Method in class org.broadinstitute.hellbender.engine.WalkerBase
-
Get the
ReadsDataSourcefor thisGATKTool. - directlyAccessEngineReferenceDataSource() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Get the
ReferenceDataSourcefor thisGATKTool. - directlyAccessEngineReferenceDataSource() - Method in class org.broadinstitute.hellbender.engine.WalkerBase
-
Get the
ReferenceDataSourcefor thisGATKTool. - Dirichlet - Class in org.broadinstitute.hellbender.utils
-
The Dirichlet distribution is a distribution on multinomial distributions: if pi is a vector of positive multinomial weights such that sum_i pi[i] = 1, the Dirichlet pdf is P(pi) = [prod_i Gamma(alpha[i]) / Gamma(sum_i alpha[i])] * prod_i pi[i]^(alpha[i] - 1) The vector alpha comprises the sufficient statistics for the Dirichlet distribution.
- Dirichlet(double...) - Constructor for class org.broadinstitute.hellbender.utils.Dirichlet
- dirichletMultinomial(double[], int[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Return the likelihood of observing the counts of categories having sampled a population whose categorical frequencies are distributed according to a Dirichlet distribution
- dirSize(GATKPath) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Returns the total file size of all files in a directory, or the file size if the path specifies a file.
- DISABLE_ANNEALING - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- DISABLE_ANNEALING_RATE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- DISABLE_ARTIFICIAL_HAPLOTYPE_RECOVERY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- DISABLE_BAM_INDEX_CACHING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- DISABLE_BAM_INDEX_CACHING_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- DISABLE_CALLER - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- DISABLE_CALLER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- DISABLE_CAP_BASE_QUALITIES_TO_MAP_QUALITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- DISABLE_READ_FILTER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- DISABLE_READ_FILTER_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- DISABLE_SAMPLER - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- DISABLE_SAMPLER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- DISABLE_SEQUENCE_DICT_VALIDATION_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- DISABLE_SORT - Variable in class picard.vcf.LiftoverVcf
- DISABLE_SPANNING_EVENT_GENOTYPING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- DISABLE_SYMMETRIC_HMM_NORMALIZING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- DISABLE_TOOL_DEFAULT_ANNOTATIONS - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- DISABLE_TOOL_DEFAULT_READ_FILTERS - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- disableAdaptivePruning - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.MutectReadThreadingAssemblerArgumentCollection
-
A single edge multiplicity cutoff for pruning doesn't work in samples with variable depths, for example exomes and RNA.
- disableArtificialHaplotypeRecovery - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
This is used to disable the recovery of paths that were dropped in the graph based on the junction trees.
- disableBamIndexCaching - Variable in class org.broadinstitute.hellbender.engine.GATKTool
- disableCapReadQualitiesToMapQ - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- disableContigOrderingCheck - Variable in class org.broadinstitute.hellbender.tools.GatherVcfsCloud
- disableOptimizations - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
-
If set, certain "early exit" optimizations in HaplotypeCaller, which aim to save compute and time by skipping calculations if an ActiveRegion is determined to contain no variants, will be disabled.
- disableProgressMeter() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Does this tool want to disable the progress meter? If so, override here to return true
- disableProgressMeter() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- disableSpanningEventGenotyping - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- disableSymmetricallyNormalizeAllelesToReference - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- disableToolDefaultReadFilters - Variable in class org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKReadFilterArgumentCollection
- DISAGREES_WITH_REF_AND_MATE_ONLY_Q - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
-
The (phred) rate of bases that disagree with both the reference and their mate (which agree with each other)
- DISAGREES_WITH_REFERENCE_ONLY_Q - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
-
The (phred) rate of bases that disagree with the reference, but agree with their mate
- DISALLOW_LARGER_PROBS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- disallowLargerProbs - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- discardNonPolytSoftclippedReads - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- discontinuousP(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- DISCORDANT - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
- discordantP(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap
-
Returns true if every allele in eval is also in comp
- DiscordantPairEvidence - Class in org.broadinstitute.hellbender.tools.sv
-
Documents evidence of a too-close or too-far-apart read pair.
- DiscordantPairEvidence(String, String, int, boolean, String, int, boolean) - Constructor for class org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence
- DiscordantPairEvidenceBCICodec - Class in org.broadinstitute.hellbender.utils.codecs
-
Codec to handle DiscordantPairEvidence in BlockCompressedInterval files
- DiscordantPairEvidenceBCICodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceBCICodec
- DiscordantPairEvidenceCodec - Class in org.broadinstitute.hellbender.utils.codecs
-
Codec to handle DiscordantPairEvidence in tab-delimited text files
- DiscordantPairEvidenceCodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceCodec
- DiscordantReadPairEvidence(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.DiscordantReadPairEvidence
- DiscordantReadPairEvidence(GATKRead, ReadMetadata, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.DiscordantReadPairEvidence
- discoverVariantsFromChimeras(SvDiscoveryInputMetaData, JavaRDD<AlignedContig>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.ContigChimericAlignmentIterativeInterpreter
- DiscoverVariantsFromContigAlignmentsArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- DiscoverVariantsFromContigAlignmentsSAMSpark - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
-
(Internal) Examines aligned contigs from local assemblies and calls structural variants
- DiscoverVariantsFromContigAlignmentsSAMSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.DiscoverVariantsFromContigAlignmentsSAMSpark
- discoverySampleInVcf - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- DISCRETE - Enum constant in enum class org.broadinstitute.hellbender.utils.SequencerFlowClass
- DISCRIMINATORY_POWER - Variable in class picard.fingerprint.FingerprintMetrics
-
The difference in fingerprinting LOD between LOD_SELF_CHECK and the LOD score found when fingerprinting it against a random permutation of the probablity vectors (PLs) in each of the haplotypes.
- disjointP(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- DiskBasedReadEndsForMarkDuplicatesMap - Class in picard.sam.markduplicates.util
-
Disk-based implementation of ReadEndsForMarkDuplicatesMap.
- DiskBasedReadEndsForMarkDuplicatesMap(int, ReadEndsForMarkDuplicatesCodec) - Constructor for class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
- dispatchJobs(JavaSparkContext, SvDiscoverFromLocalAssemblyContigAlignmentsSpark.AssemblyContigsClassifiedByAlignmentSignatures, SvDiscoveryInputMetaData, JavaRDD<GATKRead>, boolean) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark
-
Sends assembly contigs classified based on their alignment signature to a corresponding breakpoint location inference unit.
- DISRUPTED_DOMAIN - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- distance(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- distance(BarcodeEditDistanceQuery) - Method in enum class picard.illumina.DistanceMetric
- DISTANCE_MODE - Variable in class picard.illumina.ExtractBarcodesProgram
- distance0(SingleBarcodeDistanceMetric) - Method in enum class picard.illumina.DistanceMetric
- distanceAcrossContigs(GenomeLoc, SAMFileHeader) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
Calculates the distance between two genomeLocs across contigs (if necessary).
- DistanceMetric - Enum Class in picard.illumina
- DistancesBetweenAlignmentsOnRefAndOnRead(int, int, int, int, int, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera.DistancesBetweenAlignmentsOnRefAndOnRead
- distanceSquared(double[], double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- distanceToCombineVariants - Variable in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
- DISTANT_MATE_TAG - Static variable in class org.broadinstitute.hellbender.tools.PrintDistantMates
- distinctAlleleCount() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Returns the number of different alleles that participate in the genotype.
- divide(double[], double[]) - Static method in class picard.util.MathUtil
-
Calculates the ratio of two arrays of the same length.
- divide(double, double) - Static method in class picard.util.MathUtil
-
Divide two Doubles but return 0.0 if the denominator is 0
- DIVIDE_BY_GENOME_LENGTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- DIVIDE_BY_GENOME_LENGTH_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- divideByGenomeLength - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
-
If true, the score contributed by each read is divided by the mapped organism's genome length in the reference.
- divideIntervalIntoShards(SimpleInterval, int, int, int, SAMSequenceDictionary) - Static method in interface org.broadinstitute.hellbender.engine.Shard
-
Divide an interval into ShardBoundaries.
- divideIntervalIntoShards(SimpleInterval, int, int, SAMSequenceDictionary) - Static method in interface org.broadinstitute.hellbender.engine.Shard
-
Divide an interval into ShardBoundaries.
- DNP - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantType
- DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS - Variable in class picard.arrays.GtcToVcf
- DO_NOT_ASSIGN_GENOTYPES - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod
-
do not even bother changing the GTs
- DO_NOT_CHANGE - Enum constant in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- DO_NOT_CHANGE_INVALID - Enum constant in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- DO_NOT_CORRECT_OVERLAPPING_BASE_QUALITIES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- DO_NOT_GZIP_VCF_OUTPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
- DO_NOT_MARK_UNMAPPED_MATES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- DO_NOT_RECOVER_DANGLING_BRANCHES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerReadThreadingAssemblerArgumentCollection
- DO_NOT_RUN_PHYSICAL_PHASING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- DO_NOT_SORT - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.Sorting
- DO_NOT_TRUST_ALL_POLYMORPHIC_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
- DO_NOT_USE_STANDARD_COVARIATES - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
- DO_NOT_VALIDATE_FILTERED_RECORDS - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants
- doAllTxAlleleCombinationsHaveTheSameFields() - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
- doBwaAlignment(JavaRDD<GATKRead>, boolean, Broadcast<SAMFileHeader>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaAlignerSpark
- DOC_CAT_ANNOTATORS - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
-
Definition of the group names / descriptions for documentation/help purposes.
- DOC_CAT_ANNOTATORS_SUMMARY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_BASE_CALLING - Static variable in class picard.util.help.HelpConstants
-
Definition of the group names / descriptions for documentation/help purposes.
- DOC_CAT_BASE_CALLING_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_CNV - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_CNV_SUMMARY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_COVERAGE_ANALYSIS - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_COVERAGE_ANALYSIS_SUMMARY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_DIAGNOSTICS_AND_QC - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_DIAGNOSTICS_AND_QC_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_EXAMPLE - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_EXAMPLE_SUMMARY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_FLOW_ANNOTATORS - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_FLOW_ANNOTATORS_SUMMARY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_GENOTYPING_ARRAYS_MANIPULATION - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_GENOTYPING_ARRAYS_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_INTERVALS_MANIPULATION - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_INTERVALS_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_METAGENOMICS - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_METAGENOMICS_SUMMARY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_METHYLATION_DISCOVERY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_METHYLATION_DISCOVERY_SUMMARY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_METRICS - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_METRICS_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_OTHER - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_OTHER_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_READ_DATA_MANIPULATION - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_READ_DATA_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_READFILTERS - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_READFILTERS_SUMMARY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_REFERENCE - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_REFERENCE_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_RNA - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_RNA_SUMMARY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_SHORT_FLOW_BASED - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_SHORT_FLOW_BASED_SUMMARY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_SHORT_VARIANT_DISCOVERY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_SHORT_VARIANT_DISCOVERY_SUMMARY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_SV_DISCOVERY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_SV_DISCOVERY_SUMMARY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_TEST - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_TEST - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_TEST_SUMMARY - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- DOC_CAT_TEST_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_VARIANT_EVALUATION - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_VARIANT_EVALUATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_VARIANT_FILTERING - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_VARIANT_FILTERING_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_VARIANT_MANIPULATION - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_VARIANT_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_SUPERCAT_EXCLUDE - Static variable in class picard.util.help.HelpConstants
- DOC_SUPERCAT_TOOLS - Static variable in class picard.util.help.HelpConstants
-
List of "supercategory" values used for doc purposes.
- DOC_SUPERCAT_UTILITIES - Static variable in class picard.util.help.HelpConstants
- doCallGenotypes() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBOptions
- doCopy() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- DoCOutputType - Class in org.broadinstitute.hellbender.tools.walkers.coverage
-
Models a single output file in the DoC walker.
- DoCOutputType(DoCOutputType.Partition, DoCOutputType.Aggregation, DoCOutputType.FileType) - Constructor for class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType
- DoCOutputType.Aggregation - Enum Class in org.broadinstitute.hellbender.tools.walkers.coverage
- DoCOutputType.FileType - Enum Class in org.broadinstitute.hellbender.tools.walkers.coverage
- DoCOutputType.Partition - Enum Class in org.broadinstitute.hellbender.tools.walkers.coverage
- doDictionaryCrossValidation() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalker
-
Should this tool cross-validate the sequence dictionaries for input feature files? If a large number of inputs are expected, the tools should override to return false and require a reference.
- doDictionaryCrossValidation() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- doDistantMateAlterations(GATKRead) - Static method in class org.broadinstitute.hellbender.tools.PrintDistantMates
- doesReadContainAllele(PileupElement, Allele) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
TODO: Test.
- doFilter(JavaRDD<GATKRead>, PSFilterLogger) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilter
-
Main PathSeq filtering method.
- doIndelRefConfCalc(int, byte[], ReadPileup, int, ReferenceConfidenceResult) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
- doIndelRefConfCalc(int, byte[], ReadPileup, int, ReferenceConfidenceResult) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticReferenceConfidenceModel
- done - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- doNotCorrectOverlappingBaseQualities - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
-
Base quality is capped at half of PCR error rate for bases where read and mate overlap, to account for full correlation of PCR errors at these bases.
- doNotMerge - Enum constant in enum class org.broadinstitute.hellbender.engine.spark.GATKSparkTool.ReadInputMergingPolicy
- doNotRecoverDanglingBranches - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerReadThreadingAssemblerArgumentCollection
-
By default, the read threading assembler will attempt to recover dangling heads and tails.
- doNotRunPhysicalPhasing - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
-
As of GATK 3.3, HaplotypeCaller outputs physical (read-based) information (see version 3.3 release notes and documentation for details).
- DoNotSubclass - Annotation Interface in org.broadinstitute.hellbender.engine
-
Classes annotated with this annotation are NOT intended or designed to be extended and should be treated as final.
- doNotUseTristateCorrection - Variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- doNotUseTristateCorrection() - Method in class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM
- doNotUseTristateCorrection() - Method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- DONT_GENOTYPE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- DONT_INCREASE_KMER_SIZE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- DONT_MERGE_ABUTTING - Variable in class picard.util.IntervalListTools
- DONT_MIX_CONTIGS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- DONT_MODIFY - Enum constant in enum class org.broadinstitute.hellbender.utils.baq.BAQ.QualityMode
- DONT_REMOVE_DUPLICATE_INFORMATION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- DONT_REQUIRE_SOFT_CLIPS_BOTH_ENDS_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- DONT_RESTORE_ORIGINAL_QUALITIES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- DONT_SKIP_ALREADY_FILTERED_VARIANTS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- DONT_TRIM_ALLELES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
- DONT_TRIM_ALLELES_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
- DONT_USE_DRAGSTR_PAIRHMM_FULLNAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- DONT_USE_SOFT_CLIPPED_BASES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- dontClipITRArtifacts - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
When opposite ends of a fragment are inverted tandem repeats of each other, the sequence past one end may be copied onto the other during library prep.
- dontGenotype - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
-
This argument is intended for benchmarking and scalability testing.
- dontIncreaseKmerSizesForCycles - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
When graph cycles are detected, the normal behavior is to increase kmer sizes iteratively until the cycles are resolved.
- dontMarkUnmappedMates - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- dontMixContigs - Variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- dontRestoreOriginalQualities - Variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- DontTag - Enum constant in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
- dontTrimAlleles - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
-
If this argument is set, bases common to all alleles will not be removed and will not leave their minimal representation.
- dontUseDragstrPairHMMScores - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- dontUseDragstrPriors - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- dontUseSoftClippedBases - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- doPaired(FastqReader, FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
-
More complicated method that takes two fastq files and builds pairing information in the SAM.
- doProfiling - Static variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- doQualApprox - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- doReadFilterArgumentWarnings(GATKReadFilterPluginDescriptor, Logger) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- DOT - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.GenomicPhase
- dotProduct(double[], double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- DOTTER_CONFIRMED - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Transcript QC checked using dotplot to identify features eg splice junctions, end of homology.
- DOUBLE_FORMAT - Static variable in class org.broadinstitute.hellbender.tools.copynumber.formats.CopyNumberFormatsUtils
- DOUBLE_FORMAT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- doubles(double, double, double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Composes and array of doubles given the start, end (enclosed*) and the step or interval between consecutive values in the sequence.
- doubles(int, double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Returns an array of doubles filled with a particular value.
- DoubleSequence - Class in org.broadinstitute.hellbender.utils.dragstr
-
User argument to specify a sequence of doubles with 3 values in the format
"start:step:limit". - DoubleSequence(String) - Constructor for class org.broadinstitute.hellbender.utils.dragstr.DoubleSequence
- doUnpaired(FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
-
Creates a simple SAM file from a single fastq file.
- DOWN_SAMPLE_SIZE_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- downloadBytesPerMilliSecond - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- DownsampleableSparkReadShard - Class in org.broadinstitute.hellbender.tools
-
A simple shard implementation intended to be used for splitting reads by partition in Spark tools
- DownsampleableSparkReadShard(ShardBoundary, Iterable<GATKRead>, ReadsDownsampler) - Constructor for class org.broadinstitute.hellbender.tools.DownsampleableSparkReadShard
- DownsampleByDuplicateSet - Class in org.broadinstitute.hellbender.tools.walkers.consensus
-
Given a bam grouped by the same unique molecular identifier (UMI), this tool drops a specified fraction of duplicate sets and returns a new bam.
- DownsampleByDuplicateSet() - Constructor for class org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSet
- DOWNSAMPLED_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- Downsampler<T> - Class in org.broadinstitute.hellbender.utils.downsampling
-
The basic downsampler API, with no reads-specific operations.
- Downsampler() - Constructor for class org.broadinstitute.hellbender.utils.downsampling.Downsampler
- DownsampleSam - Class in picard.sam
-
Summary
- DownsampleSam() - Constructor for class picard.sam.DownsampleSam
- DownsampleType - Enum Class in org.broadinstitute.hellbender.utils.downsampling
-
Type of downsampling method to invoke.
- DOWNSAMPLING_STRIDE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DOWNSAMPLING_STRIDE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- DownsamplingMethod - Class in org.broadinstitute.hellbender.utils.downsampling
-
Describes the method for downsampling reads at a given locus.
- DownsamplingMethod(DownsampleType, Integer, Double) - Constructor for class org.broadinstitute.hellbender.utils.downsampling.DownsamplingMethod
-
If type is null, then DEFAULT_DOWNSAMPLING_TYPE will be used.
- downsamplingStride - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
Downsample a pool of reads starting within a range of one or more bases.
- DOWNSTREAM - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- DOWNSTREAM_ATG - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
an upstream ATG is used where a downstream ATG seems more evolutionary conserved.
- downstreamBreakpointRefContig - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference
- downstreamBreakpointRefPos - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference
- downwards - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph.TraversalDirection
- doWork() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineArgumentValidator
- doWork() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
-
Do the work after command line has been parsed.
- doWork() - Method in class org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor
- doWork() - Method in class org.broadinstitute.hellbender.engine.GATKTool
- doWork() - Method in class org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram
- doWork() - Method in class org.broadinstitute.hellbender.tools.BwaMemIndexImageCreator
- doWork() - Method in class org.broadinstitute.hellbender.tools.CompareIntervalLists
- doWork() - Method in class org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBam
- doWork() - Method in class org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegments
- doWork() - Method in class org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts
- doWork() - Method in class org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy
- doWork() - Method in class org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
- doWork() - Method in class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller
- doWork() - Method in class org.broadinstitute.hellbender.tools.copynumber.ModelSegments
- doWork() - Method in class org.broadinstitute.hellbender.tools.copynumber.plotting.PlotDenoisedCopyRatios
- doWork() - Method in class org.broadinstitute.hellbender.tools.copynumber.plotting.PlotModeledSegments
- doWork() - Method in class org.broadinstitute.hellbender.tools.DumpTabixIndex
- doWork() - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader
- doWork() - Method in class org.broadinstitute.hellbender.tools.GatherVcfsCloud
- doWork() - Method in class org.broadinstitute.hellbender.tools.HtsgetReader
- doWork() - Method in class org.broadinstitute.hellbender.tools.IndexFeatureFile
- doWork() - Method in class org.broadinstitute.hellbender.tools.PrintBGZFBlockInformation
- doWork() - Method in class org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndex
- doWork() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
-
Get the list of distinct kmers in the reference, and write them to a file as a HopScotch set or Bloom filter.
- doWork() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
- doWork() - Method in class org.broadinstitute.hellbender.tools.SplitCRAM
- doWork() - Method in class org.broadinstitute.hellbender.tools.validation.CompareBaseQualities
- doWork() - Method in class org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates
- doWork() - Method in class org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReports
- doWork() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination
- doWork() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.GatherPileupSummaries
- doWork() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.GatherNormalArtifactData
- doWork() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.MergeMutectStats
- doWork() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel
- doWork() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNVariantTrain
- doWork() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNVariantWriteTensors
- doWork() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.GatherTranches
- doWork() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
- doWork() - Method in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- doWork() - Method in class picard.analysis.CollectJumpingLibraryMetrics
-
Calculates the detailed statistics about the jumping library and then generates the results.
- doWork() - Method in class picard.analysis.CollectMultipleMetrics
- doWork() - Method in class picard.analysis.CollectOxoGMetrics
- doWork() - Method in class picard.analysis.CollectRrbsMetrics
- doWork() - Method in class picard.analysis.CollectWgsMetrics
- doWork() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
- doWork() - Method in class picard.analysis.CompareMetrics
- doWork() - Method in class picard.analysis.directed.CollectTargetedMetrics
-
Asserts that files are readable and writable and then fires off an HsMetricsCalculator instance to do the real work.
- doWork() - Method in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- doWork() - Method in class picard.analysis.SinglePassSamProgram
-
Final implementation of doWork() that checks and loads the input and optionally reference sequence files and the runs the sublcass through the setup() acceptRead() and finish() steps.
- doWork() - Method in class picard.annotation.SortGff
- doWork() - Method in class picard.arrays.CollectArraysVariantCallingMetrics
- doWork() - Method in class picard.arrays.CombineGenotypingArrayVcfs
- doWork() - Method in class picard.arrays.CreateBafRegressMetricsFile
- doWork() - Method in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
- doWork() - Method in class picard.arrays.GtcToVcf
- doWork() - Method in class picard.arrays.illumina.BpmToNormalizationManifestCsv
- doWork() - Method in class picard.arrays.illumina.CompareGtcFiles
- doWork() - Method in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- doWork() - Method in class picard.arrays.MergePedIntoVcf
- doWork() - Method in class picard.arrays.VcfToAdpc
- doWork() - Method in class picard.cmdline.CommandLineProgram
-
Do the work after command line has been parsed.
- doWork() - Method in class picard.fastq.BamToBfq
- doWork() - Method in class picard.fingerprint.CalculateFingerprintMetrics
- doWork() - Method in class picard.fingerprint.CheckFingerprint
- doWork() - Method in class picard.fingerprint.ClusterCrosscheckMetrics
- doWork() - Method in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
- doWork() - Method in class picard.fingerprint.CrosscheckFingerprints
- doWork() - Method in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
Deprecated.
- doWork() - Method in class picard.fingerprint.ExtractFingerprint
- doWork() - Method in class picard.fingerprint.IdentifyContaminant
- doWork() - Method in class picard.fingerprint.LiftOverHaplotypeMap
- doWork() - Method in class picard.illumina.CheckIlluminaDirectory
- doWork() - Method in class picard.illumina.CollectIlluminaBasecallingMetrics
- doWork() - Method in class picard.illumina.CollectIlluminaLaneMetrics
- doWork() - Method in class picard.illumina.ExtractIlluminaBarcodes
- doWork() - Method in class picard.illumina.IlluminaBasecallsToFastq
- doWork() - Method in class picard.illumina.IlluminaBasecallsToSam
- doWork() - Method in class picard.illumina.MarkIlluminaAdapters
- doWork() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- doWork() - Method in class picard.reference.ExtractSequences
- doWork() - Method in class picard.reference.NonNFastaSize
- doWork() - Method in class picard.reference.NormalizeFasta
- doWork() - Method in class picard.sam.AddCommentsToBam
- doWork() - Method in class picard.sam.AddOATag
- doWork() - Method in class picard.sam.AddOrReplaceReadGroups
- doWork() - Method in class picard.sam.BamIndexStats
-
Main method for the program.
- doWork() - Method in class picard.sam.BuildBamIndex
-
Main method for the program.
- doWork() - Method in class picard.sam.CalculateReadGroupChecksum
- doWork() - Method in class picard.sam.CheckTerminatorBlock
- doWork() - Method in class picard.sam.CleanSam
-
Do the work after command line has been parsed.
- doWork() - Method in class picard.sam.CompareSAMs
-
Do the work after command line has been parsed.
- doWork() - Method in class picard.sam.CreateSequenceDictionary
-
Do the work after command line has been parsed.
- doWork() - Method in class picard.sam.DownsampleSam
- doWork() - Method in class picard.sam.FastqToSam
- doWork() - Method in class picard.sam.FilterSamReads
- doWork() - Method in class picard.sam.FixMateInformation
- doWork() - Method in class picard.sam.GatherBamFiles
- doWork() - Method in class picard.sam.markduplicates.CheckDuplicateMarking
- doWork() - Method in class picard.sam.markduplicates.EstimateLibraryComplexity
-
Method that does most of the work.
- doWork() - Method in class picard.sam.markduplicates.MarkDuplicates
-
Main work method.
- doWork() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
-
Main work method.
- doWork() - Method in class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
-
Main work method.
- doWork() - Method in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
- doWork() - Method in class picard.sam.MergeBamAlignment
- doWork() - Method in class picard.sam.MergeSamFiles
-
Combines multiple SAM/BAM/CRAM files into one.
- doWork() - Method in class picard.sam.PositionBasedDownsampleSam
- doWork() - Method in class picard.sam.ReorderSam
- doWork() - Method in class picard.sam.ReplaceSamHeader
-
Do the work after command line has been parsed.
- doWork() - Method in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- doWork() - Method in class picard.sam.RevertSam
- doWork() - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- doWork() - Method in class picard.sam.SamFormatConverter
- doWork() - Method in class picard.sam.SamToFastq
- doWork() - Method in class picard.sam.SetNmMdAndUqTags
- doWork() - Method in class picard.sam.SortSam
- doWork() - Method in class picard.sam.SplitSamByLibrary
- doWork() - Method in class picard.sam.SplitSamByNumberOfReads
- doWork() - Method in class picard.sam.ValidateSamFile
-
Do the work after command line has been parsed.
- doWork() - Method in class picard.sam.ViewSam
- doWork() - Method in class picard.util.AccumulateQualityYieldMetrics
- doWork() - Method in class picard.util.BaitDesigner
- doWork() - Method in class picard.util.BedToIntervalList
- doWork() - Method in class picard.util.FifoBuffer
- doWork() - Method in class picard.util.IntervalListToBed
- doWork() - Method in class picard.util.IntervalListTools
- doWork() - Method in class picard.util.LiftOverIntervalList
-
Do the work after command line has been parsed.
- doWork() - Method in class picard.util.ScatterIntervalsByNs
- doWork() - Method in class picard.vcf.AccumulateVariantCallingMetrics
- doWork() - Method in class picard.vcf.CollectVariantCallingMetrics
- doWork() - Method in class picard.vcf.filter.FilterVcf
- doWork() - Method in class picard.vcf.FixVcfHeader
- doWork() - Method in class picard.vcf.GatherVcfs
- doWork() - Method in class picard.vcf.GenotypeConcordance
- doWork() - Method in class picard.vcf.LiftoverVcf
- doWork() - Method in class picard.vcf.MakeSitesOnlyVcf
- doWork() - Method in class picard.vcf.MakeVcfSampleNameMap
- doWork() - Method in class picard.vcf.MendelianViolations.FindMendelianViolations
- doWork() - Method in class picard.vcf.MergeVcfs
- doWork() - Method in class picard.vcf.RenameSampleInVcf
- doWork() - Method in class picard.vcf.SortVcf
- doWork() - Method in class picard.vcf.SplitVcfs
- doWork() - Method in class picard.vcf.UpdateVcfSequenceDictionary
- doWork() - Method in class picard.vcf.VcfFormatConverter
- doWork() - Method in class picard.vcf.VcfToIntervalList
- DPs - Variable in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- DRAGEN_GATK_MODE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- DRAGENGenotypesModel - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
-
This is the DRAGEN-GATK genotyper model.
- DRAGENGenotypesModel(boolean, boolean, int, int, DragstrParams) - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.DRAGENGenotypesModel
- DRAGENGenotypesModel(int, int, boolean, boolean, int, int, DragstrParams) - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.DRAGENGenotypesModel
- DRAGENGenotypesModel.ReadFeatherEndForwardComparator - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
- DRAGENGenotypesModel.ReadFeatherEndReverseComparator - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
- DRAGENMappingQualityReadTransformer - Class in org.broadinstitute.hellbender.transformers
-
Read transformer intended to replicate DRAGEN behavior for handling mapping qualities.
- DRAGENMappingQualityReadTransformer() - Constructor for class org.broadinstitute.hellbender.transformers.DRAGENMappingQualityReadTransformer
- dragenMode - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
-
DRAGEN-GATK mode changes a long list of arguments to support running DRAGEN-GATK with FRD + BQD + STRE (with or without a provided STRE table provided):
- dragenWriter(OutputStream, OutputStream, String) - Static method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusUtils
-
Generates the str_table.bin format produced by DRAGEN.
- DRAGSTR_HET_HOM_RATIO_FULLNAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- DRAGSTR_PARAMS_PATH_FULLNAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- dragstrHetHomRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- DragstrHyperParameters - Class in org.broadinstitute.hellbender.tools.dragstr
- DragstrHyperParameters() - Constructor for class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- DragstrLocus - Class in org.broadinstitute.hellbender.tools.dragstr
-
Holds information about a locus on the reference that might be used to estimate the DRAGstr model parameters.
- DragstrLocus.WriteAction - Interface in org.broadinstitute.hellbender.tools.dragstr
- DragstrLocusCase - Class in org.broadinstitute.hellbender.tools.dragstr
-
Represents the DRAGstr model fitting relevant stats at a given locus on the genome for the target sample.
- DragstrLocusCase(DragstrLocus, int, int, int, int) - Constructor for class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCase
- DragstrLocusCases - Class in org.broadinstitute.hellbender.tools.dragstr
-
Collection of Dragstr Locus cases constraint to a particular period and (minimum) repeat-length
- DragstrLocusCases(int, int) - Constructor for class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCases
-
Creates a new collection with default initial capacity.
- DragstrLocusCases(int, int, int) - Constructor for class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCases
-
Creates a new dragstr cases collection providing it period and repeat-length constraints.
- DragstrLocusUtils - Class in org.broadinstitute.hellbender.tools.dragstr
- DragstrLocusUtils() - Constructor for class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusUtils
- DragstrLocusUtils.BinaryTableIndex - Class in org.broadinstitute.hellbender.tools.dragstr
- DragstrPairHMMInputScoreImputator - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Pair-HMM score imputator based on the DRAGstr model parameters.
- dragstrParams - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- DragstrParams - Class in org.broadinstitute.hellbender.utils.dragstr
-
Holds the values of the DRAGstr model parameters for different combinations of repeat unit length (period) and number of repeat units.
- DragstrParamsBuilder - Class in org.broadinstitute.hellbender.utils.dragstr
-
Partial mutable collection of Dragstr Parameters used to compose the final immutable
DragstrParams. - DragstrParamsBuilder(int, int) - Constructor for class org.broadinstitute.hellbender.utils.dragstr.DragstrParamsBuilder
- DragstrParamUtils - Class in org.broadinstitute.hellbender.utils.dragstr
-
Utils to read and write
DragstrParamsinstances from an to files and other resources. - DragstrParamUtils() - Constructor for class org.broadinstitute.hellbender.utils.dragstr.DragstrParamUtils
- DragstrReadSTRAnalyzer - Class in org.broadinstitute.hellbender.utils.pairhmm
-
Utility to find short-tandem-repeats on read sequences.
- DragstrReferenceAnalyzer - Class in org.broadinstitute.hellbender.utils.dragstr
-
Tool to figure out the period and repeat-length (in units) of STRs in a reference sequence.
- draw() - Method in class picard.analysis.TheoreticalSensitivity.RouletteWheel
- drivingVariantFile - Variable in class org.broadinstitute.hellbender.engine.spark.VariantWalkerSpark
- drivingVariantFile - Variable in class org.broadinstitute.hellbender.engine.VariantLocusWalker
- drivingVariantFile - Variable in class org.broadinstitute.hellbender.engine.VariantWalker
- drivingVariantPaths - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MultiVariantInputArgumentCollection.DefaultMultiVariantInputArgumentCollection
- DROP_LOW_QUALS_ARG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- DROP_MISSING_CONTIGS - Variable in class picard.util.BedToIntervalList
- DROP_SOMATIC_FILTERING_ANNOTATIONS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
- dropAggregateData() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
-
Remove all VariantDatum's from the data list which are marked as aggregate data
- dropLowQuals - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- dropRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
-
BWA-mem extension drop ratio
- dropSomaticFilteringAnnotations - Variable in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
-
Rather than move the per-sample INFO annotations used for filtering to the FORMAT field, drop them entirely.
- dropSomaticFilteringAnnotations - Variable in class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
- DS_CHECKSUM_EXTENSION - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- DS_EXTENSION - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- DS_GERMLINE_NAME_MODIFIER - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- DS_SOMATIC_NAME_MODIFIER - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- DUAL_INDEXED - Enum constant in enum class org.broadinstitute.hellbender.utils.illumina.IlluminaAdapterPair
- DUAL_INDEXED - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- dumpAllFeatureCacheStats() - Method in class org.broadinstitute.hellbender.engine.FeatureManager
- dumpConfigSettings(T, Path) - Static method in class org.broadinstitute.hellbender.utils.config.ConfigFactory
-
Dump the configuration to a file that can be easily read into
Properties. - dumpMatrices() - Method in class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM
-
Print out the core hmm matrices for debugging
- dumpTabixIndex(PushbackInputStream, PrintStream) - Static method in class org.broadinstitute.hellbender.tools.DumpTabixIndex
- DumpTabixIndex - Class in org.broadinstitute.hellbender.tools
- DumpTabixIndex() - Constructor for class org.broadinstitute.hellbender.tools.DumpTabixIndex
- DUP - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.SupportedType
- DUP - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.StructuralVariantAnnotationType
- DUP_ALLELE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- DUP_ANNOTATIONS_IMPRECISE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- DUP_IMPRECISE_AFFECTED_RANGE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- DUP_INV - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.SupportedType
- DUP_INV_INTERNAL_ID_START_STRING - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- DUP_ORIENTATIONS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- DUP_PARTIAL - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- DUP_REPEAT_UNIT_REF_SPAN - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- DUP_SEQ_CIGARS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- DUP_TAN_CONTRACTION_INTERNAL_ID_START_STRING - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- DUP_TAN_CONTRACTION_STRING - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- DUP_TAN_EXPANSION_INTERNAL_ID_START_STRING - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- DUP_TAN_EXPANSION_STRING - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- dupBytes(byte, int) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Create a new byte array that's n copies of b
- dupChar(char, int) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Create a new string that's n copies of c
- DUPE - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
The record passes validation but is a duplicate (another assay at the same locus with the same alleles)
- DUPE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- dupINV - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.ComplexVariantSubtype
- dupINVdel - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.ComplexVariantSubtype
- dupINVdup - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.ComplexVariantSubtype
- DUPLEX_CONSENSUS - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
-
Consensus read which has two or more observations in both directions.
- DUPLEX_SINGLETON - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
-
Read which has two observations, one from each direction.
- DUPLEX_UMI - Variable in class picard.sam.markduplicates.MarkDuplicates
- DUPLICATE_MARKINGS_DIFFER - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records for which duplicate markings are different.
- DUPLICATE_READS_FILTERED - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterMetrics
-
The number of filtered duplicate reads
- DUPLICATE_SCORING_STRATEGY - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- DUPLICATE_SCORING_STRATEGY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- DUPLICATE_SCORING_STRATEGY_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- DUPLICATE_SET_INDEX_TAG - Static variable in class picard.sam.markduplicates.MarkDuplicates
-
The attribute in the SAM/BAM file used to store which read was selected as representative out of a duplicate set
- DUPLICATE_SET_SIZE_TAG - Static variable in class picard.sam.markduplicates.MarkDuplicates
-
The attribute in the SAM/BAM file used to store the size of a duplicate set
- DUPLICATE_SETS_IGNORING_UMI - Variable in class picard.sam.markduplicates.UmiMetrics
-
Number of duplicate sets found before taking UMIs into account
- DUPLICATE_SETS_WITH_UMI - Variable in class picard.sam.markduplicates.UmiMetrics
-
Number of duplicate sets found after taking UMIs into account
- DUPLICATE_TAGGING_POLICY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- DUPLICATE_TYPE_LIBRARY - Static variable in class picard.sam.markduplicates.MarkDuplicates
-
The duplicate type tag value for duplicate type: library.
- DUPLICATE_TYPE_SEQUENCING - Static variable in class picard.sam.markduplicates.MarkDuplicates
-
The duplicate type tag value for duplicate type: sequencing (optical & pad-hopping, or "co-localized").
- DUPLICATE_TYPE_TAG - Static variable in class picard.sam.markduplicates.MarkDuplicates
-
The optional attribute in SAM/BAM/CRAM files used to store the duplicate type.
- DUPLICATED_EVIDENCE_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- DuplicatedAltReadFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- DuplicatedAltReadFilter(int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.DuplicatedAltReadFilter
- duplicateIndexes - Variable in class picard.sam.markduplicates.MarkDuplicates
- duplicateSetSize - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- DuplicateSetWalker - Class in org.broadinstitute.hellbender.engine
-
A walker that processes duplicate reads that share the same Unique molecule Identifier (UMI) as a single unit.
- DuplicateSetWalker() - Constructor for class org.broadinstitute.hellbender.engine.DuplicateSetWalker
- duplicatesScoringStrategy - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- DUPLICATION_NUMBERS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- DUPLICATION_QS_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- DuplicationInverted(NovelAdjacencyAndAltHaplotype, BasicReference) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.DuplicationInverted
- DuplicationMetrics - Class in picard.sam
-
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.
- DuplicationMetrics() - Constructor for class picard.sam.DuplicationMetrics
- DuplicationMetricsFactory - Class in picard.sam
-
Factory class that creates either regular or flow-based duplication metrics.
- DuplicationMetricsFactory() - Constructor for class picard.sam.DuplicationMetricsFactory
- DuplicationTandem(String, int, int, String, Allele, Allele, int, Map<String, Object>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.DuplicationTandem
- DuplicationTandem(NovelAdjacencyAndAltHaplotype, BasicReference) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.DuplicationTandem
- dupSeqRepeatNumOnCtg - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- dupSeqRepeatNumOnRef - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- dupSeqRepeatUnitRefSpan - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- dupSeqStrandOnCtg - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- dupSeqStrandOnRef - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- dupString(String, int) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Create a new string thats a n duplicate copies of s
- DUST_MASK_QUALITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- DUST_T_SCORE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- DUST_WINDOW_SIZE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- dustMask - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- DUSTReadTransformer - Class in org.broadinstitute.hellbender.transformers
-
Masks read bases and base qualities using the symmetric DUST algorithm
- DUSTReadTransformer(int, int, double) - Constructor for class org.broadinstitute.hellbender.transformers.DUSTReadTransformer
- dustT - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
-
Controls the stringency of low-complexity filtering.
- dustW - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- dynamic - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.RevertSamSpark.FileType
- dynamic - Enum constant in enum class picard.sam.RevertSam.FileType
- DYNAMIC_QUAL_THRESHOLD_TABLE_ENTRY_LENGTH - Static variable in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
- DYNAMIC_QUAL_THRESHOLD_TABLE_ENTRY_MEAN_OFFSET - Static variable in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
- DYNAMIC_READ_DISQUALIFICATION_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- DYNAMIC_SEEK - Enum constant in enum class org.broadinstitute.hellbender.utils.variant.GATKVCFIndexType
- DYNAMIC_SIZE - Enum constant in enum class org.broadinstitute.hellbender.utils.variant.GATKVCFIndexType
- dynamicReadQualThreshLookupTable - Static variable in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
E
- E - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier.AlnModType.ModTypeString
- EarliestFragmentPrimaryAlignmentSelectionStrategy - Class in org.broadinstitute.hellbender.utils.read.mergealignment
-
When it is necessary to pick a primary alignment from a group of alignments for a read, pick the one that maps the earliest base in the read.
- EarliestFragmentPrimaryAlignmentSelectionStrategy - Class in picard.sam
-
When it is necessary to pick a primary alignment from a group of alignments for a read, pick the one that maps the earliest base in the read.
- EarliestFragmentPrimaryAlignmentSelectionStrategy() - Constructor for class org.broadinstitute.hellbender.utils.read.mergealignment.EarliestFragmentPrimaryAlignmentSelectionStrategy
- EarliestFragmentPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy
- ebeAdd(double[], double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- ebeAdd(int[], int[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- eChromosomeCount - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- EDGE_MULTIPLICITY_ORDER - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge
-
Sorts a collection of BaseEdges in decreasing order of weight, so that the most heavily weighted is at the start of the list
- editIntervals(List<SimpleInterval>) - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark
-
Note that this sets
intervalShardsas a side effect, in order to add padding to the intervals. - editIntervals(List<SimpleInterval>) - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Transform the intervals during loading.
- EFFECT_KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.SnpEffPositionModifier
- effectiveLog10MultinomialWeights() - Method in class org.broadinstitute.hellbender.utils.Dirichlet
- effectiveLogMultinomialWeights() - Method in class org.broadinstitute.hellbender.utils.Dirichlet
- effectiveMultinomialWeights() - Method in class org.broadinstitute.hellbender.utils.Dirichlet
- element(int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- element(GATKRead) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- EM_CONVERGENCE_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel
- EMISSION_LOD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- EMISSION_LOG_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- emit(DragstrLocus) - Method in class org.broadinstitute.hellbender.utils.dragstr.STRTableFileBuilder
-
Emits a locus in the str table.
- EMIT_ALL_ACTIVE_SITES - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.genotyper.OutputMode
-
Produces calls at any region over the activity threshold regardless of confidence.
- EMIT_ALL_CONFIDENT_SITES - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.genotyper.OutputMode
-
produces calls at variant sites and confident reference sites
- EMIT_REF_CONFIDENCE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- EMIT_REF_CONFIDENCE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- EMIT_VARIANTS_ONLY - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.genotyper.OutputMode
-
produces calls only at variant sites
- emitAllActiveSites() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
-
Whether or not all calls at any region over the activity threshold should be emitted regardless of confidence.
- emitEmptyLoci() - Method in class org.broadinstitute.hellbender.engine.LocusWalker
-
Does this tool emit information for uncovered loci? Tools that do should override to return
true. - emitEmptyLoci() - Method in class org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark
-
Does this tool emit information for uncovered loci? Tools that do should override to return
true. - emitEmptyLoci() - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCounts
- emitEmptyLoci() - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSpark
- emitEmptyLoci() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage
- emitOriginalQuals - Variable in class org.broadinstitute.hellbender.tools.ApplyBQSRUniqueArgumentCollection
-
The tool is capable of writing out the original quality scores of each read in the recalibrated output file under the "OQ" tag.
- emitReferenceConfidence - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper
- emitReferenceConfidence - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
-
The reference confidence mode makes it possible to emit a per-bp or summarized confidence estimate for a site being strictly homozygous-reference.
- emitReferenceConfidence() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
-
Are we emitting a reference confidence in some form, or not?
- emitReferenceConfidence() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
-
Are we emitting a reference confidence in some form, or not?
- EMPIRICAL - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistributionShape
-
Arbitrary densities are set for each possible insert size.
- EMPIRICAL_Q_REPORTED_DECIMAL_PLACES - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- EMPIRICAL_QUAL_DECIMAL_PLACES - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- EMPIRICAL_QUALITY_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- empiricalDistribution(int) - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram
-
Composes an empirical distribution based on the current contents fo the histogram.
- EmpiricalPhasingMetricsOutReader - Class in picard.illumina.parser.readers
- EmpiricalPhasingMetricsOutReader(File) - Constructor for class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader
- EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics - Class in picard.illumina.parser.readers
- EMPTY - Enum constant in enum class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
- EMPTY - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
- EMPTY - Static variable in class org.broadinstitute.hellbender.utils.runtime.StreamOutput
-
Empty stream output when no output is captured due to an error.
- EMPTY - Static variable in class picard.vcf.GenotypeConcordanceScheme
- EMPTY_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The empty (no contingency info) count across all variants
- EMPTY_FRAGMENT - Enum constant in enum class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord.Type
- EMPTY_GZIP_BLOCK_WITH_INDEX_POINTER - Static variable in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream
- EMPTY_LIST - Static variable in interface org.broadinstitute.hellbender.utils.genotyper.AlleleList
- EMPTY_LIST - Static variable in interface org.broadinstitute.hellbender.utils.genotyper.SampleList
- emptyAlleleList() - Static method in interface org.broadinstitute.hellbender.utils.genotyper.AlleleList
-
Returns an unmodifiable empty allele-list.
- EmptyFragment - Class in org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
-
Dummy class representing a mated read fragment at a particular start position to be used for accounting when deciding whether to duplicate unmatched fragments.
- EmptyFragment(GATKRead, SAMFileHeader, Map<String, Byte>) - Constructor for class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.EmptyFragment
-
special constructor for creating empty fragments this only includes the necessary data to locate the read, the rest is unnecessary because it will appear in the paired bucket
- EmptyIntersection(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.EmptyIntersection
- EmptyOutputArgumentCollection - Class in picard.cmdline.argumentcollections
- EmptyOutputArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.EmptyOutputArgumentCollection
- emptyRead(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Creates an "empty", unmapped read with the provided read's read group and mate information, but empty (not-null) fields: - Cigar String - Read Bases - Base Qualities Use this method if you want to create a new empty read based on another read
- emptyReader() - Static method in class org.broadinstitute.hellbender.utils.BinaryTableReader
- emptySampleList() - Static method in interface org.broadinstitute.hellbender.utils.genotyper.SampleList
-
Empty list.
- emptyTranche(List<VariantDatum>, int, double, VariantRecalibratorArgumentCollection.Mode) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- emptyTranche(List<VariantDatum>, int, double, VariantRecalibratorArgumentCollection.Mode) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VQSLODTranche
- ena - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.AnnotationSource
- ENABLE_ALL_ANNOTATIONS - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- ENABLE_BIAS_FACTORS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
- ENABLE_CNV_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- ENABLE_DYNAMIC_READ_DISQUALIFICATION_FOR_GENOTYPING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- ENABLE_LEGACY_GRAPH_CYCLE_DETECTION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- enableBAQ - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
- enableDynamicReadDisqualification - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
-
If enabled, rather than disqualifying all reads over a threshold of minimum hmm scores we will instead choose a less strict and less aggressive cap for disqualification based on the read length and base qualities.
- enableLegacyAssemblyRegionTrimming - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- enableLegacyGraphCycleDetection - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
This option exists purely to support concordance with DRAGEN-GATK, it is not recommended to enable this in most use cases.
- enableTestSparkContext() - Static method in class org.broadinstitute.hellbender.engine.spark.SparkContextFactory
-
Register a shared global
JavaSparkContextfor this JVM; this should only be used for testing. - encode(F, S) - Method in interface org.broadinstitute.hellbender.utils.codecs.FeatureOutputCodec
-
Push a feature into the consumer.
- encode(SAMRecord) - Method in class htsjdk.samtools.SAMRecordSparkCodec
-
Write object to OutputStream.
- encode(List<Integer>) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils
-
Helper method to convert StrandBias values to string format
- encode(SimpleCount) - Static method in class org.broadinstitute.hellbender.utils.codecs.copynumber.SimpleCountCodec
- encode(BafEvidence) - Static method in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceCodec
- encode(BafEvidence, BlockCompressedIntervalStream.Writer<BafEvidence>) - Method in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceBCICodec
- encode(BafEvidence, FeatureOutputStream<BafEvidence>) - Method in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceCodec
- encode(DepthEvidence) - Static method in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceCodec
- encode(DepthEvidence, BlockCompressedIntervalStream.Writer<DepthEvidence>) - Method in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceBCICodec
- encode(DepthEvidence, FeatureOutputStream<DepthEvidence>) - Method in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceCodec
- encode(DiscordantPairEvidence) - Static method in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceCodec
- encode(DiscordantPairEvidence, BlockCompressedIntervalStream.Writer<DiscordantPairEvidence>) - Method in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceBCICodec
- encode(DiscordantPairEvidence, FeatureOutputStream<DiscordantPairEvidence>) - Method in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceCodec
- encode(SiteDepth) - Static method in class org.broadinstitute.hellbender.utils.codecs.SiteDepthCodec
- encode(SiteDepth, BlockCompressedIntervalStream.Writer<SiteDepth>) - Method in class org.broadinstitute.hellbender.utils.codecs.SiteDepthBCICodec
- encode(SiteDepth, FeatureOutputStream<SiteDepth>) - Method in class org.broadinstitute.hellbender.utils.codecs.SiteDepthCodec
- encode(SplitReadEvidence) - Static method in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceCodec
- encode(SplitReadEvidence, BlockCompressedIntervalStream.Writer<SplitReadEvidence>) - Method in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceBCICodec
- encode(SplitReadEvidence, FeatureOutputStream<SplitReadEvidence>) - Method in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceCodec
- encode(ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- encode(ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
- encode(RepresentativeReadIndexer) - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- encodeAnyASListWithRawDelim(List<?>) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils
-
Helper function to convert a List of Strings to a @{value ALLELE_SPECIFIC_RAW_DELIM)-separated String, as for raw annotations
- encodeAsByte() - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns this nucleotide's exclusive upper-case
byteencoding. - encodeAsByte(boolean) - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns the
bytetyped encoding that corresponds to this nucleotide. - encodeAsChar() - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns the nucleotide's exclusive upper-case
charencoding. - encodeAsChar(boolean) - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns the
chartyped encoding that corresponds to this nucleotide. - encodeASFilters(List<List<String>>) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.AlleleFilterUtils
-
Create the encoded string for AS_FilterStatus from the list of filters for each alt allele.
- encodeAsString() - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns the nucleotide's exclusive upper-case
Stringencoding. - encodeAsString(boolean) - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns the nucleotide's exclusive
Stringtyped encoding. - encodeBQTag(GATKRead, byte[]) - Static method in class org.broadinstitute.hellbender.utils.baq.BAQ
- encodeDictionary(BufferedWriter, Iterator<SAMSequenceRecord>) - Static method in class picard.util.SequenceDictionaryUtils
-
Encodes a sequence dictionary
- encodeMappingInformation(SAMRecord) - Static method in class picard.sam.AbstractAlignmentMerger
-
Encodes mapping information from a record into a string according to the format sepcified in the Sam-Spec under the SA tag.
- encodeStringList(List<String>) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils
-
Helper function to convert a List of Strings to a comma-separated String
- encodeValueList(List<Double>, String) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils
-
Helper function to parse the list into the annotation string
- end - Variable in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.FlowModeFragment
- end - Variable in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- end - Variable in class picard.annotation.Gene.Transcript.Exon
- end - Variable in class picard.illumina.parser.Range
- end() - Method in class org.broadinstitute.hellbender.utils.logging.BunnyLog
- end() - Method in class picard.annotation.Gene.Transcript
- END - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection.SimpleCountTableColumn
- END_BIAS_BASES - Variable in class picard.analysis.CollectRnaSeqMetrics
- END_BREAKPOINT - Enum constant in enum class org.broadinstitute.hellbender.utils.IntervalUtils.IntervalBreakpointType
- END_COL_COMMENT - Static variable in class org.broadinstitute.hellbender.utils.codecs.AnnotatedIntervalCodec
- END_EXON_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
Used when generating end exon field name for segment funcotations.
- END_GENE_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
Used when generating the end gene (gene that overlaps the ending breakpoint of a segment) field name for segment funcotations.
- END_OF_CONTIG - Static variable in class org.broadinstitute.hellbender.utils.SimpleInterval
- END_TRANSCRIPT_DELIMITER - Static variable in class org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer
-
The delimiter to use when ending the information regarding a transcript.
- END2_ATTRIBUTE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- endInAssembledContig - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- endOfShard(int, int) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
last offset in this shard (1-based).
- endpointSpan(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
Returns a new GenomeLoc that represents the region between the endpoints of this and that.
- ENDS_READ_UNCERTAINTY - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- ENFORCE_SAME_SAMPLES - Variable in class picard.vcf.FixVcfHeader
- engine - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval
- enqueueAndHandleVariant(VariantContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.Funcotator
-
Creates an annotation on the given
variantor enqueues it to be processed during a later call to this method. - ENSEMBL - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.AnnotationSource
- EnsemblGtfCodec - Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
Codec to decode data in GTF format from ENSEMBL.
- EnsemblGtfCodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.gtf.EnsemblGtfCodec
- ensureAnnotations(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- ensureReadCapacity(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculator
-
Makes sure that temporal arrays and matrices are prepared for a number of reads to process.
- ensureUntouched() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator
-
make sure we haven't been used as an iterator yet; this is to miror the MergingSamIterator2 action.
- entryCollides() - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMapSpark
-
in a map, uniqueness is on the key value, so we compare keys to see if we already have an entry for that key
- entryCollides() - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchSetSpark
-
in a set, uniqueness is on the entry, so we just compare entries to see if we already have an identical one
- entryCollides() - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchUniqueMultiMapSpark
-
in a unique multimap, uniqueness is on the entry, so we just compare entries to see if we already have one
- entryCollides() - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
-
in a general multiset there is no uniqueness criterion, so there is never a collision
- entryCollides() - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchMap
-
in a map, uniqueness is on the key value, so we compare keys to see if we already have an entry for that key
- entryCollides() - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchSet
-
in a set, uniqueness is on the entry, so we just compare entries to see if we already have an identical one
- entryCollides() - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchUniqueMultiMap
-
in a unique multimap, uniqueness is on the entry, so we just compare entries to see if we already have one
- entrySet() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- epsilon - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance
- EPSILON - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- EQUAL - Enum constant in enum class org.broadinstitute.hellbender.engine.filters.ReadTagValueFilter.Operator
- equalRange(byte[], int, byte[], int, int) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Compares sections from to byte arrays to verify whether they contain the same values.
- equals(Object) - Method in class org.broadinstitute.hellbender.engine.FeatureInput
-
Test FeatureInputs for equality
- equals(Object) - Method in class org.broadinstitute.hellbender.engine.GATKPath
- equals(Object) - Method in class org.broadinstitute.hellbender.engine.ReadContextData
- equals(Object) - Method in class org.broadinstitute.hellbender.engine.ReadlessAssemblyRegion
- equals(Object) - Method in class org.broadinstitute.hellbender.engine.ReferenceShard
- equals(Object) - Method in class org.broadinstitute.hellbender.engine.ShardBoundary
- equals(Object) - Method in class org.broadinstitute.hellbender.engine.VariantShard
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractRecordCollection
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AnnotatedIntervalCollection
-
Columns, encoder, and decoder are not used.
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleLocatableMetadata
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleLocatableMetadata
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleMetadata
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
-
If all fields are specified for both
AllelicCountobjects, they are all used to check for equality. - equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AnnotatedInterval
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationKey
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationMap
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledCopyRatioSegment
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledLegacySegment
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyNumberPosteriorDistribution
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatio
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatioSegment
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CoveragePerContig
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntervalCopyNumberGenotypingData
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LegacySegment
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LinearCopyRatio
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.gcnv.IntegerCopyNumberState
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocus
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.FlagStat.FlagStatus
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.funcotator.metadata.TumorNormalPair
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.funcotator.metadata.VcfFuncotationMetadata
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedAllele
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedReferenceBases
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Kmer
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.TransitPairCount
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.reference.ReferencePair
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableEntry
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableRow
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerBloomFilter
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedAssembly
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig.GoodAndBadMappings
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.InvertedDuplicationBreakpointComplications
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantCanonicalRepresentation
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInducingAssemblyContig
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera.DistancesBetweenAlignmentsOnRefAndOnRead
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.DiscordantReadPairEvidence
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.InterContigPair
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.LargeIndel
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.MateUnmapped
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.OutiesPair
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SameStrandPair
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SplitRead
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.TemplateSizeAnomaly
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.WeirdTemplateSize
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerAndInterval
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistribution
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervals
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVLocation
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.MDElement
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchSetSpark
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.sv.BafEvidence
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.sv.DepthEvidence
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepth
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.sv.SplitReadEvidence
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleAndContext
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.InverseAllele
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqVertex
-
Two SeqVertex are equal only if their ids are equal
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.Kmer
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LocationAndAlleles
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.Splice
- equals(Object) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine.SVSegment
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfExonFeature
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.OptionalField
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfGeneFeature
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchSet
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.collections.IndexedSet
-
Compares this with another indexed set.
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParams
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
Check to see whether two genomeLocs are equal.
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.IndexRange
- equals(Object) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Insert
-
Returns true iff and only iff the
otherobject is also an insert and has exactly the same bases and qualities. - equals(Object) - Method in class org.broadinstitute.hellbender.utils.KV
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.ReadsKey.KeyForFragment
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.ReadsKey.KeyForPair
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.read.PrimaryAlignmentKey
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.reference.ReferenceBases
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.samples.Sample
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.SVInterval
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree.OverlapIterator
-
equality of iterators is defined as having the same current position in the tree
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.variant.MinimalVariant
- equals(Object) - Method in class org.broadinstitute.hellbender.utils.variant.VariantContextVariantAdapter
- equals(Object) - Method in class picard.annotation.Gene
- equals(Object) - Method in class picard.annotation.Gene.Transcript
- equals(Object) - Method in class picard.fingerprint.FingerprintIdDetails
- equals(Object) - Method in class picard.fingerprint.HaplotypeBlock
- equals(Object) - Method in class picard.fingerprint.Snp
- equals(Object) - Method in class picard.illumina.parser.Range
- equals(Object) - Method in class picard.illumina.parser.ReadDescriptor
- equals(Object) - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
- equals(Object) - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
- equals(Object) - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- equals(Object) - Method in class picard.illumina.parser.ReadStructure
- equals(Object) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
- equals(Object) - Method in class picard.sam.util.Pair
-
Calculate whether this pair object is equal to another object.
- equals(Object) - Method in class picard.sam.util.PrimaryAlignmentKey
- equals(Object) - Method in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
- equals(KmerAndInterval) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerAndInterval
- equals(QNameAndInterval) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval
- equals(SVKmerLong) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
- equals(SVKmerShort) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
- equals(SiteDepth) - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepth
- equals(IndexedSet<?>) - Method in class org.broadinstitute.hellbender.utils.collections.IndexedSet
-
Compare to another indexed set.
- equals(DragstrParams) - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParams
- equals(AlleleList<A>, AlleleList<A>) - Static method in interface org.broadinstitute.hellbender.utils.genotyper.AlleleList
-
Checks whether two allele lists are in fact the same.
- equals(SampleList, SampleList) - Static method in interface org.broadinstitute.hellbender.utils.genotyper.SampleList
-
Checks whether two sample lists are in fact the same.
- equals(GATKReport) - Method in class org.broadinstitute.hellbender.utils.report.GATKReport
-
Checks that the reports are exactly the same.
- equals(GATKReportTable) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Checks that the tables are exactly the same.
- equals(GATKReportVersion) - Method in enum class org.broadinstitute.hellbender.utils.report.GATKReportVersion
- equalUpToHmerChange(byte[], byte[]) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
- equateIntervals(List<GenomeLoc>, List<GenomeLoc>) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
computes whether the test interval list is equivalent to master.
- ERROR_BAR_WIDTH - Variable in class picard.analysis.GcBiasDetailMetrics
-
The radius of error bars in this bin based on the number of observations made.
- ERROR_BASES - Variable in class picard.sam.SamErrorMetric.BaseErrorMetric
-
The number of bases that disagree with the reference
- ERROR_CORRECT_READS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- ERROR_METRICS - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- ERROR_PROB_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactData
- ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The bait bias error rate, calculated as max(1e-10, FWD_ERROR_RATE - REV_ERROR_RATE).
- ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The estimated error rate due to this artifact.
- ERROR_SUMMARY_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
- ERROR_VALUE - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- errorCorrectReads - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
Enabling this argument may cause fundamental problems with the assembly graph itself.
- errorIfMissingData - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTable
-
By default, this tool will write NA for missing data.
- ErrorMetric - Class in picard.sam.SamErrorMetric
-
Created by farjoun on 6/26/18.
- ErrorMetric() - Constructor for class picard.sam.SamErrorMetric.ErrorMetric
- ErrorMetric(String, long) - Constructor for class picard.sam.SamErrorMetric.ErrorMetric
- errorProb - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactData
- errorProbabilities(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2AlleleFilter
-
Returns a list of probabilities, one for each alternate allele which is the probability that the allele should be filtered out.
- errorProbabilities(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2Filter
-
Should be overridden by the implementing class to return the probability that the allele should filtered out.
- errorProbabilities(VariantContext, Mutect2FilteringEngine, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2VariantFilter
-
Converts the single probability calculated for the site to be the probability for each allele
- ErrorProbabilities - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- ErrorProbabilities(List<Mutect2Filter>, VariantContext, Mutect2FilteringEngine, ReferenceContext) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorProbabilities
- errorProbToQual(double) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Convert a probability of being wrong to a phred-scaled quality score (0.01 => 20).
- errorProbToQual(double, byte) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Convert a probability of being wrong to a phred-scaled quality score (0.01 => 20).
- errorProbToQual(double, int) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
- ErrorSummaryMetrics - Class in picard.analysis.artifacts
-
Summary metrics produced by
CollectSequencingArtifactMetricsas a roll up of the context-specific error rates, to provide global error rates per type of base substitution. - ErrorSummaryMetrics() - Constructor for class picard.analysis.artifacts.ErrorSummaryMetrics
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.BaseQualityFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ClusteredEventsFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ContaminationFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.DuplicatedAltReadFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteredHaplotypeFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FragmentLengthFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.GermlineFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MappingQualityFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MinAlleleFractionFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MultiallelicFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2Filter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NormalArtifactFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NRatioFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.PanelOfNormalsFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.PolymeraseSlippageFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadOrientationFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadPositionFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrictStrandBiasFilter
- errorType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.TumorEvidenceFilter
- ErrorType - Enum Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
-
Errors in Mutect2 fall into three major categories -- technical artifacts that depend on (usually hidden) features and do not follow the independent reads assumption of the somatic likelihoods model, non-somatic variants such as germline mutations and contamination, and sequencing errors that are captured by the base qualities and the somatic likelihoods model.
- ESCAPE_CHARACTER - Static variable in class org.broadinstitute.hellbender.utils.tsv.TableUtils
-
Escape character .
- ESCAPE_STRING - Static variable in class org.broadinstitute.hellbender.utils.tsv.TableUtils
-
Escape character as a string.
- escapeExpressions(String) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Splits expressions in command args by spaces and returns the array of expressions.
- escapePeriods(String) - Static method in class picard.illumina.parser.ParameterizedFileUtil
-
Escape the period character.
- EStep(double, double, int, int, int, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter.EStep
- ESTIMATE - Variable in class picard.arrays.BafRegressMetrics
-
The estimate of contamination from the model (on the 0.0-1.0 scale)
- ESTIMATED_LIBRARY_SIZE - Variable in class picard.sam.DuplicationMetrics
-
The estimated number of unique molecules in the library based on PE duplication.
- ESTIMATED_Q_REPORTED_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- EstimateLibraryComplexity - Class in picard.sam.markduplicates
-
Attempts to estimate library complexity from sequence alone.
- EstimateLibraryComplexity() - Constructor for class picard.sam.markduplicates.EstimateLibraryComplexity
- estimateLibrarySize(long, long) - Static method in class picard.sam.DuplicationMetrics
-
Estimates the size of a library based on the number of paired end molecules observed and the number of unique pairs observed.
- estimateRoi(long, double, long, long) - Static method in class picard.sam.DuplicationMetrics
-
Estimates the ROI (return on investment) that one would see if a library was sequenced to x higher coverage than the observed coverage.
- EVAL_BLOCK_HISTOGRAM_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance
- EVAL_BLOCK_HISTOGRAM_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance
- EVAL_VARIANTS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- EVAL_VARIANTS_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- evalBlockHistogramFile - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance
- EvalFeatureInput - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Required stratification grouping output by each eval
- EvalFeatureInput(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.EvalFeatureInput
- evalInfoKey - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance
- evals - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
-
The variant file(s) to evaluate.
- evaluateData(List<VariantDatum>, GaussianMixtureModel, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorEngine
- EvaluateInfoFieldConcordance - Class in org.broadinstitute.hellbender.tools.walkers.validation
-
Compare INFO field values between two VCFs or compare two different INFO fields from one VCF.
- EvaluateInfoFieldConcordance() - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance
- evaluateIntervalsAndNarls(List<SVInterval>, List<NovelAdjacencyAndAltHaplotype>, SAMSequenceDictionary, StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection, Logger) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryUtils
- EvaluationContext - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.util
- EvaluationContext(VariantEvalEngine, Set<Class<? extends VariantEvaluator>>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.util.EvaluationContext
- evalVariantsFile - Variable in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- EVENT_COUNT_IN_HAPLOTYPE_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- EVENT_TYPE_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- eventFrom(int) - Static method in enum class org.broadinstitute.hellbender.utils.recalibration.EventType
-
Get the EventType corresponding to its ordinal index
- eventFrom(String) - Static method in enum class org.broadinstitute.hellbender.utils.recalibration.EventType
-
Get the EventType with short string representation
- EventMap - Class in org.broadinstitute.hellbender.utils.haplotype
-
Extract simple VariantContext events from a single haplotype
- EventMap(Collection<VariantContext>) - Constructor for class org.broadinstitute.hellbender.utils.haplotype.EventMap
-
For testing.
- EventMap(Haplotype, byte[], Locatable, String, int) - Constructor for class org.broadinstitute.hellbender.utils.haplotype.EventMap
- EventType - Enum Class in org.broadinstitute.hellbender.utils.recalibration
- evidence - Variable in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods.BestAllele
-
The query evidence.
- evidence() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix
- evidence() - Method in interface org.broadinstitute.hellbender.utils.genotyper.LikelihoodMatrix
-
List of evidence in the matrix sorted by their index therein.
- EVIDENCE_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.PrintSVEvidence
- evidenceCount() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix
- evidenceCount() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Returns the total count of evidence in the evidence-likelihood collection.
- evidenceCount() - Method in interface org.broadinstitute.hellbender.utils.genotyper.LikelihoodMatrix
-
Count of evidence in the matrix.
- evidenceDir - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- evidenceParams - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- EvidenceTargetLink - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
This class holds information about pairs of intervals on the reference that are connected by one or more BreakpointEvidence objects that have distal targets.
- EvidenceTargetLink(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
- EvidenceTargetLink(StrandedInterval, StrandedInterval, int, int, Set<String>, Set<String>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
- EvidenceTargetLink.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- EvidenceTargetLinkClusterer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
This class is responsible for iterating over a collection of BreakpointEvidence to find clusters of evidence with distal targets (discordant read pairs or split reads) that agree in their location and target intervals and strands.
- EvidenceTargetLinkClusterer(ReadMetadata, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLinkClusterer
- exac - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations.AlleleFrequencyDataSource
- EXACT - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection.CopyNumberPosteriorExpectationMode
- EXACT - Enum constant in enum class org.broadinstitute.hellbender.utils.pairhmm.PairHMM.Implementation
- EXACT_MATCH - Enum constant in enum class org.broadinstitute.hellbender.tools.reference.ReferencePair.Status
- ExampleAssemblyRegionWalker - Class in org.broadinstitute.hellbender.tools.examples
-
Example/toy program that shows how to implement the AssemblyRegionWalker interface.
- ExampleAssemblyRegionWalker() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalker
- ExampleAssemblyRegionWalkerSpark - Class in org.broadinstitute.hellbender.tools.examples
-
Example/toy program that shows how to implement the AssemblyRegionWalker interface.
- ExampleAssemblyRegionWalkerSpark() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerSpark
- ExampleCollectMultiMetricsSpark - Class in org.broadinstitute.hellbender.tools.examples.metrics.multi
-
Example Spark tool for collecting multi-level metrics.
- ExampleCollectMultiMetricsSpark() - Constructor for class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleCollectMultiMetricsSpark
- ExampleCollectSingleMetricsSpark - Class in org.broadinstitute.hellbender.tools.examples.metrics.single
-
Example Spark tool for collecting example single-level metrics.
- ExampleCollectSingleMetricsSpark() - Constructor for class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleCollectSingleMetricsSpark
- ExampleFeatureWalker - Class in org.broadinstitute.hellbender.tools.examples
-
Example/toy program that shows how to implement the FeatureWalker interface.
- ExampleFeatureWalker() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleFeatureWalker
- ExampleIntervalWalker - Class in org.broadinstitute.hellbender.tools.examples
-
Example/toy program that shows how to implement the IntervalWalker interface.
- ExampleIntervalWalker() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalker
- ExampleIntervalWalkerSpark - Class in org.broadinstitute.hellbender.tools.examples
-
Example/toy program that shows how to implement the IntervalWalker interface.
- ExampleIntervalWalkerSpark() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalkerSpark
- ExampleLocusWalker - Class in org.broadinstitute.hellbender.tools.examples
-
Example/toy program that shows how to implement the LocusWalker interface.
- ExampleLocusWalker() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleLocusWalker
- ExampleLocusWalkerSpark - Class in org.broadinstitute.hellbender.tools.examples
-
Example/toy program that shows how to implement the LocusWalker interface.
- ExampleLocusWalkerSpark() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleLocusWalkerSpark
- ExampleMultiFeatureWalker - Class in org.broadinstitute.hellbender.tools.examples
-
Example subclass that shows how to use the MultiFeatureWalker class.
- ExampleMultiFeatureWalker() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleMultiFeatureWalker
- ExampleMultiMetrics - Class in org.broadinstitute.hellbender.tools.examples.metrics.multi
-
An example multi-level metrics collector that just counts the number of reads (per unit/level)
- ExampleMultiMetrics(String, String, String) - Constructor for class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetrics
- ExampleMultiMetricsArgumentCollection - Class in org.broadinstitute.hellbender.tools.examples.metrics.multi
-
Example argument collection for multi-level metrics.
- ExampleMultiMetricsArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsArgumentCollection
- ExampleMultiMetricsCollector - Class in org.broadinstitute.hellbender.tools.examples.metrics.multi
-
Example multi-level metrics collector for illustrating how to collect metrics on specified accumulation levels.
- ExampleMultiMetricsCollector() - Constructor for class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollector
- ExampleMultiMetricsCollectorSpark - Class in org.broadinstitute.hellbender.tools.examples.metrics.multi
-
Example implementation of a multi-level Spark metrics collector.
- ExampleMultiMetricsCollectorSpark() - Constructor for class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollectorSpark
- ExamplePartialReadWalker - Class in org.broadinstitute.hellbender.tools.examples
-
Example/toy program that prints reads from the provided file or files with corresponding reference bases (if a reference is provided).
- ExamplePartialReadWalker() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExamplePartialReadWalker
- ExamplePostTraversalPythonExecutor - Class in org.broadinstitute.hellbender.tools.examples
-
Example/toy ReadWalker program that uses a Python script.
- ExamplePostTraversalPythonExecutor() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExamplePostTraversalPythonExecutor
- ExampleProgramGroup - Class in org.broadinstitute.hellbender.cmdline.programgroups
-
Program group for Example programs
- ExampleProgramGroup() - Constructor for class org.broadinstitute.hellbender.cmdline.programgroups.ExampleProgramGroup
- ExampleReadWalkerWithReference - Class in org.broadinstitute.hellbender.tools.examples
-
Example/toy program that prints reads from the provided file or files with corresponding reference bases (if a reference is provided).
- ExampleReadWalkerWithReference() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReference
- ExampleReadWalkerWithReferenceSpark - Class in org.broadinstitute.hellbender.tools.examples
-
Example/toy program that prints reads from the provided file or files with corresponding reference bases (if a reference is provided).
- ExampleReadWalkerWithReferenceSpark() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceSpark
- ExampleReadWalkerWithVariants - Class in org.broadinstitute.hellbender.tools.examples
-
Example/toy program that prints reads from the provided file or files along with overlapping variants (if a source of variants is provided).
- ExampleReadWalkerWithVariants() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariants
- ExampleReadWalkerWithVariantsSpark - Class in org.broadinstitute.hellbender.tools.examples
-
Example/toy program that prints reads from the provided file or files along with overlapping variants (if a source of variants is provided).
- ExampleReadWalkerWithVariantsSpark() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariantsSpark
- ExampleReferenceWalker - Class in org.broadinstitute.hellbender.tools.examples
-
Counts the number of times each reference context is seen as well as how many times it's overlapped by reads and variants.
- ExampleReferenceWalker() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalker
- ExampleSingleMetrics - Class in org.broadinstitute.hellbender.tools.examples.metrics.single
- ExampleSingleMetrics() - Constructor for class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetrics
- ExampleSingleMetricsArgumentCollection - Class in org.broadinstitute.hellbender.tools.examples.metrics.single
-
Argument argument collection for Example single level metrics.
- ExampleSingleMetricsArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetricsArgumentCollection
- ExampleSingleMetricsCollectorSpark - Class in org.broadinstitute.hellbender.tools.examples.metrics.single
-
ExampleSingleMetricsCollector for Spark.
- ExampleSingleMetricsCollectorSpark() - Constructor for class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetricsCollectorSpark
- ExampleStreamingPythonExecutor - Class in org.broadinstitute.hellbender.tools.examples
-
Example ReadWalker program that uses a Python streaming executor to stream summary data from a BAM input file to a Python process through an asynchronous stream writer.
- ExampleStreamingPythonExecutor() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleStreamingPythonExecutor
- ExampleTwoPassVariantWalker - Class in org.broadinstitute.hellbender.tools.examples
-
This walker makes two traversals through variants in a vcf.
- ExampleTwoPassVariantWalker() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalker
- ExampleVariantWalker - Class in org.broadinstitute.hellbender.tools.examples
-
Example/toy program that shows how to implement the VariantWalker interface.
- ExampleVariantWalker() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker
- ExampleVariantWalkerSpark - Class in org.broadinstitute.hellbender.tools.examples
-
Example/toy program that shows how to implement the VariantWalker interface.
- ExampleVariantWalkerSpark() - Constructor for class org.broadinstitute.hellbender.tools.examples.ExampleVariantWalkerSpark
- exception - Variable in class picard.util.ThreadPoolExecutorWithExceptions
- EXCESS_HET_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- ExcessHet - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Phred-scaled p-value for exact test of excess heterozygosity.
- ExcessHet() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet
- ExcessHet(Set<String>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet
- ExcessHet(GATKPath) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet
- ExcessiveEndClippedReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads where the number of soft-/hard-clipped bases on either end is above a certain threshold.
- ExcessiveEndClippedReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ExcessiveEndClippedReadFilter
- EXCLUDE_INTERVALS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
- EXCLUDE_INTERVALS_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
- excludeAligned - Enum constant in enum class picard.sam.FilterSamReads.Filter
- excludedFields - Variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
- excludeIntervalStrings - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
Use this argument to exclude certain parts of the genome from the analysis (like -L, but the opposite).
- excludeNaNScores - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
exclude NaN score records?
- excludeReadFromBAQ(GATKRead) - Method in class org.broadinstitute.hellbender.utils.baq.BAQ
-
Returns true if we don't think this read is eligible for the BAQ calculation.
- excludeReadList - Enum constant in enum class picard.sam.FilterSamReads.Filter
- excludeTagValues - Enum constant in enum class picard.sam.FilterSamReads.Filter
- excludingAllele(LikelihoodMatrix<EVIDENCE, A>, Allele) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix
- excludingNonOverlaps(VcfFileSegmentGenerator, OverlapDetector<T>) - Static method in class picard.vcf.processor.VcfFileSegmentGenerator
-
Deprecated.Returns a decorated
VcfFileSegmentGeneratorthat filters outVcfFileSegments that have no overlap with the providedOverlapDetector. - excludingNonOverlaps(VcfPathSegmentGenerator, OverlapDetector<T>) - Static method in class picard.vcf.processor.VcfPathSegmentGenerator
-
Returns a decorated
VcfPathSegmentGeneratorthat filters outVcfPathSegments that have no overlap with the providedOverlapDetector. - EXCLUSION_FIELDS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
-
List of final rendered fields to exclude from a final rendering
- exclusionIntervalPadding - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- exclusionIntervalsFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
-
This is a file that calls out the coordinates of intervals in the reference assembly to exclude from consideration when calling putative breakpoints.
- exec() - Method in class org.broadinstitute.hellbender.utils.R.RScriptExecutor
- exec(String[]) - Static method in class org.broadinstitute.hellbender.utils.runtime.ProcessController
-
Similar to Runtime.exec() but drains the output and error streams.
- exec(ProcessSettings) - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessController
-
Executes a command line program with the settings and waits for it to return, processing the output on a background thread.
- executableMissing() - Method in class org.broadinstitute.hellbender.utils.runtime.ScriptExecutor
- executeArgs(List<String>) - Method in class org.broadinstitute.hellbender.utils.python.PythonScriptExecutor
-
Executes the Python executor using the values in
rawArgs - executeArgsAndGetOutput(List<String>) - Method in class org.broadinstitute.hellbender.utils.python.PythonScriptExecutor
-
Executes the Python executor using the values in
rawArgs - executeCommand(String, List<String>, List<String>) - Method in class org.broadinstitute.hellbender.utils.python.PythonScriptExecutor
-
Execute a python command (-c).
- executeCuratedArgs(String[]) - Method in class org.broadinstitute.hellbender.utils.runtime.ScriptExecutor
-
Execute the script represented by the arguments in
commandLineArgumentsand handle process output. - executeCuratedArgsAndGetOutput(String[]) - Method in class org.broadinstitute.hellbender.utils.runtime.ScriptExecutor
-
Execute the script represented by the arguments in
commandLineArgumentsand return process output. - executeFromClasspath(String, String...) - Static method in class picard.util.RExecutor
-
Executes the given R script that is stored in a file on the classpath.
- executeFromFile(File, String...) - Static method in class picard.util.RExecutor
-
Executes the given R script that is stored in a file by a call to Rscript.
- executeModule(String, List<String>, List<String>) - Method in class org.broadinstitute.hellbender.utils.python.PythonScriptExecutor
-
Execute a python module (-m).
- executeMummer(File, File, File) - Method in class org.broadinstitute.hellbender.utils.alignment.MummerExecutor
-
Execute a full alignment of a sequence across a given pair of references to get a File containing the SNPs and INDELs.
- executeQuery(BigQuery, String, boolean) - Static method in class org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils
-
Executes the given
queryStringon the provided BigQuery instance. - executeQuery(BigQuery, String, String, String) - Static method in class org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils
-
Executes the given
queryStringon the provided BigQuery instance. - executeQuery(String) - Static method in class org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils
-
Executes the given
queryStringon the default instance ofBigQueryas created byBigQueryUtils.getBigQueryEndPoint(). - executeQuery(String, boolean) - Static method in class org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils
-
Executes the given
queryStringon the default instance ofBigQueryas created byBigQueryUtils.getBigQueryEndPoint(). - executeQueryWithStorageAPI(String, List<String>, String) - Static method in class org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils
- executeQueryWithStorageAPI(String, List<String>, String, boolean) - Static method in class org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils
- executeScript(String, List<String>, List<String>) - Method in class org.broadinstitute.hellbender.utils.python.PythonScriptExecutor
-
Execute a python script.
- executeScript(Resource, List<String>, List<String>) - Method in class org.broadinstitute.hellbender.utils.python.PythonScriptExecutor
-
Execute a python script from a Resource file.
- executeScriptAndGetOutput(String, List<String>, List<String>) - Method in class org.broadinstitute.hellbender.utils.python.PythonScriptExecutor
-
Execute a python script.
- executeScriptAndGetOutput(Resource, List<String>, List<String>) - Method in class org.broadinstitute.hellbender.utils.python.PythonScriptExecutor
-
Execute a python script from a Resource file and get process output.
- executorService - Static variable in class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase
- existingRecalibrationReport - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
- EXIT_CODE_WHEN_CONTIG_NOT_IN_REFERENCE - Static variable in class picard.vcf.LiftoverVcf
- EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND - Variable in class picard.fingerprint.CheckFingerprint
- EXIT_CODE_WHEN_MISMATCH - Variable in class picard.fingerprint.CrosscheckFingerprints
- EXIT_CODE_WHEN_NO_VALID_CHECKS - Variable in class picard.fingerprint.CheckFingerprint
- EXIT_CODE_WHEN_NO_VALID_CHECKS - Variable in class picard.fingerprint.CrosscheckFingerprints
- ExomeStandardArgumentDefinitions - Class in org.broadinstitute.hellbender.cmdline
-
Created by davidben on 11/30/15.
- ExomeStandardArgumentDefinitions() - Constructor for class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- Exon(int, int) - Constructor for class picard.annotation.Gene.Transcript.Exon
- EXON - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- EXON - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureType
- EXON_COUNT - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- EXON_DELETED - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- EXON_ENDS - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- EXON_FRAMES_INDEX - Static variable in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- EXON_STARTS - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- EXON_STARTS_INDEX - Static variable in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- EXON_STOPS_INDEX - Static variable in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- exonId - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
- exonNumber - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
- exons - Variable in class picard.annotation.Gene.Transcript
- EXP_CLUSTERS_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- EXP_CONF - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Transcript was tested and confirmed experimentally.
- expandAssemblyGraph - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- expandCache(int) - Method in class org.broadinstitute.hellbender.utils.IntToDoubleFunctionCache
-
Ensures that the cache contains a value for n.
- expandWithinContig(int, int) - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
-
Returns a new SimpleInterval that represents this interval as expanded by the specified amount in both directions, bounded by the contig start/stop if necessary.
- expandWithinContig(int, SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
-
Returns a new SimpleInterval that represents this interval as expanded by the specified amount in both directions, bounded by the contig start/stop if necessary.
- EXPECT_ALL_GROUPS_TO_MATCH - Variable in class picard.fingerprint.CrosscheckFingerprints
- EXPECT_ALL_READ_GROUPS_TO_MATCH - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
Deprecated.
- EXPECTED_ALLELE_FRACTION_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithExpectedAlleleFraction
- EXPECTED_COLUMN_COUNT - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- EXPECTED_COPY_NUMBER_FORMAT - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- EXPECTED_GENDER - Variable in class picard.arrays.GtcToVcf
- EXPECTED_GENDER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- EXPECTED_GENOTYPE - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The expected genotype of the sample at the SNP locus.
- EXPECTED_HET - Variable in class picard.fingerprint.FingerprintMetrics
-
Expected number of heterozygous calls
- EXPECTED_HOM_ALLELE1 - Variable in class picard.fingerprint.FingerprintMetrics
-
Expected number of major allele homozygous calls
- EXPECTED_HOM_ALLELE2 - Variable in class picard.fingerprint.FingerprintMetrics
-
Expected number of major allele homozygous calls
- EXPECTED_INSERT_SIZE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- EXPECTED_MATCH - Enum constant in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
- EXPECTED_MISMATCH - Enum constant in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
- EXPECTED_MISMATCH_RATE_FOR_READ_DISQUALIFICATION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- EXPECTED_ORIENTATIONS - Variable in class picard.sam.MergeBamAlignment
- EXPECTED_PAIR_ORIENTATIONS - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
- EXPECTED_SAMPLE_ALIAS - Variable in class picard.fingerprint.CheckFingerprint
- EXPECTED_VERSION - Static variable in class picard.illumina.parser.readers.FilterFileReader
-
Expected Version
- expectedChecksum - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- expectedErrorRatePerBase - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- expectedNumberOfReads() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- exportWorkUnitTemplate(Configuration, DocWorkUnit, String, File) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLDoclet
-
Export the generated files from templates for a single work unit.
- EXPRESSION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
- EXPRESSION_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
- expressionAlleleConcordance - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
-
If this argument is specified, add annotations (specified by --expression) from an external resource (specified by --resource) to the input VCF (specified by --variant) only if the alleles are concordant between input and the resource VCFs.
- expressionsToUse - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
-
This option enables you to add annotations from one VCF to another.
- EXT_COLLAPSED_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- EXT_COLLAPSED_TAG - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- EXT_SPECIAL_TAG - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- extend(char) - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.PathPart
- extend(char) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartContig
- extend(char) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartGap
- extendChainByOne(MultiDeBruijnVertex, byte[], int, int, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Workhorse routine of the assembler.
- EXTENDED_ILLUMINA_MANIFEST - Variable in class picard.arrays.GtcToVcf
- EXTENDED_ILLUMINA_MANIFEST_FILE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- EXTENDED_ILLUMINA_MANIFEST_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- EXTENDED_MANIFEST_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The version of the Extended Illumina Manifest used for calling this sample
- EXTENDED_MAPPING_QUALITY_READ_TAG - Static variable in class org.broadinstitute.hellbender.transformers.DRAGENMappingQualityReadTransformer
- EXTENDED_MQ_READ_TRANSFORMER - Static variable in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- extendedBaseToBaseIndex(byte) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
-
Converts a base including extended bases (ATCG + D and N bases) to a base index
- extendedIterator() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifest
- extendJunctionThreadingByOne(MultiDeBruijnVertex, byte[], int, JunctionTreeLinkedDeBruijnGraph.JunctionTreeThreadingHelper, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
-
Extends the current vertex chain by one, making sure to build junction tree objects at each node with out-degree > 1.
- extension - Variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- extension - Variable in class picard.illumina.parser.ParameterizedFileUtil
-
The file extension for this class, file extension does not have the standard meaning in this instance.
- EXTENSION - Static variable in class picard.arrays.illumina.InfiniumEGTFile
- EXTERNAL_CNV_CALLS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- ExternalEvidence(int, int, int, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ExternalEvidence
- ExternalEvidence(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ExternalEvidence
- ExternalEvidence(SVInterval, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ExternalEvidence
- externalEvidenceFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- externalEvidenceUncertainty - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- externalEvidenceWeight - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- externalExecutableExists() - Method in class org.broadinstitute.hellbender.utils.runtime.ScriptExecutor
- externalScriptExecutableName - Variable in class org.broadinstitute.hellbender.utils.runtime.ScriptExecutor
- EXTRA_ARGUMENT - Variable in class picard.analysis.CollectMultipleMetrics
- EXTRA_FIELD_KEY_VALUE_SPLITTER - Static variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- extract(VariantContext, BasicReference) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor.MultiSegmentsCpxVariantExtractor
- extract(VariantContext, BasicReference) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor.ZeroAndOneSegmentCpxVariantExtractor
-
Depending on how the ref segment is present in alt arrangement (if at all), logic as follows (order is important): if ref segment appear inverted and large enough INV call is warranted INS call(s) before and after the INV, if inserted sequence long enough otherwise if ref segment is present as-is, i.e.
- extract(JavaRDD<VariantContext>, SvDiscoveryInputMetaData, JavaRDD<GATKRead>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor
- EXTRACT_AFTER_DOWNLOAD - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader
- EXTRACT_CONTAMINATED - Variable in class picard.fingerprint.IdentifyContaminant
- EXTRACT_CONTAMINATION - Variable in class picard.fingerprint.ExtractFingerprint
- ExtractBarcodesProgram - Class in picard.illumina
- ExtractBarcodesProgram() - Constructor for class picard.illumina.ExtractBarcodesProgram
- extractDataSourcesAfterDownload - Variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader
- EXTRACTED_FROM_LARGER_ALIGNMENT - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier.AlnModType
- ExtractedSimpleVariants(List<VariantContext>, List<VariantContext>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants
- extractFields(VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTable
-
Utility function that returns the list of values for each field in fields from vc.
- ExtractFingerprint - Class in picard.fingerprint
-
Program to create a fingerprint for the contaminating sample when the level of contamination is both known and uniform in the genome.
- ExtractFingerprint() - Constructor for class picard.fingerprint.ExtractFingerprint
- extractFuncotatorKeysFromHeaderDescription(String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
- ExtractIlluminaBarcodes - Class in picard.illumina
-
Determine the barcode for each read in an Illumina lane.
- ExtractIlluminaBarcodes() - Constructor for class picard.illumina.ExtractIlluminaBarcodes
- ExtractIlluminaBarcodes.PerTileBarcodeExtractor - Class in picard.illumina
-
Extracts barcodes and accumulates metrics for an entire tile.
- extractInts(Object) - Static method in class org.broadinstitute.hellbender.tools.walkers.variantutils.PosteriorProbabilitiesUtils
-
Check the formatting on the Object returned by a call to VariantContext::getAttribute() and parse appropriately
- ExtractOriginalAlignmentRecordsByNameSpark - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
-
Subsets reads by name (basically a parallel version of "grep -f", or "grep -vf")
- ExtractOriginalAlignmentRecordsByNameSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.ExtractOriginalAlignmentRecordsByNameSpark
- extractPossibleTumorNormalPairs(VCFHeader) - Static method in class org.broadinstitute.hellbender.tools.funcotator.metadata.SamplePairExtractor
-
This method should not be needed in germline use cases, but should produce an empty list in such cases.
- extractSamples(Set<String>, Object) - Method in class org.broadinstitute.hellbender.tools.sv.BafEvidence
- extractSamples(Set<String>, Object) - Method in class org.broadinstitute.hellbender.tools.sv.DepthEvidence
- extractSamples(Set<String>, Object) - Method in class org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence
- extractSamples(Set<String>, Object) - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepth
- extractSamples(Set<String>, Object) - Method in class org.broadinstitute.hellbender.tools.sv.SplitReadEvidence
- extractSamples(Set<String>, Object) - Method in interface org.broadinstitute.hellbender.tools.sv.SVFeature
- ExtractSequences - Class in picard.reference
-
Simple command line program that allows sub-sequences represented by an interval list to be extracted from a reference sequence file.
- ExtractSequences() - Constructor for class picard.reference.ExtractSequences
- extractSimpleChimera(SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- ExtractSVEvidenceSpark - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
(Internal) Extracts evidence of structural variations from reads
- ExtractSVEvidenceSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.ExtractSVEvidenceSpark
- extractTarGz(Path) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Extracts the tar.gz file given by
tarGzFilePath. - extractTarGz(Path, Path) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Extracts the tar.gz file given by
tarGzFilePath. - extractTarGz(Path, Path, boolean) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Extracts the tar.gz file given by
tarGzFilePath. - ExtractVariantAnnotations - Class in org.broadinstitute.hellbender.tools.walkers.vqsr.scalable
-
Extracts site-level variant annotations, labels, and other metadata from a VCF file to HDF5 files.
- ExtractVariantAnnotations() - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations
- EXTREME_COUNT_FILTER_MAXIMUM_PERCENTILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
- EXTREME_COUNT_FILTER_MINIMUM_PERCENTILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
- EXTREME_COUNT_FILTER_PERCENTAGE_OF_SAMPLES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
- EXTREME_OUTLIER_TRUNCATION_PERCENTILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormals
- EXTREME_SAMPLE_MEDIAN_PERCENTILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormals
F
- F - Static variable in class picard.sam.markduplicates.util.ReadEnds
- F_SCORE_BETA_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- F1F2 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
- F1R2 - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ReadOrientation
- F1R2 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
- F1R2_A - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- F1R2_C - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- F1R2_G - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- F1R2_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- F1R2_T - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- F1R2_TAR_GZ_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- f1r2Args - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- F1R2CountsCollector - Class in org.broadinstitute.hellbender.tools.walkers.readorientation
- F1R2CountsCollector(CollectF1R2CountsArgumentCollection, SAMFileHeader, File, Collection<String>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2CountsCollector
- F1R2FilterConstants - Class in org.broadinstitute.hellbender.tools.walkers.readorientation
-
Created by tsato on 3/14/18.
- F1R2FilterConstants() - Constructor for class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterConstants
- F1R2FilterUtils - Class in org.broadinstitute.hellbender.tools.walkers.readorientation
- F1R2FilterUtils() - Constructor for class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterUtils
- f1r2TarGz - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- F2R1 - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ReadOrientation
- F2R1 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
- F2R1_A - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- F2R1_C - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- F2R1_G - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- F2R1_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- F2R1_T - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- FAIL - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- FAIL_REF - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- FAILED - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult.Status
-
Something went wrong, and we couldn't produce a meaningful graph
- failMissingValues - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
-
By default, if JEXL cannot evaluate your expression for a particular record because one of the annotations is not present, the whole expression evaluates as PASSing.
- FailsStrictValidation(String, ValidateVariants.ValidationType, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.FailsStrictValidation
- failsVendorQualityCheck() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- failsVendorQualityCheck() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- FAKE_FILES - Variable in class picard.illumina.CheckIlluminaDirectory
- fakeBciFile(File, List<Integer>) - Method in class picard.illumina.parser.fakers.BciFileFaker
- fakeBciFile(File, TileIndex) - Method in class picard.illumina.parser.fakers.BclIndexFaker
- fakeFile(File, int, int, String) - Method in class picard.illumina.parser.fakers.FileFaker
- fakeFile(File, Integer) - Method in class picard.illumina.parser.fakers.FileFaker
- fakeFile(File, List<Integer>, int, String) - Method in class picard.illumina.parser.fakers.FileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BciFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BclFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BclIndexFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.ClocsFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.FileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.FilterFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.LocsFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.PosFileFaker
- fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.MultiTileBclFileUtil
- fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.MultiTileFileUtil
- fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Given the expected tiles/expected cycles for this file type create a set of fake files such that the verification criteria are met.
- fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.PerTileFileUtil
- fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
- fakeMultiTileBclFile(File, TileIndex) - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
- faker - Variable in class picard.illumina.parser.ParameterizedFileUtil
- FALSE - Enum constant in enum class org.broadinstitute.hellbender.utils.Trilean
- FALSE_DISCOVERY_RATE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ThresholdCalculator.Strategy
- FALSE_DISCOVERY_RATE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- FALSE_NEGATIVE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceState
- FALSE_POSITIVE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceState
- falseNegative(VariantContext) - Static method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval
- falsePositive(VariantContext) - Static method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval
- FalsePositiveRecord - Class in org.broadinstitute.hellbender.tools.walkers.validation
-
Created by tsato on 2/14/17.
- FalsePositiveRecord(String, long, long, long) - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord
- falseSnpCompensation - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- Family - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies the eval RODs by each family in the eval ROD, as described by the pedigree.
- Family(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Family
- FAMILY_ID - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.PedReader.Field
- FAMILY_ID - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The family ID assigned to the trio for which these metrics are calculated.
- FamilyLikelihoods - Class in org.broadinstitute.hellbender.tools.walkers.variantutils
-
Utility to compute genotype posteriors given family priors.
- FamilyLikelihoods(SampleDB, double, Set<String>, Map<String, Set<Sample>>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.variantutils.FamilyLikelihoods
- FAST_MODE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- FastaAlternateReferenceMaker - Class in org.broadinstitute.hellbender.tools.walkers.fasta
-
Generate an alternative reference sequence over the specified interval
- FastaAlternateReferenceMaker() - Constructor for class org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker
- fastaFile - Variable in class org.broadinstitute.hellbender.tools.LocalAssembler
- FastaReferenceMaker - Class in org.broadinstitute.hellbender.tools.walkers.fasta
-
Create a subset of a FASTA reference sequence
- FastaReferenceMaker() - Constructor for class org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker
- fastBernoulliEntropy(double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Computes the entropy -p*ln(p) - (1-p)*ln(1-p) of a Bernoulli distribution with success probability p using an extremely fast Pade approximation that is very accurate for all values of 0 <= p <= 1.
- fastCalculateDiploidBasedOnGLs(GenotypingLikelihoods<Allele>, int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator
-
Identical to AlleleFrequencyCalculator but does not require VariantContext, and assumes only a single alternative allele.
- FASTEST_AVAILABLE - Enum constant in enum class org.broadinstitute.hellbender.utils.pairhmm.PairHMM.Implementation
- FASTEST_AVAILABLE - Enum constant in enum class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner.Implementation
-
use the fastest available Smith-Waterman aligner that runs on your hardware
- FASTQ - Variable in class picard.sam.FastqToSam
- FASTQ - Variable in class picard.sam.SamToFastq
- FASTQ2 - Variable in class picard.sam.FastqToSam
- fastqDir - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- FastqRead(GATKRead) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead
- FastqRead(GATKRead, boolean) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead
- FastqToSam - Class in picard.sam
-
Converts a FASTQ file to an unaligned BAM or SAM file.
- FastqToSam() - Constructor for class picard.sam.FastqToSam
- fastRound(double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- FastWgsMetricsCollector - Class in picard.analysis
-
Class represents fast algorithm for collecting data from
AbstractLocusInfowith a list of alignedEdgingRecordAndOffsetobjects. - FastWgsMetricsCollector(CollectWgsMetrics, int, IntervalList) - Constructor for class picard.analysis.FastWgsMetricsCollector
-
Creates a collector and initializes the inner data structures
- FATHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The ID of the father within the trio.
- fbargs - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper
- fbargs - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- fbargs - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- fbargs - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- FDR - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- FDR_METADATA_TAG - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterStats
- fdrToTiTv(double, double) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager
- FEATURE_ARGUMENT_TAG_DELIMITER - Static variable in class org.broadinstitute.hellbender.engine.FeatureInput
-
Delimiter between the logical name and the file name in the --argument_name logical_name:feature_file syntax
- FEATURE_CACHE_LOOKAHEAD - Static variable in class org.broadinstitute.hellbender.engine.ReadWalker
-
This number controls the size of the cache for our FeatureInputs (specifically, the number of additional bases worth of overlapping records to cache when querying feature sources).
- FEATURE_CACHE_LOOKAHEAD - Static variable in class org.broadinstitute.hellbender.engine.spark.ReadWalkerSpark
-
This number controls the size of the cache for our FeatureInputs (specifically, the number of additional bases worth of overlapping records to cache when querying feature sources).
- FEATURE_CACHE_LOOKAHEAD - Static variable in class org.broadinstitute.hellbender.engine.spark.VariantWalkerSpark
-
This number controls the size of the cache for our primary and auxiliary FeatureInputs (specifically, the number of additional bases worth of overlapping records to cache when querying feature sources).
- FEATURE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- FEATURE_QUERY_LOOKAHEAD - Static variable in class org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervals
- FEATURE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- FeatureContext - Class in org.broadinstitute.hellbender.engine
-
Wrapper around FeatureManager that presents Feature data from a particular interval to a client tool without improperly exposing engine internals.
- FeatureContext() - Constructor for class org.broadinstitute.hellbender.engine.FeatureContext
-
Creates an empty FeatureContext with no backing data source.
- FeatureContext(FeatureContext, SimpleInterval) - Constructor for class org.broadinstitute.hellbender.engine.FeatureContext
-
Creates a new FeatureContext given a FeatureContext and a query interval.
- FeatureContext(FeatureManager, SimpleInterval) - Constructor for class org.broadinstitute.hellbender.engine.FeatureContext
-
Creates a new FeatureContext given a FeatureManager and a query interval.
- FeatureDataSource<T extends htsjdk.tribble.Feature> - Class in org.broadinstitute.hellbender.engine
-
Enables traversals and queries over sources of Features, which are metadata associated with a location on the genome in a format supported by our file parsing framework, Tribble.
- FeatureDataSource(File) - Constructor for class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Creates a FeatureDataSource backed by the provided File.
- FeatureDataSource(File, String) - Constructor for class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Creates a FeatureDataSource backed by the provided File and assigns this data source the specified logical name.
- FeatureDataSource(File, String, int) - Constructor for class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Creates a FeatureDataSource backed by the provided File and assigns this data source the specified logical name.
- FeatureDataSource(String) - Constructor for class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Creates a FeatureDataSource backed by the provided path.
- FeatureDataSource(String, String, int, Class<? extends Feature>) - Constructor for class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Creates a FeatureDataSource backed by the resource at the provided path.
- FeatureDataSource(String, String, int, Class<? extends Feature>, int, int) - Constructor for class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Creates a FeatureDataSource backed by the resource at the provided path.
- FeatureDataSource(FeatureInput<T>, int, Class<? extends Feature>) - Constructor for class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Creates a FeatureDataSource backed by the provided FeatureInput.
- FeatureDataSource(FeatureInput<T>, int, Class<? extends Feature>, int, int) - Constructor for class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Creates a FeatureDataSource backed by the provided FeatureInput.
- FeatureDataSource(FeatureInput<T>, int, Class<? extends Feature>, int, int, Path) - Constructor for class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Creates a FeatureDataSource backed by the provided FeatureInput.
- FeatureDataSource(FeatureInput<T>, int, Class<? extends Feature>, int, int, Path, boolean) - Constructor for class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Creates a FeatureDataSource backed by the provided FeatureInput.
- FeatureDataSource(FeatureInput<T>, int, Class<? extends Feature>, int, int, GenomicsDBOptions) - Constructor for class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Creates a FeatureDataSource backed by the provided FeatureInput.
- FeatureDataSource(FeatureInput<T>, int, Class<? extends Feature>, int, int, GenomicsDBOptions, boolean) - Constructor for class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Creates a FeatureDataSource backed by the provided FeatureInput.
- featureFiles - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalFeatureInputArgumentCollection
- featureFiles - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredFeatureInputArgumentCollection
- featureFileToIntervals(GenomeLocParser, String) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Converts a Feature-containing file to a list of intervals
- FeatureInput<T extends htsjdk.tribble.Feature> - Class in org.broadinstitute.hellbender.engine
-
Class to represent a Feature-containing input file.
- FeatureInput(String, String, Map<String, String>) - Constructor for class org.broadinstitute.hellbender.engine.FeatureInput
-
Construct a FeatureInput from raw components: name, key value pairs and the file.
- FeatureInput(GATKPath) - Constructor for class org.broadinstitute.hellbender.engine.FeatureInput
-
Construct a FeatureInput from a GATKPath argument value.
- FeatureInput(GATKPath, String) - Constructor for class org.broadinstitute.hellbender.engine.FeatureInput
-
Construct a FeatureInput from a GATKPath argument value.
- FeatureManager - Class in org.broadinstitute.hellbender.engine
-
Handles discovery of available codecs and Feature arguments, file format detection and codec selection, and creation/management/querying of FeatureDataSources for each source of Features.
- FeatureManager(CommandLineProgram) - Constructor for class org.broadinstitute.hellbender.engine.FeatureManager
-
Create a FeatureManager given a CommandLineProgram tool instance, discovering all FeatureInput arguments in the tool and creating query-able FeatureDataSources for them.
- FeatureManager(CommandLineProgram, int) - Constructor for class org.broadinstitute.hellbender.engine.FeatureManager
-
Create a FeatureManager given a CommandLineProgram tool instance, discovering all FeatureInput arguments in the tool and creating query-able FeatureDataSources for them.
- FeatureManager(CommandLineProgram, int, int, int) - Constructor for class org.broadinstitute.hellbender.engine.FeatureManager
-
Create a FeatureManager given a CommandLineProgram tool instance, discovering all FeatureInput arguments in the tool and creating query-able FeatureDataSources for them.
- FeatureManager(CommandLineProgram, int, int, int, GenomicsDBOptions) - Constructor for class org.broadinstitute.hellbender.engine.FeatureManager
-
Create a FeatureManager given a CommandLineProgram tool instance, discovering all FeatureInput arguments in the tool and creating query-able FeatureDataSources for them.
- FeatureMapper - Interface in org.broadinstitute.hellbender.tools.walkers.featuremapping
- featureOrderNumber - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
-
The relative order of this Feature.
- FeatureOutputCodec<F extends htsjdk.tribble.Feature,
S extends FeatureSink<F>> - Interface in org.broadinstitute.hellbender.utils.codecs -
A FeatureOutputCodec can encode Features into some type of FeatureSink.
- FeatureOutputCodecFinder - Class in org.broadinstitute.hellbender.utils.codecs
-
This class knows about all FeatureOutputCodec implementations, and allows you to find an appropriate codec to create a given file type.
- FeatureOutputCodecFinder() - Constructor for class org.broadinstitute.hellbender.utils.codecs.FeatureOutputCodecFinder
- FeatureOutputStream<F extends htsjdk.tribble.Feature> - Class in org.broadinstitute.hellbender.utils.io
-
Class for output streams that encode Tribble
Features. - FeatureOutputStream(GATKPath, TabixFormat, Function<F, String>, SAMSequenceDictionary, int) - Constructor for class org.broadinstitute.hellbender.utils.io.FeatureOutputStream
- featurePath - Variable in class org.broadinstitute.hellbender.tools.IndexFeatureFile
- features - Variable in class org.broadinstitute.hellbender.engine.GATKTool
-
Our source of Feature data (null if no source of Features was provided)
- features - Variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- FEATURES_PER_READ - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.FeaturizedReadSets
- featuresFile - Variable in class org.broadinstitute.hellbender.tools.examples.ExampleFeatureWalker
- FeatureSink<F extends htsjdk.tribble.Feature> - Interface in org.broadinstitute.hellbender.utils.codecs
- featureType - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
-
Type of this feature.
- FeatureWalker<F extends htsjdk.tribble.Feature> - Class in org.broadinstitute.hellbender.engine
-
A FeatureWalker is a tool that processes a
Featureat a time from a source of Features, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features. - FeatureWalker() - Constructor for class org.broadinstitute.hellbender.engine.FeatureWalker
- FEATURIZED_READ_SETS_COUNTS_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- FEATURIZED_READ_SETS_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- FeaturizedReadSets - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
For each sample and for each allele a list feature vectors of supporting reads In order to reduce the number of delimiter characters, we flatten featurized reads.
- FeaturizedReadSets() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.FeaturizedReadSets
- FeaturizedReadSets(int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.FeaturizedReadSets
- Female - Enum constant in enum class picard.pedigree.Sex
- FEMALE - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.Sex
- FEMALE_CHROMS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- FermiLiteAssemblyHandler - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
LocalAssemblyHandler that uses FermiLite.
- FermiLiteAssemblyHandler(String, int, String, boolean, boolean, boolean, boolean, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.FermiLiteAssemblyHandler
- FF - Static variable in class picard.sam.markduplicates.util.ReadEnds
- FGBIO_MI_TAG_DELIMITER - Static variable in class org.broadinstitute.hellbender.tools.walkers.consensus.ReadsWithSameUMI
- FIELD_DELIMITER - Static variable in class org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer
-
The delimiter for each field within the VCF Funcotation field.
- FieldName_Annotation_Transcript - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_BAM_File - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_CCLE_ONCOMAP_overlapping_mutations - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_CCLE_ONCOMAP_total_mutations_in_gene - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_cDNA_Change - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Center - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_CGC_Mutation_Type - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_CGC_Other_Diseases - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_CGC_Translocation_Partner - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_CGC_Tumor_Types_Germline - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_CGC_Tumor_Types_Somatic - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Chromosome - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Codon_Change - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_COSMIC_fusion_genes - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_COSMIC_overlapping_mutations - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_COSMIC_tissue_types_affected - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_COSMIC_total_alterations_in_gene - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_dbSNP_RS - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_dbSNP_Val_Status - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Description - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_DNARepairGenes_Activity_linked_to_OMIM - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_DrugBank - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_End_Position - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Entrez_Gene_Id - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_FamilialCancerDatabase_Syndromes - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_gc_content - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Genome_Change - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_GO_Biological_Process - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_GO_Cellular_Component - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_GO_Molecular_Function - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Hugo_Symbol - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Match_Norm_Seq_Allele1 - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Match_Norm_Seq_Allele2 - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Match_Norm_Validation_Allele1 - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Match_Norm_Validation_Allele2 - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Matched_Norm_Sample_Barcode - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Matched_Norm_Sample_UUID - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Mutation_Status - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_MUTSIG_Published_Results - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_n_alt_count - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_n_ref_count - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_NCBI_Build - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_OREGANNO_ID - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_OREGANNO_Values - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Other_Transcripts - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Protein_Change - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_ref_context - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Reference_Allele - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Refseq_mRNA_Id - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Refseq_prot_Id - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Score - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Sequence_Source - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Sequencer - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Sequencing_Phase - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Start_Position - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Strand - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_SwissProt_acc_Id - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_SwissProt_entry_Id - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_t_alt_count - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_t_ref_count - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_TCGAscape_Amplification_Peaks - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_TCGAscape_Deletion_Peaks - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Transcript_Exon - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Transcript_Position - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Transcript_Strand - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_tumor_f - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Tumor_Sample_Barcode - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Tumor_Sample_UUID - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Tumor_Seq_Allele1 - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Tumor_Seq_Allele2 - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Tumor_Validation_Allele1 - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Tumor_Validation_Allele2 - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Tumorscape_Amplification_Peaks - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Tumorscape_Deletion_Peaks - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_UniProt_AApos - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_UniProt_Experimental_Info - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_UniProt_Natural_Variations - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_UniProt_Region - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_UniProt_Site - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Validation_Method - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Validation_Status - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Variant_Classification - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Variant_Type - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- FieldName_Verification_Status - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- fields - Variable in class org.broadinstitute.hellbender.utils.bigquery.TableReference
- FIELDS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.HtsgetReader
- fieldsToTake - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTable
-
Any standard VCF column (CHROM, ID, QUAL) or any annotation name in the INFO field (e.g., -F AC) to include in the output table.
- FifoBuffer - Class in picard.util
-
Summary
- FifoBuffer() - Constructor for class picard.util.FifoBuffer
-
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their start/end information logged is often undesirable.
- FifoBuffer(InputStream, PrintStream) - Constructor for class picard.util.FifoBuffer
-
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their start/end information logged is often undesirable.
- file - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase
- File - Enum constant in enum class org.broadinstitute.hellbender.utils.runtime.StreamLocation
- FILE - Enum constant in enum class picard.fingerprint.CrosscheckMetric.DataType
- FILE_EXT - Static variable in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- FILE_EXTENSION - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- FILE_EXTENSION - Variable in class picard.analysis.CollectMultipleMetrics
- FILE_EXTENSION - Static variable in class picard.arrays.CreateBafRegressMetricsFile
- FILE_EXTENSION - Static variable in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
- FILE_EXTENSION - Variable in class picard.illumina.CollectIlluminaLaneMetrics
- FILE_NAME_PATTERN - Static variable in class picard.illumina.parser.BaseIlluminaDataProvider
- FILE_POINTER_OFFSET - Static variable in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream
- FILE_PREFIX - Static variable in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
- fileExists(String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Returns true if we can read the first byte of the file.
- FileFaker - Class in picard.illumina.parser.fakers
- FileFaker() - Constructor for class picard.illumina.parser.fakers.FileFaker
- filesAvailable() - Method in class picard.illumina.parser.MultiTileBclFileUtil
- filesAvailable() - Method in class picard.illumina.parser.MultiTileFileUtil
- filesAvailable() - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Determine whether or not files are available
- filesAvailable() - Method in class picard.illumina.parser.PerTileFileUtil
- filesAvailable() - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
- filesAvailable() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
- fileSize(String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Returns the file size of a file pointed to by a GCS/HDFS/local path
- fileToPath(File) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Convert File to Path, returning null if input was null.
- fileToTile(String) - Static method in class picard.illumina.parser.BaseIlluminaDataProvider
- fileToTile(String) - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Returns only lane and tile information as PerTileFt's do not have End information.
- fill(String) - Method in class org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter.LineBuilder
-
Fills in every empty column of the pending line with the provided value
- FILL_POOLS - Variable in class picard.util.BaitDesigner
- fillIdx - Variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
- FILLING_VALUE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- fillingValue - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- fillQualsFromLikelihood(VariantContext, AlleleLikelihoods<GATKRead, Allele>, List<Double>, List<Double>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RankSumTest
- fillSoftclippedReads - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- fillTrimmedReads - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- fillTrimmedReadsQ - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- fillTrimmedReadsZ - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- fillWithRandomBases(byte[], int, int) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
-
Fill an array section with random bases.
- filter(VariantContext) - Method in class picard.vcf.filter.AlleleBalanceFilter
- filter(VariantContext) - Method in class picard.vcf.filter.FisherStrandFilter
- filter(VariantContext) - Method in class picard.vcf.filter.QdFilter
- filter(VariantContext) - Method in interface picard.vcf.filter.VariantFilter
-
Check to see if the VariantContext should have a filter applied to it.
- filter(VariantContext, Genotype) - Method in class picard.vcf.filter.DepthFilter
- filter(VariantContext, Genotype) - Method in interface picard.vcf.filter.GenotypeFilter
-
Test whether or not the genotype should be filtered out.
- filter(VariantContext, Genotype) - Method in class picard.vcf.filter.GenotypeQualityFilter
- filter(IntPredicate) - Method in class org.broadinstitute.hellbender.utils.IndexRange
-
Find the elements of this range for which an int -> boolean predicate is true
- Filter - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies by the FILTER status (PASS, FAIL) of the eval records
- Filter - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- Filter(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Filter
- FILTER - Variable in class picard.sam.FilterSamReads
- FILTER_ALLELES - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- FILTER_ALLELES_DEBUG_GRAPH - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- FILTER_ALLELES_FILTER_LONE_ALLELES - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- FILTER_ALLELES_QUAL_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- FILTER_ALLELES_SOR_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- FILTER_ANALYSIS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- FILTER_BWA_IMAGE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- FILTER_BWA_SEED_LENGTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- FILTER_CANNOT_LIFTOVER_REV_COMP - Static variable in class picard.vcf.LiftoverVcf
-
Filter name to use when a target cannot be lifted over.
- FILTER_DELIMITER - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsConstants
-
Delimiting string to place between values in the "CLINSIG" INFO field when Funcotations for a variant match multiple filters.
- FILTER_DUPLICATES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- FILTER_ENTRY_SEPARATOR - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadGroupBlackListReadFilter
- FILTER_EXPRESSION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- FILTER_INDEL_STRADDLES_TWO_INTERVALS - Static variable in class picard.vcf.LiftoverVcf
-
Filter name to use when an indel cannot be lifted over since it straddles two intervals in a chain which means that it is unclear what are the right alleles to be used.
- FILTER_METRICS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- FILTER_MISMATCHING_REF_ALLELE - Static variable in class picard.vcf.LiftoverVcf
-
Filter name to use when a target is lifted over, but the reference allele doesn't match the new reference.
- FILTER_NAME - Static variable in class picard.vcf.filter.QdFilter
- FILTER_NAME_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- FILTER_NO_TARGET - Static variable in class picard.vcf.LiftoverVcf
-
Filter name to use when a target cannot be lifted over.
- FILTER_NOT_IN_MASK_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- FILTER_READS_PER_PARTITION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- FILTER_TOO_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- FILTER_UNPAIRED_READS - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- FilterAlignmentArtifacts - Class in org.broadinstitute.hellbender.tools.walkers.realignmentfilter
-
Filter false positive alignment artifacts from a VCF callset.
- FilterAlignmentArtifacts() - Constructor for class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- filterAlleles - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- filterAlleles(AlleleLikelihoods<GATKRead, Haplotype>, int, Set<Integer>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleFiltering
-
Finds alleles that are likely not contributing much to explaining the data and remove the haplotypes that contribute them.
- filterAnalysis - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- FilterAnalysisRecord - Class in org.broadinstitute.hellbender.tools.walkers.validation
- FilterAnalysisRecord(String, int, int, int, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
- filterAndConvertToAlignedContigDirect(Iterable<AlignedAssemblyOrExcuse>, List<String>, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser
-
Filter out "failed" assemblies, unmapped and secondary (i.e.
- filterAndConvertToAlignedContigViaSAM(List<AlignedAssemblyOrExcuse>, SAMFileHeader, JavaSparkContext) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser
-
Filters out "failed" assemblies, unmapped and secondary (i.e.
- FilterApplyingVariantIterator - Class in picard.vcf.filter
-
Iterator that dynamically applies filter strings to VariantContext records supplied by an underlying iterator.
- FilterApplyingVariantIterator(Iterator<VariantContext>, Collection<VariantFilter>, Collection<GenotypeFilter>) - Constructor for class picard.vcf.filter.FilterApplyingVariantIterator
-
Constructs an iterator from an underlying iterator and the provided (possibly empty) collections of variant and genotype filters.
- filterArgs - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSpark
- filterArgs - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark
- filterCollectionByExpressions(Collection<String>, Collection<String>, boolean) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Given a collection of strings and a collection of regular expressions, generates the set of strings that match any expression
- filterDuplicates - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
-
If true, then for any two reads with identical sequences (or identical to the other's reverse complement), one will be filtered.
- FILTERED_FALSE_NEGATIVE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceState
- FILTERED_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of indels that are filtered
- FILTERED_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of SNPs that are filtered
- FILTERED_TRUE_NEGATIVE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceState
- FILTERED_TRUE_NEGATIVES_AND_FALSE_NEGATIVES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- FILTERED_TRUE_NEGATIVES_AND_FALSE_NEGATIVES_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- filteredCount - Variable in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter
- filteredCount - Variable in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter
- filteredEvidenceBySampleIndex - Variable in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Evidence disqualified by .
- filteredFalseNegative(VariantContext, VariantContext) - Static method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval
- FilteredHaplotypeFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- FilteredHaplotypeFilter(double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteredHaplotypeFilter
- filteredSampleEvidence(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Returns the units of evidence that have been removed by PairHMM error score filtering (and intentially not evidence filtered by any other mechanism).
- filteredTrueNegative(VariantContext) - Static method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval
- filteredTrueNegativesAndFalseNegativesVcf - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- filterExpressions - Variable in class org.broadinstitute.hellbender.engine.filters.JexlExpressionReadTagValueFilter
- filterExpressions - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
-
VariantFiltration accepts any number of JEXL expressions (so you can have two named filters by using --filter-name One --filter-expression "X < 1" --filter-name Two --filter-expression "X > 2").
- FilterFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- FilterFileFaker() - Constructor for class picard.illumina.parser.fakers.FilterFileFaker
- FilterFileReader - Class in picard.illumina.parser.readers
-
Illumina uses an algorithm described in "Theory of RTA" that determines whether or not a cluster passes filter("PF") or not.
- FilterFileReader(File) - Constructor for class picard.illumina.parser.readers.FilterFileReader
- filterForConsistency(List<VariantContext>, Map<String, SegmentedCpxVariantSimpleVariantExtractor.RelevantAttributes>, BasicReference) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor
- FilterFuncotations - Class in org.broadinstitute.hellbender.tools.funcotator
-
Filter variants based on clinically-significant Funcotations.
- FilterFuncotations() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations
- FilterFuncotations.AlleleFrequencyDataSource - Enum Class in org.broadinstitute.hellbender.tools.funcotator
-
The allele frequency data source that was used when Funcotating the input VCF.
- FilterFuncotations.Reference - Enum Class in org.broadinstitute.hellbender.tools.funcotator
-
The version of the Human Genome reference which was used when Funcotating the input VCF.
- FilterFuncotationsConstants - Class in org.broadinstitute.hellbender.tools.funcotator
- FilterFuncotationsConstants() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsConstants
- FilterFuncotationsUtils - Class in org.broadinstitute.hellbender.tools.funcotator
- FilterFuncotationsUtils() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsUtils
- FILTERING_STATS_EXTENSION - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls
- FILTERING_STATS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls
- FILTERING_STATUS_VCF_KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls
- filteringKmerSize - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- FilteringOutputStats - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
-
Helper class used on the final pass of
FilterMutectCallsto record total expected true positives, false positives, and false negatives, as well as false positives and false negatives attributable to each filter - FilteringOutputStats(List<Mutect2Filter>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteringOutputStats
- FilterIntervals - Class in org.broadinstitute.hellbender.tools.copynumber
-
Given specified intervals, annotated intervals output by
AnnotateIntervals, and/or counts output byCollectReadCounts, outputs a filtered Picard interval list. - FilterIntervals() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
- filterLoneAlleles - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- filterMergedVariantList(List<VariantContext>, StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.AnnotatedVariantProducer
-
Apply filters (that implements
StructuralVariantFilter) given list of variants, and write the variants to a single VCF file. - filterMetricsFileUri - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
-
If specified, records the number of reads remaining after each of the following steps: Pre-aligned host read filtering Low-quality and low-complexity sequence filtering Host read subtraction Read deduplication
- FilterMutectCalls - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
-
Filter variants in a Mutect2 VCF callset.
- FilterMutectCalls() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.BaseQualityFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ClusteredEventsFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ContaminationFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.DuplicatedAltReadFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteredHaplotypeFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FragmentLengthFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.GermlineFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MappingQualityFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MinAlleleFractionFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MTLowHeteroplasmyFilterTool
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MultiallelicFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2Filter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NormalArtifactFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NRatioFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NuMTFilterTool
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.PanelOfNormalsFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.PolymeraseSlippageFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadOrientationFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadPositionFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrictStrandBiasFilter
- filterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.TumorEvidenceFilter
- filterNames - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
-
This name is put in the FILTER field for variants that get filtered.
- filterNonPassingReads(AssemblyRegion) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- filterOut(SAMRecord) - Method in class picard.filter.CountingFilter
- filterOut(SAMRecord, SAMRecord) - Method in class picard.filter.CountingFilter
- filterPoorlyModeledEvidence(ToDoubleFunction<EVIDENCE>) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Removes those read that the best possible likelihood given any allele is just too low.
- filterPoorlyModeledEvidence(AlleleLikelihoods<GATKRead, Haplotype>, boolean, double, double) - Method in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
-
Static methods related to read disqualification to be used by implementing classes of this interface
- filterReadsPerPartition - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
-
This is a parameter for fine-tuning memory performance.
- filterRecordsNotInMask - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
-
By default, if the --mask argument is used, any variant falling in a mask will be filtered.
- filterReferenceConfidenceAnnotations(Collection<Annotation>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
-
Common method to use in order to remove unwanted annotations from the list returned by the plugin specifically for reference confidence mode.
- FilterSamReads - Class in picard.sam
-
Summary
- FilterSamReads() - Constructor for class picard.sam.FilterSamReads
- FilterSamReads.Filter - Enum Class in picard.sam
- FilterStats - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- FilterStats(String, double, double, double, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterStats
- filterSuspectSites() - Method in class picard.fingerprint.Fingerprint
-
Attempts to filter out haplotypes that may have suspect genotyping by removing haplotypes that reach a minimum confidence score yet have a significant fraction of observations from a third or fourth allele.
- filterToMaxNumberOfAltAllelesBasedOnScores(int, List<Allele>, double[]) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
- FilterType - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies by the FILTER type(s) for each line, with PASS used for passing
- FilterType(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.FilterType
- FilterVariantTranches - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
-
Apply tranche filtering to VCF based on scores from an annotation in the INFO field.
- FilterVariantTranches() - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.FilterVariantTranches
- FilterVcf - Class in picard.vcf.filter
-
Applies a set of hard filters to Variants and to Genotypes within a VCF.
- FilterVcf() - Constructor for class picard.vcf.filter.FilterVcf
-
Constructor to default to having index creation on.
- FINAL_FIT_FILE_TAG - Static variable in class org.broadinstitute.hellbender.tools.copynumber.ModelSegments
- FINAL_PAIRED_READS - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterMetrics
-
The number of non-host reads that have mates
- FINAL_TOTAL_READS - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterMetrics
-
The number of non-host reads in total
- FINAL_UNPAIRED_READS - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterMetrics
-
The number of non-host unpaired reads
- finalize() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase
- finalizeAndWriteMetrics(LibraryIdGenerator, MetricsFile<DuplicationMetrics, Double>, File) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
Writes the metrics given by the libraryIdGenerator to the outputFile.
- finalizeAnnotations(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
-
Finalize reducible annotations (those that use raw data in gVCFs)
- finalizeData() - Method in class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
-
Finalize, if appropriate, all derived data in recalibrationTables.
- finalizeEvaluation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap
- finalizeEvaluation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- finalizeEvaluation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelLengthHistogram
- finalizeEvaluation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- finalizeEvaluation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- finalizeEvaluation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ThetaVariantEvaluator
- finalizeEvaluation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator
- finalizeEvaluation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- finalizeEvaluation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantAFEvaluator
- finalizeEvaluation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
- finalizeEvaluation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- finalizeGenotype(VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyperEngine
- finalizeGenotype(VariantContext, VariantContextBuilder) - Method in class org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyperEngine
-
Calculates final annotation value for VC and calls genotypes, if necessary
- finalizeMetrics(Map<String, BarcodeMetric>, BarcodeMetric) - Static method in class picard.illumina.ExtractBarcodesProgram
- finalizeRawData(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth
-
Uses the "AS_QUAL" key, which must be computed by the genotyping engine in GenotypeGVCFs, to calculate the final AS_QD annotation on the read.
- finalizeRawData(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
-
Parses the raw data histograms generated for each allele and outputs the median value for each histogram as a representative double value.
- finalizeRawData(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality
-
Takes combined raw annotation data sums, and calculates per allele the average root mean squared from the raw data using expected Allele Depth counts data.
- finalizeRawData(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
-
Parses the raw data stings of combined contingency matrix data and calls client methods calculateReducedData(myData) implementation to generate double digest of provided allele information which is stored in '|' delineated lists.
- finalizeRawData(VariantContext, VariantContext) - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation
-
Calculate the final annotation value from the raw data which was generated by either annotateRawData or calculateRawData
- finalizeRawData(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet
-
Calculate the final annotation value from the raw data which was generated by either annotateRawData or calculateRawData
- finalizeRawData(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RawGtCount
- finalizeRawData(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
- finalizeRawGVCFVarDPValues(String, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth
- finalizeRawMQ(VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
-
converts
GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEYintoVCFConstants.RMS_MAPPING_QUALITY_KEYannotation if present NOTE: this is currently only used by HaplotypeCaller in VCF mode and GnarlyGenotyper - finalizeRecalibrationTables(RecalibrationTables) - Static method in class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
-
Finalize, if appropriate, all derived data in recalibrationTables.
- finalizeRegion(AssemblyRegion, boolean, boolean, byte, SAMFileHeader, SampleList, boolean, boolean, boolean, FlowBasedArgumentCollection, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- finalizeReport(File) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- finalPos - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator
- find(long, LocalAssembler.KmerSet<LocalAssembler.KmerAdjacency>) - Static method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- find(Object) - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
-
find an entry equivalent to the key, or return null
- find(GATKPath) - Static method in class org.broadinstitute.hellbender.utils.codecs.FeatureOutputCodecFinder
- find(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Find an interval.
- FIND_SNPS_ONLY - Enum constant in enum class org.broadinstitute.hellbender.tools.reference.CompareReferences.BaseComparisonMode
- findAdapterPairAndIndexForSingleRead(byte[], int) - Method in class picard.util.AdapterMarker
-
Return the adapter to be trimmed from a read represented as an array of bytes[]
- findAdapterPairAndIndexForSingleRead(byte[], int, double, int) - Method in class picard.util.AdapterMarker
-
Return the adapter to be trimmed from a read represented as an array of bytes[]
- findAdapterPairAndIndexForSingleRead(byte[], int, double, int, AdapterPair...) - Static method in class picard.util.ClippingUtility
-
Return the adapter to be trimmed from a read represented as an array of bytes[]
- findAndProcessHeaderLine() - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Process the first lines of the input source until the header line.
- FindAssemblyRegionsSpark - Class in org.broadinstitute.hellbender.engine.spark
-
Find assembly regions from reads in a distributed Spark setting.
- FindAssemblyRegionsSpark() - Constructor for class org.broadinstitute.hellbender.engine.spark.FindAssemblyRegionsSpark
- FindBadGenomicKmersSpark - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
Identifies sequences that occur at high frequency in a reference
- FindBadGenomicKmersSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBadGenomicKmersSpark
- findBestHaplotypes() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotypeFinder
- findBestHaplotypes(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.GraphBasedKBestHaplotypeFinder
-
Implement Dijkstra's algorithm as described in https://en.wikipedia.org/wiki/K_shortest_path_routing
- findBestHaplotypes(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
-
The primary engine for finding haplotypes based on junction trees.
- findBestHaplotypes(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotypeFinder
- FindBreakpointEvidenceSpark - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
(Internal) Produces local assemblies of genomic regions that may harbor structural variants
- FindBreakpointEvidenceSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark
- FindBreakpointEvidenceSpark.AssembledEvidenceResults - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- FindBreakpointEvidenceSpark.IntPair - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- FindBreakpointEvidenceSparkArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- findByIndex(int) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Find the nth interval in the tree.
- findByKey(int) - Static method in enum class picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
- findChangepoints(int, BiFunction<DATA, DATA, Double>, int, List<Integer>, double, double, KernelSegmenter.ChangepointSortOrder) - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.segmentation.KernelSegmenter
-
Returns a list of the indices of the changepoints, either sorted by decreasing change to the global segmentation cost or by increasing index order.
- findContig(List<LocalAssembler.Contig>, LocalAssembler.Contig) - Static method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- findEach(Object) - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
-
get an iterator over each of the elements equivalent to the key
- findFirstPositionWhereHaplotypesDiffer(byte[], byte[]) - Static method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
-
Compute the first position at which two haplotypes differ If the haplotypes are exact copies of each other, returns the min length of the two haplotypes.
- findFirstUsableFlowOrder(SAMFileHeader, FlowBasedArgumentCollection) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
-
Finds a usable FlowOrder to be used for engine calculation (when no specufic flow order already established for a specific read)
- findIndexOfClipSequence(byte[], byte[], int, double) - Static method in class picard.util.ClippingUtility
-
Finds the first index of the adapterSequence sequence in the read sequence requiring at least minMatch bases of pairwise alignment with a maximum number of errors dictated by maxErrorRate.
- findJointAlignments(List<List<BwaMemAlignment>>, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentEngine
-
Find all common alignments of a set of unitigs.
- findKmer(Kmer) - Method in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KmerSearchableGraph
-
Returns the vertex that represents or contains the last base of a given kmer.
- findKmer(Kmer) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
- findLeftClipping(int) - Method in class org.broadinstitute.hellbender.utils.haplotype.FlowBasedHaplotype
- findLeftClipping(int, int[], int[]) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- FindMendelianViolations - Class in picard.vcf.MendelianViolations
-
Summary
- FindMendelianViolations() - Constructor for class picard.vcf.MendelianViolations.FindMendelianViolations
- findNumberOfRepetitions(byte[], byte[], boolean) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Finds number of repetitions a string consists of.
- findNumberOfRepetitions(byte[], int, int, byte[], int, int, boolean) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Finds number of repetitions a string consists of.
- findOpticalDuplicates(List<? extends PhysicalLocation>, PhysicalLocation) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
-
Finds which reads within the list of duplicates that are likely to be optical/co-localized duplicates of one another.
- findOrAdd(long, LocalAssembler.KmerSet<LocalAssembler.KmerAdjacency>) - Static method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- findOrAdd(Object, Function<Object, T>) - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
-
find an entry equivalent to the key, or use producer to add a new value
- findPreferredFormat(IlluminaDataType, IlluminaFileUtil) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Given a data type find the most preferred file format even if files are not available
- findRepeatedSubstring(byte[]) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Find out if a string can be represented as a tandem number of substrings.
- findRightClipping(int) - Method in class org.broadinstitute.hellbender.utils.haplotype.FlowBasedHaplotype
- findRightClipping(int, int[], int[]) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- findSegmentation(int, double, double, double, int, List<Integer>, double, double) - Method in class org.broadinstitute.hellbender.tools.copynumber.segmentation.MultisampleMultidimensionalKernelSegmenter
-
Segments the internally held
CopyRatioCollectionandAllelicCountCollectionusing a separateKernelSegmenterfor each chromosome. - findSegmentation(int, double, int, List<Integer>, double, double) - Method in class org.broadinstitute.hellbender.tools.copynumber.segmentation.AlleleFractionKernelSegmenter
- findSegmentation(int, double, int, List<Integer>, double, double) - Method in class org.broadinstitute.hellbender.tools.copynumber.segmentation.CopyRatioKernelSegmenter
- findSegments(List<PileupSummary>) - Static method in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationSegmenter
-
Partition the genome into segments of allelic copy number state using kernel segmentation of likely hets.
- FindSNPsOnlyTableWriter(Path, TableColumnCollection) - Constructor for class org.broadinstitute.hellbender.tools.reference.CompareReferences.FindSNPsOnlyTableWriter
- findStart(AbstractReadThreadingGraph.SequenceForKmers) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Find vertex and its position in seqForKmers where we should start assembling seqForKmers
- findStartForJunctionThreading(AbstractReadThreadingGraph.SequenceForKmers) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
-
Find vertex and its position in seqForKmers where we should start assembling seqForKmers
- findTandemRepeatUnits(byte[], int) - Static method in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
- findTile(int) - Method in class picard.illumina.parser.TileIndex
- findTileMetricsFiles(File, int) - Static method in class picard.illumina.parser.TileMetricsUtil
-
Finds all of the tile metrics files for a given run directory and cycle count.
- findTranche(List<VariantDatum>, TrancheManager.SelectionMetric, double, VariantRecalibratorArgumentCollection.Mode) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager
- findTranches(List<VariantDatum>, List<Double>, TrancheManager.SelectionMetric, VariantRecalibratorArgumentCollection.Mode) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager
- findTranches(List<VariantDatum>, List<Double>, TrancheManager.SelectionMetric, VariantRecalibratorArgumentCollection.Mode, File) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager
- findUnmatchedTypes(Set<IlluminaDataType>, Map<IlluminaFileUtil.SupportedIlluminaFormat, Set<IlluminaDataType>>) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Given a set of formats to data types they provide, find any requested data types that do not have a format associated with them and return them
- findVQSLODTranche(List<VariantDatum>, TrancheManager.SelectionMetric, double, VariantRecalibratorArgumentCollection.Mode) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager
- findVQSLODTranches(List<VariantDatum>, List<Double>, TrancheManager.SelectionMetric, VariantRecalibratorArgumentCollection.Mode) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager
- Fingerprint - Class in picard.fingerprint
-
class to represent a genetic fingerprint as a set of HaplotypeProbabilities objects that give the relative probabilities of each of the possible haplotypes at a locus.
- Fingerprint(String, Path, String) - Constructor for class picard.fingerprint.Fingerprint
- FINGERPRINT_DETAIL_FILE_SUFFIX - Static variable in class picard.fingerprint.CheckFingerprint
- FINGERPRINT_GENDER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- FINGERPRINT_GENOTYPES_VCF_FILE - Variable in class picard.arrays.GtcToVcf
- FINGERPRINT_SUMMARY_FILE_SUFFIX - Static variable in class picard.fingerprint.CheckFingerprint
- FingerprintChecker - Class in picard.fingerprint
-
Major class that coordinates the activities involved in comparing genetic fingerprint data whether the source is from a genotyping platform or derived from sequence data.
- FingerprintChecker(File) - Constructor for class picard.fingerprint.FingerprintChecker
-
Creates a fingerprint checker that will work with the set of haplotypes stored in the supplied file.
- FingerprintChecker(HaplotypeMap) - Constructor for class picard.fingerprint.FingerprintChecker
-
Creates a fingerprint checker that will work with the set of haplotyped provided.
- fingerprintFiles(Collection<Path>, int, int, TimeUnit) - Method in class picard.fingerprint.FingerprintChecker
-
Deprecated.
- fingerprintFiles(Collection<Path>, Map<Path, Path>, Boolean, int, int, TimeUnit) - Method in class picard.fingerprint.FingerprintChecker
- FingerprintIdDetails - Class in picard.fingerprint
-
class to hold the details of a element of fingerprinting PU tag
- FingerprintIdDetails() - Constructor for class picard.fingerprint.FingerprintIdDetails
- FingerprintIdDetails(SAMReadGroupRecord, String) - Constructor for class picard.fingerprint.FingerprintIdDetails
- FingerprintIdDetails(String, String) - Constructor for class picard.fingerprint.FingerprintIdDetails
- FingerprintingDetailMetrics - Class in picard.analysis
-
Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.
- FingerprintingDetailMetrics() - Constructor for class picard.analysis.FingerprintingDetailMetrics
- FingerprintingSummaryMetrics - Class in picard.analysis
-
Summary fingerprinting metrics and statistics about the comparison of the sequence data from a single read group (lane or index within a lane) vs.
- FingerprintingSummaryMetrics() - Constructor for class picard.analysis.FingerprintingSummaryMetrics
- FingerprintMetrics - Class in picard.fingerprint
-
Class for holding metrics on a single fingerprint.
- FingerprintMetrics() - Constructor for class picard.fingerprint.FingerprintMetrics
- FingerprintResults - Class in picard.fingerprint
-
Class that is used to represent the results of comparing a read group within a SAM file, or a sample within a VCF against one or more set of fingerprint genotypes.
- FingerprintResults(Path, String, String) - Constructor for class picard.fingerprint.FingerprintResults
- fingerprintSamFile(Path, IntervalList) - Method in class picard.fingerprint.FingerprintChecker
-
Deprecated.
- fingerprintSamFile(Path, Path, boolean, Function<HaplotypeBlock, HaplotypeProbabilities>) - Method in class picard.fingerprint.FingerprintChecker
- fingerprintSamFile(Path, Function<HaplotypeBlock, HaplotypeProbabilities>) - Method in class picard.fingerprint.FingerprintChecker
-
Deprecated.
- FingerprintUtils - Class in picard.fingerprint
-
A set of utilities used in the fingerprinting environment
- FingerprintUtils() - Constructor for class picard.fingerprint.FingerprintUtils
- FingerprintUtils.VariantContextSet - Class in picard.fingerprint
-
A class that holds VariantContexts sorted by genomic position
- fingerprintVcf(Path) - Method in class picard.fingerprint.FingerprintChecker
-
Deprecated.
- fingerprintVcf(Path, Path, boolean) - Method in class picard.fingerprint.FingerprintChecker
- finish() - Method in class org.broadinstitute.hellbender.metrics.MultiLevelCollector
-
Call finish on all PerUnitMetricCollectors
- finish() - Method in class org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector
-
Call finish on all PerUnitMetricCollectors
- finish() - Method in class org.broadinstitute.hellbender.metrics.PerUnitInsertSizeMetricsCollector
- finish() - Method in interface org.broadinstitute.hellbender.metrics.PerUnitMetricCollector
-
When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
- finish() - Method in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
- finish() - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetrics
-
Complete any calculations/processing.
- finish() - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.PerUnitExampleMultiMetricsCollector
- finish() - Method in class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetrics
- finish() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
- finish() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- finish() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- finish() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
- finish() - Method in class picard.analysis.CollectBaseDistributionByCycle
- finish() - Method in class picard.analysis.CollectGcBiasMetrics
- finish() - Method in class picard.analysis.CollectInsertSizeMetrics
- finish() - Method in class picard.analysis.CollectQualityYieldMetrics
- finish() - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
- finish() - Method in class picard.analysis.CollectRnaSeqMetrics
- finish() - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
- finish() - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
- finish() - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
- finish() - Method in class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
- finish() - Method in class picard.analysis.MeanQualityByCycle
- finish() - Method in class picard.analysis.QualityScoreDistribution
- finish() - Method in class picard.analysis.SinglePassSamProgram
-
Should be implemented by subclasses to do one-time finalization work.
- finish() - Method in class picard.metrics.MultiLevelCollector
-
Call finish on all PerUnitMetricCollectors
- finish() - Method in interface picard.metrics.PerUnitMetricCollector
-
When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
- finish() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
- finish(MetricsFile<InsertSizeMetrics, Integer>, String) - Method in class org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollector
-
Finish the metrics collection by saving any results to a metrics file.
- first(int) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Instantiates the first genotype possible provided a total ploidy.
- FIRST - Enum constant in enum class picard.illumina.parser.TileTemplateRead
- FIRST - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
- FIRST_DOMINATES - Enum constant in enum class org.broadinstitute.hellbender.utils.MannWhitneyU.TestType
- FIRST_OF_PAIR - Enum constant in enum class picard.analysis.AlignmentSummaryMetrics.Category
- FIRST_OF_PAIR - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- FIRST_READ_TRANSCRIPTION_STRAND - Enum constant in enum class picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
- FIRST_TILE - Variable in class picard.illumina.IlluminaBasecallsToFastq
- FIRST_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
- FIRST_UNCERTAIN_FLOW_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- firstAlignmentIsTooShort(AlignmentInterval, AlignmentInterval, Integer) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.ContigChimericAlignmentIterativeInterpreter
- firstBase(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer
- firstBase(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
- firstBase(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
- firstIntervalFile - Variable in class org.broadinstitute.hellbender.tools.CompareIntervalLists
- FirstOfPairReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.FirstOfPairReadFilter
- firstPassApply(VariantContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ArHetvarFilter
- firstPassApply(VariantContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.TwoPassFuncotationFilter
- firstPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.TwoPassVariantWalker
- firstPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalker
- firstPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations
- firstPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MTLowHeteroplasmyFilterTool
- firstPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants
- firstPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.FilterVariantTranches
- firstTile(Integer) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures the first tile that the converter will begin processing at.
- firstTrimer(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer
- firstTrimer(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
- firstTrimer(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
- FISHER_STRAND_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- FisherExactTest - Class in org.broadinstitute.hellbender.utils
-
Implements the Fisher's exact test for 2x2 tables assuming the null hypothesis of odd ratio of 1.
- FisherExactTest() - Constructor for class org.broadinstitute.hellbender.utils.FisherExactTest
- FisherStrand - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Strand bias estimated using Fisher's Exact Test
- FisherStrand() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.FisherStrand
- FisherStrandFilter - Class in picard.vcf.filter
-
Filters records based on the phred scaled p-value from the Fisher Strand test stored in the FS attribute.
- FisherStrandFilter(double) - Constructor for class picard.vcf.filter.FisherStrandFilter
- FIVE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToFastq
- FIVE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToSam
- FIVE_PRIME_ADAPTER - Variable in class picard.illumina.MarkIlluminaAdapters
- FIVE_PRIME_ADAPTER_LOCATION_TAG - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- FIVE_PRIME_FLANK - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
The variant is upstream of the chosen transcript
- FIVE_PRIME_FLANK_SIZE_DEFAULT_VALUE - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- FIVE_PRIME_FLANK_SIZE_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- FIVE_PRIME_NESTED_SUPPORTED_EXTENSION - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
5' end extended based on RNA-seq data.
- FIVE_PRIME_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- FIVE_PRIME_STANDARD_SUPPORTED_EXTENSION - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
5' end extended based on RNA-seq data.
- FIVE_PRIME_TRIMMING_TAG - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- FIVE_PRIME_UTR - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Variant is on the 5'UTR for the chosen transcript.
- fivePrimeFlankSize - Variable in class org.broadinstitute.hellbender.tools.funcotator.FlankSettings
- fivePrimeFlankSize - Variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorVariantArgumentCollection
- FixedOffset - Enum constant in enum class picard.util.BaitDesigner.DesignStrategy
-
Design that places baits at fixed offsets over targets, allowing them to hang off the ends as dictated by the target size and offset.
- FixedWindowFunction(int, int) - Constructor for class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceWindowFunctions.FixedWindowFunction
- fixGenotypes(GenotypesContext, List<Allele>, List<Allele>) - Static method in class picard.util.LiftoverUtils
- FixMateInformation - Class in picard.sam
-
Summary
- FixMateInformation() - Constructor for class picard.sam.FixMateInformation
- FixMisencodedBaseQualityReads - Class in org.broadinstitute.hellbender.tools
- FixMisencodedBaseQualityReads() - Constructor for class org.broadinstitute.hellbender.tools.FixMisencodedBaseQualityReads
- fixNmMdAndUq(SAMRecord, ReferenceSequenceFileWalker, boolean) - Static method in class picard.sam.AbstractAlignmentMerger
-
Calculates and sets the NM, MD, and and UQ tags from the record and the reference
- fixOverlaps() - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Fixes the quality of all the elements that come from an overlapping pair in the same way as samtools does .
- fixTooHighQD(double) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.QualByDepth
-
The haplotype caller generates very high quality scores when multiple events are on the same haplotype.
- fixUq(SAMRecord, ReferenceSequenceFileWalker, boolean) - Static method in class picard.sam.AbstractAlignmentMerger
-
Calculates and sets UQ tag from the record and the reference
- FixVcfHeader - Class in picard.vcf
-
Tool for replacing or fixing up a VCF header.
- FixVcfHeader() - Constructor for class picard.vcf.FixVcfHeader
- FLAG - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestField
- FLAG_DUPLICATES - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- FlagStat - Class in org.broadinstitute.hellbender.tools
-
Accumulate flag statistics given a BAM file, e.g.
- FlagStat() - Constructor for class org.broadinstitute.hellbender.tools.FlagStat
- FlagStat.FlagStatus - Class in org.broadinstitute.hellbender.tools
- FlagStatSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines
-
Spark tool to accumulate flag statistics given a BAM file, e.g.
- FlagStatSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.FlagStatSpark
- FlagStatus() - Constructor for class org.broadinstitute.hellbender.tools.FlagStat.FlagStatus
- FlankSettings - Class in org.broadinstitute.hellbender.tools.funcotator
-
Simple struct container class for the 5'/3' flank settings.
- FlankSettings(int, int) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.FlankSettings
- FLAT_BETA - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.BetaDistributionShape
- FLAT_SNP_HET_PRIOR - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.DRAGENGenotypesModel
- flatBAQArray(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
-
Create a BAQ style array that indicates no alignment uncertainty
- flatDeletionPenalty - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- flatInsertionPenatly - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- FlatMapGluer<I,
O> - Class in org.broadinstitute.hellbender.tools.spark.utils -
A little shim that let's you implement a mapPartitions operation (which takes an iterator over all items in the partition, and returns an iterator over all items to which they are mapped) in terms of a flatMap function (which takes a single input item, and returns an iterator over any number of output items).
- FlatMapGluer(Function<I, Iterator<O>>, Iterator<? extends I>) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.FlatMapGluer
- FlatMapGluer(Function<I, Iterator<O>>, Iterator<? extends I>, I) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.FlatMapGluer
- flatSize() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- flattenSplitIntervals(List<List<GenomeLoc>>) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
- flip() - Method in class picard.fingerprint.Snp
-
Returns a new SNP object with the alleles swapped and MAF corrected.
- floatToByteArray(float) - Static method in class picard.arrays.illumina.InfiniumDataFile
-
Utility method to convert a float to a byte array
- floorBlocks - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper
- floorBlocks - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
-
Output the band lower bound for each GQ block instead of the min GQ -- for better compression
- FLOW - Enum constant in enum class org.broadinstitute.hellbender.utils.SequencerFlowClass
- FLOW_ASSEMBLY_COLLAPSE_HMER_SIZE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- FLOW_ASSEMBLY_COLLAPSE_PARTIAL_MODE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- FLOW_BASED_INSIGNIFICANT_END - Static variable in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- FLOW_BASED_TP_ATTRIBUTE_SYMETRIC_READ_FILTER - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- FLOW_BASED_TP_ATTRIBUTE_VALID_READ_FILTER - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- FLOW_CYCLESKIP_STATUS - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- FLOW_DUPLICATE_SCORE_ATTR_NAME - Static variable in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.FlowModeFragment
- FLOW_EFFECTIVE_QUALITY_THRESHOLD - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- FLOW_END_LOCATION_SIGNIFICANT - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- FLOW_END_POS_UNCERTAINTY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- FLOW_GATK_MODE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- FLOW_GC_CONTENT - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- FLOW_HMER_INDEL_LENGTH - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- FLOW_HMER_INDEL_NUC - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- FLOW_HMM_ENGINE_FLAT_DELETION_PENATLY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- FLOW_HMM_ENGINE_FLAT_INSERTION_PENATLY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- FLOW_HMM_ENGINE_MIN_INDEL_ADJUST_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- FLOW_INDEL_CLASSIFY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- FLOW_INDEL_LENGTH - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- FLOW_KEEP_BOUNDARY_FLOWS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- FLOW_LEFT_MOTIF - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- FLOW_LIKELIHOOD_OPTIMIZED_COMP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentArgumentCollection
- FLOW_LIKELIHOOD_PARALLEL_THREADS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentArgumentCollection
- FLOW_M2_MODE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- FLOW_MATRIX_MODS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- FLOW_MATRiX_OLD_TAG_KD - Static variable in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- FLOW_MATRiX_OLD_TAG_KF - Static variable in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- FLOW_MATRiX_OLD_TAG_KH - Static variable in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- FLOW_MATRiX_OLD_TAG_KR - Static variable in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- FLOW_MATRiX_OLD_TAG_TI - Static variable in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- FLOW_MATRIX_T0_TAG_NAME - Static variable in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- FLOW_MATRIX_TAG_NAME - Static variable in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- FLOW_MD_MODE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- FLOW_MODE - Variable in class picard.analysis.CollectQualityYieldMetrics
- FLOW_MODE - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- FLOW_ORDER_CYCLE_LENGTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- FLOW_ORDER_FOR_ANNOTATIONS - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- FLOW_Q_IS_KNOWN_END - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- FLOW_Q_IS_KNOWN_END - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- FLOW_Q_IS_KNOWN_END_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- FLOW_QUALITY_SUM_STRATEGY - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- FLOW_QUALITY_SUM_STRATEGY - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- FLOW_QUALITY_SUM_STRATEGY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- FLOW_RIGHT_MOTIF - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- FLOW_SIZE - Static variable in class org.broadinstitute.hellbender.utils.pairhmm.FlowBasedPairHMM
- FLOW_SKIP_FIRST_N_FLOWS - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- FLOW_SKIP_START_HOMOPOLYMERS - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- FLOW_SKIP_START_HOMOPOLYMERS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- FLOW_SUM_OF_BASE_QUALITIES - Enum constant in enum class org.broadinstitute.hellbender.utils.read.markduplicates.MarkDuplicatesScoringStrategy
- FLOW_SUM_OF_BASE_QUALITY_THRESHOLD - Static variable in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- FLOW_USE_CLIPPED_LOCATIONS - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- FLOW_USE_T0_TAG - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- FLOW_VARIANT_TYPE - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- FlowAnnotatorBase - Class in org.broadinstitute.hellbender.tools.walkers.annotator.flow
-
Base class for flow based annotations Some flow based annotations depend on the results from other annotations, regardless if they were called for by user arguments.
- FlowAnnotatorBase() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- FlowAnnotatorBase.LocalContext - Class in org.broadinstitute.hellbender.tools.walkers.annotator.flow
- flowAssemblyCollapseHKerSize - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- flowAssemblyCollapsePartialMode - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- FlowBased - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine.Implementation
- FlowBasedAlignmentArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
- FlowBasedAlignmentArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentArgumentCollection
- FlowBasedAlignmentLikelihoodEngine - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Flow based replacement for PairHMM likelihood calculation.
- FlowBasedAlignmentLikelihoodEngine(FlowBasedAlignmentArgumentCollection, double, double, boolean, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
-
Default constructor
- FlowBasedArgumentCollection - Class in org.broadinstitute.hellbender.tools
- FlowBasedArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- flowBasedArguments - Variable in class picard.sam.markduplicates.MarkDuplicates
- FlowBasedDuplicationMetrics - Class in picard.sam
- FlowBasedDuplicationMetrics() - Constructor for class picard.sam.FlowBasedDuplicationMetrics
- FlowBasedHaplotype - Class in org.broadinstitute.hellbender.utils.haplotype
-
Haplotype that also keeps information on the flow space @see FlowBasedRead Haplotype can't be extended, so this extends Allele
- FlowBasedHaplotype(Haplotype, String) - Constructor for class org.broadinstitute.hellbender.utils.haplotype.FlowBasedHaplotype
- FlowBasedHmerBasedReadFilterHelper - Class in org.broadinstitute.hellbender.engine.filters.flow
-
A common base class for flow based filters which test for conditions on an hmer basis
- FlowBasedHmerBasedReadFilterHelper() - Constructor for class org.broadinstitute.hellbender.engine.filters.flow.FlowBasedHmerBasedReadFilterHelper
- FlowBasedHMM - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine.Implementation
- FlowBasedHMMEngine - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Flow Based HMM, intended to incorporate the scoring model of the
FlowBasedAlignmentLikelihoodEnginewhile allowing for frame-shift insertions and deletions for better genotyping. - FlowBasedHMMEngine(FlowBasedArgumentCollection, byte, double, double, PairHMMLikelihoodCalculationEngine.PCRErrorModel, DragstrParams, boolean, double, int, byte, byte) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedHMMEngine
-
Default constructor
- FlowBasedKeyCodec - Class in org.broadinstitute.hellbender.utils.read
- FlowBasedKeyCodec() - Constructor for class org.broadinstitute.hellbender.utils.read.FlowBasedKeyCodec
- FlowBasedPairHMM - Class in org.broadinstitute.hellbender.utils.pairhmm
-
Class for performing the pair HMM for global alignment in FlowSpace.
- FlowBasedPairHMM() - Constructor for class org.broadinstitute.hellbender.utils.pairhmm.FlowBasedPairHMM
- FlowBasedProgramGroup - Class in org.broadinstitute.hellbender.cmdline.programgroups
-
Tools that perform variant calling and genotyping for short variants (SNPs, SNVs and Indels) on flow-based sequencing platforms
- FlowBasedProgramGroup() - Constructor for class org.broadinstitute.hellbender.cmdline.programgroups.FlowBasedProgramGroup
- FlowBasedRead - Class in org.broadinstitute.hellbender.utils.read
-
Adds flow information to the usual GATKRead.
- FlowBasedRead(SAMRecord, String, int, FlowBasedArgumentCollection) - Constructor for class org.broadinstitute.hellbender.utils.read.FlowBasedRead
-
Same as above but constructs from SAMRecord
- FlowBasedRead(GATKRead, String, int, FlowBasedArgumentCollection) - Constructor for class org.broadinstitute.hellbender.utils.read.FlowBasedRead
-
Constructor from GATKRead.
- FlowBasedRead.Direction - Enum Class in org.broadinstitute.hellbender.utils.read
- FlowBasedReadUtils - Class in org.broadinstitute.hellbender.utils.read
-
utility class for flow based read
- FlowBasedReadUtils() - Constructor for class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- FlowBasedReadUtils.ReadGroupInfo - Class in org.broadinstitute.hellbender.utils.read
- FlowBasedTPAttributeSymetricReadFilter - Class in org.broadinstitute.hellbender.engine.filters.flow
-
A read filter to test if the TP values for each hmer in a flow based read form a polindrome (as they should)
- FlowBasedTPAttributeSymetricReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.flow.FlowBasedTPAttributeSymetricReadFilter
- FlowBasedTPAttributeValidReadFilter - Class in org.broadinstitute.hellbender.engine.filters.flow
-
A read filter to test if the TP values for each hmer in a flow based read form are wihin the allowed range (being the possible lengths of hmers - maxHmer)
- FlowBasedTPAttributeValidReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.flow.FlowBasedTPAttributeValidReadFilter
- FLOWCELL_BARCODE - Variable in class picard.fastq.BamToBfq
- FLOWCELL_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToFastq
- flowCellTileStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies base into their read's tile which is parsed from the read-name.
- FlowCellTileStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellTileStratifier
- flowCellXStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies base into their read's tile which is parsed from the read-name.
- FlowCellXStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
- flowCellYStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies base into their read's tile which is parsed from the read-name.
- FlowCellYStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellYStratifier
- FlowFeatureMapper - Class in org.broadinstitute.hellbender.tools.walkers.featuremapping
-
Finds specific features in reads, scores the confidence of each feature relative to the reference in each read and writes them into a VCF file.
- FlowFeatureMapper() - Constructor for class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper
- FlowFeatureMapper.MappedFeature - Class in org.broadinstitute.hellbender.tools.walkers.featuremapping
- FlowFeatureMapper.ReadContext - Class in org.broadinstitute.hellbender.tools.walkers.featuremapping
- FlowFeatureMapperArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.featuremapping
-
Set of arguments for the
FlowFeatureMapper - FlowFeatureMapperArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
- flowFirstUncertainFlowBase - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- flowLikelihoodOptimizedComp - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentArgumentCollection
- flowLikelihoodParallelThreads - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentArgumentCollection
- flowMatrixMods - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- flowMissingOneShotLogger - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- flowMode - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- flowMode - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- FlowModeFragment - Class in org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
-
Class representing a single read fragment at a particular start location without a mapped mate.
- FlowModeFragment(GATKRead, SAMFileHeader, int, MarkDuplicatesScoringStrategy, Map<String, Byte>, MarkDuplicatesSparkArgumentCollection) - Constructor for class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.FlowModeFragment
- flowNumUncertainFlows - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- flowOrder - Variable in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils.ReadGroupInfo
- flowOrderCycleLength - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- flowSumOfBaseQualities(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
-
Computes the sum of base qualities of the given flow read.
- FLUIDIGM - Enum constant in enum class org.broadinstitute.hellbender.utils.illumina.IlluminaAdapterPair
- FLUIDIGM - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- flush() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine
-
Gets any available finalized clusters.
- flush() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager
-
Close out the manager stream by clearing the read cache
- flush() - Method in class org.broadinstitute.hellbender.utils.BinaryTableWriter
- flush() - Method in class org.broadinstitute.hellbender.utils.tsv.TableWriter
-
Pushes in-memory buffered content to the output stream.
- flush(boolean) - Method in class org.broadinstitute.hellbender.tools.sv.concordance.ClosestSVFinder
-
Should be run frequently to reduce memory usage.
- flushSingleSampleMultiplicity() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MultiSampleEdge
-
update the single sample multiplicities by adding the current single sample multiplicity to the priority queue, and reset the current single sample multiplicity to 0.
- FN - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
- FN - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- FN_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The FN (false negative) count across all variants
- FN_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
- fnvByteArray64(byte[]) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
-
64-bit FNV-1a hash for byte arrays
- fnvByteArray64(long, byte[]) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
- fnvLong64(long) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
-
64-bit FNV-1a hash for long's
- fnvLong64(long, long) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
- FOLD_80_BASE_PENALTY - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.
- FOLD_80_BASE_PENALTY - Variable in class picard.analysis.WgsMetrics
-
The fold over-coverage necessary to raise 80% of bases to the mean coverage level.
- FOLD_90_BASE_PENALTY - Variable in class picard.analysis.WgsMetrics
-
The fold over-coverage necessary to raise 90% of bases to the mean coverage level.
- FOLD_95_BASE_PENALTY - Variable in class picard.analysis.WgsMetrics
-
The fold over-coverage necessary to raise 95% of bases to the mean coverage level.
- FOLD_ENRICHMENT - Variable in class picard.analysis.directed.HsMetrics
-
The fold by which the baited region has been amplified above genomic background.
- FOLD_ENRICHMENT - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The fold by which the amplicon region has been amplified above genomic background.
- FOLD_ENRICHMENT - Variable in class picard.analysis.directed.TargetMetrics
-
The fold by which the probed region has been amplified above genomic background, (ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES))/(PROBE_TERRITORY/GENOME_SIZE)
- foldInto(CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics, Collection<CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics>) - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
- foldInto(T, Collection<T>) - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
- FORCE_ACTIVE_REGIONS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- FORCE_B37_TO_HG19_REFERENCE_CONTIG_CONVERSION - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- FORCE_CALL_ALLELES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- FORCE_CALL_FILTERED_ALLELES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- FORCE_CALL_FILTERED_ALLELES_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- FORCE_ESTIMATION_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- FORCE_GC - Variable in class picard.illumina.IlluminaBasecallsToFastq
- FORCE_OUTPUT_INTERVALS_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- FORCE_PLATFORM - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
- forceActive - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- forceB37ToHg19ContigNameConversion - Variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
- forceCallFiltered - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- forceFlush() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine
-
Flushes all active clusters, adding them to the output buffer.
- forceJVMLocaleToUSEnglish() - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Set the Locale to US English so that numbers will always be formatted in the US style.
- forceKeepAllele(Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
-
Checks whether even if the allele is not well supported by the data, we should keep it for genotyping.
- forceKeepAllele(Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine
- forceKeepAllele(Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine
- forceOutputIntervalStrings - Variable in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- forEach(Consumer<? super String>) - Method in class org.broadinstitute.hellbender.utils.nio.PathLineIterator
- forEach(IntConsumer) - Method in class org.broadinstitute.hellbender.utils.IndexRange
-
Iterate through all indexes in the range in ascending order to be processed by the provided
integer consumerlambda function. - forEachAbsentAlleleIndex(IntConsumer, int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Perform an action for every allele index not represented in this genotype.
- forEachAlleleIndexAndCount(IntBiConsumer) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
- forEachOnRead(GATKRead, ReferenceContext, Consumer<? super FlowFeatureMapper.MappedFeature>) - Method in interface org.broadinstitute.hellbender.tools.walkers.featuremapping.FeatureMapper
- forEachOnRead(GATKRead, ReferenceContext, Consumer<? super FlowFeatureMapper.MappedFeature>) - Method in class org.broadinstitute.hellbender.tools.walkers.featuremapping.SNVMapper
- forEachRead(MultiplePassReadWalker.GATKReadConsumer) - Method in class org.broadinstitute.hellbender.engine.MultiplePassReadWalker
-
Provides a single traversal over all input reads.
- forEachRemaining(Consumer<? super E>) - Method in class org.broadinstitute.hellbender.utils.iterators.CloseAtEndIterator
- format() - Element in annotation interface org.broadinstitute.hellbender.tools.walkers.varianteval.util.DataPoint
- FORMAT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts
- FORMAT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.HtsgetReader
- FORMAT_START - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.TableDataHeaderFields
- FORMAT_SUFFIX - Static variable in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceCodec
- FORMAT_SUFFIX - Static variable in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceCodec
- FORMAT_SUFFIX - Static variable in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceCodec
- FORMAT_SUFFIX - Static variable in class org.broadinstitute.hellbender.utils.codecs.SiteDepthCodec
- FORMAT_SUFFIX - Static variable in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceCodec
- formatAssemblyID(int) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse
- formatContigName(int, int) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse
- formatDouble(double) - Static method in class org.broadinstitute.hellbender.tools.copynumber.formats.CopyNumberFormatsUtils
- formatException(String) - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Composes the exception to be thrown due to a formatting error.
- formatExceptionWithoutLocation(String) - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Composes the exception to be thrown due to a formatting error.
- formatFloatForVcf(float) - Static method in class picard.arrays.GtcToVcf
- formatKey(int) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ContextCovariate
- formatKey(int) - Method in interface org.broadinstitute.hellbender.utils.recalibration.covariates.Covariate
-
Converts the internal representation of the key to String format for file output.
- formatKey(int) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.CycleCovariate
- formatKey(int) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.QualityScoreCovariate
- formatKey(int) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadGroupCovariate
- formatMillisecondsTime(long) - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- formattedPercent(long, long) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Convenience function that formats a percentage as a %.2f string
- formattedRatio(long, long) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Convenience function that formats a ratio as a %.2f string
- formattedValue(double) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandOddsRatio
- formatTimeRemainingAsTimestamp - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- formatToDataTypes - Variable in class picard.illumina.parser.IlluminaDataProviderFactory
-
A Map of file formats to the dataTypes they will provide for this run.
- formatValue(Object) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportColumn
-
Returns a string version of the values.
- forRead(GATKRead) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.evidence.TemplateFragmentOrdinal
- forumPost(String) - Static method in class org.broadinstitute.hellbender.utils.help.HelpConstants
- forVcf(File) - Method in class picard.vcf.processor.VcfFileSegmentGenerator
-
Deprecated.
- forVcf(PicardHtsPath) - Method in class picard.vcf.processor.VcfPathSegmentGenerator
- FORWARD - Enum constant in enum class org.broadinstitute.hellbender.engine.AlignmentContext.ReadOrientation
- FORWARD - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
- FORWARD - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils
- FORWARD_TO_REVERSE - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.StrandSwitch
- forwardStrand - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- FOUND_NO_EVIDENCE - Enum constant in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
- FOURFIVEFOUR_RNA_SEQ_SUPPORTED - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
annotated based on RNA-seq data.
- FP - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
- FP - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- FP_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The FP (false positive) count across all variants
- FP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
- FP_GENDER - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The sex, as reported for the fingerprinted sample
- FP_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
- FP_TN - Static variable in class picard.vcf.GenotypeConcordanceScheme
- FP_TN_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
- FR - Static variable in class picard.sam.markduplicates.util.ReadEnds
- FRACTION - Variable in class picard.sam.PositionBasedDownsampleSam
- FRACTION_HEADER_LINE - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.AllelePseudoDepth
- FRACTION_INFO_FIELD - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals
- FRACTION_TO_KEEP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
- FRACTION_TO_KEEP_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSet
- FRACTION_TO_KEEP_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
-
The value of this argument should be a number between 0 and 1 specifying the fraction of total variants to be randomly selected from the input callset.
- FractionalDownsampler - Class in org.broadinstitute.hellbender.utils.downsampling
-
Fractional Downsampler: selects a specified fraction of the reads for inclusion.
- FractionalDownsampler(double) - Constructor for class org.broadinstitute.hellbender.utils.downsampling.FractionalDownsampler
-
Construct a FractionalDownsampler
- fractionToKeep - Variable in class org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSet
- Fragment - Class in org.broadinstitute.hellbender.utils.read
-
All available evidence coming from a single biological fragment.
- Fragment - Class in org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
-
Class representing a single read fragment at a particular start location without a mapped mate.
- Fragment(Pair<GATKRead, GATKRead>) - Constructor for class org.broadinstitute.hellbender.utils.read.Fragment
- Fragment(GATKRead) - Constructor for class org.broadinstitute.hellbender.utils.read.Fragment
- Fragment(GATKRead, SAMFileHeader, int, MarkDuplicatesScoringStrategy, Map<String, Byte>) - Constructor for class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Fragment
- FRAGMENT - Enum constant in enum class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord.Type
- FRAGMENT_ALLELE_DEPTHS - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- FRAGMENT_NUMBER_SEPARATOR_CHR - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils
- FragmentCollection<T> - Class in org.broadinstitute.hellbender.utils.fragments
-
Represents the results of the reads -> fragment calculation.
- FragmentCountReader(Path) - Constructor for class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation.FragmentCountReader
- FragmentCountWriter(Path, String, GeneExpressionEvaluation.FeatureLabelType) - Constructor for class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation.FragmentCountWriter
- FragmentDepthPerAlleleBySample - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Fragment depth of coverage of each allele per sample
- FragmentDepthPerAlleleBySample() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.FragmentDepthPerAlleleBySample
- FRAGMENTED_LOCUS - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
locus consists of non-overlapping transcript fragments either because of genome assembly issues (i.e., gaps or
- FragmentLength - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Median fragment length of reads supporting each allele.
- FragmentLength() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.FragmentLength
- FragmentLengthFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- FragmentLengthFilter(double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FragmentLengthFilter
- FragmentLengthReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only read pairs (0x1) with absolute insert length less than or equal to the specified maximum, and/or greater than or equal to the specified minimum.
- FragmentLengthReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.FragmentLengthReadFilter
- FRAGMENTS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of fragments in the SAM file
- FragmentUtils - Class in org.broadinstitute.hellbender.utils.fragments
- fragSort - Variable in class picard.sam.markduplicates.MarkDuplicates
- FRAME_SHIFT - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- FRAME_SHIFT_DEL - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Deletion that moves the sequence out of frame (i.e.
- FRAME_SHIFT_INS - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Insertion that moves the coding sequence out of frame (i.e.
- frameshift_rate_for_coding_indels - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- FREE - Enum constant in enum class picard.illumina.DistanceMetric
- freeDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
-
+++lifted from Commons Lang Text +++
- FREQUENCY_FILTER_KEY - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- FROM_SPLIT_GAPPED_ALIGNMENT - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier.AlnModType
- fromBases(byte[]) - Static method in enum class picard.fingerprint.DiploidGenotype
-
Converts a pair of bases into a DiploidGenotype regardless of base order or case
- fromBases(byte, byte) - Static method in enum class picard.fingerprint.DiploidGenotype
-
Converts a pair of bases into a DiploidGenotype regardless of base order or case
- fromCode(int) - Static method in enum class picard.pedigree.Sex
-
Decodes the Sex from a numeric code.
- fromFile(File, boolean) - Static method in class picard.pedigree.PedFile
-
Attempts to read a pedigree file into memory.
- fromFormatString(String) - Static method in enum class org.broadinstitute.hellbender.utils.report.GATKReportDataType
-
Returns a GATK report data type from the format string specified.
- fromHeader(SAMFileHeader, Metadata.Type) - Static method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.MetadataUtils
- fromHeader(String) - Static method in enum class org.broadinstitute.hellbender.utils.report.GATKReportVersion
-
Returns the GATK Report Version from the file header.
- fromIndex(int) - Method in interface org.broadinstitute.hellbender.utils.collections.Permutation
-
Given an index on the resulting list, it gives you the index of that element on the original list.
- fromIndex(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.ActualPermutation
- fromIndex(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.NonPermutation
- fromList() - Method in interface org.broadinstitute.hellbender.utils.collections.Permutation
-
Returns an unmodifiable view to the original element list.
- fromList() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.ActualPermutation
- fromList() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.NonPermutation
- fromList(List<ReadFilter>, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter
-
Return a composite (and)
CountingReadFilterconstructed from a list ofReadFilter. - fromList(List<ReadFilter>, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.engine.filters.ReadFilter
-
Return a composite (and)
ReadFilterconstructed from a list ofReadFilter. - fromList(List<VariantFilter>) - Static method in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter
-
Return a composite (and)
CountingVariantFilterconstructed from a list ofVariantFilter. - fromMeanAndStdDeviation(double, double) - Method in enum class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistributionShape
- fromObject(Object) - Static method in enum class org.broadinstitute.hellbender.utils.report.GATKReportDataType
-
Returns a GATK report data type from the Object specified.
- fromPath(Path) - Static method in class picard.nio.PicardHtsPath
-
Construct a
PicardHtsPathfrom aPath - fromPaths(Collection<String>) - Static method in class picard.nio.PicardHtsPath
-
Create a
List<PicardHtsPath>from path representations. - fromRead(GATKRead, SAMFileHeader) - Static method in enum class org.broadinstitute.hellbender.utils.NGSPlatform
-
Convenience get -- get the NGSPlatform from a Read.
- fromReadGroupPL(String) - Static method in enum class org.broadinstitute.hellbender.utils.NGSPlatform
-
Returns the NGSPlatform corresponding to the PL tag in the read group
- fromReadMetadataFile(String) - Method in enum class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistributionShape
- fromSerializationFile(String) - Method in enum class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistributionShape
- fromSexMap(Map<String, Sex>) - Static method in class picard.pedigree.PedFile
-
Function that accepts a map from sample-name to its sex and creates a PEDFile documenting the sexes.
- fromSize() - Method in interface org.broadinstitute.hellbender.utils.collections.Permutation
-
Length of the original element list.
- fromSize() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.ActualPermutation
- fromSize() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.NonPermutation
- fromString(String) - Static method in enum class picard.pedigree.Sex
-
Decodes the Sex from a String.
- fromTextFile(String) - Method in enum class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistributionShape
- fScoreBeta - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- FULL_ALIGNMENT - Enum constant in enum class org.broadinstitute.hellbender.tools.reference.CompareReferences.BaseComparisonMode
- FULL_CONTIG - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapStatus
-
Gene or transcript completely mapped to the target genome with all features intact.
- FULL_FRAGMENT - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapStatus
-
Gene or transcript completely mapped to the target genome with insertions in some features.
- FULL_NAME_STOP_ON_READ_NAME - Static variable in class org.broadinstitute.hellbender.tools.examples.ExamplePartialReadWalker
- fullString() - Method in class picard.arrays.illumina.ArraysControlInfo
- FuncotateSegments - Class in org.broadinstitute.hellbender.tools.funcotator
-
Perform functional annotation on a segment file (tsv).
- FuncotateSegments() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.FuncotateSegments
- Funcotation - Interface in org.broadinstitute.hellbender.tools.funcotator
-
Abstract class representing a
Funcotatorannotation. - FuncotationFilter - Class in org.broadinstitute.hellbender.tools.funcotator.filtrationRules
-
A filter to apply to Funcotations in
FilterFuncotations. - FuncotationMap - Class in org.broadinstitute.hellbender.tools.funcotator
-
A linked map of transcript IDs to funcotations.
- FuncotationMetadata - Interface in org.broadinstitute.hellbender.tools.funcotator.metadata
-
Represents metadata information for fields in in a Funcotation.
- FuncotationMetadataUtils - Class in org.broadinstitute.hellbender.tools.funcotator.metadata
- Funcotator - Class in org.broadinstitute.hellbender.tools.funcotator
-
Funcotator (FUNCtional annOTATOR) analyzes given variants for their function (as retrieved from a set of data sources) and produces the analysis in a specified output file.
- Funcotator() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.Funcotator
- FUNCOTATOR_VCF_FIELD_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer
-
The name of the field inside the VCF INFO field in which to put
Funcotatorresults. - FUNCOTATOR_VERSION_VCF_HEADERLINE_KEY - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorConstants
-
Name of the header line key which indicates that a file has already been annotated.
- FuncotatorArgumentDefinitions - Class in org.broadinstitute.hellbender.tools.funcotator
-
Class to store argument definitions specific to
Funcotator. - FuncotatorArgumentDefinitions() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- FuncotatorArgumentDefinitions.DataSourceType - Enum Class in org.broadinstitute.hellbender.tools.funcotator
-
An enum to handle the different types of input files for data sources.
- FuncotatorArgumentDefinitions.OutputFormatType - Enum Class in org.broadinstitute.hellbender.tools.funcotator
-
The file format of the output file.
- FuncotatorConstants - Class in org.broadinstitute.hellbender.tools.funcotator
- FuncotatorConstants() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.FuncotatorConstants
- FuncotatorDataSourceDownloader - Class in org.broadinstitute.hellbender.tools.funcotator
-
FuncotatorDataSourceDownloaderis a tool to download the latest data sources forFuncotator. - FuncotatorDataSourceDownloader() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader
- funcotatorEngine - Variable in class org.broadinstitute.hellbender.tools.funcotator.Funcotator
- FuncotatorEngine - Class in org.broadinstitute.hellbender.tools.funcotator
-
Class that performs functional annotation of variants.
- FuncotatorEngine(BaseFuncotatorArgumentCollection, SAMSequenceDictionary, FuncotationMetadata, List<DataSourceFuncotationFactory>) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine
-
Create a
FuncotatorEngineusing the givenmetadataandfuncotationFactoriesrepresenting the kinds ofFuncotations to be created and the data sources from which they should be created, respectively. - FuncotatorReferenceVersionB37 - Static variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
-
String representing the b37 version of the homo sapiens reference.
- FuncotatorReferenceVersionHg19 - Static variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
-
String representing the hg19 version of the homo sapiens reference.
- FuncotatorReferenceVersionHg38 - Static variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
-
String representing the hg38 version of the homo sapiens reference.
- FuncotatorSegmentArgumentCollection - Class in org.broadinstitute.hellbender.tools.funcotator
- FuncotatorSegmentArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.FuncotatorSegmentArgumentCollection
- FuncotatorUtils - Class in org.broadinstitute.hellbender.tools.funcotator
- FuncotatorUtils.Genus - Enum Class in org.broadinstitute.hellbender.tools.funcotator
-
A type to keep track of different specific genuses.
- FuncotatorUtils.TranscriptCodingSequenceException - Exception in org.broadinstitute.hellbender.tools.funcotator
-
Class representing exceptions that arise when trying to create a coding sequence for a variant:
- FuncotatorVariantArgumentCollection - Class in org.broadinstitute.hellbender.tools.funcotator
- FuncotatorVariantArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.FuncotatorVariantArgumentCollection
- FunctionalClass - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies by nonsense, missense, silent, and all annotations in the input ROD, from the INFO field annotation.
- FunctionalClass(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.FunctionalClass
- FunctionalClass.FunctionalType - Enum Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
- FWD - Enum constant in enum class org.broadinstitute.hellbender.tools.LocalAssembler.ContigOrientation
- FWD_CXT_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The number of REF_BASE:ALT_BASE alignments at sites with the given reference context.
- FWD_CXT_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The number of REF_BASE:REF_BASE alignments at sites with the given reference context.
- FWD_ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The substitution rate of REF_BASE:ALT_BASE, calculated as max(1e-10, FWD_CXT_ALT_BASES / (FWD_CXT_ALT_BASES + FWD_CXT_REF_BASES)).
- FwdIterator(SVIntervalTree.Node<V>) - Constructor for class org.broadinstitute.hellbender.utils.SVIntervalTree.FwdIterator
G
- G - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer.Base
- G - Enum constant in enum class org.broadinstitute.hellbender.utils.BaseUtils.Base
- G - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- G - Enum constant in enum class picard.analysis.artifacts.Transition.Base
- G - Enum constant in enum class picard.illumina.parser.IntensityChannel
- G_FOLLOWED_BY_INSERTION_BASE - Static variable in class org.broadinstitute.hellbender.utils.pileup.PileupElement
- G_REF_ALT_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of alt (A/T) basecalls observed at sites where the genome reference == G.
- G_REF_OXO_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The rate at which C>A and G>T substitutions are observed at G reference sites above the expected rate if there were no bias between sites with a C reference base vs.
- G_REF_OXO_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
G_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
- G_REF_REF_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of ref basecalls observed at sites where the genome reference == G.
- GA4GHScheme - Class in picard.vcf
-
The scheme is defined in the constructor.
- GA4GHScheme() - Constructor for class picard.vcf.GA4GHScheme
- GA4GHSchemeWithMissingAsHomRef - Class in picard.vcf
-
The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme.
- GA4GHSchemeWithMissingAsHomRef() - Constructor for class picard.vcf.GA4GHSchemeWithMissingAsHomRef
- GALLUS - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.Genus
-
Chicken
- GAP - Static variable in interface org.broadinstitute.hellbender.utils.IntervalPileup
- GAP_CHARACTER - Static variable in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
- gapContinuationPenalties() - Method in interface org.broadinstitute.hellbender.utils.pairhmm.PairHMMInputScoreImputation
- gapLen(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVInterval
-
Assumes interval half-open and this
SVInterval.isUpstreamOf(SVInterval). - GAPPED_ALIGNMENT_BREAK_DEFAULT_SENSITIVITY - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- GATHER_TYPE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.GatherVcfsCloud
- GatherBamFiles - Class in picard.sam
-
Concatenate efficiently BAM files that resulted from a scattered parallel analysis.
- GatherBamFiles() - Constructor for class picard.sam.GatherBamFiles
- GatherBQSRReports - Class in org.broadinstitute.hellbender.tools.walkers.bqsr
- GatherBQSRReports() - Constructor for class org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReports
- gatherEvidenceAndWriteContigSamFile(JavaSparkContext, StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection, SAMFileHeader, JavaRDD<GATKRead>, String, Logger) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark
-
Gathers evidence reads and outputs them in a directory where reads are written out as interleaved FASTQ's.
- GatherNormalArtifactData - Class in org.broadinstitute.hellbender.tools.walkers.mutect
- GatherNormalArtifactData() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.GatherNormalArtifactData
- GatherPileupSummaries - Class in org.broadinstitute.hellbender.tools.walkers.contamination
- GatherPileupSummaries() - Constructor for class org.broadinstitute.hellbender.tools.walkers.contamination.GatherPileupSummaries
- gatherReports(List<File>) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport
-
Gathers a set of files containing
RecalibrationReports into a singleGATKReport. - gatherReportsIntoOneFile(List<File>, File) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport
-
Gather multiple
RecalibrationReports into a single file - GatherTranches - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
- GatherTranches() - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.GatherTranches
- gatherType - Variable in class org.broadinstitute.hellbender.tools.GatherVcfsCloud
- GatherVcfs - Class in picard.vcf
-
Simple little class that combines multiple VCFs that have exactly the same set of samples and nonoverlapping sets of loci.
- GatherVcfs() - Constructor for class picard.vcf.GatherVcfs
- GatherVcfsCloud - Class in org.broadinstitute.hellbender.tools
-
This tool combines together rows of variant calls from multiple VCFs, e.g.
- GatherVcfsCloud() - Constructor for class org.broadinstitute.hellbender.tools.GatherVcfsCloud
- GatherVcfsCloud.GatherType - Enum Class in org.broadinstitute.hellbender.tools
- GATK_CONFIG_FILE - Variable in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- GATK_CONFIG_FILE_OPTION - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
-
The option specifying a main configuration file.
- GATK_FORUM_URL - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- GATK_INTERVAL_FILE_EXTENSIONS - Static variable in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Recognized extensions for interval files
- GATK_MAIN_SITE - Static variable in class org.broadinstitute.hellbender.utils.help.HelpConstants
- gatk_stacktrace_on_user_exception() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- GATKAnnotationArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.GATKPlugin
-
An abstract ArgumentCollection for defining the set of annotation descriptor plugin arguments that are exposed to the user on the command line.
- GATKAnnotationArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationArgumentCollection
- GATKAnnotationPluginDescriptor - Class in org.broadinstitute.hellbender.cmdline.GATKPlugin
-
A plugin descriptor for managing the dynamic discovery of both
InfoFieldAnnotationandGenotypeAnnotationobjects within the packages defined by the method getPackageNames() (defaultorg.broadinstitute.hellbender.tools.walkers.annotator). - GATKAnnotationPluginDescriptor(List<Annotation>, List<Class<? extends Annotation>>) - Constructor for class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
-
Constructor that allows client tools to specify what annotations (optionally with parameters specified) to use as their defaults before discovery of user specified annotations.
- GATKAnnotationPluginDescriptor(GATKAnnotationArgumentCollection, List<Annotation>, List<Class<? extends Annotation>>) - Constructor for class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
-
Constructor that allows client tools to specify what annotations (optionally with parameters specified) to use as their defaults before discovery of user specified annotations.
- GATKAvroReader - Interface in org.broadinstitute.hellbender.utils.bigquery
- GATKConfig - Interface in org.broadinstitute.hellbender.utils.config
-
Configuration file for GATK options.
- GATKDataSource<T> - Interface in org.broadinstitute.hellbender.engine
-
A GATKDataSource is something that can be iterated over from start to finish and/or queried by genomic interval.
- GATKDocWorkUnit - Class in org.broadinstitute.hellbender.utils.help
-
Custom DocWorkUnit used for generating GATK help/documentation.
- GATKDocWorkUnit(DocWorkUnitHandler, Element, Class<?>, DocumentedFeature) - Constructor for class org.broadinstitute.hellbender.utils.help.GATKDocWorkUnit
- GATKDuplicationMetrics - Class in org.broadinstitute.hellbender.utils.read.markduplicates
-
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.
- GATKDuplicationMetrics() - Constructor for class org.broadinstitute.hellbender.utils.read.markduplicates.GATKDuplicationMetrics
- GATKException - Exception in org.broadinstitute.hellbender.exceptions
-
Class GATKException.
- GATKException(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.GATKException
- GATKException(String, Throwable) - Constructor for exception org.broadinstitute.hellbender.exceptions.GATKException
- GATKException.MissingReadField - Exception in org.broadinstitute.hellbender.exceptions
- GATKException.ReadAttributeTypeMismatch - Exception in org.broadinstitute.hellbender.exceptions
- GATKException.ShouldNeverReachHereException - Exception in org.broadinstitute.hellbender.exceptions
-
For wrapping errors that are believed to never be reachable
- GATKGenomicsDBUtils - Class in org.broadinstitute.hellbender.tools.genomicsdb
-
Utility class containing various methods for working with GenomicsDB Contains code to modify the GenomicsDB import input using the Protobuf API References: GenomicsDB Protobuf structs: https://github.com/GenomicsDB/GenomicsDB/blob/master/src/resources/genomicsdb_vid_mapping.proto Protobuf generated Java code guide: https://developers.google.com/protocol-buffers/docs/javatutorial#the-protocol-buffer-api https://developers.google.com/protocol-buffers/docs/reference/java-generated
- GATKGenomicsDBUtils() - Constructor for class org.broadinstitute.hellbender.tools.genomicsdb.GATKGenomicsDBUtils
- GATKGSONWorkUnit - Class in org.broadinstitute.hellbender.utils.help
-
Class representing a GSONWorkUnit for GATK work units.
- GATKGSONWorkUnit(DocWorkUnit) - Constructor for class org.broadinstitute.hellbender.utils.help.GATKGSONWorkUnit
- GATKHelpDoclet - Class in org.broadinstitute.hellbender.utils.help
-
Custom Barclay-based Javadoc Doclet used for generating GATK help/documentation.
- GATKHelpDoclet() - Constructor for class org.broadinstitute.hellbender.utils.help.GATKHelpDoclet
- GATKHelpDocWorkUnitHandler - Class in org.broadinstitute.hellbender.utils.help
-
The GATK Documentation work unit handler class that is the companion to GATKHelpDoclet.
- GATKHelpDocWorkUnitHandler(HelpDoclet) - Constructor for class org.broadinstitute.hellbender.utils.help.GATKHelpDocWorkUnitHandler
- GATKPath - Class in org.broadinstitute.hellbender.engine
-
GATK tool command line arguments that are input or output resources.
- GATKPath(String) - Constructor for class org.broadinstitute.hellbender.engine.GATKPath
-
The raw value for this specifier as provided by the user.
- GATKPath(GATKPath) - Constructor for class org.broadinstitute.hellbender.engine.GATKPath
-
Create a GATKPath from an existing GATKPath.
- GATKRead - Interface in org.broadinstitute.hellbender.utils.read
-
Unified read interface for use throughout the GATK.
- GATKReadComparator() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampUtils.GATKReadComparator
- GATKReadFilterArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.GATKPlugin
-
An abstract ArgumentCollection for defining the set of read filter descriptor plugin arguments that are exposed to the user on the command line.
- GATKReadFilterArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterArgumentCollection
- GATKReadFilterPluginDescriptor - Class in org.broadinstitute.hellbender.cmdline.GATKPlugin
-
A CommandLinePluginDescriptor for ReadFilter plugins
- GATKReadFilterPluginDescriptor(List<ReadFilter>) - Constructor for class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
- GATKReadFilterPluginDescriptor(GATKReadFilterArgumentCollection, List<ReadFilter>) - Constructor for class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
- GATKReadToBDGAlignmentRecordConverter - Class in org.broadinstitute.hellbender.utils.read
-
Converts a GATKRead to a BDG AlignmentRecord
- GATKReadToBDGAlignmentRecordConverter(SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.utils.read.GATKReadToBDGAlignmentRecordConverter
- GATKReadWriter - Interface in org.broadinstitute.hellbender.utils.read
-
Interface for classes that are able to write GATKReads to some output destination.
- GATKRegistrator - Class in org.broadinstitute.hellbender.engine.spark
-
GATKRegistrator registers Serializers for our project.
- GATKRegistrator() - Constructor for class org.broadinstitute.hellbender.engine.spark.GATKRegistrator
- GATKReport - Class in org.broadinstitute.hellbender.utils.report
-
Container class for GATK report tables
- GATKReport() - Constructor for class org.broadinstitute.hellbender.utils.report.GATKReport
-
Create a new, empty GATKReport.
- GATKReport(File) - Constructor for class org.broadinstitute.hellbender.utils.report.GATKReport
-
Create a new GATKReport with the contents of a GATKReport on disk.
- GATKReport(InputStream) - Constructor for class org.broadinstitute.hellbender.utils.report.GATKReport
- GATKReport(String) - Constructor for class org.broadinstitute.hellbender.utils.report.GATKReport
-
Create a new GATKReport with the contents of a GATKReport on disk.
- GATKReport(GATKReportTable...) - Constructor for class org.broadinstitute.hellbender.utils.report.GATKReport
-
Create a new GATK report from GATK report tables
- GATKREPORT_HEADER_PREFIX - Static variable in class org.broadinstitute.hellbender.utils.report.GATKReport
- GATKReportColumn - Class in org.broadinstitute.hellbender.utils.report
-
column information within a GATK report table
- GATKReportColumn(String, String) - Constructor for class org.broadinstitute.hellbender.utils.report.GATKReportColumn
-
Construct the column object, specifying the column name, default value, whether or not the column should be displayed, and the format string.
- GATKReportColumnFormat - Class in org.broadinstitute.hellbender.utils.report
-
Column width and left/right alignment.
- GATKReportColumnFormat(int, GATKReportColumnFormat.Alignment) - Constructor for class org.broadinstitute.hellbender.utils.report.GATKReportColumnFormat
- GATKReportColumnFormat.Alignment - Enum Class in org.broadinstitute.hellbender.utils.report
- GATKReportDataType - Enum Class in org.broadinstitute.hellbender.utils.report
-
The gatherable data types acceptable in a GATK report column.
- GATKReportTable - Class in org.broadinstitute.hellbender.utils.report
- GATKReportTable(BufferedReader, GATKReportVersion) - Constructor for class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Construct a new GATK report table from the reader Note that the row ID mappings are just the index -> index
- GATKReportTable(String, String, int) - Constructor for class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Construct a new GATK report table with the specified name and description Sorting will be done with
GATKReportTable.Sorting.SORT_BY_ROW - GATKReportTable(String, String, int, GATKReportTable.Sorting) - Constructor for class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Construct a new GATK report table with the specified name and description and whether to sort rows by the row ID.
- GATKReportTable.Sorting - Enum Class in org.broadinstitute.hellbender.utils.report
- GATKReportTable.TableDataHeaderFields - Enum Class in org.broadinstitute.hellbender.utils.report
- GATKReportTable.TableNameHeaderFields - Enum Class in org.broadinstitute.hellbender.utils.report
- GATKReportVersion - Enum Class in org.broadinstitute.hellbender.utils.report
- GATKSparkTool - Class in org.broadinstitute.hellbender.engine.spark
-
Base class for GATK spark tools that accept standard kinds of inputs (reads, reference, and/or intervals).
- GATKSparkTool() - Constructor for class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- GATKSparkTool.ReadInputMergingPolicy - Enum Class in org.broadinstitute.hellbender.engine.spark
- GATKSV_CONTIG_ALIGNMENTS_READ_GROUP_ID - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
- GATKSVVariantContextUtils - Class in org.broadinstitute.hellbender.utils.variant
- GATKSVVariantContextUtils() - Constructor for class org.broadinstitute.hellbender.utils.variant.GATKSVVariantContextUtils
- GATKSVVCFConstants - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- GATKSVVCFConstants() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- GATKSVVCFConstants.ComplexVariantSubtype - Enum Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- GATKSVVCFConstants.StructuralVariantAnnotationType - Enum Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- GATKSVVCFHeaderLines - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- GATKSVVCFHeaderLines() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFHeaderLines
- GATKTool - Class in org.broadinstitute.hellbender.engine
-
Base class for all GATK tools.
- GATKTool() - Constructor for class org.broadinstitute.hellbender.engine.GATKTool
- GATKVariant - Interface in org.broadinstitute.hellbender.utils.variant
-
Variant is (currently) a minimal variant interface needed by the Hellbender pipeline.
- GATKVariantContextUtils - Class in org.broadinstitute.hellbender.utils.variant
- GATKVariantContextUtils() - Constructor for class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- GATKVariantContextUtils.AlleleMapper - Class in org.broadinstitute.hellbender.utils.variant
- GATKVariantContextUtils.FilteredRecordMergeType - Enum Class in org.broadinstitute.hellbender.utils.variant
- GATKVariantContextUtils.GenotypeMergeType - Enum Class in org.broadinstitute.hellbender.utils.variant
- GATKVCFConstants - Class in org.broadinstitute.hellbender.utils.variant
-
This class contains any constants (primarily FORMAT/INFO keys) in VCF files used by the GATK.
- GATKVCFConstants() - Constructor for class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- GATKVCFHeaderLines - Class in org.broadinstitute.hellbender.utils.variant
-
This class contains the
VCFHeaderLinedefinitions for the annotation keys inGATKVCFConstants. - GATKVCFHeaderLines() - Constructor for class org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines
- GATKVCFIndexType - Enum Class in org.broadinstitute.hellbender.utils.variant
-
Choose the Tribble indexing strategy
- GATKWDLDoclet - Class in org.broadinstitute.hellbender.utils.help
-
Custom Barclay-based Javadoc Doclet used for generating tool WDL.
- GATKWDLDoclet() - Constructor for class org.broadinstitute.hellbender.utils.help.GATKWDLDoclet
- GATKWDLWorkUnitHandler - Class in org.broadinstitute.hellbender.utils.help
-
The GATK WDL work unit handler.
- GATKWDLWorkUnitHandler(HelpDoclet) - Constructor for class org.broadinstitute.hellbender.utils.help.GATKWDLWorkUnitHandler
- GC - Variable in class picard.analysis.GcBiasDetailMetrics
-
The G+C content of the reference sequence represented by this bin.
- GC_CONTENT - Static variable in class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.CopyNumberAnnotations
- GC_CONTENT_SIZE - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- GC_CURVE_STANDARD_DEVIATION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
- GC_DROPOUT - Variable in class picard.analysis.directed.PanelMetricsBase
-
A measure of how undercovered >= 50% GC regions are relative to the mean.
- GC_DROPOUT - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Illumina-style GC dropout metric.
- GC_NC_0_19 - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Normalized coverage over quintile of GC content ranging from 0 - 19.
- GC_NC_20_39 - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Normalized coverage over each quintile of GC content ranging from 20 - 39.
- GC_NC_40_59 - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Normalized coverage over each quintile of GC content ranging from 40 - 59.
- GC_NC_60_79 - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Normalized coverage over each quintile of GC content ranging from 60 - 79.
- GC_NC_80_100 - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Normalized coverage over each quintile of GC content ranging from 80 - 100.
- GC_SCORE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- GCBiasCorrector - Class in org.broadinstitute.hellbender.tools.copynumber.denoising
-
Learn multiplicative correction factors as a function of GC content using a simple regression.
- GcBiasDetailMetrics - Class in picard.analysis
-
Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.
- GcBiasDetailMetrics() - Constructor for class picard.analysis.GcBiasDetailMetrics
- GcBiasMetrics - Class in picard.metrics
- GcBiasMetrics() - Constructor for class picard.metrics.GcBiasMetrics
- GcBiasMetricsCollector - Class in picard.analysis
-
Calculates GC Bias Metrics on multiple levels Created by kbergin on 3/23/15.
- GcBiasMetricsCollector(Set<MetricAccumulationLevel>, int[], List<SAMReadGroupRecord>, int, boolean) - Constructor for class picard.analysis.GcBiasMetricsCollector
- GcBiasMetricsCollector(Set<MetricAccumulationLevel>, int[], List<SAMReadGroupRecord>, int, boolean, boolean) - Constructor for class picard.analysis.GcBiasMetricsCollector
- GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector - Class in picard.analysis
- GcBiasSummaryMetrics - Class in picard.analysis
-
High level metrics that capture how biased the coverage in a certain lane is.
- GcBiasSummaryMetrics() - Constructor for class picard.analysis.GcBiasSummaryMetrics
- GcBiasUtils - Class in picard.analysis
-
Utilities to calculate GC Bias Created by kbergin on 9/23/15.
- GcBiasUtils() - Constructor for class picard.analysis.GcBiasUtils
- gcContent(VariantContext, FlowAnnotatorBase.LocalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- GcContent - Class in org.broadinstitute.hellbender.tools.walkers.annotator.flow
-
Flow Annotation: percentage of G or C in the window around hmer
- GcContent() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.flow.GcContent
- gcContentStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
A stratifier that uses GC (of the read) to stratify.
- GCContentStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.GCContentStratifier
- gcp - Variable in class org.broadinstitute.hellbender.utils.dragstr.DragstrParamsBuilder
- gcp(int, int) - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParams
-
Returns the GCP for a specific period and repeat length in Phred scale.
- GCP_TABLE_NAME - Static variable in class org.broadinstitute.hellbender.utils.dragstr.DragstrParamUtils
- gcpHMM - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- GCS - Enum constant in enum class picard.nio.PathProvider
- GCS_PREFIX - Static variable in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
- gcsMaxRetries() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- gcsProjectForRequesterPays() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- GENBANK_CATALOG_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
- GENBANK_CATALOG_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
- genbankCatalogPath - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
-
This may be supplied alone or in addition to the RefSeq catalog in the case that sequences from GenBank are present in the reference.
- gencallVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
- GENCODE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.DataSourceType
-
This value indicates a GENCODE GTF data file.
- GENCODE_GTF_FILE_PREFIX - Static variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfCodec
- GencodeFuncotation - Class in org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode
-
A class to represent a Functional Annotation.
- GencodeFuncotation.VariantClassification - Enum Class in org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode
-
Represents the type and severity of a variant.
- GencodeFuncotation.VariantType - Enum Class in org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode
- GencodeFuncotationBuilder - Class in org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode
-
A builder object to create
GencodeFuncotations. - GencodeFuncotationBuilder() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
- GencodeFuncotationBuilder(GencodeFuncotation) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
- GencodeFuncotationFactory - Class in org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode
-
A factory to create
GencodeFuncotations. - GencodeFuncotationFactory(Path, String, String, TranscriptSelectionMode, Set<String>, LinkedHashMap<String, String>, FeatureInput<? extends Feature>, String) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
Creates a
GencodeFuncotationFactorywith the 5'/3' flank sizes both set to 0 and will funcotate segments. - GencodeFuncotationFactory(Path, String, String, TranscriptSelectionMode, Set<String>, LinkedHashMap<String, String>, FeatureInput<? extends Feature>, FlankSettings, boolean, String, boolean) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
Create a
GencodeFuncotationFactory. - GencodeFuncotationFactory(Path, String, String, TranscriptSelectionMode, Set<String>, LinkedHashMap<String, String>, FeatureInput<? extends Feature>, FlankSettings, boolean, String, boolean, int) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
Create a
GencodeFuncotationFactory. - GencodeFuncotationFactory(Path, String, String, TranscriptSelectionMode, Set<String>, LinkedHashMap<String, String>, FeatureInput<? extends Feature>, FlankSettings, String) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
Create a
GencodeFuncotationFactorythat will funcotate segments. - GencodeGtfCDSFeature - Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
A Gencode GTF Feature representing a CDS.
- GencodeGtfCodec - Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
TribbleCodec to read data from a GENCODE GTF file. - GencodeGtfCodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfCodec
- GencodeGtfExonFeature - Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
A Gencode GTF Feature representing an exon.
- GencodeGtfFeature - Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
A
GencodeGtfFeaturerepresents data in a GENCODE GTF file. - GencodeGtfFeature(String[], String) - Constructor for class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
-
Populate this GencodeGtfFeature with the given data.
- GencodeGtfFeature(GencodeGtfFeatureBaseData) - Constructor for class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
-
Populate this GencodeGtfFeature with the given data.
- GencodeGtfFeature.AnnotationSource - Enum Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
Keyword identifying the source of the feature, like a program (e.g.
- GencodeGtfFeature.FeatureTag - Enum Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
Additional relevant information appended to a feature.
- GencodeGtfFeature.FeatureType - Enum Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
Type of the feature represented in a single line of a GENCODE GTF File.
- GencodeGtfFeature.GeneTranscriptStatus - Enum Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
Indication of whether a feature is new, tenatative, or already known.
- GencodeGtfFeature.GenomicPhase - Enum Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
Whether the first base of the CDS segment is the first (frame 0), second (frame 1) or third (frame 2) \ in the codon of the ORF.
- GencodeGtfFeature.KnownGeneBiotype - Enum Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
Biotype / transcript type for the transcript or gene represented in a feature.
- GencodeGtfFeature.LocusLevel - Enum Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
Status of how a position was annotated / verified: 1 - verified locus 2 - manually annotated locus 3 - automatically annotated locus For more information, see: https://www.gencodegenes.org/data_format.html https://en.wikipedia.org/wiki/General_feature_format
- GencodeGtfFeature.OptionalField<T> - Class in org.broadinstitute.hellbender.utils.codecs.gtf
- GencodeGtfFeature.RemapStatus - Enum Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
Attribute that indicates the status of the mapping.
- GencodeGtfFeature.RemapTargetStatus - Enum Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
Attribute that compares the mapping to the existing target annotations.
- GencodeGtfFeature.TranscriptSupportLevel - Enum Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
Transcript score according to how well mRNA and EST alignments match over its full length.
- GencodeGtfFeatureBaseData - Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
Struct-like container class for the fields in a
GencodeGtfFeatureThis is designed to be a basic dummy class to make feature instantiation easier. - GencodeGtfFeatureBaseData() - Constructor for class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
- GencodeGtfFeatureBaseData(String, int, String, String, GencodeGtfFeature.FeatureType, int, int, Strand, GencodeGtfFeature.GenomicPhase, String, String, String, GencodeGtfFeature.GeneTranscriptStatus, String, String, GencodeGtfFeature.GeneTranscriptStatus, String, int, String, GencodeGtfFeature.LocusLevel, List<GencodeGtfFeature.OptionalField<?>>, String) - Constructor for class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
- GencodeGtfGeneFeature - Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
A Gencode GTF Feature representing a gene.
- GencodeGtfSelenocysteineFeature - Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
A Gencode GTF Feature representing a selenocysteine.
- GencodeGtfStartCodonFeature - Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
A Gencode GTF Feature representing a start codon.
- GencodeGtfStopCodonFeature - Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
A Gencode GTF Feature representing a stop codon.
- GencodeGtfTranscriptFeature - Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
A Gencode GTF Feature representing a transcript.
- GencodeGtfUTRFeature - Class in org.broadinstitute.hellbender.utils.codecs.gtf
-
A Gencode GTF Feature representing an untranslated region.
- GENDER - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.PedReader.Field
- GENDER_CONCORDANCE_PF - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
Whether or not the three sexs agree
- GENDER_GTC - Variable in class picard.arrays.GtcToVcf
- gene - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Aggregation
- Gene - Class in picard.annotation
-
Holds annotation of a gene for storage in an OverlapDetector.
- Gene(String, int, int, boolean, String) - Constructor for class picard.annotation.Gene
- GENE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.SnpEffPositionModifier.PositionModifier
- GENE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- GENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureType
- GENE_CONFLICT - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapStatus
-
Transcripts in the gene mapped to multiple locations.
- GENE_NAME - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory.XsvDataKeyType
-
The key specified is a Gene Name which will be used to match and annotate a
VariantContext. - GENE_NAME - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- GENE_NAME_INDEX - Static variable in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- GENE_SIZE_CHANGE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapStatus
-
Transcripts caused gene length to change by more than 50%.
- Gene.Transcript - Class in picard.annotation
-
A single transcript of a gene.
- Gene.Transcript.Exon - Class in picard.annotation
-
1-based, inclusive representation of an exon.
- GeneAnnotationReader - Class in picard.annotation
-
Load gene annotations into an OverlapDetector of Gene objects.
- GeneAnnotationReader() - Constructor for class picard.annotation.GeneAnnotationReader
- GeneExpressionEvaluation - Class in org.broadinstitute.hellbender.tools.walkers.rnaseq
-
Evaluate gene expression from RNA-seq reads aligned to genome.
- GeneExpressionEvaluation() - Constructor for class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation
- GeneExpressionEvaluation.Coverage - Class in org.broadinstitute.hellbender.tools.walkers.rnaseq
- GeneExpressionEvaluation.FragmentCountReader - Class in org.broadinstitute.hellbender.tools.walkers.rnaseq
- GeneExpressionEvaluation.FragmentCountWriter - Class in org.broadinstitute.hellbender.tools.walkers.rnaseq
- GeneExpressionEvaluation.SingleStrandFeatureCoverage - Class in org.broadinstitute.hellbender.tools.walkers.rnaseq
- geneId - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
- GeneListOutputRenderer - Class in org.broadinstitute.hellbender.tools.funcotator.genelistoutput
-
This class can - only work on segments.
- GeneListOutputRenderer(Path, LinkedHashMap<String, String>, LinkedHashMap<String, String>, Set<String>, String) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.genelistoutput.GeneListOutputRenderer
- GeneListOutputRenderer(Path, LinkedHashMap<String, String>, LinkedHashMap<String, String>, Set<String>, String, int) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.genelistoutput.GeneListOutputRenderer
- geneName - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
- GENERATE_SITES_TEXT_OUTPUT_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFile
- generateAD(int[], int[]) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
-
Generates a new AD array by adding zeros for missing alleles given the set of indexes of the Genotype's current alleles from the original AD.
- generateAdditionalWriters(List<SAMReadGroupRecord>, FastqWriterFactory) - Method in class picard.sam.SamToFastq
- generateAdditionalWriters(List<SAMReadGroupRecord>, FastqWriterFactory) - Method in class picard.sam.SamToFastqWithTags
- generateAF(double[], int[]) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
-
Generates a new AF (allele fraction) array
- generateAnnotationValueVector(VCFHeaderLineCount, List<T>, int[]) - Static method in class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
-
Generates a new annotation value array by adding zeros for missing alleles given the set of indexes of the Genotype's current alleles from the original annotation value array.
- generateCsv(File, Map<String, RecalibrationReport>) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
-
Prints out a collection of reports into a file in Csv format in a way that can be used by R scripts (such as the plot generator script).
- generateDuplicateIndexes(boolean, boolean) - Method in class picard.sam.markduplicates.MarkDuplicates
-
Goes through the accumulated ReadEndsForMarkDuplicates objects and determines which of them are to be marked as duplicates.
- generateDuplicateIndexes(boolean, boolean) - Method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
-
This method is identical in function to generateDuplicateIndexes except that it accomodates for the possible significance of the end side of the reads (w/ or w/o uncertainty).
- generateDuplicateIndexes(boolean, boolean) - Method in interface picard.sam.markduplicates.MarkDuplicatesHelper
- generateEmptyLLocalAssemblyResult(AssemblyRegion, Haplotype, byte[], SimpleInterval, LongHomopolymerHaplotypeCollapsingEngine) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- generateFastaForSequence(GATKPath, String, GATKPath) - Static method in class org.broadinstitute.hellbender.tools.reference.CompareReferences
-
Method to generate a fasta file for an individual sequence in a reference
- generateFilterString(double) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSR
-
Generate the VCF filter string for this record based on the provided lod score
- generateFilterStringFromAlleles(VariantContext, double) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSR
-
Generate the VCF filter string for this record based on the ApplyVQSR modes run so far
- generateJunctionTrees() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
- generateMissingDataWarning(VariantContext, Genotype, AlleleLikelihoods<GATKRead, Allele>) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils
- generateModel(List<VariantDatum>, int) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorEngine
- generateNoMatchBarcode(ReadStructure) - Static method in class picard.illumina.BarcodeExtractor
- generatePlots(File, File, File) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
-
s Write recalibration plots into a file
- generatePythonArguments() - Method in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- generatePythonArguments(DetermineGermlineContigPloidy.RunMode) - Method in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineContigPloidyModelArgumentCollection
- generatePythonArguments(GermlineCNVCaller.RunMode) - Method in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCallingArgumentCollection
- generatePythonArguments(GermlineCNVCaller.RunMode) - Method in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
-
Generates arguments for the python CLI tool.
- generateReadName(ClusterData, Integer) - Method in class picard.fastq.Casava18ReadNameEncoder
- generateReadName(ClusterData, Integer) - Method in class picard.fastq.IlluminaReadNameEncoder
- generateReadName(ClusterData, Integer) - Method in interface picard.fastq.ReadNameEncoder
-
Generates a read name string for the provided cluster.
- generateReferencePairs() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
-
Generate ReferencePairs for pairwise comparison of all references present in the table
- generateReferencePairsAgainstDictionary(GATKPath) - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
-
Generate ReferencePairs for comparison of all references present in the table against a provided dictionary.
- generateReportTable() - Method in class org.broadinstitute.hellbender.utils.recalibration.QuantizationInfo
- generateReportTable(String) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
- generateReportTables(RecalibrationTables, StandardCovariateList) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- generateShortName(ClusterData) - Method in class picard.fastq.Casava18ReadNameEncoder
- generateShortName(ClusterData) - Method in class picard.fastq.IlluminaReadNameEncoder
- generateShortName(ClusterData) - Method in interface picard.fastq.ReadNameEncoder
-
Generates a short read name that includes a minimal amount of information, this is used primarily for read sorting.
- generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Method in class picard.analysis.CollectRawWgsMetrics
- generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Method in class picard.analysis.CollectWgsMetrics
- generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
- generatingAccumulatorsBy(VariantProcessor.AccumulatorGenerator<A, R>) - Static method in class picard.vcf.processor.VariantProcessor.Builder
- GENES_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
Used when generating the genes field name for segment funcotations.
- geneStatus - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
- geneType - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
-
There are no formal definitions for what can be a valid geneType and the number of possible values seem to increase as new versions of Gencode are released.
- GENOME_ASSEMBLY - Variable in class picard.sam.CreateSequenceDictionary
- GENOME_BUILD_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- GENOME_SIZE - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of bases in the reference genome used for alignment.
- GENOME_TERRITORY - Variable in class picard.analysis.WgsMetrics
-
The number of non-N bases in the genome reference over which coverage will be evaluated.
- GenomeLoc - Class in org.broadinstitute.hellbender.utils
-
Genome location representation.
- GenomeLoc(String, int, int, int) - Constructor for class org.broadinstitute.hellbender.utils.GenomeLoc
- GenomeLocParser - Class in org.broadinstitute.hellbender.utils
-
Factory class for creating GenomeLocs
- GenomeLocParser(ReferenceSequenceFile) - Constructor for class org.broadinstitute.hellbender.utils.GenomeLocParser
-
set our internal reference contig order
- GenomeLocParser(SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Create a new GenomeLocParser based on seqDictionary with the standard validation level
- GenomeLocParser(SAMSequenceDictionary, GenomeLocParser.ValidationLevel) - Constructor for class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Create a genome loc parser based on seqDict with the specified level of validation
- GenomeLocParser.ValidationLevel - Enum Class in org.broadinstitute.hellbender.utils
-
How much validation should we do at runtime with this parser?
- genomeLocsFromLocatables(GenomeLocParser, Collection<? extends Locatable>) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Generates a list of
GenomeLocinstances given the appropriateGenomeLocParserfactory and a collection ofLocatableinstances. - GenomeLocSortedSet - Class in org.broadinstitute.hellbender.utils
-
Class GenomeLocCollection
- GenomeLocSortedSet(GenomeLocParser) - Constructor for class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
Create a new, empty GenomeLocSortedSet
- GenomeLocSortedSet(GenomeLocParser, Collection<GenomeLoc>) - Constructor for class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
Create a new GenomeLocSortedSet containing locations l The elements in l can be in any order, and can be overlapping.
- GenomeLocSortedSet(GenomeLocParser, GenomeLoc) - Constructor for class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
Create a new GenomeLocSortedSet containing location e
- GENOMIC_DB_URI_SCHEME - Static variable in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Schemes starting with gendb could be GenomicsDB paths
- genomicCoordinatesToBinIndexMap - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.BinnedCNVLinkage
- genomicPhase - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
-
Frame/phase of this feature.
- genomicPosition - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
-
Location of this feature on the genome.
- genomicsDBApppendPaths(String, String) - Static method in class org.broadinstitute.hellbender.tools.genomicsdb.GATKGenomicsDBUtils
-
Appends path to the given parent path.
- GenomicsDBArgumentCollection - Class in org.broadinstitute.hellbender.tools.genomicsdb
- GenomicsDBArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection
- GenomicsDBConstants - Class in org.broadinstitute.hellbender.tools.genomicsdb
-
Constants related to GenomicsDB
- genomicsDBGetAbsolutePath(String) - Static method in class org.broadinstitute.hellbender.tools.genomicsdb.GATKGenomicsDBUtils
- GenomicsDBImport - Class in org.broadinstitute.hellbender.tools.genomicsdb
-
Import single-sample GVCFs into GenomicsDB before joint genotyping.
- GenomicsDBImport() - Constructor for class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- genomicsDBOptions - Variable in class org.broadinstitute.hellbender.engine.VariantWalkerBase
- GenomicsDBOptions - Class in org.broadinstitute.hellbender.tools.genomicsdb
-
Encapsulates the GenomicsDB-specific options relevant to the FeatureDataSource
- GenomicsDBOptions() - Constructor for class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBOptions
- GenomicsDBOptions(Path) - Constructor for class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBOptions
- GenomicsDBOptions(Path, GenomicsDBArgumentCollection) - Constructor for class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBOptions
- GenomicsDBOptions(Path, GenomicsDBArgumentCollection, GenotypeCalculationArgumentCollection) - Constructor for class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBOptions
- genomicStrand - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
-
Which strand this feature is on.
- genotype - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- GENOTYPE_AND_VALIDATE_STATUS_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- GENOTYPE_ASSIGNMENT_METHOD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- GENOTYPE_CONCORDANCE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The genotype concordance for all possible states.
- GENOTYPE_CONCORDANCE_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- GENOTYPE_FILTER_EXPRESSION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- GENOTYPE_FILTER_NAME_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- GENOTYPE_GERMLINE_SITES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- GENOTYPE_LOD_THRESHOLD - Variable in class picard.fingerprint.CalculateFingerprintMetrics
- GENOTYPE_LOD_THRESHOLD - Variable in class picard.fingerprint.CheckFingerprint
- GENOTYPE_PON_SITES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- GENOTYPE_PRIOR_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- GENOTYPE_SELECT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
- GENOTYPE_SELECT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
-
JEXL expressions to be applied to genotype (FORMAT) fields e.g.
- GenotypeAlleleCounts - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
-
Collection of allele counts for a genotype.
- genotypeAlleleCountsAt(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculator
-
Returns the genotype associated to a particular likelihood index.
- GenotypeAnnotation - Interface in org.broadinstitute.hellbender.tools.walkers.annotator
-
Represents an annotation that is computed for a single genotype.
- genotypeArgs - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection
- genotypeArgs - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- genotypeAssignmentMethod - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- GenotypeAssignmentMethod - Enum Class in org.broadinstitute.hellbender.tools.walkers.genotyper
-
Created by davidben on 6/10/16.
- GenotypeCalculationArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
- GenotypeCalculationArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
-
Creates a GenotypeCalculationArgumentCollection with default values.
- GenotypeConcordance - Class in picard.vcf
-
Summary
- GenotypeConcordance() - Constructor for class picard.vcf.GenotypeConcordance
- GenotypeConcordance.Alleles - Class in picard.vcf
-
A simple structure to return the results of getAlleles.
- GenotypeConcordanceContingencyMetrics - Class in picard.vcf
-
Class that holds metrics about the Genotype Concordance contingency tables.
- GenotypeConcordanceContingencyMetrics() - Constructor for class picard.vcf.GenotypeConcordanceContingencyMetrics
-
Empty constructor - needed for unit tests
- GenotypeConcordanceContingencyMetrics(VariantContext.Type, GenotypeConcordanceCounts, String, String, boolean) - Constructor for class picard.vcf.GenotypeConcordanceContingencyMetrics
- GenotypeConcordanceCounts - Class in picard.vcf
-
A class to store the counts for various truth and call state classifications relative to a reference.
- GenotypeConcordanceCounts() - Constructor for class picard.vcf.GenotypeConcordanceCounts
- GenotypeConcordanceDetailMetrics - Class in picard.vcf
-
Class that holds detail metrics about Genotype Concordance
- GenotypeConcordanceDetailMetrics() - Constructor for class picard.vcf.GenotypeConcordanceDetailMetrics
- GenotypeConcordanceScheme - Class in picard.vcf
-
This defines for each valid TruthState and CallState tuple, the set of contingency table entries that to which the tuple should contribute.
- GenotypeConcordanceScheme() - Constructor for class picard.vcf.GenotypeConcordanceScheme
- GenotypeConcordanceSchemeFactory - Class in picard.vcf
-
Created by kbergin on 6/19/15.
- GenotypeConcordanceSchemeFactory() - Constructor for class picard.vcf.GenotypeConcordanceSchemeFactory
- GenotypeConcordanceStateCodes - Enum Class in picard.vcf
-
Created by kbergin on 7/30/15.
- GenotypeConcordanceStates - Class in picard.vcf
-
A class to store the various classifications for: 1.
- GenotypeConcordanceStates() - Constructor for class picard.vcf.GenotypeConcordanceStates
- GenotypeConcordanceStates.CallState - Enum Class in picard.vcf
-
These states represent the relationship between the call genotype and the truth genotype relative to a reference sequence.
- GenotypeConcordanceStates.ContingencyState - Enum Class in picard.vcf
-
A specific state for a 2x2 contingency table.
- GenotypeConcordanceStates.TruthAndCallStates - Class in picard.vcf
-
A minute class to store the truth and call state respectively.
- GenotypeConcordanceStates.TruthState - Enum Class in picard.vcf
-
These states represent the relationship between a truth genotype and the reference sequence.
- GenotypeConcordanceSummaryMetrics - Class in picard.vcf
-
Class that holds summary metrics about Genotype Concordance
- GenotypeConcordanceSummaryMetrics() - Constructor for class picard.vcf.GenotypeConcordanceSummaryMetrics
-
Empty constructor - needed for unit tests
- GenotypeConcordanceSummaryMetrics(VariantContext.Type, GenotypeConcordanceCounts, String, String, boolean) - Constructor for class picard.vcf.GenotypeConcordanceSummaryMetrics
- genotypeCount() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculator
-
Returns the number of possible genotypes given ploidy and the maximum allele index.
- genotypeCount(int, int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculators
-
Returns the number of possible genotypes given the ploidy and number of different alleles.
- GenotypeCounts - Class in org.broadinstitute.hellbender.utils
- GenotypeCounts(double, double, double) - Constructor for class org.broadinstitute.hellbender.utils.GenotypeCounts
- genotypeDistance(SVCallRecord, SVCallRecord) - Static method in class org.broadinstitute.hellbender.tools.sv.concordance.ClosestSVFinder
-
Genotype distance, defined as the negative fraction of matching genotypes, or
Integer.MAX_VALUEif one record is null. - GenotypeFilter - Interface in picard.vcf.filter
-
An interface for classes that perform Genotype filtration.
- genotypeFilterExpressions - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
-
Similar to the INFO field based expressions, but used on the FORMAT (genotype) fields instead.
- genotypeFilterNames - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
-
Similar to the INFO field based expressions, but used on the FORMAT (genotype) fields instead.
- GenotypeFilterSummary - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
-
Created by bimber on 5/17/2017.
- GenotypeFilterSummary(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.GenotypeFilterSummary
- genotypeGermlineSites - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
Usually we exclude germline sites from active region determination to save runtime.
- GenotypeGVCFs - Class in org.broadinstitute.hellbender.tools.walkers
-
Perform joint genotyping on one or more samples pre-called with HaplotypeCaller
- GenotypeGVCFs() - Constructor for class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- GenotypeGVCFsAnnotationArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers
- GenotypeGVCFsAnnotationArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsAnnotationArgumentCollection
- GenotypeGVCFsEngine - Class in org.broadinstitute.hellbender.tools.walkers
-
Engine class to allow for other classes to replicate the behavior of GenotypeGVCFs.
- GenotypeGVCFsEngine(VariantAnnotatorEngine, GenotypeCalculationArgumentCollection, boolean, VCFHeader, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine
-
Create and initialize a new GenotypeGVCFsEngine given a collection of GenotypeGVCF arguments and a VCF header
- genotypeHets(List<AllelicCountCollection>, AllelicCountCollection, SimpleIntervalCollection, int, int, double, double) - Static method in class org.broadinstitute.hellbender.tools.copynumber.utils.genotyping.NaiveHeterozygousPileupGenotypingUtils
-
Filters allelic counts based on total count, overlap with copy-ratio intervals, and a naive test for heterozygosity.
- genotypeIndexMap(int[], GenotypeLikelihoodCalculators) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculator
-
Composes a genotype index map given a allele index recoding.
- genotypeIsUsableForAFCalculation(Genotype) - Static method in class org.broadinstitute.hellbender.utils.GenotypeUtils
-
Do we have (or can we infer) likelihoods necessary for allele frequency calculation? Some reblocked and/or DRAGEN GVCFs omit likelihoods for ref blocks, but we can estimate them If GenomicsDB max alt threshold is too low, non-reference genotypes may also be missing PLs -- we can't estimate, so reject those
- genotypeLikelihoodByRead(double[], int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculator
-
Calculates the likelihood component of each read on each genotype.
- GenotypeLikelihoodCalculator - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
- GenotypeLikelihoodCalculator(int, int, int[][], GenotypeAlleleCounts[][]) - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculator
- GenotypeLikelihoodCalculatorDRAGEN - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
-
Helper to calculate genotype likelihoods for DRAGEN advanced genotyping models (BQD - Base Quality Dropout, and FRD - Foreign Reads Detection).
- GenotypeLikelihoodCalculatorDRAGEN(int, int, int[][], GenotypeAlleleCounts[][]) - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculatorDRAGEN
-
Creates a new calculator providing its ploidy and number of genotyping alleles.
- GenotypeLikelihoodCalculators - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
-
Genotype likelihood calculator utility.
- GenotypeLikelihoodCalculators() - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculators
- genotypeLikelihoods(LikelihoodMatrix<EVIDENCE, A>) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculator
-
Calculate the likelihoods given the list of alleles and the likelihood map.
- genotypeLikelihoods(LikelihoodMatrix<EVIDENCE, A>) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculatorDRAGEN
- genotypePonSites - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
Usually we exclude sites in the panel of normals from active region determination, which saves time.
- GenotypePriorCalculator - Class in org.broadinstitute.hellbender.utils.genotyper
-
Class to compose genotype prior probability calculators.
- GenotypeQualityFilter - Class in picard.vcf.filter
-
Genotype filter that filters out genotypes below a given quality threshold.
- GenotypeQualityFilter(int) - Constructor for class picard.vcf.filter.GenotypeQualityFilter
- genotyperDebugOutStream - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- GENOTYPES - Variable in class picard.fingerprint.CheckFingerprint
- genotypeScore - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- GenotypeSummaries - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Summarize genotype statistics from all samples at the site level
- GenotypeSummaries() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeSummaries
- GenotypeUtils - Class in org.broadinstitute.hellbender.utils
- GENOTYPING_BASE_ERROR_RATE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticGenotypingArgumentCollection
- GENOTYPING_ERROR_RATE - Variable in class picard.fingerprint.CrosscheckFingerprints
- GENOTYPING_HOMOZYGOUS_LOG_RATIO_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticGenotypingArgumentCollection
- GenotypingArraysProgramGroup - Class in picard.cmdline.programgroups
-
Miscellaneous tools, e.g.
- GenotypingArraysProgramGroup() - Constructor for class picard.cmdline.programgroups.GenotypingArraysProgramGroup
- genotypingBaseErrorRate - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticGenotypingArgumentCollection
- GenotypingData<A extends htsjdk.variant.variantcontext.Allele> - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
-
Encapsulates the data use to make the genotype calls.
- GenotypingData(PloidyModel, AlleleLikelihoods<GATKRead, A>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingData
-
Constructs a new genotyping-data collection providing the ploidy model to apply to the input model and the read-likelihoods collection.
- genotypingEngine - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- GenotypingEngine<Config extends StandardCallerArgumentCollection> - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
-
Base class for genotyper engines.
- GenotypingEngine(Config, SampleList, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
-
Construct a new genotyper engine, on a specific subset of samples.
- genotypingHomozygousLogRatioThreshold - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticGenotypingArgumentCollection
- GenotypingLikelihoods<A extends htsjdk.variant.variantcontext.Allele> - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
-
Genotyping Likelihoods collection.
- GenotypingModel - Interface in org.broadinstitute.hellbender.tools.walkers.genotyper
-
A wrapping interface between the various versions of genotypers so as to keep them interchangeable.
- GERMLINE_ARG_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader
- GERMLINE_HET - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- GERMLINE_QUAL_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- GERMLINE_RESOURCE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- GERMLINE_RISK_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- GERMLINE_TAG_HEADER - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEvents
- GermlineCallingArgumentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.arguments
- GermlineCallingArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCallingArgumentCollection
- GermlineCNVCaller - Class in org.broadinstitute.hellbender.tools.copynumber
-
Calls copy-number variants in germline samples given their counts and the corresponding output of
DetermineGermlineContigPloidy. - GermlineCNVCaller() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller
- GermlineCNVCaller.RunMode - Enum Class in org.broadinstitute.hellbender.tools.copynumber
- GermlineCNVHybridADVIArgumentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.arguments
- GermlineCNVHybridADVIArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCNVHybridADVIArgumentCollection
- GermlineCNVIntervalVariantComposer - Class in org.broadinstitute.hellbender.tools.copynumber.gcnv
-
Helper class for
PostprocessGermlineCNVCallsfor single-sample postprocessing ofGermlineCNVCallercalls into genotyped intervals. - GermlineCNVIntervalVariantComposer(VariantContextWriter, String, IntegerCopyNumberState, Set<String>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVIntervalVariantComposer
-
Constructor for
PostprocessGermlineCNVCallsPostprocessor - GermlineCNVNamingConstants - Class in org.broadinstitute.hellbender.tools.copynumber.gcnv
-
This class stores naming standards in the
GermlineCNVCaller. - GermlineCNVNamingConstants() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVNamingConstants
- GermlineCNVSegmentVariantComposer - Class in org.broadinstitute.hellbender.tools.copynumber.gcnv
-
Helper class for
PostprocessGermlineCNVCallsfor single-sample postprocessing of segmentedGermlineCNVCallercalls. - GermlineCNVSegmentVariantComposer(VariantContextWriter, String, IntegerCopyNumberState, Set<String>, ReferenceSequenceFile) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVSegmentVariantComposer
- GermlineCNVSegmentVariantComposer(VariantContextWriter, String, IntegerCopyNumberState, Set<String>, ReferenceSequenceFile, int, int, int, double, File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVSegmentVariantComposer
-
Constructor.
- GermlineCNVVariantComposer<DATA extends htsjdk.samtools.util.Locatable> - Class in org.broadinstitute.hellbender.tools.copynumber.gcnv
-
Base class for
GermlineCNVIntervalVariantComposerandGermlineCNVSegmentVariantComposer. - GermlineContigPloidyHybridADVIArgumentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.arguments
- GermlineContigPloidyHybridADVIArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineContigPloidyHybridADVIArgumentCollection
- GermlineContigPloidyModelArgumentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.arguments
- GermlineContigPloidyModelArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineContigPloidyModelArgumentCollection
- GermlineDenoisingModelArgumentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.arguments
- GermlineDenoisingModelArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
- GermlineDenoisingModelArgumentCollection.CopyNumberPosteriorExpectationMode - Enum Class in org.broadinstitute.hellbender.tools.copynumber.arguments
- GermlineFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- GermlineFilter(List<File>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.GermlineFilter
- germlineMode - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.AssemblyComplexity
- germlineProbability(double, double, double, double, double) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.GermlineFilter
- germlineResource - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals
-
A resource, such as gnomAD, containing population allele frequencies of common and rare variants.
- germlineResource - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
A resource, such as gnomAD, containing population allele frequencies of common and rare variants.
- get() - Method in class org.broadinstitute.hellbender.utils.AutoCloseableReference
-
Returns the referred object.
- get() - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
- get(int) - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCases
- get(int) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigListRC
- get(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NearbyKmerErrorCorrector.CorrectionSet
-
Get list of corrections for a particular offset
- get(int) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- get(int) - Method in class org.broadinstitute.hellbender.utils.bigquery.QueryRecord
- get(int) - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
-
Get a value from this
XsvTableFeature. - get(int) - Method in class org.broadinstitute.hellbender.utils.collections.IndexedSet
-
Returns the element given its index within the set.
- get(int) - Method in class org.broadinstitute.hellbender.utils.dragstr.DoubleSequence
-
Returns an element of the sequence by its 0-base index.
- get(int) - Method in class org.broadinstitute.hellbender.utils.IntToDoubleFunctionCache
-
Get the value of the function, expanding the cache as necessary.
- get(int) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.CovariateKeyCache
-
Get the cached value for the given readlength or null is no value is cached.
- get(int) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList
-
Get the covariate by the index.
- get(int) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the string value in a column by its index.
- get(int) - Method in class picard.analysis.CounterManager.Counter
- get(int) - Method in class picard.illumina.parser.readers.BclIndexReader
- get(int) - Method in class picard.illumina.parser.ReadStructure.Substructure
- get(int...) - Method in class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray
- get(int, int) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix
- get(int, int) - Method in interface org.broadinstitute.hellbender.utils.genotyper.LikelihoodMatrix
-
Returns the likelihood of a unit of evidence given a haplotype.
- get(int, int) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Get a value from the given position in the table
- get(int, String) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Get a value from the given position in the table
- get(Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection
-
Get the value for an allele, REF or ALT
- get(Double) - Method in class org.broadinstitute.hellbender.utils.Histogram
-
Return the count of items in the bin corresponding to the provided value
- get(Enum<?>) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the string value of a column by its name.
- get(Object) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- get(Object) - Method in class org.broadinstitute.hellbender.utils.config.ConfigFactory
-
Wrapper around
ConfigCache.get(Object). - get(Object, String) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Get a value from the given position in the table
- get(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
-
Get the value in this
TableFuncotationcorresponding to the given key. - get(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
-
Get all funcotations for the given transcript.
- get(String) - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPriorCollection
- get(String) - Method in class org.broadinstitute.hellbender.utils.bigquery.QueryRecord
- get(String) - Method in class org.broadinstitute.hellbender.utils.codecs.table.TableFeature
-
Gets the value associated with the key.
- get(String) - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
-
Get a value from this
XsvTableFeature. - get(String) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the string value in a column by its index.
- get(String, String) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.PloidyTable
- get(String, String) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the string value in a column by its index.
- get(String, Nucleotide, ReadOrientation) - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.DepthOneHistograms
- get(List<Object>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- get(Decile) - Method in class org.broadinstitute.hellbender.utils.mcmc.DecileCollection
-
Gets the specified decile.
- get(Nucleotide) - Method in class org.broadinstitute.hellbender.utils.Nucleotide.Counter
-
Returns the current count for a given nucleotide.
- get(T, Class<U>) - Method in class org.broadinstitute.hellbender.utils.mcmc.ParameterizedState
-
Returns the value of a
Parametercontained in the collection held by theParameterizedState, given theParameterEnumkey and type of theParameter. - get1Key(int) - Method in class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray
-
Specialized version of get for 1 parameter.
- get2Keys(int, int) - Method in class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray
-
Specialized version of get for 2 parameters.
- get3Keys(int, int, int) - Method in class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray
-
Specialized version of get for 3 parameters.
- get3PrimeAdapter() - Method in interface org.broadinstitute.hellbender.utils.illumina.AdapterPair
- get3PrimeAdapter() - Method in enum class org.broadinstitute.hellbender.utils.illumina.IlluminaAdapterPair
- get3PrimeAdapter() - Method in interface picard.util.AdapterPair
- get3PrimeAdapter() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- get3PrimeAdapterBytes() - Method in interface picard.util.AdapterPair
- get3PrimeAdapterBytes() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- get3PrimeAdapterBytesInReadOrder() - Method in interface picard.util.AdapterPair
- get3PrimeAdapterBytesInReadOrder() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- get3PrimeAdapterInReadOrder() - Method in interface picard.util.AdapterPair
- get3PrimeAdapterInReadOrder() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- get3PrimeSoftClippedBases(Cigar, boolean) - Static method in class picard.analysis.AlignmentSummaryMetricsCollector
-
returns the length of the soft clip on the 3' end If there are no-non-clipping operators, method will return 0 as it is unclear which clips should be considered on the "3'" end.
- get4Keys(int, int, int, int) - Method in class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray
-
Specialized version of get for 4 parameters.
- get5PrimeAdapter() - Method in interface org.broadinstitute.hellbender.utils.illumina.AdapterPair
- get5PrimeAdapter() - Method in enum class org.broadinstitute.hellbender.utils.illumina.IlluminaAdapterPair
- get5PrimeAdapter() - Method in interface picard.util.AdapterPair
- get5PrimeAdapter() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- get5PrimeAdapterBytes() - Method in interface picard.util.AdapterPair
- get5PrimeAdapterBytes() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- get5PrimeAdapterBytesInReadOrder() - Method in interface picard.util.AdapterPair
- get5PrimeAdapterBytesInReadOrder() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- get5PrimeAdapterInReadOrder() - Method in interface picard.util.AdapterPair
- get5PrimeAdapterInReadOrder() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- getAaCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getAaEndPos() - Method in class org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo
- getAaStartPos() - Method in class org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo
- getAbbreviation() - Method in enum class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceState
- getAbCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getAbsolutePathWithGenomicsDBURIScheme(GATKPath) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Get the GenomicsDB equivalent absolute URL for a given path
- getAbsolutePathWithoutFileProtocol(Path) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Gets the absolute Path name with the URI marker, handling the special case of the default file system by removing the file:// prefix.
- getAccessionLength(String) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
- getAccessions() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
- getAccumulatedOutput() - Method in class org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor
-
Return all data accumulated since the last call to
StreamingPythonScriptExecutor.getAccumulatedOutput()(either directly, or indirectly throughStreamingPythonScriptExecutor.sendSynchronousCommand(java.lang.String). - getAccurateKmerCoverage(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getActualTiles(List<IlluminaFileUtil.SupportedIlluminaFormat>) - Method in class picard.illumina.parser.IlluminaFileUtil
-
Get the available tiles for the given formats, if the formats have tile lists that differ then throw an exception, if any of the format
- getADAMReads(GATKPath, TraversalParameters, SAMFileHeader) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource
-
Loads ADAM reads stored as Parquet.
- getAdaptorBoundary() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Finds the adaptor boundary around the read and returns the first base inside the adaptor that is closest to the read boundary.
- getAdaptorBoundary() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getAdaptorBoundary(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Finds the adaptor boundary around the read and returns the first base inside the adaptor that is closest to the read boundary.
- getAdditionalCovariates() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList
-
returns an unmodifiable view of the additional covariates stored in this list.
- getAdditionalInfo() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
- getAdditionalInfo() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex
- getAdditionalSequence(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
-
Get the sequence unique to this vertex This function may not return the entire sequence stored in the vertex, as kmer graphs really only provide 1 base of additional sequence (the last base of the kmer).
- getAdditionalSequence(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex
-
Get the sequence unique to this vertex This function may not return the entire sequence stored in the vertex, as kmer graphs really only provide 1 base of additional sequence (the last base of the kmer).
- getAdditionalSequence(BaseVertex, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Pull out the additional sequence implied by traversing this node in the graph
- getAdditionalSequence(V) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Pull out the additional sequence implied by traversing this node in the graph
- getAdditionalTables() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
- getAddressA() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getAddressAId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getAddressB() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getAddressBId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getAffection() - Method in class org.broadinstitute.hellbender.utils.samples.Sample
- getAFScale() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- getAlgorithms() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getAlgorithms(VariantContext) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
- getAlignedAlternateAllele() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getAlignedAssemblyOrExcuseList() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark.AssembledEvidenceResults
- getAlignedCodingSequenceAllele(String, Integer, Integer, Allele, Integer, Strand) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Gets the coding sequence for the allele with given start and stop positions, codon-aligned to the start of the reference sequence.
- getAlignedCodingSequenceAlleleStart() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getAlignedCodingSequenceAlternateAllele() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getAlignedCodingSequenceReferenceAllele() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getAlignedContigs() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContigGenerator
- getAlignedContigs() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigAlignmentsRDDProcessor.SAMFormattedContigAlignmentParser
- getAlignedContigs() - Method in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser
- getAlignedContigsInOneAssembly(AlignedAssemblyOrExcuse, List<String>, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser
-
Work on "successful" assembly and turn its contigs' alignments to custom
AlignmentIntervalformat. - getAlignedEndPosition(int) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Get the sequence-aligned end position for the given allele end position.
- getAlignedPosition(int) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Gets the sequence aligned position (1-based, inclusive) for the given coding sequence position.
- getAlignedReadHistogram() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- getAlignedRefAllele(StrandCorrectedReferenceBases, int, Allele, Allele, int, int, Strand, Locatable) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Get the aligned coding sequence for the given reference allele.
- getAlignedReferenceAllele() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getAlignedReferenceAlleleStop() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getAligner() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SingleSequenceReferenceAligner
-
Gives access to the underlying aligner so that you can modify its options.
- getAligner(SmithWatermanAligner.Implementation) - Static method in interface org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner
-
Factory method to get an instance of an aligner corresponding to the given implementation
- getAlignment() - Method in class org.broadinstitute.hellbender.utils.report.GATKReportColumnFormat
- getAlignmentContext() - Method in class org.broadinstitute.hellbender.engine.AlignmentAndReferenceContext
-
getter for the AlignmentContect
- getAlignmentContext() - Method in class org.broadinstitute.hellbender.engine.spark.LocusWalkerContext
- getAlignmentData() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Method for obtaining the alignment data which is attached to the assembly region.
- getAlignmentEnd() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- getAlignmentEvidence() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence
- getAlignmentOffset() - Method in interface org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAlignment
- getAlignments() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
- getAlignments() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- getAlignments(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark
-
Loads alignments and the corresponding reference and features into a
JavaRDDfor the intervals specified. - getAlignmentSignatureBasicType() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- getAlignmentStart() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- getAlignmentStartHapwrtRef() - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- getAll() - Method in class org.broadinstitute.hellbender.utils.mcmc.DecileCollection
-
Gets a list of all deciles.
- getAllele() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleAndContext
- getAllele(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingData
- getAllele(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingLikelihoods
- getAllele(int) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix
- getAllele(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Returns the allele given its index.
- getAllele(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.ActualPermutation
- getAllele(int) - Method in interface org.broadinstitute.hellbender.utils.genotyper.AlleleList
-
Returns the allele at the given index in this AlleleList.
- getAllele(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.NonPermutation
- getAllele(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.IndexedAlleleList
- getAllele(int) - Method in interface org.broadinstitute.hellbender.utils.genotyper.LikelihoodMatrix
-
Returns the allele given its index.
- getAllele1() - Method in enum class picard.fingerprint.DiploidGenotype
- getAllele1() - Method in class picard.fingerprint.Snp
- getAllele2() - Method in enum class picard.fingerprint.DiploidGenotype
- getAllele2() - Method in class picard.fingerprint.Snp
- getAlleleA() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getAlleleAProbeSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getAlleleAProbeSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getAlleleB() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getAlleleBProbeSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getAlleleBProbeSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getAlleleCount(Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.HeterozygosityCalculator
- getAlleleCountAtMLE(Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculationResult
-
Returns the AC of allele a la #getAlleleCountsOfMLE
- getAlleleCountsOfMLE() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculationResult
-
Returns a vector with maxAltAlleles values containing AC values at the MLE The values of the ACs for this call are stored in the getAllelesUsedInGenotyping order, starting from index 0 (i.e., the first alt allele is at 0).
- getAlleleDepths(GenotypesContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth
- getAlleleForCopyNumber(int, int, Allele) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKSVVariantContextUtils
- getAlleleFrequency() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- getAlleleLengthListOfString(String) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils
-
Handles all the Java and htsjdk parsing shenanigans
- getAlleleLikelihoods(Locatable, String, SampleList, Map<String, List<GATKRead>>, Map<String, List<GATKRead>>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.PostFilterOnRamp
- getAlleles() - Method in class org.broadinstitute.hellbender.tools.sv.SVAlleleCounter
- getAlleles() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getAlleles() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AlleleSpecificAnnotationData
- getAlleles() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData
-
Note: parent class ReducibleAnnotationData is non-allele specific and stores all values with the no-call allele
- getAlleles() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LocationAndAlleles
- getAlleles() - Method in class picard.fingerprint.Snp
- getAlleles(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
-
Get all the alleles in all of the funcotations for a given transcript ID.
- getAllelesConsistentWithGivenAlleles(List<VariantContext>, VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- getAlleleSpecificVariantType(VariantContext, Allele) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.VariantType
-
Note that spanning deletions are expected to be filtered out upstream of this method to preserve VQSR behavior; we do not explicitly check this.
- getAlleleStart() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getAlleleString() - Method in class picard.fingerprint.Snp
- getAllelesUsedInGenotyping() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculationResult
-
Get the list of alleles actually used in genotyping, which may be smaller than the actual list of alleles requested
- getAllelicCounts() - Method in class org.broadinstitute.hellbender.tools.copynumber.datacollection.AllelicCountCollector
-
Get the allelic counts gathered so far.
- getAllFeatures() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfExonFeature
- getAllFeatures() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfGeneFeature
- getAllFeatures() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature
- getAllFilterLines() - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines
- getAllFormatLines() - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines
- getAllInfoLines() - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines
- getAllInputs() - Method in class org.broadinstitute.hellbender.engine.FeatureManager
-
Get all the sources managed by this FeatureManager.
- getAllIntervals() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.Mapping
- getAllIntervalsForReference(SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Builds a list of intervals that cover the whole given sequence.
- getAllLeaves() - Method in class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray
- getAllLibraryStatistics() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getAllNormalizationIds() - Method in class picard.arrays.illumina.IlluminaBPMFile
- getAllowedShortFragmentOverhang() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter
- getAllowedValuesForDescriptorHelp(String) - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
-
Return the allowed values for annotationNames/disableAnnotations/annotationGroups for use by the help system.
- getAllowedValuesForDescriptorHelp(String) - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
-
Return the allowed values for read-filter/disable-read-filter names for use by the help system.
- getAllowMissingHomRefDataOpt() - Method in class org.broadinstitute.hellbender.utils.variant.writers.ReblockingOptions
- getAllPossibleHeaderNames() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifest
- getAllPossibleHeaderNames() - Method in class picard.arrays.illumina.IlluminaManifest
- getAllReadsCollector() - Method in class org.broadinstitute.hellbender.metrics.MultiLevelCollector
-
Get the PerUnitMetricCollector that collects reads for all levels
- getAllReadsCollector() - Method in class org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector
-
Get the PerUnitMetricCollector that collects reads for all levels
- getAllReadsCollector() - Method in class picard.metrics.MultiLevelCollector
-
Get the PerUnitMetricCollector that collects reads for all levels
- getAllReferenceBases() - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceFileSparkSource
- getAllSamples() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getAllSamples() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
- getAllSequenceDictionaries() - Method in class org.broadinstitute.hellbender.engine.FeatureManager
-
Returns the sequence dictionaries associated with all feature sources.
- getAllSequenceNames() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
- getAllSnps() - Method in class picard.fingerprint.HaplotypeMap
-
Returns an unmodifiable collection of all SNPs in all Haplotype blocks.
- getAllStates() - Method in interface org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.Stratifier
- getAllStates() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier
- getAllTiles() - Method in class picard.illumina.parser.readers.CbclReader
- getAllValues() - Method in class org.broadinstitute.hellbender.utils.codecs.table.TableFeature
-
Gets all the values in order.
- getAllValues() - Method in class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray
- getAllVariantHeaders() - Method in class org.broadinstitute.hellbender.engine.FeatureManager
-
This method finds and returns all of the variant headers from the feature sources.
- getAlpha() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.BetaDistributionShape
- getAlt(Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection
- getAltAaSeq() - Method in class org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo
- getAltAllele() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getAltAllele() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
- getAltAllele() - Method in interface org.broadinstitute.hellbender.tools.funcotator.Funcotation
- getAltAllele() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- getAltAllele() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord
- getAltAlleleOfArtifact() - Method in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- getAltAlleles() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getAltAlleles() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection
- getAltCount() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- getAltCount() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.Datum
- getAltCount() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord
- getAltData(Genotype) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MinAlleleFractionFilter
- getAltDataByAllele(VariantContext, Predicate<Genotype>, Function<Genotype, List<T>>, Mutect2FilteringEngine) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2AlleleFilter
-
The call to use when the data is only for the alternate alleles
- getAltDepth1Resonsibilities(int) - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelEngine
- getAlternate() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- getAlternateAllele() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getAlternateAlleleFraction() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
- getAlternateSequence(StrandCorrectedReferenceBases, int, Allele, Allele, Strand) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Get the full alternate sequence given a reference coding sequence, and two alleles.
- getAltF1R2() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord
- getAltForwardCountFromFlattenedContingencyTable(int[]) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasBySample
- getAltFraction() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- getAltHaplotypeSequence() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- getAltHaplotypeSequence() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence
- getAltHistogramsFromExtractedTar(File) - Static method in class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2CountsCollector
- getAltNucleotide() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
- getAltReadCount() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
- getAltResonsibilities(int) - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelEngine
- getAltReverseCountFromFlattenedContingencyTable(int[]) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasBySample
- getAltTablesFromExtractedTar(File) - Static method in class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2CountsCollector
- getAminoAcidByLetter(char) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Returns the
AminoAcidcorresponding to the given single-letter abbreviation. - getAminoAcidByLetter(String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Returns the
AminoAcidcorresponding to the given single-letter abbreviation. - getAminoAcidCodes() - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
- getAminoAcidNames() - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
- getAnalysis() - Method in class org.broadinstitute.hellbender.tools.reference.ReferencePair
- getAnalysis() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.AnalysisModuleScanner
- getAndValidateConfigFileContentsOnPath(Path, boolean) - Static method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
-
Get the properties from the given
configFilePath, validate that all required properties are present, and return the property map. - getAndValidateDataSourcesFromPaths(String, List<String>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
-
Initializes the data sources for
Funcotator. - getAnnotationFeatureClass() - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
- getAnnotationFeatureClass() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory
- getAnnotationFeatureClass() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
- getAnnotationFeatureClass() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory
- getAnnotationFeatureClass() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.LocatableXsvFuncotationFactory
- getAnnotationFeatureClass() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory
- getAnnotationKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- getAnnotationMap() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AnnotatedInterval
- getAnnotations() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval
-
Returns a copy of the annotations as a map.
- getAnnotations() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection
- getAnnotations() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalHeader
- getAnnotationSource() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getAnnotationTranscript() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getAnnotationValue(String) - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval
- getAnnotationValueOrDefault(String, String) - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval
- getAnonymousOptionalFields() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getAntisenseCount() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation.Coverage
- getApplicableNextEdgesBasedOnJunctionTrees(List<E>, Set<E>, int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JTBestHaplotype
-
This method is the primary logic of deciding how to traverse junction paths and with what score.
- getApprisRank() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getAppropriateVCFInfoHeaders() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
- getApproximateCommandLine() - Method in class org.broadinstitute.hellbender.utils.python.PythonExecutorBase
-
Return a (not necessarily executable) string representing the current command line for this executor for error reporting purposes.
- getApproximateCommandLine() - Method in class org.broadinstitute.hellbender.utils.python.PythonScriptExecutor
-
Return a (not necessarily executable) string representing the current command line for this executor for error reporting purposes.
- getApproximateCommandLine() - Method in class org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor
-
/** Return a (not necessarily executable) string representing the current command line for this executor for error reporting purposes.
- getApproximateCommandLine() - Method in class org.broadinstitute.hellbender.utils.R.RScriptExecutor
- getApproximateCommandLine() - Method in class org.broadinstitute.hellbender.utils.runtime.ScriptExecutor
-
Return a (not necessarily executable) string representing the command line for this executor for error reporting purposes.
- getArguments() - Method in class org.broadinstitute.hellbender.tools.funcotator.Funcotator
- getArtifactProb() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.Datum
- getArtifactProbability() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter.EStep
- getArtificialReadsBasedOnSATag(SAMFileHeader) - Method in class org.broadinstitute.hellbender.utils.SATagBuilder
-
Returns a list of artificial GATKReads corresponding to the reads described by the SA tag in read.
- getAsRealMatrix(LikelihoodMatrix<EVIDENCE, Allele>) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine
- getAssayFormat() - Method in class picard.arrays.illumina.IlluminaManifest
- getAssayHeaderNames() - Method in class picard.arrays.illumina.IlluminaManifest
- getAssayHeaderNameToIndex() - Method in class picard.arrays.illumina.IlluminaManifest
- getAssayType() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getAssembledIntervals() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData.SampleSpecificData
- getAssembledIntervals() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark.AssembledEvidenceResults
- getAssembly() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse
- getAssemblyId() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse
- getAssemblyRegion() - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerContext
- getAssemblyRegionReference(ReferenceSequenceFile) - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
- getAssemblyRegionReference(ReferenceSequenceFile, int) - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Get the reference bases from referenceReader spanned by the padded span of this active region, including additional padding bp on either side.
- getAssemblyRegions(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark
-
Loads assembly regions and the corresponding reference and features into a
JavaRDDfor the intervals specified. - getAssemblyRegionsFast(JavaSparkContext, JavaRDD<GATKRead>, SAMFileHeader, SAMSequenceDictionary, String, FeatureManager, List<ShardBoundary>, Broadcast<Supplier<AssemblyRegionEvaluator>>, AssemblyRegionReadShardArgumentCollection, AssemblyRegionArgumentCollection, boolean, boolean) - Static method in class org.broadinstitute.hellbender.engine.spark.FindAssemblyRegionsSpark
-
Get an RDD of assembly regions for the given reads and intervals using the fast algorithm (looks for assembly regions in each read shard in parallel).
- getAssemblyRegionsStrict(JavaSparkContext, JavaRDD<GATKRead>, SAMFileHeader, SAMSequenceDictionary, String, FeatureManager, List<ShardBoundary>, Broadcast<Supplier<AssemblyRegionEvaluator>>, AssemblyRegionReadShardArgumentCollection, AssemblyRegionArgumentCollection, boolean) - Static method in class org.broadinstitute.hellbender.engine.spark.FindAssemblyRegionsSpark
-
Get an RDD of assembly regions for the given reads and intervals using the strict algorithm (looks for assembly regions in each contig in parallel).
- getAssembyResult(AssemblyRegion, String, SAMFileHeader, HaplotypeCallerArgumentCollection, Logger, SmithWatermanAligner, ReferenceSequenceFile) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.PostAssemblerOnRamp
- getAssignedContig() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getAssignedContig() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getAssignedReferenceIndex(GATKRead, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Returns the reference index in the given header of the read's assigned contig.
- getAssignedStart() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getAssignedStart() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getAsynchronousStreamWriter(OutputStream, Function<T, ByteArrayOutputStream>) - Method in class org.broadinstitute.hellbender.utils.runtime.StreamingProcessController
-
Return a
AsynchronousStreamWriterto be used to write to a stream on a background thread. - getAttribute(Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData
- getAttribute(String) - Method in class org.broadinstitute.hellbender.engine.FeatureInput
-
Gets the value for the given key associated with this Feature source or
nullif no value is associated with a given key. - getAttributeAsByteArray(String) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Retrieve the value of a particular attribute typed as a byte array.
- getAttributeAsByteArray(String) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getAttributeAsDouble(Genotype, String, double) - Static method in class org.broadinstitute.hellbender.utils.variant.VariantContextGetters
-
Returns an attribute as a double.
- getAttributeAsDoubleArray(Genotype, String, Supplier<double[]>, double) - Static method in class org.broadinstitute.hellbender.utils.variant.VariantContextGetters
-
Composes the double array from a genotype annotation.
- getAttributeAsDoubleArray(VariantContext, String) - Static method in class org.broadinstitute.hellbender.utils.variant.VariantContextGetters
-
Composes the double array from a genotype annotation.
- getAttributeAsDoubleArray(VariantContext, String, Supplier<double[]>, double) - Static method in class org.broadinstitute.hellbender.utils.variant.VariantContextGetters
-
Composes the double array from a genotype annotation.
- getAttributeAsDoubleList(VariantContext, String, double) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- getAttributeAsFloat(String) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Retrieve the value of a particular attribute typed as a floating point value.
- getAttributeAsFloat(String) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getAttributeAsInt(Genotype, String, int) - Static method in class org.broadinstitute.hellbender.utils.variant.VariantContextGetters
-
Returns an attribute as an integer.
- getAttributeAsIntArray(Genotype, String, Supplier<int[]>, int) - Static method in class org.broadinstitute.hellbender.utils.variant.VariantContextGetters
-
Composes the double array from a genotype annotation.
- getAttributeAsIntArray(VariantContext, String, Supplier<int[]>, int) - Static method in class org.broadinstitute.hellbender.utils.variant.VariantContextGetters
-
Composes the int array from an INFO annotation.
- getAttributeAsInteger(String) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Retrieve the value of a particular attribute typed as an integer.
- getAttributeAsInteger(String) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getAttributeAsLong(VariantContext, String, Long) - Static method in class org.broadinstitute.hellbender.utils.variant.VariantContextGetters
-
Get Long attribute from a variant context.
- getAttributeAsLongList(VariantContext, String, Long) - Static method in class org.broadinstitute.hellbender.utils.variant.VariantContextGetters
-
Composes the Long List from a variant context.
- getAttributeAsString(Genotype, String, String) - Static method in class org.broadinstitute.hellbender.utils.variant.VariantContextGetters
-
Returns an attribute as a string.
- getAttributeAsString(String) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Retrieve the value of a particular attribute typed as a String.
- getAttributeAsString(String) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getAttributeAsStringList(VariantContext, String) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
-
todo: this should be fixed in a new major version of htsjdk this exist because for whatever reason, VC.getAttributeAsStringList() sometimes returns a giant single string, while using VC.getAttributeAsString() gives back an array.....
- getAttributeAsStringStream(VariantContext, String) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
- getAttributeMap() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData
-
Get the stored raw per-allele data
- getAttributes() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getAttributesToReverse() - Method in class picard.sam.AbstractAlignmentMerger
-
Gets the set of attributes to be reversed on reads marked as negative strand.
- getAttributesToReverseComplement() - Method in class picard.sam.AbstractAlignmentMerger
-
Gets the set of attributes to be reverse complemented on reads marked as negative strand.
- getAuthenticatedGcs(String, String, byte[]) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Get an authenticated GCS-backed NIO FileSystem object representing the selected projected and bucket.
- getAutoCallDate() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getAutoCallVersion() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getAvailableTiles() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Return the list of tiles available for this flowcell and lane.
- getAvgReadLen() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getB37Chr() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getB37Pos() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getBadMappings() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig.GoodAndBadMappings
- getbAlleleFreqs() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getBamIndexPath(Path) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase
- getBAMOutputHeader() - Method in class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMDestination
-
Get the SAMFileHeader that is used for writing the output for this destination.
- getBandSize() - Method in class org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile
-
Get the size (in bp) of the band pass filter
- getBandWidth() - Method in class org.broadinstitute.hellbender.utils.baq.BAQ
- getBAQTag(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.baq.BAQ
-
Get the BAQ attribute from the tag in read.
- getBarcode() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
- getBarcodeValue(SAMRecord) - Method in class picard.sam.markduplicates.EstimateLibraryComplexity
- getBase() - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
-
Get the base at the given locus.
- getBase() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupElement
-
Get the base
- getBase() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the base aligned to the genome at this location If the current element is a deletion returns
PileupElement.DELETION_BASE. - getBase(int) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getBase(int) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getBaseCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getBaseCounts() - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Get counts of A, C, G, T in order, which returns a int[4] vector with counts according to BaseUtils.simpleBaseToBaseIndex for each base.
- getBaseDeletionQual() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the Base Deletion quality at this pileup position
- getBaseDeletionQualities(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Default utility to query the base deletion quality of a read.
- getBaseInsertionQual() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the Base Insertion quality at this pileup position
- getBaseInsertionQualities(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Default utility to query the base insertion quality of a read.
- getBaselineIntegerCopyNumberState() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
- getBaselineIntegerCopyNumberState() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntervalCopyNumberGenotypingData
- getBasePileup() - Method in class org.broadinstitute.hellbender.engine.AlignmentContext
- getBaseQualities() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getBaseQualities() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getBaseQualities(GATKRead, EventType) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
- getBaseQualitiesNoCopy() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getBaseQualitiesNoCopy() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getBaseQuality() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupElement
-
Get the quality
- getBaseQuality(int) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getBaseQuality(int) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getBaseQuality(GATKRead, VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.BaseQuality
- getBaseQualityCount() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getBaseQualityCount() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getBaseQualityHistogram() - Method in class picard.analysis.directed.TargetMetricsCollector
- getBaseQualityString(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Returns the base qualities for the read as a string.
- getBaseQuals() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature
-
Gets the PHRED base qualities.
- getBaseQuals() - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Returns an array of the quals in this pileup.
- getBases() - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
-
Get all reference bases in this context.
- getBases() - Method in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedReferenceBases
- getBases() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead
-
returns bases with values like 'A', 'C', 'G', and 'T'
- getBases() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.InverseAllele
- getBases() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
-
The base sequence for this path.
- getBases() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature
-
Gets the bases in byte array form Note: this call costs O(n) and allocates fresh array each time
- getBases() - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Returns an array of the bases in this pileup.
- getBases() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getBases() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getBases() - Method in class org.broadinstitute.hellbender.utils.reference.ReferenceBases
- getBases() - Method in class picard.illumina.parser.BclData
- getBases() - Method in class picard.illumina.parser.ReadData
- getBases(int, int) - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
-
Get all reference bases in this context with the given leading / trailing bases as the window.
- getBases(SimpleInterval) - Method in interface org.broadinstitute.hellbender.engine.BasicReference
-
Get the reference base calls in the specified window.
- getBases(SimpleInterval) - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
-
Get all reference bases in this context with the given window.
- getBases(SimpleInterval) - Method in interface org.broadinstitute.hellbender.engine.spark.datasources.ReferenceSparkSource
- getBasesAndBaseQualitiesAlignedOneToOne(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Returns the "IGV View" of all the bases and base qualities in a read aligned to the reference according to the cigar, dropping any bases that might be in the read but aren't in the reference.
- getBasesCoveringRefInterval(int, int, byte[], int, Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Get the byte[] from bases that cover the reference interval refStart -> refEnd given the alignment of bases to the reference (basesToRefCigar) and the start offset of the bases on the reference refStart and refEnd are 0 based offsets that we want to obtain.
- getBasesExcludedBy(CountingFilter) - Method in class picard.analysis.CollectWgsMetrics
-
If INTERVALS is specified, this will count bases beyond the interval list when the read overlaps the intervals and extends beyond the edge.
- getBasesInWindowAroundReferenceAllele(Allele, ReferenceContext, Strand, int) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Get a string of bases around a variant (specified by reference and alternate alleles), including the reference allele itself.
- getBasesNoCopy() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getBasesNoCopy() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getBasesOfImmediatelyFollowingInsertion() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the bases for an insertion that immediately follows this alignment state, or null if none exists
- getBasesReverseComplement(byte[]) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Returns the reverse complement of the read bases
- getBasesReverseComplement(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Returns the reverse complement of the read bases
- getBasesStream() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature
-
Get the bases as a stream
- getBasesString() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature
-
Returns pile of observed bases over the genomic location.
- getBasesString() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getBaseString() - Method in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedReferenceBases
- getBaseString(Strand) - Method in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedReferenceBases
-
Get the string of bases in this
StrandCorrectedReferenceBasesobject as if it were on the givenstrand. - getBasicInformation() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- getBbCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getBciFile() - Method in class picard.illumina.parser.readers.BclIndexReader
- getBeadSetId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getBestAvailableSequenceDictionary() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- getBestAvailableSequenceDictionary() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns the "best available" sequence dictionary or
nullif there is no single best dictionary. - getBestAvailableSequenceDictionary() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Returns the "best available" sequence dictionary.
- getBestAvailableSequenceDictionary() - Method in class org.broadinstitute.hellbender.engine.spark.VariantWalkerSpark
- getBestAvailableSequenceDictionary() - Method in class org.broadinstitute.hellbender.engine.VariantWalkerBase
-
Overriding the superclass method to preferentially choose the sequence dictionary from the driving source of variants.
- getBestAvailableSequenceDictionary() - Method in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
-
Inputs to this tool are directories, not files, so we need a custom method to find an appropriate file inside the directories to pull a dictionary out of
- getBestAvailableSequenceDictionary() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
-
Overriding getBestAvailableSequenceDictionary() to prefer the mergedVCFHeader's sequence directory, if present, over any other dictionaries
- getBestAvailableSequenceDictionary() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionary
- getBeta() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.BetaDistributionShape
- getBetweenNextPosition() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the cigar elements that occur after the current position but before the next position on the genome
- getBetweenPrevPosition() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the cigar elements that occur before the current position but after the previous position on the genome For example, if we are in the 3M state of 1M2I3M state then 2I occurs before this position.
- getBigQueryEndPoint() - Static method in class org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils
- getBlocks() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetResponse
- getBoolean(int) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the boolean value in a column by its index.
- getBoolean(String) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the boolean value in a column by its index.
- getBQSRSpecificReadFilterList() - Static method in class org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator
-
Return the list of basic, raw read filters used for BQSR contexts, not including WellFormed.
- getBreakPointIntervals(int, SAMSequenceDictionary, boolean) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVContext
-
Returns break point intervals for this structural variant.
- getBucket(String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Given a path of the form "gs://bucket/folder/folder/file", returns "bucket".
- getBufferBytes() - Method in class org.broadinstitute.hellbender.utils.runtime.CapturedStreamOutput
- getBufferBytes() - Method in class org.broadinstitute.hellbender.utils.runtime.StreamOutput
-
Returns the content as a string.
- getBufferedReaderGz(String) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBuildReferenceTaxonomyUtils
-
Gets a buffered reader for a gzipped file
- getBufferedReaderTarGz(String, String) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBuildReferenceTaxonomyUtils
-
Gets a Reader for a file in a gzipped tarball
- getBufferEnd() - Method in class org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFBlockCombiner
- getBufferSize() - Method in class org.broadinstitute.hellbender.utils.runtime.OutputStreamSettings
- getBufferStart() - Method in class org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFBlockCombiner
- getBufferString() - Method in class org.broadinstitute.hellbender.utils.runtime.StreamOutput
-
Returns the content as a string.
- getBuildDir() - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLDoclet
- getBuilder() - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getByte() - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the byte value in a column at the current column index and advance it.
- getByte(int) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
- getByte(String) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the byte value of a column by its name.
- getByteBufferIterator(int, int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
- getByteIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
- getBytesAvailableToRead() - Method in class picard.util.CircularByteBuffer
-
Returns the number of bytes that are in the buffer at the time of the method invocation.
- getCacheHits() - Method in class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
- getCacheMisses() - Method in class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
- getCacheSize() - Method in class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
- getCall() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledCopyRatioSegment
- getCall() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledLegacySegment
- getCallComparator(SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
-
Gets a comparator for
SVCallRecordobjects. - getCalledHaplotypes() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.CalledHaplotypes
-
Get the set of haplotypes that we actually called (i.e., underlying one of the VCs in getCalls().
- getCallIntegerCopyNumberState() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
- getCallRate() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getCalls() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.CalledHaplotypes
-
Get the list of calls made at this location
- getCanonicalChromosomes(String, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
-
Canonical chromosomes are defined, for homo sapiens, as chromosomes 1-22, chromosome X and Y.
- getCanonicalChromosomesBroadcast() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData.ReferenceData
- getCanonicalPath(File) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
-
File paths that are passed to
PythonScriptExecutormust be canonical (rather than absolute). - getCanonicalPath(String) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
-
File paths that are passed to
PythonScriptExecutormust be canonical (rather than absolute). - getCapacity() - Method in class picard.util.CircularByteBuffer
-
Returns the total capacity of the buffer (empty+filled).
- getCarrierGenotypeList() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getCarrierSampleSet() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getCategory() - Method in class picard.arrays.illumina.ArraysControlInfo
- getCDF() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics
- getCDF() - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram
- getcDnaChange() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getCds() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfExonFeature
- getChainedPgIds(SAMFileHeader) - Method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
We have to re-chain the program groups based on this algorithm.
- getChannels() - Method in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.TensorType
- getChecksum() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeterResults
-
Get the checksum calculated against
NioFileCopierWithProgressMeterResults.dest. - getChecksumAlgorithm() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeterResults
-
Get the checksum algorithm used to calculate the checksum of the downloaded file.
- getChild() - Method in class org.broadinstitute.hellbender.utils.samples.Trio
- getChildID() - Method in class org.broadinstitute.hellbender.utils.samples.Trio
- getChildren() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- getChildrenNodes() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph.ThreadingNode
- getChildrenOf(int) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- getChr() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature
-
Deprecated.
- getChr() - Method in class org.broadinstitute.hellbender.utils.haplotype.FlowBasedHaplotype
- getChr() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getChrom() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getChrom() - Method in class picard.fingerprint.Snp
- getChromosome() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getChromosomeIndex() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocus
- getChromosomeName() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getChromosomes() - Method in class picard.arrays.illumina.InfiniumNormalizationManifest
- getCigar() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.Mapping
-
Returns the cigar of the primary interval, or the empty cigar if
unmapped. - getCigar() - Method in class org.broadinstitute.hellbender.utils.haplotype.FlowBasedHaplotype
- getCigar() - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
-
Get the cigar for this haplotype.
- getCigar() - Method in class org.broadinstitute.hellbender.utils.read.CigarBuilder.Result
- getCigar() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getCigar() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getCigar() - Method in interface org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAlignment
- getCigarElement(int) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Return the cigar element at a given index.
- getCigarElement(int) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
-
This implementation avoids the creation of the unmodifiable view of the underlying list of CigarElements and simply retrieves the element that is requested.
- getCigarElements() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getCigarElements() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
-
This implementation does not make a new Cigar object but instead provides an unmodifiable view of the underlying list of CigarElements.
- getCigarModifiedOffset(PileupElement) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
-
Calculate the index of the current pileup position against the reference-aligned read This offset should be representative of the "IGV view" for the read where insertions are collapsed and deletions are padded so that we can easily count the mismatches against the reference
- getCigarOperator() - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
-
Convenience accessor of the CigarOperator of the current cigar element Robust to the case where we're on the edge, and currentElement is null, in which case this function returns null as well
- getCigarString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
- getClassesOfType(Class<?>, List<Class<?>>) - Static method in class org.broadinstitute.hellbender.utils.ClassUtils
-
Gets a list of classes that are either the same as, or a subclass/subinterface of a parent target class.
- getClassForPluginHelp(String) - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
-
Return the class representing the instance of the plugin specified by
pluginName - getClassForPluginHelp(String) - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
-
Return the class object for the plugin with simple class name
pluginNameUsed for help/usage and documentation generation. - getClassList() - Method in class org.broadinstitute.hellbender.Main
-
The single classes we wish to include in our command line.
- getClassName() - Method in class org.broadinstitute.hellbender.tools.sv.SVFeaturesHeader
- getClient() - Static method in class org.broadinstitute.hellbender.utils.HttpUtils
- getClosest() - Method in class org.broadinstitute.hellbender.tools.sv.concordance.ClosestSVFinder.ClosestPair
- getClosestExonIndex(int, List<? extends Locatable>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Get the index of the exon that is closest to the given start position of a variant.
- getClosestItem(SVCallRecord, Set<Map.Entry<Long, SVCallRecord>>) - Method in class org.broadinstitute.hellbender.tools.sv.concordance.ClosestSVFinder
-
Compares a set of records to the given item and returns the "closest" one.
- getCloudStorageConfiguration(int, String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
The config we want to use.
- getClusterCount() - Method in class picard.illumina.parser.Tile
-
Returns the number of on this tile.
- getClusterDensity() - Method in class picard.illumina.parser.Tile
-
Returns the cluster density of this tile, in units of [cluster/mm^2].
- getClusterFile() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getCnvCallsBroadcast() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData.SampleSpecificData
- getCNVGenotypeAllelesFromCopyNumber(List<Allele>, Allele, int, Integer) - Static method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
-
Generates genotype alleles, i.e.
- getCode() - Method in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- getCode() - Method in enum class picard.vcf.GenotypeConcordanceStates.CallState
- getCode() - Method in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- getCodecForFile(Path) - Static method in class org.broadinstitute.hellbender.engine.FeatureManager
-
Utility method that determines the correct codec to use to read Features from the provided file.
- getCodecForFile(Path, Class<? extends Feature>) - Static method in class org.broadinstitute.hellbender.engine.FeatureManager
-
Utility method that determines the correct codec to use to read Features from the provided file, optionally considering only codecs that produce a particular type of Feature.
- getCodingLocation() - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
-
Returns genomic interval of the coding sequence (does not include UTRs, but still includes introns, since it's a single interval on the DNA)
- getCodingLocation() - Method in interface org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqTranscript
-
Returns genomic interval of the coding sequence (does not include UTRs, but still includes introns, since it's a single interval on the DNA)
- getCodingSequence(ReferenceContext, List<? extends Locatable>, Strand) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Deprecated.
- getCodingSequenceAlleleStart() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getCodingSequenceChangeString(int, String, String, Strand, Integer, Integer, Integer) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Get the coding sequence change string from the given variant information.
- getCodonChange() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getCodonChangeString(SequenceComparison, Locatable) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Creates the string representation of the codon change for the given
SequenceComparison. - getCodons() - Method in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- getCollapser() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine
- getCollector(int, IntervalList) - Method in class picard.analysis.CollectWgsMetrics
-
Creates
AbstractWgsMetricsCollectorimplementation according toCollectWgsMetrics.USE_FAST_ALGORITHMvalue. - getCollector(int, IntervalList) - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
- getColumnFormat() - Method in class org.broadinstitute.hellbender.utils.report.GATKReportColumn
-
Get the display width for this column.
- getColumnIndices() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
- getColumnInfo() - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
- getColumnMedians(RealMatrix) - Static method in class org.broadinstitute.hellbender.utils.MatrixSummaryUtils
-
Return an array containing the median for each column in the given matrix.
- getColumnName() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableEntry
- getColumnName() - Method in class org.broadinstitute.hellbender.utils.report.GATKReportColumn
- getColumnNames() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
- getColumnNames() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableRow
- getColumnNames() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- getColumnNames() - Method in class picard.util.TabbedTextFileWithHeaderParser
- getColumnValue() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableEntry
- getCombinedErrorProbabilities() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorProbabilities
- getCommand() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- getCommandLine() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- getCommandLine() - Method in class picard.cmdline.CommandLineProgram
- getCommandLineName() - Method in class org.broadinstitute.hellbender.Main
-
Returns the command line that will appear in the usage.
- getCommandLineParser() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- getCommandLineParser() - Method in class picard.cmdline.CommandLineProgram
- getCommandLineParserForArgs(String[]) - Method in class picard.cmdline.CommandLineProgram
- getCommandString() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- getComments() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection
-
Creates a copy from the SAM File header or an empty list if no sam file header and no comments.
- getCommonContigsByName(SAMSequenceDictionary, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
-
Returns the set of contig names found in both dicts.
- getCompAFStratifier() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- getComparator() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractLocatableCollection
- getComparator(Set<String>) - Method in enum class org.broadinstitute.hellbender.tools.funcotator.TranscriptSelectionMode
- getComparisonOrder() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap
- getComparisonOrder() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- getComparisonOrder() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.GenotypeFilterSummary
- getComparisonOrder() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelLengthHistogram
- getComparisonOrder() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- getComparisonOrder() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- getComparisonOrder() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MetricsCollection
- getComparisonOrder() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- getComparisonOrder() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.PrintMissingComp
- getComparisonOrder() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ThetaVariantEvaluator
- getComparisonOrder() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator
- getComparisonOrder() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- getComparisonOrder() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantAFEvaluator
- getComparisonOrder() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
- getComparisonOrder() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- getComplement(byte) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
- getComplexSubtype() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getComplexSubtype(VariantContext) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
- getComplication() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- getCompressedBlockSize() - Method in class picard.illumina.parser.readers.BaseBclReader.TileData
- getComps() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- getCompsProvided() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- getConcordance() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval
- getConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceScheme
-
Get the concordance state array associate with the given truth state and call state tuple.
- getConcordanceStateArray(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceScheme
-
Get the concordance state array associate with the given truth state and call state tuple.
- getConfigFilenameFromArgs(String[], String) - Static method in class org.broadinstitute.hellbender.utils.config.ConfigFactory
-
Get the configuration file name from the given arguments.
- getConfigFilePath(Path) - Static method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
-
Gets the path to the corresponding configuration file for the given
inputFilePath. - getConfiguration() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
-
Returns a reference to the engine configuration
- getConsensusCorrection(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NearbyKmerErrorCorrector.CorrectionSet
-
Get consensus correction for a particular offset.
- getConsolidatedPaddedCigar(int) - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
-
Get the haplotype cigar extended by padSize M at the tail, consolidated into a clean cigar
- getContamination() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationRecord
- getContext() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker.PQEntry
- getContig() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval
- getContig() - Method in class org.broadinstitute.hellbender.engine.AlignmentContext
- getContig() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
- getContig() - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
- getContig() - Method in class org.broadinstitute.hellbender.engine.ReferenceShard
- getContig() - Method in interface org.broadinstitute.hellbender.engine.Shard
- getContig() - Method in class org.broadinstitute.hellbender.engine.ShardBoundary
- getContig() - Method in class org.broadinstitute.hellbender.engine.VariantShard
- getContig() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
- getContig() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AnnotatedInterval
- getContig() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatio
- getContig() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatioSegment
- getContig() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
- getContig() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntervalCopyNumberGenotypingData
- getContig() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LegacySegment
- getContig() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LinearCopyRatio
- getContig() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment
- getContig() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount
- getContig() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval
- getContig() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getContig() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigEndKmer
- getContig() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- getContig() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- getContig() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- getContig() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.PathPart
- getContig() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartContig
- getContig() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartGap
- getContig() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.Mapping
-
Returns the contig as per the primary interval, or
nullif unmapped. - getContig() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVLocation
- getContig() - Method in class org.broadinstitute.hellbender.tools.sv.BafEvidence
- getContig() - Method in class org.broadinstitute.hellbender.tools.sv.DepthEvidence
- getContig() - Method in class org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence
- getContig() - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepth
- getContig() - Method in class org.broadinstitute.hellbender.tools.sv.SplitReadEvidence
- getContig() - Method in class org.broadinstitute.hellbender.tools.walkers.consensus.ReadsWithSameUMI
- getContig() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.MinorAlleleFractionRecord
- getContig() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- getContig() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleAndContext
- getContig() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- getContig() - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
- getContig() - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileStateRange
- getContig() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getContig() - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
- getContig() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature
- getContig() - Method in class org.broadinstitute.hellbender.utils.codecs.table.TableFeature
- getContig() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
- getContig() - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- getContig() - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
-
Get the contig of the underlying read
- getContig() - Method in class org.broadinstitute.hellbender.utils.read.Fragment
- getContig() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getContig() - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
- getContig() - Method in class org.broadinstitute.hellbender.utils.SVInterval
- getContig() - Method in class org.broadinstitute.hellbender.utils.variant.MinimalVariant
- getContig() - Method in class org.broadinstitute.hellbender.utils.variant.VariantContextVariantAdapter
- getContig() - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- getContigA() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getContigA() - Method in interface org.broadinstitute.hellbender.tools.sv.SVLocatable
-
Gets the contig name for first coordinate
- getContigAlignments() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse
-
List is equal in length to the number of contigs in the assembly.
- getContigB() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getContigB() - Method in interface org.broadinstitute.hellbender.tools.sv.SVLocatable
-
Gets the contig name for second coordinate
- getContigColumn() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
-
Do not call before
XsvLocatableTableCodec.readActualHeader(LineIterator)or exception will be thrown.. - getContigColumnName() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalHeader
- getContigID(String) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getContigIDFromName(String, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
-
Get numeric contig ID from string contig name based on SAMSequenceDictionary
- getContigIndex() - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- getContigIndex(String) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Returns the contig index of a specified string version of the contig
- getContigIndex(String) - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Writer
- getContigIndexWithoutException(String) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
- getContigInfo(String) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
get the contig's SAMSequenceRecord
- getContigName() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
- getContigName() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- getContigName(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getContigNameMap() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getContigNames(SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
- getContigNamesList(SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
- getContigOffset() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- getContigOffset() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- getContigOffset() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- getContigOrientation() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigEndKmer
- getContigs() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- getContigSequence() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
- getContigSequence() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- getContigSizes(Path) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Returns a map of contig names with their sizes.
- getContigsWithSignatureClassifiedAsComplex() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark.AssemblyContigsClassifiedByAlignmentSignatures
- getContigsWithSignatureClassifiedAsSimpleChimera() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark.AssemblyContigsClassifiedByAlignmentSignatures
- getContigsWithSignatureClassifiedAsUnknown() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark.AssemblyContigsClassifiedByAlignmentSignatures
- getContingencyStateCounts(GenotypeConcordanceScheme) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the total number of times each contingency state is encountered, summed across all truth/call state pairs.
- getContingencyStateSet(GenotypeConcordanceStates.ContingencyState[]) - Method in class picard.vcf.GenotypeConcordanceScheme
-
Get the contingency state array as a set
- getContingencyStateString(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceScheme
-
Get the contingency state array as a parse-able string
- getContingencyTable(AlleleLikelihoods<GATKRead, Allele>, Allele, List<Allele>, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest
- getContingencyTable(AlleleLikelihoods<GATKRead, Allele>, VariantContext, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest
-
Allocate and fill a 2x2 strand contingency table.
- getContingencyTable(AlleleLikelihoods<GATKRead, Allele>, VariantContext, int, Collection<String>) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest
-
Allocate and fill a 2x2 strand contingency table.
- getContingencyTableWrtAll(AlleleLikelihoods<GATKRead, Allele>, Allele, List<Allele>, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest
-
Generates a contingency table where the strand bias of an allele is estimated relative to all alleles (total coverage) in the location.
- getControl() - Method in class picard.arrays.illumina.ArraysControlInfo
- getControlConfig() - Method in class picard.arrays.illumina.IlluminaBPMFile
- getCopyNumber() - Method in class org.broadinstitute.hellbender.tools.copynumber.gcnv.IntegerCopyNumberState
- getCopyNumberPosterior(IntegerCopyNumberState) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyNumberPosteriorDistribution
-
Get the probability for a given copy number state
- getCopyNumberPosteriorDistribution() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntervalCopyNumberGenotypingData
- getCorrectReferenceContext(VariantContext, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine
-
Gets the correct
ReferenceContextfor thevariantbeing processed based on if the B37->HG19 conversion is required. - getCount() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount
- getCount() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.TransitPairCount
- getCount() - Method in class org.broadinstitute.hellbender.tools.sv.SplitReadEvidence
- getCount(AnalyzeSaturationMutagenesis.ReportType) - Method in class org.broadinstitute.hellbender.tools.AnalyzeSaturationMutagenesis.ReportTypeCounts
- getCount(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the count defined by the truth state set and call state set.
- getCount(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the count defined by the truth state set and call state set.
- getCountedKmers() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.KMerCounter
-
Get an unordered collection of the counted kmers in this counter
- getCounterSize() - Method in class picard.vcf.GenotypeConcordanceCounts
- getCountMap() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.AllelePileupCounter
- getCounts() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection
- getCounts() - Method in class org.broadinstitute.hellbender.tools.sv.DepthEvidence
- getCounts() - Method in class org.broadinstitute.hellbender.tools.sv.SVAlleleCounter
- getCovariateByParsedName(String) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList
-
Retrieves a covariate by the parsed name
Covariate.parseNameForReport()or null if no covariate with that name exists in the list. - getCovariateForTable(NestedIntegerArray<RecalDatum>) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
- getCovariates() - Method in class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
- getCovariates() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport
- getCovariatesValues() - Method in class org.broadinstitute.hellbender.utils.recalibration.ReadRecalibrationInfo
-
Get the ReadCovariates object carrying the mapping from offsets -> covariate key sets
- getCoverage() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics
- getCoverage() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getCoverage(String) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CoveragePerContig
- getCoverageByAggregationType(DoCOutputType.Partition) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoveragePartitionedDataStore
- getCoverageByTarget() - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Returns the accumulated coverage per target.
- getCoverageProportions(String) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
-
Return a list of the cumulative depth counts as a perportion of total number of loci
- getCurrentCigarElement() - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
-
Get the cigar element we're currently aligning with.
- getCurrentCigarElement() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the cigar element aligning this element to the genome
- getCurrentCigarElementOffset() - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
-
Get the offset of the current cigar element among all cigar elements in the read Suppose our read's cigar is 1M2D3M, and we're at the first 1M.
- getCurrentCigarOffset() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the offset of this cigar element in the Cigar of the current read (0-based) Suppose the cigar is 1M2D3I4D.
- getCurrentContig() - Method in class org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFBlockCombiner
- getCurrentLine() - Method in class picard.util.BasicInputParser
-
Provides access to the current (just parsed) line in pre-parsed format.
- getCurrentLine() - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
- getCurrentLine() - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
- getCurrentLineNumber() - Method in class picard.util.BasicInputParser
-
NOTE: Because AbstractInputParser pre-fetches the next line, this method actually returns the next line, not the most recent line returned by next().
- getCurrentLineNumber() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- getCurrentLineNumber() - Method in class picard.util.TabbedTextFileWithHeaderParser
- getCustomerStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getCycleData() - Method in class picard.illumina.parser.readers.CbclReader
- getCycleFromDir(File) - Static method in class picard.illumina.parser.PerTilePerCycleFileUtil
- getCycleIndexRanges() - Method in class picard.illumina.parser.OutputMapping
- getCycleIndexRanges() - Method in class picard.illumina.parser.ReadStructure.Substructure
- getCycles() - Method in class picard.illumina.parser.ReadStructure.Substructure
- getDanglingEndSWParameters() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- getData() - Method in class org.broadinstitute.hellbender.tools.ClipReads.ReadClipperWithData
- getData() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetResponse.Block
-
Returns InputStream containing data of a single block from the htsget response Large blocks (those behind an http(s) URI) are first saved to a temp file that is deleted upon program exit
- getData() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.AnalysisModuleScanner
- getData() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- getData(Genotype) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MTLowHeteroplasmyFilterTool
- getData(Genotype) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NuMTFilterTool
- getDataByAllele(VariantContext, Predicate<Genotype>, Function<Genotype, List<T>>, Mutect2FilteringEngine) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2AlleleFilter
-
The call to use when the data includes data for the reference
- getDataClass() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- getDataClass() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetResponse.Block
- getDataSourceInfoString() - Method in class org.broadinstitute.hellbender.tools.funcotator.OutputRenderer
- getDataSourceMaxVersionString() - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
-
Get the string representing the Max version information for funcotator as it would be written in the data sources release files.
- getDataSourceMinVersionString() - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
-
Get the string representing the Min version information for funcotator as it would be written in the data sources release files.
- getDataSourceName() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getDataSourceName() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
- getDataSourceName() - Method in interface org.broadinstitute.hellbender.tools.funcotator.Funcotation
- getDataSourceName() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
- getDataSourceVersionString(int, int, LocalDate) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
-
Get the string representing the given version information for funcotator as it would be written in the data sources release files.
- getDataType() - Method in class org.broadinstitute.hellbender.utils.report.GATKReportColumn
- getDataTypesFromReadStructure(ReadStructure, boolean, File) - Static method in class picard.illumina.BasecallsConverter
-
Given a read structure return the data types that need to be parsed for this run
- getDateFromVcfOtherHeaderLine(VCFHeader, String, SimpleDateFormat) - Static method in class picard.arrays.illumina.InfiniumVcfFields
- getDateManufactured() - Method in class picard.arrays.illumina.IlluminaManifest
- getDateTimeForDisplay(ZonedDateTime) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Return the given
dateTimeformatted as string for display. - getDecile10() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment.SimplePosteriorSummary
- getDecile50() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment.SimplePosteriorSummary
- getDecile90() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment.SimplePosteriorSummary
- getDeciles(T) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.ParameterDecileCollection
- getDecisionEdgesTakenSinceLastJunctionTreeEvidence() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JTBestHaplotype
-
Return an accounting of how many edge decision (where there is a choice) have consecutively been based on the raw graph weights (as opposed to being based on junction tree evidence).
- getDefaultAlleleFrequency() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- getDefaultCloudIndexPrefetchBufferSize() - Method in class org.broadinstitute.hellbender.engine.GATKTool
- getDefaultCloudIndexPrefetchBufferSize() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- getDefaultCloudPrefetchBufferSize() - Method in class org.broadinstitute.hellbender.engine.GATKTool
- getDefaultCloudPrefetchBufferSize() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- getDefaultHeaders() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
-
Returns the (live) list of default metrics headers used by this tool.
- getDefaultHeaders() - Method in class picard.cmdline.CommandLineProgram
- getDefaultInstances() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
-
Get the list of default plugins used for this instance of this descriptor.
- getDefaultInstances() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
-
Get the list of default plugins used for this instance of this descriptor.
- getDefaultMaxMnpDistance() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- getDefaultMaxMnpDistance() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- getDefaultMaxMnpDistance() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- getDefaultPartsDirectory(String) - Static method in class org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink
-
Gets the default parts directory for a given file by appending .parts/ to the end of it
- getDefaultPlatform() - Method in enum class org.broadinstitute.hellbender.utils.NGSPlatform
-
Returns a representative PL string for this platform
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionWalker
-
Returns the default list of CommandLineReadFilters that are used for this tool.
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.engine.DuplicateSetWalker
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns the default list of ReadFilters that are used for this tool.
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.engine.LocusWalker
-
Returns the default list of CommandLineReadFilters that are used for this tool.
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.engine.ReadWalker
-
Returns the default list of CommandLineReadFilters that are used for this tool.
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Returns the default list of ReadFilters that are used for this tool.
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollector
-
Return the read filter for InsertSizeMetrics collector.
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCounts
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleCollectMultiMetricsSpark
-
Return the read filters required for this collector
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollector
-
Return the read filter for example metrics collector.
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollectorSpark
-
Return the read filters to be used for this collector.
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleCollectSingleMetricsSpark
-
Return the read filter required for this collector
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.HaplotypeCallerSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.PrintDistantMates
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.bwa.BwaSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.PileupSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectBaseDistributionByCycleSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectInsertSizeMetricsSpark
-
Return the read filters required for this collector
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.InsertSizeMetricsCollectorSpark
-
Return the read filters to be used for this collector.
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MeanQualityByCycleSpark
- getDefaultReadFilters() - Method in interface org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSpark
-
Return the read filters used for this collector.
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSparkTool
-
The following
MetricsCollectorSparkmethods must be implemented by subclasses and should be forwarded to the embedded collector. - getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityScoreDistributionSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.SortSamSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.DiscoverVariantsFromContigAlignmentsSAMSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantReInterpreterSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.StructuralVariantDiscoverer
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactData
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.PairWalker
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.CheckPileup
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.Pileup
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.PostProcessReadsForRSEM
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.ReadAnonymizer
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2Counts
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.RevertBaseQualityScores
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.UnmarkDuplicates
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeBasedVariantRecaller
- getDefaultReadFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants
- getDefaultSampleID() - Method in class picard.fingerprint.FingerprintChecker
- getDefaultSeverity() - Method in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
- getDefaultToolVCFHeaderLines() - Method in class org.broadinstitute.hellbender.engine.GATKTool
- getDefaultToolVCFHeaderLines() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- getDefaultToolVCFHeaderLines() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData
- getDefaultValue(HybridADVIArgumentCollection.HybridADVIArgument) - Method in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCNVHybridADVIArgumentCollection
- getDefaultValue(HybridADVIArgumentCollection.HybridADVIArgument) - Method in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineContigPloidyHybridADVIArgumentCollection
- getDefaultValue(HybridADVIArgumentCollection.HybridADVIArgument) - Method in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- getDefaultValueForType(ArgumentDefinition) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLWorkUnitHandler
-
Return a value that will satisfy the constructor for argDef's underlying class.
- getDefaultVariantAnnotationGroups() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns the default list of annotation groups that are used for this tool.
- getDefaultVariantAnnotationGroups() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- getDefaultVariantAnnotationGroups() - Method in class org.broadinstitute.hellbender.tools.HaplotypeCallerSpark
- getDefaultVariantAnnotationGroups() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- getDefaultVariantAnnotationGroups() - Method in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
- getDefaultVariantAnnotationGroups() - Method in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- getDefaultVariantAnnotationGroups() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
- getDefaultVariantAnnotationGroups() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- getDefaultVariantAnnotationGroups() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- getDefaultVariantAnnotations() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns the default list of
Annotations that are used for this tool. - getDefaultVariantAnnotations() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- getDefaultVariantTransformer() - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine
- getDefaultVCFHeaderLines(String, String, String, String, String) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
A method that constructs a mutable set of VCF header lines containing the tool name, version, date and command line, and return to the requesting tool.
- getDelegatee() - Method in class org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec
- getDeletionAllelesFromCopyNumber(Allele, int, int) - Static method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
-
Generates genotype alleles for deletion genotypes from the given copy number.
- getDeletionsKeySet() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadCovariates
- getDeletionsKeySet(int) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadCovariates
- getDenoisedCopyRatios() - Method in class org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisedCopyRatioResult
- getDensity() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
- getDeprecatedRawKeyName() - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
- getDepth() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCase
-
Returns the total number of qualifying reads that overlap the STR that starts at this locus for the target sample.
- getDepth() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord
- getDepth(int) - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepth
- getDepth(GenotypesContext, AlleleLikelihoods<GATKRead, Allele>) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.QualByDepth
- getDepthHistogram() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
- getDepthHistogram() - Method in class picard.analysis.directed.TargetMetricsCollector
- getDepthOnlyParams() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- getDepthParameters() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- getDepths() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Gets the coverage depths as an array of ints.
- getDescendentScore() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- getDescription() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.CopyNumberProgramGroup
- getDescription() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.CoverageAnalysisProgramGroup
- getDescription() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.ExampleProgramGroup
- getDescription() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.FlowBasedProgramGroup
- getDescription() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.MetagenomicsProgramGroup
- getDescription() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.MethylationProgramGroup
- getDescription() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.ShortVariantDiscoveryProgramGroup
- getDescription() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.StructuralVariantDiscoveryProgramGroup
- getDescription() - Method in class org.broadinstitute.hellbender.cmdline.TestProgramGroup
- getDescription() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead
- getDescription() - Method in class org.broadinstitute.hellbender.utils.dragstr.DoubleSequence
- getDescription() - Method in class picard.cmdline.programgroups.BaseCallingProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.GenotypingArraysProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.IntervalsManipulationProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.OtherProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.ReadDataManipulationProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.ReferenceProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.Testing
- getDescription() - Method in class picard.cmdline.programgroups.VariantEvaluationProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.VariantFilteringProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.VariantManipulationProgramGroup
- getDescriptions() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.AllelePseudoDepth
- getDescriptions() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RawGtCount
- getDescriptions() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
- getDescriptions() - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotation
- getDescriptorFileName() - Method in class picard.arrays.illumina.IlluminaManifest
- getDescriptorLengths() - Method in class picard.illumina.parser.ReadStructure.Substructure
- getDest() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- getDestination() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeterResults
- getDestinationFilename(DocWorkUnit) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLWorkUnitHandler
-
Return the flat filename (no paths) that the handler would like the Doclet to write out the documentation for workUnit.
- getDetectedCycles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
- getDictionary() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker.DictSource
- getDictionary() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker
-
Get the dictionary we settled on
- getDictionary() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker.PQContext
- getDictionary() - Method in class org.broadinstitute.hellbender.tools.sv.SVFeaturesHeader
- getDictionary() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- getDictionaryAsString(SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
-
Returns a compact String representation of the sequence dictionary it's passed The format of the returned String is: [ contig1Name(length: contig1Length) contig2Name(length: contig2Length) ...
- getDictionaryForMergedBam() - Method in class picard.sam.AbstractAlignmentMerger
- getDictionaryForMergedBam() - Method in class picard.sam.SamAlignmentMerger
- getDictionaryOrderComparator(SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
The order of contigs/sequences in the dictionary is the order of the sorting here.
- getDifferingPositions(Kmer, int, int[], byte[]) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.Kmer
-
Gets a set of differing positions and bases from another k-mer, limiting up to a max distance.
- getDimensions() - Method in class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray
- getDiploidHaplotype(Snp, DiploidGenotype) - Method in class picard.fingerprint.HaplotypeBlock
-
Gets the diploid haplotype for this haplotype block given the provided SNP and SNP genotype.
- getDirection() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- getDirectory() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- getDisableToolDefaultAnnotations() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKVariantAnnotationArgumentCollection
- getDisableToolDefaultAnnotations() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationArgumentCollection
-
Returns
trueif all tool-default annotations are disabled;falseotherwise. - getDisableToolDefaultReadFilters() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKReadFilterArgumentCollection
-
Returns
trueif all default filters are disabled;falseotherwise. - getDisableToolDefaultReadFilters() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterArgumentCollection
-
Returns
trueif all default filters are disabled;falseotherwise. - getDiscoveredHaplotypes() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult
- getDiscoverStageArgs() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData
- getDiscoveryAltCount() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- getDiscoveryRefCount() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- getDisplayMessage() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessControllerAckResult
- getDisplayName() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
-
Return a display name to identify this plugin to the user
- getDisplayName() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
-
Return a display name to identify this plugin to the user
- getDisplayNameForToolClass(Class<?>) - Method in class org.broadinstitute.hellbender.Main
- getDisplayString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.InverseAllele
- getDisplaySummaryForTool(Class<?>, CommandLineProgramProperties) - Method in class org.broadinstitute.hellbender.Main
-
Return a summary string for a command line tool suitable for display.
- getDistalTargets(ReadMetadata, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.DiscordantReadPairEvidence
-
In the case of a discordant read pair, the distal target interval is a StrandedInterval where the interval location is the possible breakpoint interval given by the inferred rest-of-fragment interval for the mate read (ie the region that would contain the mate's mated read if its fragment size had been drawn from the non-outlier fragment size distribution), and the strand can be easily computed as the strand of the reference the mate mapped to.
- getDistalTargets(ReadMetadata, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
-
Returns the distal interval implicated as a candidate adjacency to the breakpoint by this piece of evidence.
- getDistalTargets(ReadMetadata, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SplitRead
-
In the case of a split read with an SA tag, the distal target interval is a StrandedInterval where the interval location is the possible breakpoint interval given by the clipping location on the supplementary alignment, and the strand indicates whether or not the rest of the supplementary alignment is upstream or downstream of of the breakpoint.
- getDistance() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
-
Distance between the two intervals.
- getDistanceBetweenNovelAdjacencies() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- getDotLabel() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge
-
Get the DOT format label for this edge, to be displayed when printing this edge to a DOT file
- getDotLabel() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MultiSampleEdge
- getDotName() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph.ThreadingNode
- getDouble(int) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the double value in a column by its index.
- getDouble(int, Function<String, RuntimeException>) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the double value in a column by its index.
- getDouble(Enum<?>) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the double value of a column by its name.
- getDouble(String) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the double value in a column by its index.
- getDownsampling() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.NormalArtifactRecord
- getDownsamplingInfo() - Method in class org.broadinstitute.hellbender.engine.LocusWalker
-
Returns the downsampling info using
LocusWalker.maxDepthPerSampleas target coverage. - getDownsamplingInfo() - Method in class org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark
-
Returns the downsampling info using
LocusWalkerSpark.maxDepthPerSampleas target coverage. - getDragenNameValuePairs() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- getDrivingFeaturePath() - Method in class org.broadinstitute.hellbender.engine.FeatureWalker
-
Returns the file that contains the driving features.
- getDrivingFeaturePath() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleFeatureWalker
- getDrivingFeaturePath() - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotateSegments
- getDrivingFeaturePath() - Method in class org.broadinstitute.hellbender.tools.sv.CondenseDepthEvidence
- getDrivingFeaturePath() - Method in class org.broadinstitute.hellbender.tools.sv.PrintReadCounts
- getDrivingFeaturesHeader() - Method in class org.broadinstitute.hellbender.engine.FeatureWalker
-
Returns the header of the driving features file.
- getDrivingVariantCacheLookAheadBases() - Method in class org.broadinstitute.hellbender.engine.VariantWalkerBase
-
When performing a query on the driving variants input(s), the number of additional bases beyond the end of the query for which overlapping variants should be pre-fetched and cached.
- getDrivingVariantPaths() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.MultiVariantInputArgumentCollection.DefaultMultiVariantInputArgumentCollection
- getDrivingVariantPaths() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.MultiVariantInputArgumentCollection
- getDrivingVariantsFeatureInput() - Method in class org.broadinstitute.hellbender.engine.VariantLocusWalker
-
Returns the feature input for the driving variants file.
- getDrivingVariantsFeatureInput() - Method in class org.broadinstitute.hellbender.engine.VariantWalker
-
Returns the feature input for the driving variants file.
- getDrivingVariantsFeatureInputs() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalker
-
Returns a list of feature inputs used for the driving variants for this source.
- getDropLowQualsOpt() - Method in class org.broadinstitute.hellbender.utils.variant.writers.ReblockingOptions
- getDuplicateCountHist() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getDuplicatedItems(Collection<T>) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Gets duplicated items in the collection.
- getDuplicateMarkingsDiffer() - Method in class picard.sam.util.SamComparison
- getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator, SAMRecordDuplicateComparator) - Method in class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
- getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator, SAMRecordDuplicateComparator) - Method in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
- getDuplicationAllelesFromCopyNumber(Allele, int, int) - Static method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
-
Generates genotype alleles for duplication genotypes from the given copy number.
- getDupSeqOrientationsOnCtg() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- getDupSeqRepeatNumOnCtg() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- getDupSeqRepeatNumOnRef() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- getDupSeqRepeatUnitRefSpan() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.InvertedDuplicationBreakpointComplications
- getDupSeqRepeatUnitRefSpan() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- getDx() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getEdges() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
-
Get the edges of this path in order.
- getEffectiveCounts() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelEngine
- getEffectiveCounts(RealMatrix, double[]) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticLikelihoodsEngine
- getEffectiveCounts(RealMatrix, double[], double[]) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticLikelihoodsEngine
-
Given data log likelihoods and a Dirichlet prior for a categorical distribution, obtain the array of total responsibilities for each category
- getEffectiveCounts(ArtifactState) - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelEngine
- getEigensampleVectors() - Method in class org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals
- getEigensampleVectors() - Method in interface org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals
-
Returns a modifiable copy of an array containing the orthnonormal matrix of eigensample vectors.
- getElementForRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_BaseQualityRankSumTest
-
Get the element for the given read at the given reference position
- getElementForRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_MappingQualityRankSumTest
- getElementForRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_ReadPosRankSumTest
- getElementForRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityRankSumTest
- getElementForRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ClippingRankSumTest
- getElementForRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.LikelihoodRankSumTest
- getElementForRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.MappingQualityRankSumTest
- getElementForRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RankSumTest
-
Get the element for the given read at the given reference position
- getElementForRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosRankSumTest
- getElementForRead(GATKRead, VariantContext, AlleleLikelihoods.BestAllele) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.LikelihoodRankSumTest
- getElementForRead(GATKRead, VariantContext, AlleleLikelihoods.BestAllele) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RankSumTest
-
Get the element for the given read at the given reference position
- getEmissionLogOdds() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- getEmpiricalErrorRate() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
-
Returns the error rate (in real space) of this interval, or 0 if there are no observations
- getEmpiricalQuality() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- getEmpiricalQuality(double) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- getEmpiricalQualityAsByte() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- getEmptyBins(int) - Static method in class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterConstants
- getEmptyRawValue() - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AlleleSpecificAnnotation
- getEmptyRawValue() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
- getEmptyRawValue() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality
- getEmptyRawValue() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
- getEnableAllAnnotations() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKVariantAnnotationArgumentCollection
- getEnableAllAnnotations() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationArgumentCollection
-
Returns
trueif all annotations are enabled;falseotherwise. - getEncapsulatedSamRecord() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getEnd() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval
- getEnd() - Method in class org.broadinstitute.hellbender.engine.AlignmentContext
- getEnd() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
- getEnd() - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
- getEnd() - Method in interface org.broadinstitute.hellbender.engine.Shard
- getEnd() - Method in class org.broadinstitute.hellbender.engine.ShardBoundary
- getEnd() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
- getEnd() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AnnotatedInterval
- getEnd() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatio
- getEnd() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatioSegment
- getEnd() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
- getEnd() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntervalCopyNumberGenotypingData
- getEnd() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LegacySegment
- getEnd() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LinearCopyRatio
- getEnd() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment
- getEnd() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount
- getEnd() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval
- getEnd() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocus
- getEnd() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getEnd() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVContext
-
The end position of this variant context.
- getEnd() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.Mapping
-
Returns the primary interval end position, or
SAMRecord.NO_ALIGNMENT_STARTif unmapped. - getEnd() - Method in class org.broadinstitute.hellbender.tools.sv.BafEvidence
- getEnd() - Method in class org.broadinstitute.hellbender.tools.sv.DepthEvidence
- getEnd() - Method in class org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence
-
Used for sorting/checking evidence file order, where end coordinates should not be compared.
- getEnd() - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepth
- getEnd() - Method in class org.broadinstitute.hellbender.tools.sv.SplitReadEvidence
- getEnd() - Method in class org.broadinstitute.hellbender.tools.walkers.consensus.ReadsWithSameUMI
- getEnd() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.MinorAlleleFractionRecord
- getEnd() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- getEnd() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- getEnd() - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
- getEnd() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getEnd() - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
- getEnd() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature
- getEnd() - Method in class org.broadinstitute.hellbender.utils.codecs.table.TableFeature
- getEnd() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
- getEnd() - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- getEnd() - Method in class org.broadinstitute.hellbender.utils.haplotype.FlowBasedHaplotype
- getEnd() - Method in class org.broadinstitute.hellbender.utils.IndexRange
- getEnd() - Method in class org.broadinstitute.hellbender.utils.read.Fragment
- getEnd() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.FlowModeFragment
- getEnd() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getEnd() - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
- getEnd() - Method in class org.broadinstitute.hellbender.utils.SVInterval
- getEnd() - Method in class org.broadinstitute.hellbender.utils.variant.MinimalVariant
- getEnd() - Method in class org.broadinstitute.hellbender.utils.variant.VariantContextVariantAdapter
- getEnd() - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- getEndColumn() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
-
Do not call before
XsvLocatableTableCodec.readActualHeader(LineIterator)or exception will be thrown.. - getEndColumnName() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalHeader
- getEndContig() - Method in class org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence
- getEndpoint() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- getEndpoints() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
- getEndPosition() - Method in class org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence
- getEndStrand() - Method in class org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence
- getEngine() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
- getEngine() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier
- getEntries() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableRow
- getEntry(Locatable, String) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OnRampBase
- getEnum(String) - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.DataSourceType
- getEnum(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
- getEnum(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureType
- getEnum(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.GenomicPhase
- getEnum(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- getEnum(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.LocusLevel
- getEnum(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapStatus
- getEnum(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapTargetStatus
- getEnum(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.TranscriptSupportLevel
- getEnvironment() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- getEquivalentFormatHeaderLine(String) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines
- getError() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetErrorResponse
- getError() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationRecord
- getErrorFraction(EventType, int) - Method in class org.broadinstitute.hellbender.utils.recalibration.ReadRecalibrationInfo
-
Get the error fraction for event type at offset The error fraction is a value between 0 and 1 that indicates how much certainty we have in the error occurring at offset.
- getErrorMessage() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse
-
Either this is null, or the assembly and list of alignments is null.
- getErrorRate() - Method in class org.broadinstitute.hellbender.utils.recalibration.QualQuantizer.QualInterval
- getEstimatedQReported() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- getEstimatedQReportedAsByte() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- getEukaryoticAminoAcidByCodon(String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Returns the
AminoAcidcorresponding to the given three-letter EukaryoticcodonThe codons given are expected to be valid for Eukaryotic DNA. - getEval() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval
- getEvalHeader() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- getEvalItem() - Method in class org.broadinstitute.hellbender.tools.sv.concordance.ClosestSVFinder.ClosestPair
- getEvalKey() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.InfoConcordanceRecord
- getEvals() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- getEvalState(Genotype) - Method in class org.broadinstitute.hellbender.tools.sv.concordance.SVConcordanceAnnotator
- getEvaluationClasses() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.EvaluationContext
-
Returns a set of VariantEvaluator classes to be used
- getEvaluationContexts(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
-
Given specific eval and comp VCs and the sample name, return an iterable over all of the applicable state keys.
- getEvaluationData() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- getEvaluationInstances() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.EvaluationContext
-
Return a list of instances of each VariantEvaluator (see getEvaluationClasses).
- getEvaluatorClasses() - Static method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getEventMap() - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- getEvidence(int) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix
- getEvidence(int) - Method in interface org.broadinstitute.hellbender.utils.genotyper.LikelihoodMatrix
-
Returns the allele given its index.
- getEvidenceCount() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph.ThreadingNode
- getEvidenceParams() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- getEvidenceTargetLinks() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData.SampleSpecificData
- getEvidenceTargetLinks() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark.AssembledEvidenceResults
- getException() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
- getExceptionMessageFromScriptError(ProcessOutput) - Method in class org.broadinstitute.hellbender.utils.runtime.ScriptExecutor
-
Inspect process output exit code and construct a corresponding exception message.
- getExecutableName() - Method in enum class org.broadinstitute.hellbender.utils.python.PythonExecutorBase.PythonExecutableName
- getExistingBaseDeletionQualities(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
- getExistingBaseInsertionQualities(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
- getExitValue() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessOutput
- getExonEndPosition() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getExonId() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getExonLocation(int) - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
-
Genomic location of the n-th exon; throws an exception if n is out of bounds
- getExonNumber() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getExons() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature
- getExons() - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
-
Returns the list of all exons in this transcript, as genomic intervals
- getExons() - Method in interface org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqTranscript
-
Returns the list of all exons in this transcript, as genomic intervals
- getExonStartPosition() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getExpClusters() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getExpClusters() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getExpectedChecksum() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeterResults
-
Get the expected checksum value for
NioFileCopierWithProgressMeterResults.destas set by the user inNioFileCopierWithProgressMeter.setChecksumAlgorithmAndExpectedChecksum(String, String). - getExpectedCopyNumber(Genotype) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getExpectedErrorRatePerBase() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
- getExpectedSortOrder() - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleCollectMultiMetricsSpark
-
Return the sort order required/expected by this collector.
- getExpectedSortOrder() - Method in class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleCollectSingleMetricsSpark
-
Return the sort order required/expected by this collector.
- getExpectedSortOrder() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectInsertSizeMetricsSpark
- getExpectedSortOrder() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark
- getExpectedSortOrder() - Method in interface org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSpark
-
Return the sort order this collect requires.
- getExpectedSortOrder() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSparkTool
- getExpectedTiles() - Method in class picard.illumina.parser.IlluminaFileUtil
-
Return the list of tiles we would expect for this lane based on the metrics found in InterOp/TileMetricsOut.bin
- getExtendedManifestVersion() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifest
- getExtension() - Static method in class picard.illumina.IlluminaLaneMetrics
-
This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
- getExtension() - Static method in class picard.illumina.IlluminaPhasingMetrics
-
This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
- getExtension() - Static method in class picard.vcf.MendelianViolations.MendelianViolationMetrics
- getExtraGraphFileLines() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
- getExtraGraphFileLines() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
- getF1R2(Genotype) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadOrientationFilter
- getF1R2StateForAlt(Nucleotide) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- getF2R1(Genotype) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadOrientationFilter
- getF2R1StateForAlt(Nucleotide) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- getFalseDiscoveryRate() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterStats
- getFalseNegativeCount() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterStats
- getFalseNegativeCount() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
- getFalseNegativeRate() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterStats
- getFalseNegatives() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceSummaryRecord
- getFalsePositiveCount() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterStats
- getFalsePositiveProbability() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerBloomFilter
- getFalsePositiveProbability() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet
- getFalsePositives() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceSummaryRecord
- getFamilies() - Method in class org.broadinstitute.hellbender.utils.samples.SampleDB
-
Returns a map from family ID -> set of family members.
- getFamilies(Collection<String>) - Method in class org.broadinstitute.hellbender.utils.samples.SampleDB
- getFamily(String) - Method in class org.broadinstitute.hellbender.utils.samples.SampleDB
-
Return all samples with a given family ID
- getFamilyCalledCount() - Method in class org.broadinstitute.hellbender.utils.samples.MendelianViolation
- getFamilyId() - Method in class picard.pedigree.PedFile.PedTrio
- getFamilyID() - Method in class org.broadinstitute.hellbender.utils.samples.Sample
- getFamilyIDs() - Method in class org.broadinstitute.hellbender.utils.samples.SampleDB
-
Returns a sorted set of the family IDs in all samples
- getFamilyLowQualsCount() - Method in class org.broadinstitute.hellbender.utils.samples.MendelianViolation
- getFamilyNamesForEvaluation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getFamilyNamesForStratification() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getFamilyNoCallCount() - Method in class org.broadinstitute.hellbender.utils.samples.MendelianViolation
- getFaqLink() - Static method in class picard.cmdline.CommandLineProgram
- getFastaDictionaryFileName(String) - Static method in class org.broadinstitute.hellbender.utils.reference.ReferenceUtils
-
Given a fasta filename, return the name of the corresponding dictionary file.
- getFastaIndexFileName(String) - Static method in class org.broadinstitute.hellbender.utils.reference.ReferenceUtils
-
Given a fasta filename, return the name of the corresponding index file.
- getFather() - Method in class org.broadinstitute.hellbender.utils.samples.Trio
- getFather(Sample) - Method in class org.broadinstitute.hellbender.utils.samples.SampleDB
-
Get the sample's father
- getFeature() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker.PQEntry
- getFeatureCodecClass() - Method in class org.broadinstitute.hellbender.engine.FeatureInput
- getFeatureCodecHeader() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- getFeatureContext() - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerContext
- getFeatureContext() - Method in class org.broadinstitute.hellbender.engine.spark.IntervalWalkerContext
- getFeatureContext() - Method in class org.broadinstitute.hellbender.engine.spark.LocusWalkerContext
- getFeatureContext() - Method in class org.broadinstitute.hellbender.engine.spark.ReadWalkerContext
- getFeatureContext() - Method in class org.broadinstitute.hellbender.engine.spark.VariantWalkerContext
- getFeatureInputsForDrivingVariants() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- getFeatureIterator(FeatureInput<T>) - Method in class org.broadinstitute.hellbender.engine.FeatureManager
-
Given a FeatureInput argument field from our tool, returns an iterator to its features starting from the first one.
- getFeatureIterator(FeatureInput<T>, List<SimpleInterval>) - Method in class org.broadinstitute.hellbender.engine.FeatureManager
-
As above, but takes an optional list of intervals to examine.
- getFeatureOrderNumber() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getFeaturePath() - Method in class org.broadinstitute.hellbender.engine.FeatureInput
-
Gets the file backing this source of Features
- getFeatures(FeatureInput<T>, Locatable) - Method in class org.broadinstitute.hellbender.engine.FeatureManager
-
Given a FeatureInput argument field from our tool, queries the data source for that FeatureInput over the specified interval, and returns a List of the Features overlapping that interval from that data source.
- getFeatureType() - Method in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceBCICodec
- getFeatureType() - Method in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceBCICodec
- getFeatureType() - Method in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceBCICodec
- getFeatureType() - Method in interface org.broadinstitute.hellbender.utils.codecs.FeatureOutputCodec
-
Each codec knows how to handle one subtype of Feature, and this is the one.
- getFeatureType() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getFeatureType() - Method in class org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec
- getFeatureType() - Method in class org.broadinstitute.hellbender.utils.codecs.SiteDepthBCICodec
- getFeatureType() - Method in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceBCICodec
- getField(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getField(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
- getField(String) - Method in interface org.broadinstitute.hellbender.tools.funcotator.Funcotation
-
Get the value of a field in this
Funcotation. - getField(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
- getField(String) - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
- getFieldNames() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getFieldNames() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
- getFieldNames() - Method in interface org.broadinstitute.hellbender.tools.funcotator.Funcotation
-
Get the names of the fields in this
Funcotation. - getFieldNames(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
-
Get all field names found in the funcotations for the given transcript ID.
- getFieldNameToListIndexInProtobufVidMappingObject(GenomicsDBVidMapProto.VidMappingPB) - Static method in class org.broadinstitute.hellbender.tools.genomicsdb.GATKGenomicsDBUtils
-
In vidMapPB, fields is a list of GenomicsDBVidMapProto.GenomicsDBFieldInfo objects Each GenomicsDBFieldInfo object contains information about a specific field in the GenomicsDB store We iterate over the list and create a field name to list index map
- getFieldOrDefault(String, String) - Method in interface org.broadinstitute.hellbender.tools.funcotator.Funcotation
-
Get the value of a field in this
Funcotation. - getFields() - Method in class org.broadinstitute.hellbender.tools.funcotator.AliasProvider
-
Get the fields that have aliases.
- getFields() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- getFields() - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
- getFields() - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
- getFieldValue(String, String, Allele) - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
- getFile() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
- getFile() - Method in class picard.illumina.parser.TileIndex
- getFileExtension() - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
- getFileExtension() - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
- getFileExtension() - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
- getFileExtension() - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
- getFileExtension() - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
- getFileName() - Method in class picard.util.AbstractInputParser
- getFileName() - Method in class picard.util.BasicInputParser
-
Gets the name of the file being parsed
- getFilePath(String) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType
- getFilePosition() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.IndexEntry
- getFiles() - Method in class picard.illumina.parser.PerTileFileUtil
- getFiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
- getFiles(int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
Returns a cycleIlluminaFileMap with all available tiles but limited to the cycles passed in.
- getFiles(List<Integer>) - Method in class picard.illumina.parser.PerTileFileUtil
- getFiles(List<Integer>) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
- getFiles(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileBclFileUtil
- getFiles(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
Returns a cycleIlluminaFileMap that contains only the tiles and cycles specified (and fewer if the original CycleIlluminaFileMap, created on util instantiation, doesn't contain any of these tiles/cycles).
- getFilesForCycle(int) - Method in class picard.illumina.parser.readers.CbclReader
- getFilter() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
- getFilteredBases() - Method in class picard.filter.CountingFilter
-
Gets the number of bases that have been filtered out thus far.
- getFilteredCount() - Method in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter
- getFilteredCount() - Method in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter
- getFilteredHaplotypeCount() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
- getFilteredRecords() - Method in class picard.filter.CountingFilter
-
Gets the number of records that have been filtered out thus far.
- getFilteredSize() - Method in class org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile
-
Get the filter size (which is the size of each wing of the band, minus the center point)
- getFilterLine(String) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFHeaderLines
- getFilterLine(String) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines
- getFilterLines() - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFHeaderLines
- getFilterName() - Method in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.FuncotationFilter
- getFilterName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterStats
- getFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- getFinalCall() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Kmer
- getFinalRecalibrationTables() - Method in class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
-
Get the final recalibration tables, after finalizeData() has been called This returns the finalized recalibration table collected by this engine.
- getFinalSampleDB() - Method in class org.broadinstitute.hellbender.utils.samples.SampleDBBuilder
- getFingerprintFile() - Method in class picard.fingerprint.MatchResults
- getFingerprintIdDetailsStringFunction(CrosscheckMetric.DataType) - Static method in class picard.fingerprint.Fingerprint
- getFingerprintMetrics(Fingerprint) - Method in class picard.fingerprint.CalculateFingerprintMetrics
- getFingerprintPanels() - Method in class picard.fingerprint.Snp
- getFirstAlignedBaseOffset(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Returns the offset (0-based index) of the first base in the read that is aligned against the reference.
- getFirstCall() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.PathPart
- getFirstCall() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartContig
- getFirstCall() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartGap
- getFirstContig() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- getFirstContig() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionStatistics
- getFirstContigID() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionBounds
- getFirstInsertionOffset(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
If a read starts in INSERTION, returns the first element length.
- getFirstKmer() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- getFirstKmer() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- getFirstKmer() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- getFirstLocation() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionStatistics
- getFirstOfPair() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.ReadPair
- getFirstOfPair(int) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
- getFirstSnp() - Method in class picard.fingerprint.HaplotypeBlock
-
Gets the arbitrarily first SNP in the haplotype.
- getFirstStart() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionBounds
- getFirstVertex() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
-
Get the first vertex in this path
- getFlag() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getFlags() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getFlags() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getFlatPrior(Nucleotide) - Static method in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelEngine
- getFloatIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
- getFlowMatrixModsInstructions(String, int) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
-
Retrieve flow matrix modifications matrix from its string argument format.
- getFlowModeArgValues() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- getFlowOrder() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- getFlowOrderArray() - Method in class org.broadinstitute.hellbender.utils.haplotype.FlowBasedHaplotype
- getFlowOrderArray() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- getFlowSumOfBaseQualities(SAMRecord, int) - Static method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
-
A quality summing scoring strategy used for flow based reads.
- getFlowToBase(String, int) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedKeyCodec
-
For every flow of the key output the nucleotide that is being read for this flow
- getForceSort() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.SamAlignmentMerger
- getForceSort() - Method in class picard.sam.SamAlignmentMerger
- getFormat() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- getFormat() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetResponse
- getFormat() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.AlleleCount
- getFormat() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.IndelSize
- getFormat() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier
- getFormat() - Method in class org.broadinstitute.hellbender.utils.report.GATKReportColumn
- getFormatLine(String) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFHeaderLines
- getFormatLine(String) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines
- getFormatLine(String, boolean) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines
- getFormatLines() - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFHeaderLines
- getForwardAltCount() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter.EStep
- getForwardArtifactResponsibility() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter.EStep
- getForwardBases() - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
-
Get the bases in this context, from the beginning of the interval to the end of the window.
- getForwardCount() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter.EStep
- getForwardStrand() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
- getFounderGenotypes(VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation
- getFounderIds() - Method in class org.broadinstitute.hellbender.utils.samples.SampleDB
- getFQTableName() - Method in class org.broadinstitute.hellbender.utils.bigquery.TableReference
- getFracA() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getFracC() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getFracG() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getFracT() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getFraction(int) - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.CDF
- getFractionUnexpectedAlleleObs() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- getFragment(int) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
- getFragmentLength() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Returns the observed length of the read's fragment (equivalent to TLEN in SAM).
- getFragmentLength() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getFragmentOrdinal() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
- getFrequencies() - Method in class org.broadinstitute.hellbender.tools.sv.SVAlleleCounter
- getFullPath() - Method in class org.broadinstitute.hellbender.utils.io.Resource
- getFullReferenceWithPadding() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Returns the current full reference with padding.
- getFuncotationFactories() - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine
- getGA4GHEnd() - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
- getGA4GHStart() - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
- getGapExtensionProb() - Method in class org.broadinstitute.hellbender.utils.baq.BAQ
- getGapOpenProb() - Method in class org.broadinstitute.hellbender.utils.baq.BAQ
- getGATKConfig() - Method in class org.broadinstitute.hellbender.utils.config.ConfigFactory
-
Quick way to get the GATK configuration.
- getGatkReadJavaRDD(TraversalParameters, ReadsSparkSource, GATKPath) - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- getGcContent() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getGcContent() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getGencodeVersion() - Method in enum class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations.Reference
- getGender() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getGene() - Method in class picard.annotation.Gene.Transcript
- getGeneId() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getGeneName() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getGeneName() - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
-
Name of the gene this transcript corresponds to (NOT gene id such as Entrez etc)
- getGeneName() - Method in interface org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqTranscript
-
Name of the gene this transcript corresponds to (typically NOT gene id such as Entrez etc, but the implementation can decide otherwise)
- getGenesForPickTranscripts() - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
-
Derived class may override this method in order to return a different set of genes for picking transcripts for computing coverage, or to cache the value returned by geneOverlapDetector.getAll(), because it can be expensive to compute repeatedly.
- getGeneStatus() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getGeneTranscriptType() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getGeneType() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getGenomeBuild() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getGenomeBuild() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getGenomeChange() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getGenomeLocation() - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
-
Get the span of this haplotype (may be null)
- getGenomeLocParser() - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
Gets the GenomeLocParser used to create this sorted set.
- getGenomeOffset() - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
-
What is the current offset w.r.t.
- getGenomePosition() - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
-
Get the position (1-based as standard) of the current alignment on the genome w.r.t.
- getGenomicEndLocation() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getGenomicPhase() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getGenomicPosition() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getGenomicsDBAbsolutePath(GATKPath) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Gets the absolute Path for a GenomicsDB path
- getGenomicsDBFeatureReader(GATKPath, File, GenomicsDBOptions) - Static method in class org.broadinstitute.hellbender.engine.FeatureDataSource
- getGenomicsDBOptions() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Get the GenomicsDB read settings for the current tool
- getGenomicsDBOptions() - Method in class org.broadinstitute.hellbender.engine.VariantWalkerBase
- getGenomicsDBOptions() - Method in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- getGenomicsDBOptions() - Method in class org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyper
- getGenomicsDBOptions() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals
- getGenomicsDBOptions() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
- getGenomicsDBPath(String) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
If path is prefaced with gendb:// or gendb.CloudURIScheme://, this method returns an absolute path acceptable by GenomicsDB by stripping off gendb:// for files or gendb. for Cloud URIs respectively .
- getGenomicsDBPath(GATKPath) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
If path is prefaced with gendb:// or gendb.CloudURIScheme://, this method returns an absolute path acceptable by GenomicsDB by stripping off gendb:// for files or gendb. for Cloud URIs respectively .
- getGenomicStartLocation() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getGenomicStrand() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getGenotype(String, InfiniumGTCRecord, IlluminaManifestRecord, Allele, Allele) - Method in class picard.arrays.GtcToVcf
- getGenotypeAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
-
Returns the list of genotype annotations that will be applied.
- getGenotypeBytes() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getGenotypes() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getGenotypeScores() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getGoldStand() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- getGoodMappings() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig.GoodAndBadMappings
- getGraph() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
-
Get the graph of this path
- getGreen() - Method in class picard.arrays.illumina.ArraysControlInfo
- getGroupMap(DocWorkUnit) - Method in class org.broadinstitute.hellbender.utils.help.GATKHelpDoclet
-
Adds a super-category so that we can custom-order the categories in the doc index
- getGroupMap(DocWorkUnit) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLDoclet
-
Return the group map for this workunit.
- getGroupMap(DocWorkUnit) - Method in class picard.util.help.PicardHelpDoclet
-
Adds a super-category so that we can custom-order the categories in the doc index
- getGtfSourceFileType() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getHaplotype() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the haplotype for which the probabilities apply.
- getHaplotype(String) - Method in class picard.fingerprint.HaplotypeMap
-
Queries a HaplotypeBlock by Snp name.
- getHaplotype(String, int) - Method in class picard.fingerprint.HaplotypeMap
-
Queries a HaplotypeBlock by Snp chromosome and position.
- getHaplotype(Snp) - Method in class picard.fingerprint.HaplotypeMap
-
Queries a HaplotypeBlock by Snp object.
- getHaplotypeCollapsingEngine() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
- getHaplotypeCount() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Returns the number of haplotypes in the assembly result set.
- getHaplotypeFrequencies() - Method in class picard.fingerprint.HaplotypeBlock
-
Gets the set of haplotype frequencies.
- getHaplotypeFrequency(int) - Method in class picard.fingerprint.HaplotypeBlock
-
Gets the frequency of the i'th diploid haplotype where haplotypes are ordered accorinding to DiploidHaplotype.
- getHaplotypeList() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Returns the haplotypes as a list.
- getHaplotypeReadGroupID() - Method in class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMDestination
-
Get the read group ID that is used by this writer when writing halpotypes as reads.
- getHaplotypes() - Method in class picard.fingerprint.HaplotypeMap
-
Returns an unmodifiable collection of all the haplotype blocks in the map.
- getHaplotypes(Locatable, String) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OnRampBase
- getHaplotypeSampleTag() - Method in class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMDestination
-
Get the sample tag that is used by this writer when writing halpotypes as reads.
- getHaplotypeToReferenceSWParameters() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- getHardClippedPileupReads() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Get an unmodifiable copy of the list of reads currently in this assembly region.
- getHeadAlignment() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
- getHeadAlignment() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- getHeader() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Returns the header for the reads in this region.
- getHeader() - Method in class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Gets the header associated with this data source
- getHeader() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker.PQContext
- getHeader() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker.PQEntry
- getHeader() - Method in class org.broadinstitute.hellbender.engine.MultiVariantDataSource
-
Gets the merged header associated with this data source
- getHeader() - Method in interface org.broadinstitute.hellbender.engine.ReadsDataSource
-
Returns the SAM header for this data source.
- getHeader() - Method in class org.broadinstitute.hellbender.engine.ReadsPathDataSource
-
Returns the SAM header for this data source.
- getHeader() - Method in class org.broadinstitute.hellbender.tools.spark.bwa.BwaSparkEngine
- getHeader() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead
-
Returns the header line of this Fastq read starting with '@' followed by the read id and description separated by tab characters.
- getHeader() - Method in class org.broadinstitute.hellbender.utils.codecs.table.TableFeature
-
Gets the column names.
- getHeader() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
-
Get the header from this
XsvTableFeature. - getHeader() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- getHeader() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- getHeader() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- getHeader() - Method in class picard.fingerprint.FingerprintChecker
- getHeader() - Method in class picard.fingerprint.HaplotypeMap
- getHeader() - Method in class picard.sam.AbstractAlignmentMerger
- getHeader(SamReader) - Method in class org.broadinstitute.hellbender.tools.walkers.variantrecalling.TrimmedReadsReader
- getHeader(String) - Static method in class org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSource
- getHeader(FeatureInput<T>) - Method in class org.broadinstitute.hellbender.engine.FeatureContext
-
Gets the header associated with the provided FeatureInput
- getHeader(FeatureInput<T>) - Method in class org.broadinstitute.hellbender.engine.FeatureManager
-
Get the header associated with a particular FeatureInput
- getHeader(GATKPath, GATKPath) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource
-
Loads the header using Hadoop-BAM.
- getHeaderBroadcast() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData.SampleSpecificData
- getHeaderContents() - Method in class picard.arrays.illumina.IlluminaManifest
- getHeaderForFeatures(FeatureInput<T>) - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns the header for the specified source of Features
- getHeaderForFeatures(FeatureInput<T>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getHeaderForReads() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns the SAM header for the reads data source.
- getHeaderForReads() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- getHeaderForReadsInput(GATKPath) - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Returns the header for a given input.
- getHeaderForSAMWriter() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns the SAM header suitable for writing SAM/BAM/CRAM files produced by this tool.
- getHeaderForSAMWriter() - Method in class org.broadinstitute.hellbender.tools.AnalyzeSaturationMutagenesis
- getHeaderForVariants() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalker
-
Gets the header associated with our driving source of variants as a VCFHeader.
- getHeaderForVariants() - Method in class org.broadinstitute.hellbender.engine.spark.VariantWalkerSpark
-
Gets the header associated with our driving source of variants as a VCFHeader.
- getHeaderForVariants() - Method in class org.broadinstitute.hellbender.engine.VariantLocusWalker
-
Gets the header associated with our driving source of variants as a VCFHeader.
- getHeaderForVariants() - Method in class org.broadinstitute.hellbender.engine.VariantWalker
-
Gets the header associated with our driving source of variants as a VCFHeader.
- getHeaderForVariants() - Method in class org.broadinstitute.hellbender.engine.VariantWalkerBase
-
Return the VCFHeader to be used for the driving variants for this tool.
- getHeaders() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetResponse.Block
- getHeaderSize() - Method in class picard.illumina.parser.readers.CbclReader
- getHeaderWithoutLocationColumns() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
-
Get the header from this
XsvLocatableTableCodecwithout the columns that contain location information. - getHeaderWithoutLocationColumns() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
-
Get the header from this
XsvTableFeaturewithout the columns that contain location information. - getHelpDoc() - Method in enum class org.broadinstitute.hellbender.tools.spark.RevertSamSpark.FileType
- getHelpDoc() - Method in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.TensorType
- getHelpDoc() - Method in enum class picard.analysis.CollectMultipleMetrics.Program
- getHelpDoc() - Method in enum class picard.illumina.DistanceMetric
- getHelpDoc() - Method in enum class picard.sam.FilterSamReads.Filter
- getHelpDoc() - Method in enum class picard.sam.markduplicates.CheckDuplicateMarking.Mode
- getHelpDoc() - Method in enum class picard.sam.RevertSam.FileType
- getHelpDoc() - Method in enum class picard.util.IntervalList.IntervalListScatterMode
- getHelpDoc() - Method in enum class picard.util.IntervalListTools.Action
- getHet(int, int) - Static method in enum class picard.vcf.GenotypeConcordanceStates.CallState
- getHetAllelicCountsPerSample() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.genotyping.NaiveHeterozygousPileupGenotypingUtils.NaiveHeterozygousPileupGenotypingResult
- getHetCount(Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.HeterozygosityCalculator
-
Get the count of heterozygotes in vc for a specific altAllele (both reference and non-reference hets, e.g.
- getHeterogyzousGenotype() - Method in class picard.fingerprint.Snp
- getHetNormalAllelicCounts() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.genotyping.NaiveHeterozygousPileupGenotypingUtils.NaiveHeterozygousPileupGenotypingResult
- getHetPercent() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getHets() - Method in class org.broadinstitute.hellbender.utils.GenotypeCounts
- getHgGenomeBuild() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getHighQualityDepthHistogram() - Method in class picard.analysis.AbstractWgsMetricsCollector
- getHistogram(long[], String, String) - Method in class picard.analysis.AbstractWgsMetricsCollector
- getHistograms() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
- getHistograms() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.DepthOneHistograms
- getHom(int) - Static method in enum class picard.vcf.GenotypeConcordanceStates.CallState
- getHom(int) - Static method in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- getHomologyForwardStrandRep() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications
- getHomozygousAllele1Genotype() - Method in class picard.fingerprint.Snp
- getHomozygousAllele2Genotype() - Method in class picard.fingerprint.Snp
- getHoms() - Method in class org.broadinstitute.hellbender.utils.GenotypeCounts
- getHugoSymbol() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getId() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- getId() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- getId() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- getId() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead
- getId() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getId() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqVertex
-
Get the unique ID for this SeqVertex
- getId() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord
- getId() - Method in class org.broadinstitute.hellbender.utils.UniqueIDWrapper
- getID() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- getID() - Method in class org.broadinstitute.hellbender.utils.samples.Sample
- getID(SAMReadGroupRecord) - Static method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadGroupCovariate
-
Get the ID of the readgroup.
- getIdentifier() - Method in class picard.arrays.illumina.InfiniumDataFile
- getIlmnId() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getIlmnId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getIlmnStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getIlmnStrand() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getImagingDate() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getImagingUser() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getIncompatibleEvaluators() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.AlleleCount
- getIncompatibleEvaluators() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Family
- getIncompatibleEvaluators() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Sample
- getIncompatibleEvaluators() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier
-
The way for a stratifier to specify that it's incompatible with specific evaluations.
- getIndelAdjustedAlleleChangeStartPosition(VariantContext) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Get the start position of the difference between the reference and alternate alleles in the given
VariantContext. - getIndelAdjustedAlleleChangeStartPosition(VariantContext, Allele) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Get the start position of the difference between the reference and alternate alleles in the given
VariantContext. - getIndelCounter() - Method in class picard.vcf.GenotypeConcordance
- getIndelElement(SamLocusIterator.RecordAndOffset) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
- getIndelFalsePositiveRate() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord
- getIndelFalsePositives() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord
- getIndelLength() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.Datum
- getIndels() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCase
-
Returns the total number of indel events on reads that overlap the STR a this locus.
- getIndentString(int) - Method in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter
- getIndentString(int) - Method in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter
- getIndependentSets(List<Pair<C, C>>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.OccurrenceMatrix
-
Analyse columns for being independent of each other.
- getIndex() - Method in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils.IndexPair
- getIndex() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getIndex() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getIndex(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Find the rank of the specified interval.
- getIndexesOfRelevantAlleles(List<Allele>, List<Allele>, int, Genotype) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
- getIndexesOfRelevantAllelesForGVCF(List<Allele>, List<Allele>, int, Genotype, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
-
Determines the allele mapping from myAlleles to the targetAlleles, substituting the generic "
" as appropriate. - getIndexFileExtension() - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLDoclet
- getIndexForColumn(String) - Method in class org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter
- getIndexTemplateName() - Method in class org.broadinstitute.hellbender.utils.help.GATKHelpDoclet
-
Return the name of the freemarker template to be used for the index generated by Barclay.
- getIndexTemplateName() - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLDoclet
-
Return the name of the freemarker template to be used for the index generated by Barclay.
- getIndexTemplateName() - Method in class picard.util.help.PicardHelpDoclet
-
Return the name of the freemarker template to be used for the index generated by Barclay.
- getIndices() - Method in class picard.illumina.parser.ReadStructure.Substructure
- getIndividualId() - Method in class picard.pedigree.PedFile.PedTrio
- getInfo() - Method in class picard.fingerprint.Fingerprint
- getInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
-
Returns the list of info annotations that will be applied.
- getInfoLine(String) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFHeaderLines
- getInfoLine(String) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines
- getInfoLine(String, boolean) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines
- getInfoLines() - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFHeaderLines
- getInfoString() - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
- getInfoString() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
- getInheritance() - Method in class org.broadinstitute.hellbender.utils.samples.MendelianViolation
- getInitialCall() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Kmer
- getInitialLogOdds() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- getInputArguments() - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleCollectMultiMetricsSpark
-
Return the embedded argument collection.
- getInputArguments() - Method in class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleCollectSingleMetricsSpark
-
Return the embedded argument collection.
- getInputArguments() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectInsertSizeMetricsSpark
- getInputArguments() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark
- getInputArguments() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSparkTool
-
To be implemented by subclasses; return the fully initialized and populated argument collection that will be passed to the collector
- getInputBuffer() - Method in class org.broadinstitute.hellbender.utils.runtime.InputStreamSettings
- getInputFile() - Method in class org.broadinstitute.hellbender.utils.runtime.InputStreamSettings
- getInputFile() - Method in class picard.fingerprint.FingerprintResults
- getInputStream() - Method in class org.broadinstitute.hellbender.engine.GATKPath
- getInputStream() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- getInputStream() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- getInsertedSequence() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVContext
-
Returns the inserted sequence.
- getInsertedSequenceForwardStrandRep() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications
- getInsertionMappings() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- getInsertionsKeySet() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadCovariates
- getInsertionsKeySet(int) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadCovariates
- getInstance() - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
- getInstance() - Static method in class org.broadinstitute.hellbender.utils.config.ConfigFactory
- getInstance() - Static method in class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner
-
return the stateless singleton instance of SmithWatermanJavaAligner
- getInstance(int, int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculators
-
Returns an instance given its ploidy and the number of alleles.
- getInstance(String) - Static method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndexCache
-
Returns a
BwaMemIndexinstance that corresponds to given index image file. - getInstanceDRAGEN(int, int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculators
-
Returns an instance of the DRAGEN genotypeLikelihoodCalculator given its ploidy and the number of alleles.
- getInt() - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the int value in a column at the current column index and advance it.
- getInt(int) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the int value in a column by its index.
- getInt(Enum<?>) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the int value of a column by its name.
- getInt(String) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the int value in a column by its index.
- getIntegerCopyNumberStateList() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyNumberPosteriorDistribution
- getIntegerField(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
- getIntegerField(String) - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
- getIntegerFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
- getIntegerIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
- getIntensityOnly() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getIntermediateStopSites(SimpleInterval, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
- getInternalVariantId() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- getInterval() - Method in class org.broadinstitute.hellbender.engine.FeatureContext
-
Gets our query interval (the interval that all Features returned by this FeatureContext overlap).
- getInterval() - Method in class org.broadinstitute.hellbender.engine.ReadsContext
-
Gets the interval spanned by this context (returned reads will overlap this interval).
- getInterval() - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
-
Get the location on the reference represented by this context, without including any extra bases of requested context around this interval.
- getInterval() - Method in interface org.broadinstitute.hellbender.engine.Shard
- getInterval() - Method in class org.broadinstitute.hellbender.engine.ShardBoundary
- getInterval() - Method in class org.broadinstitute.hellbender.engine.ShardBoundaryShard
- getInterval() - Method in class org.broadinstitute.hellbender.engine.ShardToMultiIntervalShardAdapter
- getInterval() - Method in class org.broadinstitute.hellbender.engine.spark.IntervalWalkerContext
- getInterval() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
- getInterval() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AnnotatedInterval
- getInterval() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatio
- getInterval() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatioSegment
- getInterval() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
- getInterval() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntervalCopyNumberGenotypingData
- getInterval() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LegacySegment
- getInterval() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LinearCopyRatio
- getInterval() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment
- getInterval() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount
- getInterval() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval
-
Returns a copy
- getInterval() - Method in class org.broadinstitute.hellbender.tools.DownsampleableSparkReadShard
- getInterval() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- getInterval() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval
- getInterval() - Method in class org.broadinstitute.hellbender.tools.walkers.consensus.ReadsWithSameUMI
- getInterval() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine.SVSegment
- getInterval() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- getInterval() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.IndexEntry
- getInterval() - Method in class org.broadinstitute.hellbender.utils.reference.ReferenceBases
- getInterval() - Method in interface org.broadinstitute.hellbender.utils.SVIntervalTree.Entry
- getIntervalExclusionPadding() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
Get the interval exclusion padding specified on the command line.
- getIntervalFile() - Method in class picard.analysis.CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
- getIntervalFile() - Method in interface picard.cmdline.argumentcollections.IntervalArgumentCollection
- getIntervalForFatInsertion() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
-
Return the interval being replaced, anchored 1 bp from left, i.e.
- getIntervalId() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerAndInterval
- getIntervalId() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval
- getIntervalList() - Method in class picard.fingerprint.HaplotypeMap
-
Returns an IntervalList with an entry for every SNP in every Haplotype in the map.
- getIntervalMergingRule() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
Get the interval merging rule specified on the command line.
- getIntervalObjectsToQueryOver() - Method in class org.broadinstitute.hellbender.engine.LocusWalkerByInterval
-
Tool-specified list of Locatable objects (which have been read into memory) that will have overlaps queried at each locus
- getIntervalObjectsToQueryOver() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage
-
We want to keep track of per-interval information for both the user specified intervals and for user specified genes
- getIntervalPadding() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
Get the interval padding specified on the command line.
- getIntervals() - Method in class org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard
- getIntervals() - Method in interface org.broadinstitute.hellbender.engine.MultiIntervalShard
- getIntervals() - Method in class org.broadinstitute.hellbender.engine.ShardToMultiIntervalShardAdapter
- getIntervals() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- getIntervals() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractLocatableCollection
- getIntervals(SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
Get the intervals specified on the command line.
- getIntervals(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.IntervalWalkerSpark
-
Loads intervals and the corresponding reads, reference and features into a
JavaRDD. - getIntervalSetRule() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
Get the interval set rule specified on the command line.
- getIntervalsFile() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- getIntervalsForTraversal() - Method in class org.broadinstitute.hellbender.engine.TraversalParameters
- getIntervalsToExamine() - Method in class picard.analysis.CollectWgsMetrics
-
Gets the intervals over which we will calculate metrics.
- getIntervalStrings() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
Subclasses must provide a -L argument and override this to return the results of that argument.
- getIntervalStrings() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalIntervalArgumentCollection
- getIntervalStrings() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredIntervalArgumentCollection
- getIntervalSVType() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine.SVSegment
- getIntervalsWithFlanks(List<SimpleInterval>, int, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Pads the provided intervals by the specified amount, sorts the resulting intervals, and merges intervals that are adjacent/overlapping after padding.
- getIntervalsWithFlanks(GenomeLocParser, List<GenomeLoc>, int) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Returns a list of intervals between the passed int locs.
- getIntervalsWithoutMerging(SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
Returns the full set of traversal intervals specified on the command line, including parsed intervals without merging intervals specified by the user on the command line.
- getItems() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine.OutputCluster
- getIterator() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker.PQContext
- getJexlExpressions() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getJSONFilename(DocWorkUnit) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLWorkUnitHandler
-
Returns the JSON output file name.
- getJunctionTreeForNode(MultiDeBruijnVertex) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
- getKeepSpecifiedCombinedAnnotationNames() - Method in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsAnnotationArgumentCollection
- getKernel() - Method in class org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile
-
Get the kernel of this band pass filter.
- getKey() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerAndInterval
- getKey() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval
- getKey() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.KmerAndCount
- getKey() - Method in class org.broadinstitute.hellbender.utils.haplotype.FlowBasedHaplotype
- getKey() - Method in class org.broadinstitute.hellbender.utils.KV
- getKey() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- getKey(List<Object>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- getKeyForFragment(int, boolean, int, byte) - Static method in class org.broadinstitute.hellbender.utils.read.markduplicates.ReadsKey
- getKeyForPair(SAMFileHeader, GATKRead, GATKRead, Map<String, Byte>) - Static method in class org.broadinstitute.hellbender.utils.read.markduplicates.ReadsKey
- getKeyLength() - Method in class org.broadinstitute.hellbender.utils.haplotype.FlowBasedHaplotype
- getKeyLength() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.AlleleFraction
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.AllelePseudoDepth
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_BaseQualityRankSumTest
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_FisherStrand
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_InbreedingCoeff
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_MappingQualityRankSumTest
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_ReadPosRankSumTest
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandOddsRatio
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.AS_StrandBiasMutectAnnotation
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.AssemblyComplexity
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityHistogram
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityRankSumTest
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ChromosomeCounts
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ClippingRankSumTest
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.CountNs
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.Coverage
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.DepthPerAlleleBySample
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.DepthPerSampleHC
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.FeaturizedReadSets
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.FisherStrand
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.CycleSkipStatus
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.GcContent
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.HmerIndelLength
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.HmerIndelNuc
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.HmerMotifs
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.IndelClassify
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.IndelLength
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.VariantType
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.FragmentDepthPerAlleleBySample
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeSummaries
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.HaplotypeFilteringAnnotation
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.LikelihoodRankSumTest
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.MappingQualityRankSumTest
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.MappingQualityZero
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.OrientationBiasReadCounts
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.OriginalAlignment
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.PerAlleleAnnotation
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.PossibleDeNovo
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.QualByDepth
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RawGtCount
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosRankSumTest
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ReferenceBases
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.SampleList
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasBySample
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandOddsRatio
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.TandemRepeat
- getKeyNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.UniqueAltReadCount
- getKeyNames() - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotation
-
Return the keys
- getKeys() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationMap
- getKeys(List<List<Object>>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- getKeySet(int, EventType) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadCovariates
-
Get the keys for all covariates at read position for error model
- getKeySet(EventType) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadCovariates
- getKeyToBase(int[]) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedKeyCodec
-
For every flow of the key output the index of the last base that was output prior to this flow
- getKingdomTaxonId() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- getKmerAround(int, int) - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
-
Get a kmer around a position in reference without altering the internal state of the object The position must lie within the window Returns null when, at the ends of a contig, we cannot expand the window to the requested size
- getKmerCount(Kmer) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.KMerCounter
-
Get the count of kmer in this kmer counter
- getKmers(Collection<SeqVertex>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.GraphUtils
-
Get the list of kmers as byte[] from the vertices in the graph
- getKmerSize() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult
- getKmerSize() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
How big of a kmer did we use to create this graph?
- getKmerSize() - Method in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KmerSearchableGraph
-
The kmer-size of indexed kmers.
- getKmerSize() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex
-
Get the kmer size for this DeBruijnVertex
- getKmerSize() - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- getKmersWithCountsAtLeast(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.KMerCounter
-
Get kmers that have minCount or greater in this counter
- getKmerVertex(Kmer, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Get the unique vertex for kmer, or null if not possible.
- getKnownCNVsFile() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- getKnowns() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getKnownTypes() - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- getKVal() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Kmer
- getLane() - Method in class picard.illumina.parser.ClusterData
- getLane() - Method in class picard.illumina.parser.IlluminaFileUtil
-
Return the lane we're inspecting
- getLane() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
- getLaneFactories() - Method in class picard.illumina.BasecallsConverter
-
Gets the data provider factory used to create the underlying data provider.
- getLaneNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
- getLaneNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- getLaneNumber() - Method in class picard.illumina.parser.Tile
-
Returns the number of this tile's parent lane.
- getLaneTileCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- getLastCall() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.PathPart
- getLastCall() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartContig
- getLastCall() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartGap
- getLastContig() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- getLastContig() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionStatistics
- getLastContigID() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionBounds
- getLastEdge() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
- getLastEnd() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionBounds
- getLastInsertionOffset(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
If a read ends in INSERTION, returns the last element length.
- getLastKmer() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- getLastKmer() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- getLastKmer() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- getLastLocation() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionStatistics
- getLastThreeFields(String, char, int[]) - Static method in class picard.sam.util.ReadNameParser
-
Given a string, splits the string by the delimiter, and returns the the last three fields parsed as integers.
- getLastVertex() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
-
Get the final vertex of the path
- getLCA(Collection<Integer>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
-
Get lowest common ancester of the set of given nodes.
- getLeadingDeletionBasesRemoved() - Method in class org.broadinstitute.hellbender.utils.read.CigarBuilder
-
Count the number of leading deletion bases that have been removed by this builder and that will not show up in any call to make().
- getLeadingDeletionBasesRemoved() - Method in class org.broadinstitute.hellbender.utils.read.CigarBuilder.Result
- getLeft() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervals
- getLeft() - Method in class picard.sam.util.Pair
- getLeftClipPoint(byte[]) - Method in class org.broadinstitute.hellbender.transformers.BaseQualityClipReadTransformer
-
Returns left clip point or -1 if no clip
- getLeftJustifiedLeftRefLoc() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- getLeftJustifiedRightRefLoc() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- getLeftMotif(VariantContext, FlowAnnotatorBase.LocalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- getLegalSizeAbove(long) - Static method in class org.broadinstitute.hellbender.utils.collections.SetSizeUtils
- getLegalSizeAbove(long, double) - Static method in class org.broadinstitute.hellbender.utils.collections.SetSizeUtils
-
Computes next largest legal table size for a given number of elements, accounting for load factor
- getLegalSizeBelow(long) - Static method in class org.broadinstitute.hellbender.utils.collections.SetSizeUtils
- getLegalSizeBelow(long, double) - Static method in class org.broadinstitute.hellbender.utils.collections.SetSizeUtils
-
Computes next smallest legal table size for a given number of elements, accounting for load factor
- getLength() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocus
- getLength() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.PathPart
- getLength() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartContig
- getLength() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartGap
- getLength() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableRow
- getLength() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- getLength() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.DeletionMDElement
- getLength() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.MatchMDElement
- getLength() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.MDElement
- getLength() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.MismatchMDElement
- getLength() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getLength() - Method in class org.broadinstitute.hellbender.utils.clipping.ClippingOp
- getLength() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getLength() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getLength() - Method in class org.broadinstitute.hellbender.utils.SVInterval
- getLengthForDupTandemExpansion() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
-
the new copies' length + inserted sequence length for simple expansion for complex expansion: the difference between affected reference region's size and the alt haplotype's length throws UnsupportedOperationException otherwise
- getLengthOf(int) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- getLengthOfImmediatelyFollowingIndel() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the length of an immediately following insertion or deletion event, or 0 if no such event exists Only returns a positive value when this pileup element is immediately before an indel.
- getLengthOnReference() - Method in interface org.broadinstitute.hellbender.tools.sv.SVLocatable
- getLetter() - Method in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- getLibrary(GATKRead, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Returns the library associated with the provided read's read group.
- getLibraryForRead(GATKRead, SAMFileHeader, String) - Static method in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils
-
Returns the library associated with the provided read's read group.
- getLibraryId() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- getLibraryId() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
- getLibraryId() - Method in class picard.sam.markduplicates.util.ReadEnds
- getLibraryId() - Method in interface picard.sam.util.PhysicalLocation
- getLibraryId() - Method in class picard.sam.util.PhysicalLocationInt
- getLibraryId(SAMRecord) - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator
-
Get the library ID for the given SAM record.
- getLibraryId(SAMRecord) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
-
Get the library ID for the given SAM record.
- getLibraryIdGenerator() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- getLibraryIdsMap() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator
- getLibraryIdsMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getLibraryName() - Method in enum class org.broadinstitute.hellbender.utils.R.RScriptLibrary
- getLibraryName(SAMFileHeader, SAMRecord) - Static method in class org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator
-
Gets the library name from the header for the record.
- getLibraryName(SAMFileHeader, SAMRecord) - Static method in class picard.sam.markduplicates.util.LibraryIdGenerator
-
Gets the library name from the header for the record.
- getLibraryName(SAMFileHeader, String) - Static method in class org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator
-
Gets the library name from the header for the read group id.
- getLibraryName(String) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getLibraryNameToStatisticsMap() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionStatistics
- getLibraryStatistics(String) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidence
- getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
- getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
- getLikelihoods() - Method in class picard.fingerprint.CappedHaplotypeProbabilities
-
Converts the loglikelihoods into linear-space with normalizing.
- getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- getLikelihoods0() - Method in class picard.fingerprint.CappedHaplotypeProbabilities
- getLine() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getLine() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getLinearCopyRatio() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LinearCopyRatio
- getLineNumber() - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the line number for this data-line.
- getLinkage() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine
- getLoc() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleAndContext
- getLoc() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LocationAndAlleles
- getLoc() - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState
-
Get the locus associated with the ActivityProfileState
- getLocation() - Method in class org.broadinstitute.hellbender.engine.AlignmentContext
- getLocation() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
- getLocation() - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
- getLocation() - Method in interface org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqTranscript
-
Returns transcript's full genomic interval (includes all exons with UTRs)
- getLocation() - Method in class org.broadinstitute.hellbender.utils.codecs.table.TableFeature
-
Gets the position for the feature.
- getLocation() - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- getLocation() - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
-
Get the span of this haplotype (may be null)
- getLocation() - Method in interface org.broadinstitute.hellbender.utils.HasGenomeLocation
- getLocation() - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
-
Gets #getGenomePosition but as a 1 bp GenomeLoc
- getLocation() - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
- getLocation(SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCase
-
Returns a locatable for this caze's locus given the sequence dictionary.
- getLocations(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.MarkQueue
-
Returns the nonDuplicateReadEndsSet of read ends that should be considered for tracking optical duplicates.
- getLocationSet() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
- getLocFilenameSuffix(Locatable) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase
- getLocForOffset(SimpleInterval, int) - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
-
Helper function that gets the interval for a site offset from relativeLoc, protecting ourselves from falling off the edge of the contig.
- getLociCount() - Method in class picard.arrays.illumina.IlluminaManifest
- getLociToGenotype(Collection<Fingerprint>) - Method in class picard.fingerprint.FingerprintChecker
-
Takes a set of fingerprints and returns an IntervalList containing all the loci that can be productively examined in sequencing data to compare to one or more of the fingerprints.
- getLocus() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCase
-
The target locus.
- getLocusCounts() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
- getLocusEntries() - Method in class picard.arrays.illumina.IlluminaBPMFile
- getLocusIterator(SamReader) - Method in class picard.analysis.CollectWgsMetrics
-
Creates
AbstractLocusIteratorimplementation according toCollectWgsMetrics.USE_FAST_ALGORITHMvalue. - getLocusLevel() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getLocusLevel() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getLocusMaxReads() - Method in class picard.fingerprint.FingerprintChecker
- getLocusResults() - Method in class picard.fingerprint.MatchResults
- getLOD() - Method in class picard.fingerprint.MatchResults
- getLodMostProbableGenotype() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the LOD score between the most probable haplotype and the second most probable.
- getLodMostProbableGenotype() - Method in class picard.fingerprint.CappedHaplotypeProbabilities
-
Overridden to calculate the LOD from the loglikelihoods instead of the probabilities because it will allow for more accurate calculation before overflowing.
- getLodNT() - Method in class picard.fingerprint.MatchResults
- getLodTN() - Method in class picard.fingerprint.MatchResults
- getLog_of_base() - Method in class picard.util.MathUtil.LogMath
- getLog10globalReadMismappingRate() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
- getLog10PosteriorOfAlleleAbsent(Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculationResult
-
Returns the log10 probability that allele is not segregating Note that this function is p not segregating so that we can store internally the log10 value of AF == 0, which grows very quickly negative and yet has sufficient resolution for high confidence tests.
- getLog10Priors(GenotypeLikelihoodCalculator, List<Allele>) - Method in class org.broadinstitute.hellbender.utils.genotyper.GenotypePriorCalculator
-
Calculates the priors given the alleles to genetype and a likelihood calculator that determines the ploidy of the sample at that site.
- getLog2CopyRatioSimplePosteriorSummary() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment
- getLog2CopyRatioValue() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatio
- getLog2CopyRatioValues() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.CopyRatioCollection
- getLogFromProbability(double[]) - Static method in class picard.util.MathUtil
-
Takes a complete set of mutually exclusive Likelihoods and converts them to logLikelihoods.
- getLogIndelPrior() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- getLogLikelihoodArray() - Method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
-
Return the results of the computeLogLikelihoods function
- getLogLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilities
- getLogLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
- getLogLikelihoods() - Method in class picard.fingerprint.CappedHaplotypeProbabilities
-
Since this class uses log-rawLikelihoods natively, we override and return the native variable
- getLogPriorOfSomaticVariant(VariantContext, int) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel
- getLogPriorOfVariantVersusArtifact() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel
-
Given that something is not an error from the sequencing machine itself, the log prior probability that it is a technical artifact (such as from sample prep or alignment) and not a real variant.
- getLogRDev() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getLogRRatios() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getLogSnvPrior() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- getLogSomaticPrior(VariantContext, int) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- getLogValue(double) - Method in class picard.util.MathUtil.LogMath
-
Returns the log-representation of the provided decimal value.
- getLogValue(double[]) - Method in class picard.util.MathUtil.LogMath
-
Returns the log-representation of the provided decimal array.
- getLong() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
- getLong() - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
- getLong(int) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the long value in a column by its index.
- getLong(Enum<?>) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the long value in a column by its name expressed as an enum constant.
- getLong(String) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the long value in a column by its index.
- getLongIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
- getMaf() - Method in class picard.fingerprint.HaplotypeBlock
-
Returns the minor allele frequency of this haplotype.
- getMaf() - Method in class picard.fingerprint.Snp
- getMainSourceFileAsFeatureInput() - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
- getMajorGenomeBuild() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getManifest(Class<?>) - Static method in class org.broadinstitute.hellbender.utils.runtime.RuntimeUtils
- getManifestFile() - Method in class picard.arrays.illumina.IlluminaManifest
- getManifestFileHeaderNames() - Method in class picard.arrays.illumina.IlluminaManifest
- getManifestFileParser() - Method in class picard.arrays.illumina.IlluminaManifest
- getManifestName() - Method in class picard.arrays.illumina.IlluminaBPMFile
- getManifestName() - Method in class picard.arrays.illumina.InfiniumEGTFile
- getMapInfo() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getMapping() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead
- getMappingQual() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the mapping quality of the read of this element
- getMappingQuality() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
- getMappingQuality() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getMappingQuality() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getMappingQuals() - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Get an array of the mapping qualities.
- getMappingsDiffer() - Method in class picard.sam.util.SamComparison
- getMappingsMatch() - Method in class picard.sam.util.SamComparison
- getMarkDupReadEnd(GATKRead, boolean, SAMFileHeader, MarkDuplicatesSparkArgumentCollection) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- getMarkDupReadStart(GATKRead, boolean, SAMFileHeader, MarkDuplicatesSparkArgumentCollection) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
-
Get a starting location for the read, mainly for the purpose of comparing it with another one to find duplicates.
- getMask() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocus
- getMask() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerBloomFilter
- getMask() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet
- getMask(byte[], int) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
- getMaskedBaseCount(byte[], int, int) - Static method in class picard.util.BaitDesigner
-
Returns the total of soft or hard masked bases in the interval of bases.
- getMaskedKmersFromLocalReference(ReferenceFileSparkSource, int, int, SVKmerShort) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerUtils
-
Gets all kmers from a given reference as a Collection of long arrays, while logging handy progress messages.
- getMasterSequenceDictionary() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns the master sequence dictionary if it has been set, otherwise null.
- getMatchedBarcode() - Method in class picard.illumina.parser.ClusterData
- getMatchesLessDeletions(Cigar, int) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSUtils
- getMatchesOrDefault(Set<Map.Entry<String, String>>, Predicate<Map.Entry<String, String>>, String) - Method in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.FuncotationFilter
-
Given a set of extracted funcotations, return a Stream of values whose entry matches the supplied predicate
- getMatchResults() - Method in class picard.fingerprint.FingerprintResults
- getMateContig() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getMateContig() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getMateForwardStrand(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.DiscordantReadPairEvidence
- getMateReferenceIndex(GATKRead, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Returns the reference index in the given header of the contig of the read's mate, or
SAMRecord.NO_ALIGNMENT_REFERENCE_INDEXif the read's mate is unmapped. - getMaternalId() - Method in class picard.pedigree.PedFile.PedTrio
- getMaternalID() - Method in class org.broadinstitute.hellbender.utils.samples.Sample
- getMaternalID() - Method in class org.broadinstitute.hellbender.utils.samples.Trio
- getMateStart() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getMateStart() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getMateTargetInterval(GATKRead, ReadMetadata) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.DiscordantReadPairEvidence
-
Finds the coordinates implicated by the read's mate as being part of the breakpoint, ie.
- getMaxClusterableStartingPosition(Collection<T>) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterLinkage
-
Compute max feasible starting position of any other item for all items in the given collection.
- getMaxClusterableStartingPosition(SVCallRecord) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.BinnedCNVLinkage
- getMaxClusterableStartingPosition(SVCallRecord) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- getMaxClusterableStartingPosition(SVCallRecord) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CNVLinkage
-
Max clusterable position depends on the other variant's length, which is unknown, so we assume the largest possible event that would extend to the end of the contig.
- getMaxClusterableStartingPosition(T) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterLinkage
-
Returns the maximum feasible starting position of any other item with the given item.
- getMaxDiploidAltAllelesThatCanBeGenotyped() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBOptions
- getMaxGenotypeCount() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBOptions
- getMaxHmer() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- getMaximumKmerSize() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Returns the maximum kmerSize available.
- getMaximumTrackedValue() - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram
- getMaxMedianFragmentSize() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getMaxMinorAlleleFreq(Set<Map.Entry<String, String>>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AlleleFrequencyExacUtils
-
Calculate the max MAF across all ExAC sub-populations from the given Funcotations.
- getMaxNonOutlierFragmentSize() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics
- getMaxObservations() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- getMaxObservations() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- getMaxObservations() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- getMaxPairErrorRate() - Method in class picard.util.AdapterMarker
- getMaxProbPropagationDistance() - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
-
How far away can probability mass be moved around in this profile? This distance puts an upper limit on how far, in bp, we will ever propagate probability mass around when adding a new ActivityProfileState.
- getMaxProbPropagationDistance() - Method in class org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile
-
Our maximize propagation distance is whatever our parent's is, plus our filter size Stops the profile from interpreting sites that aren't yet fully determined due to propagation of the probabilities.
- getMaxReadsInPartition() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getMaxSingleEndErrorRate() - Method in class picard.util.AdapterMarker
- getMayBeNullGoodMappingToNonCanonicalChromosome() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig.GoodAndBadMappings
- getMd5() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetResponse
- getMd5() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableRow
- getMean() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.InfoConcordanceRecord
- getMeanBaseQuality() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics
- getMeanBaseQuality() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getMeanLog2CopyRatio() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatioSegment
- getMeans() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
- getMeanVector() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- getMedian() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics
- getMedianDP() - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
-
Get the median DP observed within this band If there are an even number of DPs recorded in this band the median is the mean of the two middle values
- getMedianPartitionSpan() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getMedianPhasingMap() - Method in class picard.illumina.LanePhasingMetricsCollector
- getMedianPrePhasingMap() - Method in class picard.illumina.LanePhasingMetricsCollector
- getMedianShift() - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU.Result
- getMedianValue(List<T>) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Streams and sorts a collection of objects and returns the integer median entry of the sorted list
- getMendelianViolationQualThreshold() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- getMergedASFilterString(VariantContext, List<Boolean>, String) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.AlleleFilterUtils
-
Takes a list of boolean values that indicate whether the filter applies to each of the alternate alleles
- getMergedCountingReadFilter(SAMFileHeader) - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
-
Merge the default filters with the users's command line read filter requests, then initialize the resulting filters.
- getMergedReadFilter(SAMFileHeader) - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
-
Merge the default filters with the users's command line read filter requests, then initialize the resulting filters.
- getMergedReadFilter(SAMFileHeader, BiFunction<List<ReadFilter>, SAMFileHeader, T>) - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
-
Merge the default filters with the users's command line read filter requests, then initialize the resulting filters.
- getMergedReinterpretedCalls() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants
- getMessage() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetErrorResponse
- getMessage(int) - Method in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
- getMessage(Throwable) - Static method in exception org.broadinstitute.hellbender.exceptions.UserException
- getMetadata() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractRecordCollection
- getMetadata() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getMetadata() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
- getMetadata() - Method in interface org.broadinstitute.hellbender.tools.funcotator.Funcotation
- getMetadata() - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
- getMetadataType() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractLocatableCollection
- getMetadataType() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractSampleLocatableCollection
- getMetadataType() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractSampleRecordCollection
- getMetric() - Method in interface picard.sam.SamErrorMetric.BaseCalculator
-
Returns the metric generated by the observed loci
- getMetric() - Method in class picard.sam.SamErrorMetric.IndelErrorCalculator
-
Returns the metric generated by the observed loci
- getMetric() - Method in class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
-
Returns the metric generated by the observed loci
- getMetric() - Method in class picard.sam.SamErrorMetric.SimpleErrorCalculator
-
Returns the metric generated by the observed loci
- getMetricCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
- getMetricCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- getMetrics() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- getMetrics() - Method in class picard.illumina.BarcodeExtractor
- getMetrics() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
- getMetrics() - Method in class picard.sam.SamErrorMetric.BaseErrorAggregation
- getMetrics(CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.AbstractWgsMetricsCollector
-
Creates CollectWgsMetrics.WgsMetrics - the object holding the result of CollectWgsMetrics
- getMetricsByLibrary(String) - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator
- getMetricsByLibrary(String) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getMetricsByLibraryMap() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator
- getMetricsByLibraryMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getMetricsCode() - Method in enum class picard.illumina.parser.IlluminaMetricsCode
- getMetricsFile() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
-
Gets a MetricsFile with default headers already written into it.
- getMetricsFile() - Method in class picard.cmdline.CommandLineProgram
-
Gets a MetricsFile with default headers already written into it.
- getMetricValue() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- getMiddleBase(String) - Static method in class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterUtils
- getMidpoint() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatio
-
The midpoint is used to characterize the interval for the purposes of determining overlaps so that each copy-ratio interval will be uniquely contained in a single segment.
- getMidpointOverlapDetector() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.CopyRatioCollection
-
The midpoint is used to characterize the interval for the purposes of determining overlaps so that each copy-ratio interval will be uniquely contained in a single segment.
- getMinActiveStartingPositionItem() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine
- getMinBaseQual() - Method in class org.broadinstitute.hellbender.utils.baq.BAQ
- getMinBaseQualityToUseInAssembly() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- getMinDP() - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
-
Get the min DP observed within this band
- getMinEvidenceMapQ() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter
- getMinEvidenceMatchLength() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter
- getMinimaIndices() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.optimization.PersistenceOptimizer
-
Returns an unmodifiable list of the indices of the local minima, sorted first by decreasing topological persistence and then by increasing index.
- getMinimumBaseQuality() - Method in class picard.illumina.BarcodeExtractor
- getMinimumKmerSize() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Returns the minimum kmerSize available.
- getMinMaxObservations() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- getMinMedianMappingQuality() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- getMinMQ() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCase
-
The minimum MQ amongst the reads qualifying reads that overlap this position.
- getMinorAlleleFraction() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.MinorAlleleFractionRecord
- getMinorAlleleFraction() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- getMinorAlleleFractionSimplePosteriorSummary() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment
- getMinPairMatchBases() - Method in class picard.util.AdapterMarker
- getMinSingleEndMatchBases() - Method in class picard.util.AdapterMarker
- getMinValidationReadCount() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- getMismatchCount(GATKRead, byte[], int) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
- getMismatchCount(GATKRead, byte[], int, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Count how many bases mismatch the reference.
- getMismatches() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
- getMismatchesKeySet() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadCovariates
- getMismatchesKeySet(int) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadCovariates
- getMismatchesToSecondBest() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
- getMissingLeft() - Method in class picard.sam.util.SamComparison
- getMissingRight() - Method in class picard.sam.util.SamComparison
- getMitochondrialAminoAcidByCodon(String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Returns the
AminoAcidcorresponding to the given three-letter MitochondrialrawCodon. - getMitochondrialAminoAcidByCodon(String, boolean, FuncotatorUtils.Genus) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Returns the
AminoAcidcorresponding to the given three-letter MitochondrialrawCodon. - getMixedParameters() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- getMixedParams() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- getMixingFraction() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.MixingFraction
- getModeledSegments() - Method in class org.broadinstitute.hellbender.tools.copynumber.models.MultidimensionalModeller
- getModuleClass() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.AnalysisModuleScanner
- getModulesToUse() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getMoleculeNumber() - Method in class org.broadinstitute.hellbender.tools.walkers.consensus.MoleculeID
- getMoleculeNumber() - Method in class org.broadinstitute.hellbender.tools.walkers.consensus.ReadsWithSameUMI
- getMoleculeNumberOfRead(GATKRead) - Static method in class org.broadinstitute.hellbender.tools.walkers.consensus.MoleculeID
-
Extracts the molecule number portion of the
SAMTag.MIfield of the read - getMoltenAnnotation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.AnalysisModuleScanner
- getMoltenField() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.AnalysisModuleScanner
- getMostLikelyGenotype(Snp) - Method in class picard.fingerprint.HaplotypeProbabilities
-
Gets the genotype for this Snp given the most likely haplotype.
- getMostLikelyHaplotype() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Gets the most likely haplotype given the probabilities.
- getMother() - Method in class org.broadinstitute.hellbender.utils.samples.Trio
- getMother(Sample) - Method in class org.broadinstitute.hellbender.utils.samples.SampleDB
-
Get the sample's mother
- getMultiplicity() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge
-
Get the number of observations of paths connecting two vertices
- getMultiVariantInputArgumentCollection() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalker
-
Return an argument collection that provides the driving variants.
- getMultiVariantInputArgumentCollection() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval
- getMummerExecutableDirectory() - Method in class org.broadinstitute.hellbender.utils.alignment.MummerExecutor
-
Getter method to access the location of the MUMmer executables.
- getName() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.CopyNumberProgramGroup
- getName() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.CoverageAnalysisProgramGroup
- getName() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.ExampleProgramGroup
- getName() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.FlowBasedProgramGroup
- getName() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.MetagenomicsProgramGroup
- getName() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.MethylationProgramGroup
- getName() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.ShortVariantDiscoveryProgramGroup
- getName() - Method in class org.broadinstitute.hellbender.cmdline.programgroups.StructuralVariantDiscoveryProgramGroup
- getName() - Method in class org.broadinstitute.hellbender.cmdline.TestProgramGroup
- getName() - Method in class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Get the logical name of this data source.
- getName() - Method in class org.broadinstitute.hellbender.engine.FeatureInput
-
Gets the logical name of this Feature source.
- getName() - Method in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter.CountingAndReadFilter
- getName() - Method in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter
- getName() - Method in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter.CountingAndVariantFilter
- getName() - Method in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter
- getName() - Method in class org.broadinstitute.hellbender.engine.MultiVariantDataSource
-
Get the logical name of this data source.
- getName() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationKey
- getName() - Method in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- getName() - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
- getName() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory
- getName() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
- getName() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory
- getName() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.LocatableXsvFuncotationFactory
- getName() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory
- getName() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
- getName() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- getName() - Method in interface org.broadinstitute.hellbender.tools.spark.sv.discovery.StructuralVariantFilter
- getName() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SVAlignmentLengthFilter
- getName() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SVMappingQualityFilter
- getName() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead
- getName() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.ReadPair
- getName() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- getName() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.PrintMissingComp
- getName() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier
- getName() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager.SelectionMetric
- getName() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.OptionalField
- getName() - Method in class org.broadinstitute.hellbender.utils.help.GATKDocWorkUnit
- getName() - Method in interface org.broadinstitute.hellbender.utils.illumina.AdapterPair
- getName() - Method in enum class org.broadinstitute.hellbender.utils.illumina.IlluminaAdapterPair
- getName() - Method in class org.broadinstitute.hellbender.utils.mcmc.Parameter
- getName() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getName() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord
- getName() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getName() - Method in class org.broadinstitute.hellbender.utils.recalibration.QualQuantizer.QualInterval
- getName() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getName() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getName() - Method in class picard.cmdline.programgroups.BaseCallingProgramGroup
- getName() - Method in class picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup
- getName() - Method in class picard.cmdline.programgroups.GenotypingArraysProgramGroup
- getName() - Method in class picard.cmdline.programgroups.IntervalsManipulationProgramGroup
- getName() - Method in class picard.cmdline.programgroups.OtherProgramGroup
- getName() - Method in class picard.cmdline.programgroups.ReadDataManipulationProgramGroup
- getName() - Method in class picard.cmdline.programgroups.ReferenceProgramGroup
- getName() - Method in class picard.cmdline.programgroups.Testing
- getName() - Method in class picard.cmdline.programgroups.VariantEvaluationProgramGroup
- getName() - Method in class picard.cmdline.programgroups.VariantFilteringProgramGroup
- getName() - Method in class picard.cmdline.programgroups.VariantManipulationProgramGroup
- getName() - Method in class picard.fingerprint.Snp
- getName() - Method in interface picard.util.AdapterPair
- getName() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- getNameForInput(FeatureInput<VariantContext>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getNameFormat() - Method in class org.broadinstitute.hellbender.utils.report.GATKReportColumnFormat
- getNameOf(int) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- getNameValuePairs() - Method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection.FlowMode
- getNameValuePairs() - Method in enum class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection.FlowMode
- getNBases() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.LibraryRawStatistics
- getNcbiBuild() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getNearProbeDistance() - Method in class picard.analysis.directed.TargetMetricsCollector
-
Gets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.
- getNegativeMAD() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics
- getNewLineBuilder() - Method in class org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter
-
Builds a new LineBuilder and writes out the previous line if it exists.
- getNextContig() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.TransitPairCount
- getNextKmerVertexForChainExtension(Kmer, boolean, MultiDeBruijnVertex) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
- getNextKmerVertexForChainExtension(Kmer, boolean, MultiDeBruijnVertex) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
- getNextKmerVertexForChainExtension(Kmer, boolean, MultiDeBruijnVertex) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
- getNextOnGenomeCigarElement() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the cigar element of the next genomic aligned position
- getNextReadPair(PeekableIterator<SAMRecord>) - Static method in class picard.util.QuerySortedReadPairIteratorUtil
-
Get the next read pair (where both have the same read name).
- getNextReferenceVertex(V) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Traverse the graph and get the next reference vertex if it exists
- getNextReferenceVertex(V, boolean, Optional<E>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Traverse the graph and get the next reference vertex if it exists
- getNFlows() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- getNKmers() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- getnLoci() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- getNMiddleBases(String, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.ReferenceBases
- getNObservations() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- getNObservations() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- getNObservations() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- getNObservations(int) - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram
- getNodeIDs() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- getNodes() - Method in class picard.util.GraphUtils.Graph
- getNoMatchMetric() - Method in class picard.illumina.BarcodeExtractor
- getNoMatchMetric() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
- getNonArtifactStates() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- getNonLogValue(double) - Method in class picard.util.MathUtil.LogMath
-
Returns the decimal representation of the provided log values.
- getNonOpticalDuplicateCountHist() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getNonOverlappingAltAlleleBaseString(Allele, Allele, boolean) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Get the string of bases that are different from the given alleles.
- getNonSequencingErrorProb() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.Datum
- getNonSomaticProbabilities() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorProbabilities
- getNormal() - Method in class org.broadinstitute.hellbender.tools.funcotator.metadata.TumorNormalPair
- getNormalAltCount() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.NormalArtifactRecord
- GetNormalArtifactData - Class in org.broadinstitute.hellbender.tools.walkers.mutect
-
Usage example
- GetNormalArtifactData() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactData
- getNormalDepth() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.NormalArtifactRecord
- getNormalizationId() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getNormalizedXIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getNormalizedYIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getNoTags() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- getNovelAdjacencyReferenceLocations() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence
- getNPartitions() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getnProcessedLoci() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
-
If an evaluator calls this method it must override
VariantEvaluator.requiresTerritoryToBeSpecified()to return true. - getNReads() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics
- getNReads() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getNReads() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.LibraryRawStatistics
- getNReads() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionStatistics
- getnReadsPerLocus() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- getNRefBases() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getNSamples() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- getNSup() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCase
-
Number of qualifying reads records that overlap the STR that are supplementary alignments.
- getNumAdaptersToKeep() - Method in class picard.util.AdapterMarker
- getNumAlignedBases(SAMRecord) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
- getNumAlignedBasesCountingSoftClips(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Get the number of bases aligned to the genome, including soft clips If read is not mapped (i.e., doesn't have a cigar) returns 0
- getNumAlignmentBlocks(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Returns number of alignment blocks (continuous stretches of aligned bases) in the specified alignment.
- getNumAltExamples() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPrior
- getNumAltSupportingReadsInNormal() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- getNumAssays() - Method in class picard.arrays.illumina.IlluminaManifest
- getNumBasesPassingMinimumBaseQuality(SAMRecord, AlignmentBlock, int) - Static method in class picard.analysis.directed.TargetMetricsCollector
-
Get the the number of bases in the given alignment block and record that have base quality greater or equal to the minimum
- getNumber() - Method in class org.broadinstitute.hellbender.tools.sv.SVAlleleCounter
- getNumberOfClusters(File) - Static method in class picard.illumina.parser.readers.BclReader
- getNumberOfDiscardedItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.Downsampler
-
Returns the number of items discarded (so far) during the downsampling process
- getNumberOfElements(Predicate<PileupElement>) - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Returns the number of elements that satisfy the predicate.
- getNumberOfEvents() - Method in class org.broadinstitute.hellbender.utils.haplotype.EventMap
-
How many events do we have?
- getNumberOfLociCovered() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
-
Returns a count of the number of loci summarized in this object
- getNumberOfOpticalDuplicateClusters() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator
- getNumberOfOpticalDuplicateClusters() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getNumberOfSamplesForEvaluation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getNumberOfSnps() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getNumCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getNumClustersInTile() - Method in class picard.illumina.parser.TileIndex.TileIndexRecord
- getNumColumns() - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
- getNumDescriptors() - Method in class picard.illumina.parser.ReadStructure
- getNumDuplicates() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- getNumDuplicates() - Method in class picard.sam.markduplicates.util.MarkQueue
-
Returns the number of duplicates detected
- getNumEigensamples() - Method in class org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals
- getNumEigensamples() - Method in interface org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals
-
Returns the number of eigensamples.
- getNumericalMean() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BetaBinomialDistribution
- getNumericalVariance() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BetaBinomialDistribution
- getNumExamples() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPrior
- getNumExons() - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
-
Number of exons in this transcript
- getNumHardClippedBases(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Count the number of bases hard clipped from read If read's cigar is null, return 0
- getNumIntensityOnly() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getNumMismatches() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- getNumNoCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getNumObservations() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- getNumOfTies() - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU.RankedData
- getNumPoints() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatioSegment
- getNumPoints() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
- getNumPointsAlleleFraction() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment
- getNumPointsCopyRatio() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment
- getNumProbes() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LegacySegment
- getNumReads() - Method in class picard.illumina.parser.ClusterData
- getNumReadsProcessed() - Method in class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
- getNumRecordsWithNoMateCigar() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
-
Useful for statistics after the iterator has been exhausted and closed.
- getNumRows() - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
- getNumSamples() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.SampleNameMap
- getNumTandemRepeatUnits(byte[], byte[], byte[]) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- getNumTandemRepeatUnits(VariantContext, byte[]) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- getNumTandemRepeatUnits(ReferenceContext, VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.TandemRepeat
- getNumTiles() - Method in class picard.illumina.parser.readers.BclIndexReader
- getNumTiles() - Method in class picard.illumina.parser.TileIndex
- getNumUniqueContexts() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPriorCollection
- getOAContig(GATKRead) - Static method in class org.broadinstitute.hellbender.tools.AddOriginalAlignmentTags
- getObsAllele1() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the number of observations of alleles supporting the first/major haplotype allele.
- getObsAllele1() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
Returns the number of bases/reads that support the first allele.
- getObsAllele1() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- getObsAllele2() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the number of observations of alleles supporting the second/minor haplotype allele.
- getObsAllele2() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
Returns the number of bases/reads that support the second allele.
- getObsAllele2() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- getOffset() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the offset of the this element into the read that aligns that read's base to this genomic position.
- getOffset() - Method in class picard.arrays.illumina.InfiniumFileTOC
- getOffset(Locatable) - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState
-
The offset of state w.r.t.
- getOffsetInCurrentCigar() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the offset into the *current* cigar element for this alignment position We can be anywhere from offset 0 (first position) to length - 1 of the current cigar element aligning us to this genomic position.
- getOffsetIntoCurrentCigarElement() - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
-
Get the offset of the current state into the current cigar element That is, suppose we have a read with cigar 2M3D4M, and we're right at the second M position.
- getOffsetOnRead(GATKRead, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.variantrecalling.VariantRecallerResultWriter
- getOffsets() - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Returns a list of the offsets in this pileup.
- getOffsetX() - Method in class picard.arrays.illumina.InfiniumTransformation
- getOffsetY() - Method in class picard.arrays.illumina.InfiniumTransformation
- getOneVariantFromOneContig(AssemblyContigWithFineTunedAlignments, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInterpreter
- getOps() - Method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
-
Check the list of operations set up for this read.
- getOpticalDupesByLibraryId() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- getOpticalDuplicateCountHist() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getOpticalDuplicatesByLibraryIdMap() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator
- getOpticalDuplicatesByLibraryIdMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getOptimalNumberOfBits(long, double) - Static method in class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter
- getOptionalAssemblyRegion(AssemblyRegion, String, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.PostAssemblerOnRamp
- getOptionalDouble(Map<String, String>, String, double) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- getOptionalDoubleFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
- getOptionalField(String) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getOptionalFields() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getOptionalIntAttribute(SAMRecord, String) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Encapsulates a integer attribute into an
OptionalIntinstance. - getOptionalIntAttribute(GATKRead, String) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Encapsulates a integer attribute into an
OptionalIntinstance. - getOptionalInteger(Map<String, String>, String, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- getOptionalIntegerFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
- getOptionalLong(Map<String, String>, String, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- getOptionalTransientAttribute(Object, Class<T>) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Returns a transient attribute value as an
Optional. - getOptionalValueFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
- getOrCreate(Class<? extends T>, Map<?, ?>...) - Method in class org.broadinstitute.hellbender.utils.config.ConfigFactory
-
Wrapper around
ConfigCache.getOrCreate(Class, Map[])which will ensure that path variables specified inConfig.Sourcesannotations are resolved prior to creation. - getOrCreate(Object, Class<? extends T>, Map<?, ?>...) - Method in class org.broadinstitute.hellbender.utils.config.ConfigFactory
-
Wrapper around
ConfigCache.getOrCreate(Object, Class, Map[])which will ensure that path variables specified inConfig.Sourcesannotations are resolved prior to creation. - getOrCreate(Factory, Class<? extends T>, Map<?, ?>...) - Method in class org.broadinstitute.hellbender.utils.config.ConfigFactory
-
Wrapper around
ConfigCache.getOrCreate(Factory, Class, Map[])which will ensure that path variables specified inConfig.Sourcesannotations are resolved prior to creation. - getOrCreate(Factory, Object, Class<? extends T>, Map<?, ?>...) - Method in class org.broadinstitute.hellbender.utils.config.ConfigFactory
-
Wrapper around
ConfigCache.getOrCreate(Factory, Object, Class, Map[])which will ensure that path variables specified inConfig.Sourcesannotations are resolved prior to creation. - getOrderedMates(NovelAdjacencyAndAltHaplotype, BasicReference) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.InterChromosomeBreakend
- getOrderedMates(NovelAdjacencyAndAltHaplotype, BasicReference) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.IntraChromosomalStrandSwitch33BreakEnd
- getOrderedMates(NovelAdjacencyAndAltHaplotype, BasicReference) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.IntraChromosomalStrandSwitch55BreakEnd
- getOrderedMates(NovelAdjacencyAndAltHaplotype, BasicReference) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.IntraChromosomeRefOrderSwap
- getOrientationByte(boolean, boolean) - Static method in class picard.sam.markduplicates.util.ReadEnds
-
Returns a single byte that encodes the orientation of the two reads in a pair.
- getOrientationForOpticalDuplicates() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair
-
Returns the pair orientation suitable for optical duplicates, which always goes by the first then the second end for the strands.
- getOrientationForPCRDuplicates() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.EmptyFragment
- getOrientationForPCRDuplicates() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.FlowModeFragment
- getOrientationForPCRDuplicates() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Fragment
- getOrientationForPCRDuplicates() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair
- getOrientationForPCRDuplicates() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.PairedEnds
-
This returns a byte summary spanning from 0-5 representing all combinations of single read or two read forward/reverse strand for the first and second read in the Pair.
- getOriginalBaseQualities(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Retrieve the original base qualities of the given read, if present, as stored in the OQ attribute.
- getOriginalIntervalGCContent() - Method in class org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals
- getOriginalIntervalGCContent() - Method in interface org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals
-
Returns a modifiable copy of an array containing the GC content of the original intervals (in the same order as in
SVDReadCountPanelOfNormals.getOriginalIntervals()). - getOriginalIntervals() - Method in class org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals
- getOriginalIntervals() - Method in interface org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals
-
Returns a modifiable copy of the list of the original intervals that were used to build this PoN (no filtering will have been applied).
- getOriginalReadCounts() - Method in class org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals
- getOriginalReadCounts() - Method in interface org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals
-
Returns a modifiable copy of the original matrix of integer read-counts (represented as doubles) used to build the PoN (no filtering will have been applied).
- getOriginalToQuantizedMap() - Method in class org.broadinstitute.hellbender.utils.recalibration.QualQuantizer
- getOtherAltCount() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- getOtherOrientation(ReadOrientation) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ReadOrientation
- getOtherTranscripts() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getOutputArgumentCollection() - Method in class picard.analysis.SinglePassSamProgram
- getOutputArgumentCollection() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
- getOutputCycles() - Method in class picard.illumina.parser.OutputMapping
- getOutputDescriptors() - Method in class picard.illumina.parser.OutputMapping
- getOutputFile() - Method in class org.broadinstitute.hellbender.utils.runtime.OutputStreamSettings
- getOutputFile() - Method in class picard.cmdline.argumentcollections.EmptyOutputArgumentCollection
- getOutputFile() - Method in interface picard.cmdline.argumentcollections.OutputArgumentCollection
- getOutputFile() - Method in class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
- getOutputFileName(File) - Static method in class picard.sam.CalculateReadGroupChecksum
-
Creates a file name (not including the path) for an RG MD5 file based on the name of the input file.
- getOutputIndexForCycle(int) - Method in class picard.illumina.parser.OutputMapping
-
Return an index that where: index.arrayIndex - represents either the read number the cycle will be output too, or (in some cases) an array index into a two dimensional array of byte[][] where the top level array corresponds to read number index.elementIndex - represents the element a cycle will appear in inside it's give read, or the element in an array as described above
- getOutputPath() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalTextOutputArgumentCollection
- getOutputPath() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData
- getOutputReadLengths() - Method in class picard.illumina.parser.OutputMapping
- getOutputReadStructure() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Sometimes (in the case of skipped reads) the logical read structure of the output cluster data is different from the input readStructure
- getOutputReadStructure() - Method in class picard.illumina.parser.OutputMapping
- getOutputStream() - Method in class org.broadinstitute.hellbender.engine.GATKPath
-
Open a path for writing regardless of whether it's on GCS, HDFS or local disk.
- getOutputStream() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- getOutputStream() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- getOutputString() - Method in enum class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledCopyRatioSegment.Call
- getOverallGCP() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- getOverlapDetector() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractLocatableCollection
- getOverlapNames() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator
-
Get the collection of names of overlap sets ued by this annotator.
- getOverlapping(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
Return a list of intervals overlapping loc
- getOverlappingEvents(int) - Method in class org.broadinstitute.hellbender.utils.haplotype.EventMap
-
Returns any events in the map that overlap loc, including spanning deletions and events that start at loc.
- getOverlappingExonPositions(Allele, Allele, String, int, int, Strand, List<? extends Locatable>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Get the overlapping exon start/stop as a
SimpleIntervalfor the given altAllele / reference. - getOverlappingFragmentFilteredPileup(boolean, Comparator<PileupElement>, SAMFileHeader) - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Returns a new ReadPileup where only one read from an overlapping read pair is retained.
- getOverlappingFragmentFilteredPileup(SAMFileHeader) - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Returns a new ReadPileup where only one read from an overlapping read pair is retained.
- getOverlappingFullSearch(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
Return a list of intervals overlapping loc by enumerating all locs and testing for overlap Purely for testing purposes -- this is way to slow for any production code
- getOverlappingPairs() - Method in class org.broadinstitute.hellbender.utils.fragments.FragmentCollection
-
Gets the T elements containing overlapping elements, in no particular order The returned collection is unmodifiable.
- getOverlappingReferenceBases() - Method in class org.broadinstitute.hellbender.engine.ReadContextData
- getOverlappingVariantContext(Locatable, Collection<VariantContext>) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Return the rightmost variant context in maybeOverlapping that overlaps curPos
- getOverlappingVariants() - Method in class org.broadinstitute.hellbender.engine.ReadContextData
- getP() - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU.Result
- getP05Green() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getP05Red() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getP10GC() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getP50GC() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getP50Green() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getP50Red() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getP95Green() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getP95Red() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getPackageList() - Method in class org.broadinstitute.hellbender.Main
-
The packages we wish to include in our command line.
- getPackageList() - Static method in class picard.cmdline.PicardCommandLine
-
The packages we wish to include in our command line
- getPackageNames() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
-
A list of package names which will be searched for plugins managed by the descriptor.
- getPackageNames() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
-
A list of package names which will be searched for plugins managed by the descriptor.
- getPaddedInterval() - Method in interface org.broadinstitute.hellbender.engine.Shard
- getPaddedInterval() - Method in class org.broadinstitute.hellbender.engine.ShardBoundaryShard
- getPaddedInterval() - Method in class org.broadinstitute.hellbender.engine.ShardToMultiIntervalShardAdapter
- getPaddedInterval() - Method in class org.broadinstitute.hellbender.tools.DownsampleableSparkReadShard
- getPaddedIntervals() - Method in class org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard
- getPaddedIntervals() - Method in interface org.broadinstitute.hellbender.engine.MultiIntervalShard
- getPaddedIntervals() - Method in class org.broadinstitute.hellbender.engine.ShardToMultiIntervalShardAdapter
- getPaddedRecordInterval(String, int, int) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.BinnedCNVLinkage
- getPaddedRecordInterval(String, int, int) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CNVLinkage
-
Determine an overlap interval for clustering using specified padding.
- getPaddedReferenceLoc() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Returns the padded reference location.
- getPaddedReferenceLoc(AssemblyRegion, int, ReferenceSequenceFile) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- getPaddedSpan() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Get the span of this assembly region including the padding value
- getPaddedSpan() - Method in class org.broadinstitute.hellbender.engine.ShardBoundary
- getPairedReads() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPairedUnpairedSplitterSpark
- getPairedStrandedIntervals() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
- getPairedStrandedIntervals(ReadMetadata, SAMSequenceDictionary, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVContext
- getPairHMMArgs() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMNativeArgumentCollection
- getPairOrientation() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Computes the pair orientation
- getPanelIntervalFractionalMedians() - Method in class org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals
- getPanelIntervalFractionalMedians() - Method in interface org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals
-
Returns a modifiable copy of an array containing the median (across all samples, before filtering) of the fractional coverage at each panel interval (in the same order as in
SVDReadCountPanelOfNormals.getPanelIntervals()). - getPanelIntervals() - Method in class org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals
- getPanelIntervals() - Method in interface org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals
-
Returns a modifiable copy of the list of the intervals contained in this PoN after all filtering has been applied.
- getParallelReads(GATKPath, GATKPath) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource
-
Loads Reads using Hadoop-BAM.
- getParallelReads(GATKPath, GATKPath, int) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource
-
Loads Reads using Hadoop-BAM.
- getParallelReads(GATKPath, GATKPath, TraversalParameters) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource
-
Loads Reads using Hadoop-BAM.
- getParallelReads(GATKPath, GATKPath, TraversalParameters, long) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource
-
Loads Reads using Hadoop-BAM.
- getParallelReads(GATKPath, GATKPath, TraversalParameters, long, boolean) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource
-
Loads Reads using Hadoop-BAM.
- getParallelVariantContexts(String, List<SimpleInterval>) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSource
-
Loads variants in parallel using Hadoop-BAM for vcfs and bcfs.
- getParallelVariants(String, List<SimpleInterval>) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSource
-
Loads variants in parallel using Hadoop-BAM for vcfs and bcfs.
- getParallelVariants(List<String>, List<SimpleInterval>) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSource
-
Loads variants from multiple inputs in parallel using Hadoop-BAM for vcfs and bcfs.
- getParent() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
- getParent() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- getParentOf(int) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- getParents(Sample) - Method in class org.broadinstitute.hellbender.utils.samples.SampleDB
-
Get the sample's father and mother
- getParentsRefRefChildHet() - Method in class org.broadinstitute.hellbender.utils.samples.MendelianViolation
- getPartition(Object) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.ComplexityPartitioner
- getPartitionBounds(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- getPartitionIndex() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord
- getParts() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Path
- getPassthrough(GATKRead, int) - Static method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord
- getPaternalId() - Method in class picard.pedigree.PedFile.PedTrio
- getPaternalID() - Method in class org.broadinstitute.hellbender.utils.samples.Sample
- getPaternalID() - Method in class org.broadinstitute.hellbender.utils.samples.Trio
- getPath() - Method in class org.broadinstitute.hellbender.utils.BinaryTableWriter
- getPath() - Method in class org.broadinstitute.hellbender.utils.io.Resource
- getPath(String) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Converts the given URI to a
Pathobject. - getPathOf(int) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
-
Returns path of node id's from the input id to the root.
- getPathOnGcs(String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
String -> Path.
- getPathToDataFile(String) - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
- getPathWithoutBucket(String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Given a path of the form "gs://bucket/folder/folder/file", returns "folder/folder/file".
- getPedigreeFile() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation
-
This is a getter for the pedigree file, which could be null.
- getPenalty() - Method in class org.broadinstitute.hellbender.utils.recalibration.QualQuantizer.QualInterval
- getPeriod() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocus
- getPeriod() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCase
-
The period length of this STR.
- getPeriod() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCases
- getPersistences() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.optimization.PersistenceOptimizer
-
Returns the corresponding unmodifiable list of the topological persistences of the local minima given by
PersistenceOptimizer.getMinimaIndices(). - getPerTilePerCycleFiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
For the given tiles, populate a CycleIlluminaFileMap that contains all these tiles and will iterate through all the files for these tiles in expectedBase Side Effect: Assigns numCycles
- getPESRParameters() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- getPGRecord(SAMFileHeader) - Method in class picard.cmdline.CommandLineProgram
- getPhasingCode(int, IlluminaMetricsCode) - Static method in enum class picard.illumina.parser.IlluminaMetricsCode
-
Phasing codes are between 200 and 299 (inclusive).
- getPhasingMap() - Method in class picard.illumina.parser.Tile
- getPhasingMetricsForTiles(long, Collection<Tile>, boolean) - Static method in class picard.illumina.IlluminaPhasingMetrics
-
Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them
- getPhasingValue() - Method in class picard.illumina.parser.TilePhasingValue
- getPhenotype() - Method in class picard.pedigree.PedFile.PedTrio
- getPi() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPrior
- getPi(ArtifactState) - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPrior
- getPileupForLane(String) - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Make a new pileup from elements whose reads have read groups that agree with the given lane ID.
- getPileupForSample(String, SAMFileHeader) - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Make a new pileup from elements whose reads belong to the given sample.
- getPileupsOverReference(SAMFileHeader, SimpleInterval, AlleleLikelihoods<GATKRead, Haplotype>, SampleList) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
-
Get a list of pileups that span the entire active region span, in order, one for each position
- getPileupString() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature
-
Format in a samtools-like string.
- getPileupString(char) - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Format, assuming a single-sample, in a samtools-like string.
- GetPileupSummaries - Class in org.broadinstitute.hellbender.tools.walkers.contamination
-
Summarizes counts of reads that support reference, alternate and other alleles for given sites.
- GetPileupSummaries() - Constructor for class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- getPileupVariantContexts(List<AlignmentAndReferenceContext>, PileupDetectionArgumentCollection, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.pileup.PileupBasedAlleles
-
Accepts the raw per-base pileups stored from the active region detection code and parses them for potential variants that are visible in the pileups but might be dropped from assembly for any number of reasons.
- getPinv() - Method in class org.broadinstitute.hellbender.utils.svd.SimpleSVD
- getPinv() - Method in interface org.broadinstitute.hellbender.utils.svd.SVD
-
Get the pseudoinverse as calculated using the SVD
- getPlatform(GATKRead, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Returns the platform associated with the provided read's read group.
- getPlatformUnit() - Method in class picard.fingerprint.FingerprintIdDetails
- getPlatformUnit(GATKRead, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Returns the platform unit associated with the provided read's read group.
- getPloidy() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator
- getPloidy() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- getPloidy() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getPloidy() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getPloidy() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getPloidyModel() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine
-
Returns the ploidy-model used by this genotyping engine.
- getPloidyType() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getPluginBaseClass() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
- getPluginBaseClass() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
- getPluginDescriptors() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
-
Return the list of GATKCommandLinePluginDescriptors to be used for this CLP.
- getPluginDescriptors() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Return the list of GATKCommandLinePluginDescriptors to be used for this tool.
- getPluginDescriptors() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Return the list of GATKCommandLinePluginDescriptor objects to be used for this CLP.
- getPluginDescriptors() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.CountVariantsSpark
-
Return the list of GATKCommandLinePluginDescriptor objects to be used for this CLP.
- getPluginDescriptors() - Method in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- getPluginDescriptors() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval
- getPmtGreen() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getPmtRed() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getPoorQualityFrequencies() - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
-
Returns a view of number of qualities that failed, where the key is the quality score and the value is the number of observations.
- getPopulationLikelihood() - Method in class picard.fingerprint.MatchResults
- getPos() - Method in class picard.fingerprint.Snp
- getPosition() - Method in class org.broadinstitute.hellbender.engine.AlignmentContext
- getPosition() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVLocation
- getPosition() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- getPosition() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getPosition(GATKRead, VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosition
- getPositionA() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getPositionA() - Method in interface org.broadinstitute.hellbender.tools.sv.SVLocatable
- getPositionAInterval() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getPositionB() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getPositionB() - Method in interface org.broadinstitute.hellbender.tools.sv.SVLocatable
- getPositionBInterval() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getPositionInfo() - Method in class picard.illumina.parser.CbclData
- getPositions() - Method in class picard.arrays.illumina.InfiniumNormalizationManifest
- getPositiveMAD() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics
- getPosteriorLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the probabilities, in order, of the AA, Aa and aa haplotypes.
- getPosteriorProbabilities() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the probabilities, in order, of the AA, Aa and aa haplotypes.
- getPosteriorProbabilities() - Method in class picard.fingerprint.CappedHaplotypeProbabilities
-
getter for posteriorProbs
- getPosteriorProbabilities0() - Method in class picard.fingerprint.CappedHaplotypeProbabilities
-
Returns the posterior probability of the haplotypes given the evidence (uses the internal prior)
- getPower() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- getPrecision() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceSummaryRecord
- getPredecessorCount() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- getPredecessorCount() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- getPredecessorCount() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- getPredecessorMask() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- getPredecessorMask() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- getPredecessorMask() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- getPredecessors() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- getPredecessors() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- getPredecessors() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- getPredecessorVal(int) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Kmer
- getPrefetchingWrapper(int) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Creates a wrapping function which adds a prefetcher if the buffer size is > 0 if it's <= 0 then this wrapper returns the original channel.
- getPrePhasingMap() - Method in class picard.illumina.parser.Tile
- getPrePhasingValue() - Method in class picard.illumina.parser.TilePhasingValue
- getPrevContig() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.TransitPairCount
- getPreviousOnGenomeCigarElement() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the cigar element of the previous genomic aligned position For example, we might have 1M2I3M, and be sitting at the someone in the 3M.
- getPrevReferenceVertex(V) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Traverse the graph and get the previous reference vertex if it exists
- getPrimaryInterval() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.Mapping
- getPrimaryRawKey() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_BaseQualityRankSumTest
-
Get the string that's used to combine data for this annotation
- getPrimaryRawKey() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_MappingQualityRankSumTest
-
Get the string that's used to combine data for this annotation
- getPrimaryRawKey() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth
- getPrimaryRawKey() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_ReadPosRankSumTest
-
Get the string that's used to combine data for this annotation
- getPrimaryRawKey() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality
- getPrimaryRawKey() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
- getPrimaryRawKey() - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation
-
Get the string that's used to combine data for this annotation
- getPrimaryRawKey() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RawGtCount
- getPrimaryRawKey() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
- getPrintableId() - Method in class picard.fingerprint.Fingerprint
- getPriorProbablities() - Method in class picard.fingerprint.HaplotypeProbabilities
- getProb(int, int) - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
-
get a specific cell from the flow matrix.
- getProbabilitiesAsArray() - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
-
Get the probabilities of the states as a single linear array of doubles
- getProbabilitiesByFilter() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorProbabilities
- getProbabilitiesForAlleleFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorProbabilities
- getProbabilitiesForVariantFilters() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorProbabilities
- getProbabilityFromLog(double[]) - Static method in class picard.util.MathUtil
-
Takes a complete set of mutually exclusive logLikelihoods and converts them to probabilities with no rescaling.
- getProbeIntervals() - Method in class picard.analysis.directed.CollectHsMetrics
- getProbeIntervals() - Method in class picard.analysis.directed.CollectTargetedMetrics
- getProbeIntervals() - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
- getProbeSetName() - Method in class picard.analysis.directed.CollectHsMetrics
- getProbeSetName() - Method in class picard.analysis.directed.CollectTargetedMetrics
- getProbeSetName() - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
- getProcess() - Method in class org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor
-
Get the Process object associated with this executor.
- getProcess() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase
- getProcessOutput() - Method in class org.broadinstitute.hellbender.utils.runtime.StreamingProcessController
-
Wait for *any* output from the process (to stdout or stderr), by draining the stream(s) until no more output is available.
- getProgramName() - Method in class org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram
-
Returns the program's name.
- getProgramProperty(Class) - Static method in class picard.cmdline.PicardCommandLine
- getProgramProperty(Class<?>) - Static method in class org.broadinstitute.hellbender.Main
- getProgramRecord() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
- getProgramRecord() - Method in class picard.sam.AbstractAlignmentMerger
- getProgressMeterRecordLabel() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionWalker
- getProgressMeterRecordLabel() - Method in class org.broadinstitute.hellbender.engine.FeatureWalker
- getProgressMeterRecordLabel() - Method in class org.broadinstitute.hellbender.engine.GATKTool
- getProgressMeterRecordLabel() - Method in class org.broadinstitute.hellbender.engine.IntervalWalker
- getProgressMeterRecordLabel() - Method in class org.broadinstitute.hellbender.engine.LocusWalker
- getProgressMeterRecordLabel() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker
- getProgressMeterRecordLabel() - Method in class org.broadinstitute.hellbender.engine.ReadWalker
- getProgressMeterRecordLabel() - Method in class org.broadinstitute.hellbender.engine.ReferenceWalker
- getProgressMeterRecordLabel() - Method in class org.broadinstitute.hellbender.engine.VariantWalkerBase
- getProgressMeterRecordLabel() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- getPromoterInterval(GencodeGtfTranscriptFeature, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate
-
Get promoter interval for GTF transcript: user-defined window upstream (5') of TSS
- getPromoterIntervalTree() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine.GTFIntervalTreesContainer
- getProteinChange() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getProteinChangeEndPosition(Integer, Integer) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Get the Protein change end position (1-based, inclusive) given the protein change start position and aligned alternate allele length.
- getProteinChangeInfo() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getProteinChangePosition(Integer) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Get the Protein change start position (1-based, inclusive) given the aligned position of the coding sequence.
- getProtobufVidMappingFromJsonFile(String) - Static method in class org.broadinstitute.hellbender.tools.genomicsdb.GATKGenomicsDBUtils
-
Parse the vid json and create an in-memory Protobuf structure representing the information in the JSON file
- getPruningMultiplicity() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge
-
A special assessor that returns the multiplicity that should be used by pruning algorithm
- getPruningMultiplicity() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MultiSampleEdge
- getQName() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval
- getQual() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the base quality score of the base at this aligned position on the genome
- getQual() - Method in class org.broadinstitute.hellbender.utils.recalibration.QualQuantizer.QualInterval
- getQual(EventType, int) - Method in class org.broadinstitute.hellbender.utils.recalibration.ReadRecalibrationInfo
-
Get the qual score for event type at offset
- getQualities() - Method in class picard.illumina.parser.BclData
- getQualities() - Method in class picard.illumina.parser.ReadData
- getQualityAllCalled() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
- getQualityEnd() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
- getQualityScoreCovariate() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList
- getQualityScoreTable() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
- getQualitySomeCalled() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
- getQualityStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
- getQuals() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead
-
returns phred-scaled quals with no bias
- getQualsStream() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature
-
Get the qualities as a stream
- getQualsString() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature
-
Returns pile of obseved qualities over the genomic location Note: this call costs O(n) and allocates fresh array each time
- getQuantizationInfo() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport
- getQuantizationLevels() - Method in class org.broadinstitute.hellbender.utils.recalibration.QuantizationInfo
- getQuantizedQuals() - Method in class org.broadinstitute.hellbender.utils.recalibration.QuantizationInfo
- getQuerynameSortedAlignedRecords() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
- getQuerynameSortedAlignedRecords() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.SamAlignmentMerger
-
Reads the aligned SAM records into a SortingCollection and returns an iterator over that collection
- getQuerynameSortedAlignedRecords() - Method in class picard.sam.AbstractAlignmentMerger
- getQuerynameSortedAlignedRecords() - Method in class picard.sam.SamAlignmentMerger
-
Reads the aligned SAM records into a SortingCollection and returns an iterator over that collection
- getRAC() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport
- getRandomDataForPlotting(int, List<VariantDatum>, List<VariantDatum>, List<VariantDatum>) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- getRandomDataGenerator() - Static method in class org.broadinstitute.hellbender.utils.Utils
- getRandomGenerator() - Static method in class org.broadinstitute.hellbender.utils.Utils
- getRank() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
- getRank() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- getRank() - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU.RankedData
- getRankOf(int) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- getRateFactor() - Method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.PCRErrorModel
- getRawControlXIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRawControlXIntensity(int) - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRawControlYIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRawControlYIntensity(int) - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRawData() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData
- getRawDescriptions() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth
- getRawDescriptions() - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation
-
Returns the descriptions used for the VCF INFO meta field corresponding to the annotations raw key.
- getRawDescriptions() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RawGtCount
- getRawDescriptions() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
- getRawKeyName() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet
- getRawKeyNames() - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation
-
Get all the raw key names for this annotation
- getRawXIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRawYIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRC() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.TransitPairCount
- getRCContext() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPrior
- getRead() - Method in class org.broadinstitute.hellbender.engine.spark.ReadWalkerContext
- getRead() - Method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
-
The original read.
- getRead() - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
-
Get the read we are aligning to the genome
- getRead() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Get the read for this pileup element.
- getRead() - Method in class org.broadinstitute.hellbender.utils.recalibration.ReadRecalibrationInfo
-
Get the read involved in this recalibration info
- getRead(int) - Method in class picard.illumina.parser.ClusterData
- getReadBarcodeValue(SAMRecord, String) - Static method in class picard.sam.markduplicates.EstimateLibraryComplexity
- getReadBaseAtReferenceCoordinate(GATKRead, int) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
- getReadBaseQuality(GATKRead, VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityRankSumTest
- getReadBaseQualityAtReferenceCoordinate(GATKRead, int) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
- getReadCount() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.TemplateSizeAnomaly
- getReadDelQuals() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- getReadDuplicateScore(SAMRecord, ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.MarkDuplicates
-
Calculates score for the duplicate read
- getReadDuplicateScore(SAMRecord, ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
-
update score for pairedEnds
- getReadDuplicateScore(SAMRecord, ReadEndsForMarkDuplicates) - Method in interface picard.sam.markduplicates.MarkDuplicatesHelper
- getReadEndCoordinate(SAMRecord, boolean, boolean, MarkDuplicatesForFlowArgumentCollection) - Static method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- getReadEnds() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
Gets the set of read ends
- getReadEndSetForOpticalDuplicates() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
Gets the read ends for optical duplicate tracking
- getReadFlowOrder(SAMFileHeader, GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- getReadGroup() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
- getReadGroup() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- getReadGroup() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- getReadGroup() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getReadGroup() - Method in class picard.fingerprint.FingerprintResults
- getReadGroup() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
- getReadGroup() - Method in class picard.sam.markduplicates.util.ReadEnds
- getReadGroup() - Method in interface picard.sam.util.PhysicalLocation
- getReadGroup() - Method in class picard.sam.util.PhysicalLocationInt
- getReadGroupCovariate() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList
- getReadGroupIDs() - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Gets a set of the read groups represented in this pileup.
- getReadGroupIDs(SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadGroupCovariate
- getReadGroupInfo(SAMFileHeader, GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- getReadGroupLibraryName(SAMReadGroupRecord) - Static method in class org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator
- getReadGroupLibraryName(SAMReadGroupRecord) - Static method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getReadGroups() - Method in class org.broadinstitute.hellbender.utils.report.GATKReport
-
Gets the unique read groups in the table
- getReadGroupTable() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
- getReadHistogram() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- getReadIndexForReferenceCoordinate(int, Cigar, int) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Find the 0-based index within a read base array corresponding to a given 1-based position in the reference, along with the cigar operator of the element containing that base.
- getReadIndexForReferenceCoordinate(GATKRead, int) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Returns the index within the read's bases array corresponding to the requested reference coordinate -- or the read coordinate immediately preceding a deletion in which the reference coordinate falls -- along with the cigar operator in which the reference coordinate occurs.
- getReadIndexPaths() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.ReadInputArgumentCollection
- getReadInputMergingPolicy() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Does this tool support multiple inputs? Tools that do should override this method with the desired
GATKSparkTool.ReadInputMergingPolicy. - getReadInputMergingPolicy() - Method in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- getReadInsQuals() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
-
Various methods for storing arrays of pre-computed qualities to be used in
FlowBasedHMMEngine. - getReadLength() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- getReadMetadata() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData.SampleSpecificData
- getReadMetadata() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark.AssembledEvidenceResults
- getReadName() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
- getReadOffset() - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
-
What is our current offset in the read's bases that aligns us with the reference genome?
- getReadPairs() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
- getReadPairTemplateNames() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
- getReadPaths() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.ReadInputArgumentCollection
-
Get the list of BAM/SAM/CRAM inputs specified at the command line.
- getReadPathSpecifiers() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalReadInputArgumentCollection
-
Get the list of BAM/SAM/CRAM inputs specified at the command line.
- getReadPathSpecifiers() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.ReadInputArgumentCollection
-
Get the list of BAM/SAM/CRAM inputs specified at the command line.
- getReadPathSpecifiers() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredReadInputArgumentCollection
-
Get the list of BAM/SAM/CRAM inputs specified at the command line.
- getReadPosition(GATKRead, VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosRankSumTest
- getReads() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Get an unmodifiable copy of the list of reads currently in this assembly region.
- getReads() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Loads the reads into a
JavaRDDusing the intervals specified, and filters them using the filter returned byGATKSparkTool.makeReadFilter(). - getReads() - Method in class org.broadinstitute.hellbender.tools.walkers.consensus.ReadsWithSameUMI
- getReads() - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Returns a list of the reads in this pileup.
- getReads() - Method in class org.broadinstitute.hellbender.utils.read.Fragment
- getReads(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.qc.ReadPair
- getReads(Locatable, Locatable) - Method in class org.broadinstitute.hellbender.tools.walkers.variantrecalling.TrimmedReadsReader
- getReads(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.ReadWalkerSpark
-
Loads reads and the corresponding reference and features into a
JavaRDDfor the intervals specified. - getReadsContext() - Method in class org.broadinstitute.hellbender.engine.spark.IntervalWalkerContext
- getReadsContext() - Method in class org.broadinstitute.hellbender.engine.spark.VariantWalkerContext
- getReadSourceName() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Returns the name of the source of reads data.
- getReadStartFrequency() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics
- getReadSuppName(String, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase
- getReadSuppName(GATKRead) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase
- getReadThreadingAssemblerArgumentCollection() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- getReadThreadingAssemblerArgumentCollection() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- getReadThreadingAssemblerArgumentCollection() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- getReadThreadingJunctionTrees(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
- getReadToHaplotypeSWParameters() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- getReadToMateMap(ReadsContext, int) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Create a map of reads overlapping
intervalto their mates by looking for all possible mates within some maximum fragment size. - getReadType() - Method in class picard.illumina.parser.ReadData
- getReadValidationStringency() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.ReadInputArgumentCollection
-
Get the read validation stringency specified at the command line, or the default value if none was specified at the command line.
- getReadVectors(VariantContext, Collection<String>, AlleleLikelihoods<GATKRead, Allele>, AlleleLikelihoods<Fragment, Haplotype>, int, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.FeaturizedReadSets
- getReadVectors(VariantContext, Collection<String>, AlleleLikelihoods<GATKRead, Allele>, AlleleLikelihoods<Fragment, Haplotype>, int, int, Map<Allele, Integer>) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.FeaturizedReadSets
- getReasonForAlignmentClassificationFailure() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- getRecalibrationTables() - Method in class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
-
Get a possibly not-final recalibration table, to deal with distributed execution.
- getRecalibrationTables() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport
- getReciprocalOverlap() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.ClusteringParameters
- getRecommendedNumReducers() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Return the recommended number of reducers for a pipeline processing the reads.
- getRecord() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
- getRecord(int) - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRecordReadName() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
- getRecords() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractRecordCollection
- getRecords() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection
- getRecordsWithMostPreciseBreakpoints(Collection<SVCallRecord>) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
-
Gets records likely to have the most accurate breakpoint position.
- getRed() - Method in class picard.arrays.illumina.ArraysControlInfo
- getRef() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection
- getRef() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature
-
Returns the reference basse
- getRef() - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- getRef1() - Method in class org.broadinstitute.hellbender.tools.reference.ReferencePair
- getRef1AsString() - Method in class org.broadinstitute.hellbender.tools.reference.ReferencePair
- getRef1ColumnIndex() - Method in class org.broadinstitute.hellbender.tools.reference.ReferencePair
- getRef2() - Method in class org.broadinstitute.hellbender.tools.reference.ReferencePair
- getRef2AsString() - Method in class org.broadinstitute.hellbender.tools.reference.ReferencePair
- getRef2ColumnIndex() - Method in class org.broadinstitute.hellbender.tools.reference.ReferencePair
- getRefAaSeq() - Method in class org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo
- getRefAllele() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getRefAllele() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getRefAllele() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AlleleSpecificAnnotationData
-
Get the reference allele for this allele-specific data.
- getRefAllele() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleAndContext
- getRefAllele() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection
- getRefAllele() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getRefBaseAtPosition(ReferenceSequenceFile, String, int) - Static method in class org.broadinstitute.hellbender.utils.reference.ReferenceUtils
- getRefBasesAtPosition(ReferenceSequenceFile, String, int, int) - Static method in class org.broadinstitute.hellbender.utils.reference.ReferenceUtils
- getRefCount() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- getRefCount() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord
- getReference() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- getReference() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBOptions
- getReference() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- getReference() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- getReferenceAllele() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getReferenceBases() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getReferenceBases(SimpleInterval) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceFileSparkSource
- getReferenceBases(SimpleInterval) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceHadoopSparkSource
- getReferenceBases(SimpleInterval) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource
-
Return reference bases for the given interval.
- getReferenceBases(SimpleInterval) - Method in interface org.broadinstitute.hellbender.engine.spark.datasources.ReferenceSparkSource
- getReferenceBases(SimpleInterval) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceTwoBitSparkSource
-
Gets the reference bases spanning the requested interval.
- getReferenceBasesRDD(JavaSparkContext, int, ReferenceMultiSparkSource, SAMSequenceDictionary, int, int) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVReferenceUtils
-
Create an RDD from the reference sequences.
- getReferenceBroadcast() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData.ReferenceData
- getReferenceBytes(MultiDeBruijnVertex, MultiDeBruijnVertex, boolean, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
-
Walk along the reference path in the graph and pull out the corresponding bases NOTE: this attempts to generate the longest sequence of refernce bases in the event that fromVertex or toVertex are non-unique
- getReferenceBytes(V, V, boolean, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Walk along the reference path in the graph and pull out the corresponding bases
- getReferenceColumnName(GATKPath) - Static method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
-
Given a GATKPath, return the name of the file as a String.
- getReferenceContext() - Method in class org.broadinstitute.hellbender.engine.AlignmentAndReferenceContext
-
getter for the ReferenceContect
- getReferenceContext() - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerContext
- getReferenceContext() - Method in class org.broadinstitute.hellbender.engine.spark.IntervalWalkerContext
- getReferenceContext() - Method in class org.broadinstitute.hellbender.engine.spark.LocusWalkerContext
- getReferenceContext() - Method in class org.broadinstitute.hellbender.engine.spark.ReadWalkerContext
- getReferenceContext() - Method in class org.broadinstitute.hellbender.engine.spark.VariantWalkerContext
- getReferenceContext() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getReferenceContext() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord
- getReferenceContext() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPrior
- getReferenceContext() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.VariantEvalContext
- getReferenceData() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData
- getReferenceDictionary() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns the reference sequence dictionary if there is a reference (hasReference() == true), otherwise null.
- getReferenceFasta() - Method in class picard.fingerprint.FingerprintChecker
- getReferenceFile() - Method in class picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
- getReferenceFile() - Method in class picard.analysis.CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
- getReferenceFile() - Method in class picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection
- getReferenceFile() - Method in interface picard.cmdline.argumentcollections.ReferenceArgumentCollection
- getReferenceFile() - Method in class picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection
- getReferenceFile() - Method in class picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
- getReferenceFile() - Method in class picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
- getReferenceFileName() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.ReferenceInputArgumentCollection
-
Get the name of the reference file specified at the command line.
- getReferenceHaplotype() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Query the reference haplotype in the result set.
- getReferenceIndex(GATKRead, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Returns the reference index in the given header of the read's contig, or
SAMRecord.NO_ALIGNMENT_REFERENCE_INDEXif the read is unmapped. - getReferenceLength() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- getReferencePath() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.ReferenceInputArgumentCollection
-
Get the Path to the reference, may be null
- getReferencePath(MultiDeBruijnVertex, AbstractReadThreadingGraph.TraversalDirection, Optional<MultiSampleEdge>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Finds the path in the graph from this vertex to the reference sink, including this vertex
- getReferencePath(MultiDeBruijnVertex, AbstractReadThreadingGraph.TraversalDirection, Optional<MultiSampleEdge>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
-
Finds the path in the graph from this vertex to the reference sink, including this vertex
- getReferencePathIndexes() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MultiSampleEdge
- getReferenceReader(ReferenceInputArgumentCollection) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
- getReferenceSequence() - Method in class org.broadinstitute.hellbender.metrics.SAMRecordAndReference
- getReferenceSequence() - Method in class picard.metrics.SAMRecordAndReference
- getReferenceSequenceDictionary() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- getReferenceSequenceDictionary(SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceFileSparkSource
- getReferenceSequenceDictionary(SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceHadoopSparkSource
- getReferenceSequenceDictionary(SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource
-
Return a sequence dictionary for the reference.
- getReferenceSequenceDictionary(SAMSequenceDictionary) - Method in interface org.broadinstitute.hellbender.engine.spark.datasources.ReferenceSparkSource
- getReferenceSequenceDictionary(SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceTwoBitSparkSource
- getReferenceSequenceDictionaryBroadcast() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData.ReferenceData
- getReferenceSinkVertex() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
- getReferenceSinkVertex() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
-
NOTE: we override the old behavior here to allow for looping/nonunique references to be handled properly
- getReferenceSourceVertex() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
- getReferenceSourceVertex() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
-
NOTE: we override the old behavior here to allow for looping/nonunique references to be handled properly
- getReferenceSpecifier() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalReferenceInputArgumentCollection
- getReferenceSpecifier() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.ReferenceInputArgumentCollection
-
Get the name of the reference input specified at the command line.
- getReferenceSpecifier() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredReferenceInputArgumentCollection
- getReferenceStrand() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getReferenceWindow(SimpleInterval) - Method in class org.broadinstitute.hellbender.engine.ReferenceWalker
-
Determine the window to use when creating the ReferenceContext in apply.
- getReferenceWindow(SimpleInterval) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalker
- getReferenceWindowForRead(GATKRead, int) - Static method in class org.broadinstitute.hellbender.utils.baq.BAQ
-
Given a read, get an interval representing the span of reference bases required by BAQ for that read
- getReferenceWindowFunction() - Method in class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource
- getReferenceWindowFunction() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Window function that controls how much reference context to return for each read when using the reference source returned by
GATKSparkTool.getReference(). - getReferenceWindowFunction() - Method in class org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark
- getRefF1R2() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord
- getRefFrequency() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- getRefHistogramsFromExtractedTar(File) - Static method in class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2CountsCollector
- getRefNucleotide() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
- getRefReadCount() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
- getRefResonsibilities(int) - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelEngine
- getRefs() - Method in class org.broadinstitute.hellbender.utils.GenotypeCounts
- getRefStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getRefStrand() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getRefToRefArtifacts(Nucleotide) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- getRegion(Locatable, String) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OnRampBase
- getRegionForGenotyping() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Returns the current region for genotyping.
- getReInterpretMultiSegmentsCalls() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants
- getReInterpretZeroOrOneSegmentCalls() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants
- getRelativeClass() - Method in class org.broadinstitute.hellbender.utils.io.Resource
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.AlleleCount
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.AlleleFrequency
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.CompFeatureInput
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Contig
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.CpG
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Degeneracy
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.EvalFeatureInput
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Family
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Filter
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.FilterType
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.FunctionalClass
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.IndelSize
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.IntervalStratification
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.JexlExpression
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Novelty
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.OneBPIndel
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Sample
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.SnpEffPositionModifier
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.TandemRepeat
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier
- getRelevantStates(VariantEvalContext, VariantContext, String, VariantContext, String, String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantType
- getRemainingDuration(long, double) - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- getRepeatLength() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCase
-
The repeat lenght in integer repeated units.
- getRepeatLength() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCases
- getRepeats() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocus
- getReportableDiscordantReadPair(GATKRead, Set<String>, SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- getRepresentativeGenotype(Collection<Genotype>) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
- getRepresentativeRead() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
- getRepresentativeRecord(Collection<SVCallRecord>, int, int) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
- getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns a representative SNP for this haplotype.
- getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
-
Returns the SNP who's genotype was used to construct the likelihoods.
- getRepresentativeSnp() - Method in class picard.fingerprint.CappedHaplotypeProbabilities
-
Simple returns the SNP from the haplotype that has the lowest genome coordinate.
- getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- getRequestedExpressions() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
- getRequiredDouble(Map<String, String>, String) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- getRequiredInteger(Map<String, String>, String) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- getRequiredLong(Map<String, String>, String) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- getRequiredStratificationNames() - Static method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getReserved1() - Method in class picard.arrays.illumina.InfiniumTransformation
- getReserved2() - Method in class picard.arrays.illumina.InfiniumTransformation
- getReserved3() - Method in class picard.arrays.illumina.InfiniumTransformation
- getReserved4() - Method in class picard.arrays.illumina.InfiniumTransformation
- getReserved5() - Method in class picard.arrays.illumina.InfiniumTransformation
- getReserved6() - Method in class picard.arrays.illumina.InfiniumTransformation
- getResolvedInstances() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
-
Merge the default annotations with the users's command line annotation requests, then initialize the resulting annotations.
- getResolvedInstances() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
- getResolvedInstancesMap() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
-
Returns a map of the String to Annotations only in the resolved instances.
- getResolvedIntervals(String, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Given an interval query string and a sequence dictionary, determine if the query string can be resolved as a valid interval query against more than one contig in the dictionary, i.e., more than one of: prefix prefix:nnn prefix:nnn+ prefix:nnn-nnn and return the list of all possible interpretations (there can never be more than 2).
- getResourceContentsAsFile(String) - Static method in class org.broadinstitute.hellbender.utils.io.Resource
-
Given a resource path that is either on the file system or in a jar, return a File.
- getResourceContentsAsStream() - Method in class org.broadinstitute.hellbender.utils.io.Resource
-
Get the contents of this resource as an InputStream
- getResourcePath() - Method in enum class org.broadinstitute.hellbender.utils.R.RScriptLibrary
- getResultDataPrettyString(TableResult) - Static method in class org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils
-
Creates a
Stringcontaining the given results in a pretty ascii-art table. - getResultState() - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState
- getResultValue() - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState
- getRevCompState() - Method in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- getReverseAltCount() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter.EStep
- getReverseArtifactResponsibility() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter.EStep
- getReverseComplement() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPrior
- getReverseComplementOfRecord() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord
-
Contract: only call this method on an
AltSiteRecordwhose reference context is *not* in the - getReverseCount() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter.EStep
- getReversedFlowOrder() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils.ReadGroupInfo
- getReverseOutputFieldNameMap() - Method in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRenderer
-
No field ordering is preserved in the output of this method.
- getReverseValueToListMap(Map<T, List<U>>) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Take a map of a value to a list and reverse it.
- getRgqThresholdOpt() - Method in class org.broadinstitute.hellbender.utils.variant.writers.ReblockingOptions
- getRight() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervals
- getRight() - Method in class picard.sam.util.Pair
- getRightClipPoint(byte[]) - Method in class org.broadinstitute.hellbender.transformers.BaseQualityClipReadTransformer
-
Returns right clip point or -1 if no clip
- getRightMotif(VariantContext, FlowAnnotatorBase.LocalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- getRIlmn() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRoot() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- getRootNode() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph.ThreadingTree
- getRow(int) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Get entire row from the given row index in the table
- getRowMedians(RealMatrix) - Static method in class org.broadinstitute.hellbender.utils.MatrixSummaryUtils
-
Return an array containing the median for each row in the given matrix.
- getRowVariances(RealMatrix) - Static method in class org.broadinstitute.hellbender.utils.MatrixSummaryUtils
-
Return an array containing the variance for each row in the given matrix.
- getRsId() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getRunFile(File, Pattern) - Method in class picard.illumina.parser.ParameterizedFileUtil
- getRunning() - Static method in class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase
- getRunningMetric(int) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager.SelectionMetric
- getRunningMetric(int) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager.TruthSensitivityMetric
- getSAMField() - Method in class org.broadinstitute.hellbender.tools.walkers.consensus.MoleculeID
-
Format the molecule ID as stored in the sam/bam/cram file under the
SAMTag.MItag - getSamFileHeader() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection
-
Can return
null - getSamFileHeader() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalHeader
-
Can be
null - getSamFileHeader() - Method in class picard.analysis.CollectWgsMetrics
-
This method should only be called after
CollectWgsMetrics.getSamReader()is called. - getSAMFlagsForRead(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Construct a set of SAM bitwise flags from a GATKRead
- getSample() - Method in class org.broadinstitute.hellbender.tools.sv.BafEvidence
- getSample() - Method in class org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence
- getSample() - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepth
- getSample() - Method in class org.broadinstitute.hellbender.tools.sv.SplitReadEvidence
- getSample() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationRecord
- getSample() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPriorCollection
- getSample() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.MixingFraction
- getSample() - Method in class picard.fingerprint.Fingerprint
- getSample() - Method in class picard.fingerprint.FingerprintIdDetails
- getSample() - Method in class picard.fingerprint.MatchResults
- getSample(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingData
- getSample(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingLikelihoods
- getSample(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.HeterogeneousPloidyModel
- getSample(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.HomogeneousPloidyModel
- getSample(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Returns sample name given its index.
- getSample(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList
- getSample(int) - Method in interface org.broadinstitute.hellbender.utils.genotyper.SampleList
-
Returns the element given its index within the set.
- getSample(String) - Method in class org.broadinstitute.hellbender.utils.samples.SampleDB
-
Get a sample by its ID If an alias is passed in, return the main sample object
- getSampleAlias() - Method in class picard.fingerprint.FingerprintResults
- getSampleContamination() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection
-
Returns an unmodifiable view of the map of SampleId -> contamination.
- getSampleCount() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.HeterozygosityCalculator
- getSampleDB() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getSampleId() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData.SampleSpecificData
- getSampleId(SAMFileHeader) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
- getSampleIndex(String) - Method in class org.broadinstitute.hellbender.tools.sv.SVFeaturesHeader
- getSampleIndex(String) - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Writer
- getSampleLikelihood() - Method in class picard.fingerprint.MatchResults
- getSampleName() - Method in interface org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SampleLocatableMetadata
- getSampleName() - Method in interface org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SampleMetadata
- getSampleName() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleLocatableMetadata
- getSampleName() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleMetadata
- getSampleName() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CoveragePerContig
- getSampleName() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LegacySegment
- getSampleName() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getSampleName(GATKRead, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Returns the sample name associated with the provided read's read group.
- GetSampleName - Class in org.broadinstitute.hellbender.tools
-
Emit a single sample name from the bam header into an output file.
- GetSampleName() - Constructor for class org.broadinstitute.hellbender.tools.GetSampleName
- getSampleNames() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker
-
Get the list of sample names we accumulated
- getSampleNames() - Method in class org.broadinstitute.hellbender.tools.sv.SVFeaturesHeader
- getSampleNames() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- getSampleNamesForEvaluation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.VariantEvalContext
- getSampleNamesForEvaluation() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getSampleNamesForStratification() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getSampleNamesInSortedOrder() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.SampleNameMap
- getSampleNameToVcfPath() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.SampleNameMap
- getSampleOverlap() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.ClusteringParameters
- getSamplePlate() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getSamplePloidy(Set<String>, int, SampleDB, String, String, Genotype) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
-
Get the sample ploidy for a given contig based on the input pedigree (if available) defaults to for autosomes
- getSamples() - Method in class org.broadinstitute.hellbender.engine.MultiVariantDataSource
-
Return lexicographically sorted set of uniquified sample names merged from across input data sources
- getSamples() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- getSamples() - Method in class org.broadinstitute.hellbender.utils.samples.SampleDB
- getSamples(SAMFileHeader) - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Gets a set of the samples represented in this pileup.
- getSamples(V, Class<U>, int) - Method in class org.broadinstitute.hellbender.utils.mcmc.GibbsSampler
-
Returns a list of samples for a specified model parameter, discarding the first
numBurnInsamples. - getSampleSetOverlap(Collection<String>, Set<String>) - Static method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterLinkage
-
Returns number of overlapping items
- getSamplesForVariants() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalker
-
Get in name-sorted order a list of samples merged from the driving variants files.
- getSamplesFromHeader(SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Pull out the sample names from a SAMFileHeader note that we use a TreeSet so that they are sorted
- getSampleSpecificData() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData
- getSampleWell() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getSamReader() - Method in class picard.analysis.CollectWgsMetrics
-
Gets the SamReader from which records will be examined.
- getSamReader() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
- getSAMReadGroupRecord(GATKRead, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Returns a
SAMReadGroupRecordobject corresponding to the provided read's read group. - getSamRecord() - Method in class org.broadinstitute.hellbender.metrics.SAMRecordAndReference
- getSamRecord() - Method in class picard.metrics.SAMRecordAndReference
- getSamRecordComparator(SAMFileHeader.SortOrder) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
-
Given
sortOrder, provide appropriate comparator. - getSamRecordIndex() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
A number of convenience functions
- getSamSequenceDictionary(SamReader) - Method in class org.broadinstitute.hellbender.tools.walkers.variantrecalling.TrimmedReadsReader
- getSAMString() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Get a string representation of this read in SAM string format, terminated with '\n'.
- getSAMString() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getSAtagForGoodMappingToNonCanonicalChromosome() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- getSBsForAlleles(VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils
-
Get an allele-specific strand bias contingency table from a VariantContext
- getScaleX() - Method in class picard.arrays.illumina.InfiniumTransformation
- getScaleY() - Method in class picard.arrays.illumina.InfiniumTransformation
- getScannerName() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getScannerVersion() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getSchema() - Method in interface org.broadinstitute.hellbender.utils.bigquery.GATKAvroReader
- getSchema() - Method in class org.broadinstitute.hellbender.utils.bigquery.QueryRecord
- getSchema() - Method in class org.broadinstitute.hellbender.utils.bigquery.StorageAPIAvroReader
- getScheme(boolean) - Method in class picard.vcf.GenotypeConcordanceSchemeFactory
- getScore() - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
-
Get the score (an estimate of the support) of this haplotype
- getScore() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.EmptyFragment
- getScore() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.FlowModeFragment
- getScore() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Fragment
- getScore() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair
- getScore() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.PairedEnds
- getScoreNormalized() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- getScriptException(String) - Method in class org.broadinstitute.hellbender.utils.python.PythonExecutorBase
-
Return an exception specific to this executor type, to be thrown on error conditions.
- getScriptException(String) - Method in class org.broadinstitute.hellbender.utils.R.RScriptExecutor
-
Return an exception specific to this executor type, to be thrown on error conditions.
- getScriptException(String) - Method in class org.broadinstitute.hellbender.utils.runtime.ScriptExecutor
-
Called by the script executor when error is encountered.
- getSecondaryAlignments() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.ReadPair
- getSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_BaseQualityRankSumTest
-
Get additional raw key strings that are not the primary key
- getSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_MappingQualityRankSumTest
-
Get additional raw key strings that are not the primary key
- getSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth
- getSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_ReadPosRankSumTest
-
Get additional raw key strings that are not the primary key
- getSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality
-
Get additional raw key strings that are not the primary key
- getSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
-
Get additional raw key strings that are not the primary key
- getSecondaryRawKeys() - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation
-
Get additional raw key strings that are not the primary key
- getSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RawGtCount
- getSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
-
Get additional raw key strings that are not the primary key
- getSecondaryVariantClassification() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getSecondOfPair() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.ReadPair
- getSecondOfPair(int) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
- getSecondsInAssembly() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse
- getSegment() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.MinorAlleleFractionRecord
- getSegmentEndExonOverlap() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment.SegmentExonOverlaps
- getSegmentMean() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LegacySegment
- getSegmentStartExonOverlap() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment.SegmentExonOverlaps
- getSelenocysteines() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature
- getSelfScore() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- getSenseCount() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation.Coverage
- getSensitivity() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceSummaryRecord
- getSensitivity(GenotypeConcordanceScheme, GenotypeConcordanceStates.TruthState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the sensitivity defined by the scheme across the subset of truth states.
- getSentinel() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Get the special sentinel value that will be used to signal novelty when putting a new interval into the tree, or to signal "not found" when removing an interval.
- getSentrixBarcode() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getSeqGraph() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult
- getSequence() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- getSequence() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- getSequence() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- getSequence() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.PathPart
- getSequence() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartContig
- getSequence() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartGap
- getSequence() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- getSequence() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
-
Get the sequence of bases contained in this vertex Do not modify these bytes in any way!
- getSequence(String) - Method in class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
-
Retrieves the complete sequence described by this contig.
- getSequenceDictionary() - Method in class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Returns the sequence dictionary for this source of Features.
- getSequenceDictionary() - Method in class org.broadinstitute.hellbender.engine.MultiVariantDataSource
-
Returns the aggregate sequence dictionary for this source of Variants.
- getSequenceDictionary() - Method in interface org.broadinstitute.hellbender.engine.ReadsDataSource
-
Get the sequence dictionary for this ReadsDataSource
- getSequenceDictionary() - Method in class org.broadinstitute.hellbender.engine.ReadsPathDataSource
-
Get the sequence dictionary for this ReadsPathDataSource
- getSequenceDictionary() - Method in interface org.broadinstitute.hellbender.engine.ReferenceDataSource
-
Get the sequence dictionary for this reference
- getSequenceDictionary() - Method in class org.broadinstitute.hellbender.engine.ReferenceFileSource
-
Get the sequence dictionary for this reference
- getSequenceDictionary() - Method in class org.broadinstitute.hellbender.engine.ReferenceMemorySource
-
Get the sequence dictionary for this reference
- getSequenceDictionary() - Method in class org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals
- getSequenceDictionary() - Method in interface org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals
-
Returns the sequence dictionary common to all of the read counts used to build the PoN.
- getSequenceDictionary() - Method in interface org.broadinstitute.hellbender.tools.copynumber.formats.metadata.LocatableMetadata
- getSequenceDictionary() - Method in interface org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SampleLocatableMetadata
- getSequenceDictionary() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleLocatableMetadata
- getSequenceDictionary() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleLocatableMetadata
- getSequenceDictionary() - Method in class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
-
Returns the sequence dictionary associated with this reference file
- getSequenceDictionary() - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Return the master sequence dictionary used within this GenomeLocParser
- getSequenceDictionaryForDrivingVariants() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalker
- getSequenceDictionaryForDrivingVariants() - Method in class org.broadinstitute.hellbender.engine.VariantLocusWalker
- getSequenceDictionaryForDrivingVariants() - Method in class org.broadinstitute.hellbender.engine.VariantWalker
- getSequenceDictionaryForDrivingVariants() - Method in class org.broadinstitute.hellbender.engine.VariantWalkerBase
-
Return the primary sequence dictionary to be used for the driving variants for this tool.
- getSequenceDictionaryForDrivingVariants() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.VariantEvalContext
- getSequenceDictionaryForDrivingVariants() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getSequenceDictionaryValidationArgumentCollection() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Get the
SequenceDictionaryValidationArgumentCollectionfor the tool. - getSequenceDictionaryValidationArgumentCollection() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
subclasses can override this to provide different default behavior for sequence dictionary validation
- getSequenceDictionaryValidationArgumentCollection() - Method in class org.broadinstitute.hellbender.tools.reference.CheckReferenceCompatibility
- getSequenceDictionaryValidationArgumentCollection() - Method in class org.broadinstitute.hellbender.tools.spark.bwa.BwaSpark
- getSequenceDictionaryValidationArgumentCollection() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.BwaAndMarkDuplicatesPipelineSpark
- getSequenceLength() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- getSequenceNames() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- getSequenceRecord() - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
- getSequencerType() - Method in enum class org.broadinstitute.hellbender.utils.NGSPlatform
-
The broad "type" of sequencer this platform represents (discrete or flow)
- getSequenceString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
-
Get a string representation of the bases in this vertex
- getSequentialFileList(Path) - Static method in class picard.sam.FastqToSam
-
Get a list of FASTQs that are sequentially numbered based on the first (base) fastq.
- getSets() - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- getSeverity() - Method in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
- getSex() - Method in class org.broadinstitute.hellbender.utils.samples.Sample
- getSex() - Method in class picard.pedigree.PedFile.PedTrio
- getSexConcordance(String, String, String) - Static method in class picard.arrays.CollectArraysVariantCallingMetrics
- getShardBoundary() - Method in class org.broadinstitute.hellbender.engine.ShardBoundaryShard
- getShardedCollectionSortOrder(List<? extends AbstractLocatableCollection<METADATA, RECORD>>) - Static method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractLocatableCollection
-
Gets a list of locatable collections and returns the ascending sort order of collections.
- getShardFilename(Path, int) - Static method in class org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter
-
Gets filepath for the given shard and base path
- getShardNumber() - Method in class org.broadinstitute.hellbender.engine.ReferenceShard
- getShardNumber() - Method in class org.broadinstitute.hellbender.engine.VariantShard
- getShardNumberFromInterval(Locatable) - Static method in class org.broadinstitute.hellbender.engine.ReferenceShard
-
getShardNumberFromInterval returns the ReferenceShard that overlap the read's start position.
- getShear() - Method in class picard.arrays.illumina.InfiniumTransformation
- getSigma() - Method in class org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile
-
Get the Gaussian kernel sigma value
- getSimpleName() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
- getSingleBarcodeDistanceQuery(int, int) - Method in class picard.util.BarcodeEditDistanceQuery
- getSingletonReads() - Method in class org.broadinstitute.hellbender.utils.fragments.FragmentCollection
-
Gets the T elements not containing overlapping elements, in no particular order.
- getSingletonSample(VariantContext) - Static method in class picard.vcf.CallingMetricAccumulator
- getSingularValues() - Method in class org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals
- getSingularValues() - Method in interface org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals
-
Returns a modifiable copy of an array of the singular values of the eigensamples in decreasing order.
- getSingularValues() - Method in class org.broadinstitute.hellbender.utils.svd.SimpleSVD
- getSingularValues() - Method in interface org.broadinstitute.hellbender.utils.svd.SVD
-
Get the singular values as an array.
- getSinks() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Get the set of sink vertices of this graph NOTE: We return a LinkedHashSet here in order to preserve the determinism in the output order of VertexSet(), which is deterministic in output due to the underlying sets all being LinkedHashSets.
- getSize() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeterResults
- getSize() - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- getSizeOf() - Static method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- getSizeOf() - Static method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- getSizeOnRead() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- getSkipNLoci() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- getSnp() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getSnp() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getSnp(String) - Method in class picard.fingerprint.HaplotypeBlock
-
Gets a SNP by name if it belongs to this haplotype.
- getSnp(String, int) - Method in class picard.fingerprint.HaplotypeMap
-
Queries a Snp by chromosome and position.
- getSnpAlleleA() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getSnpAlleleB() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getSnpCounter() - Method in class picard.vcf.GenotypeConcordance
- getSnpFalsePositiveRate() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord
- getSnpFalsePositives() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord
- getSnpGenotype(Snp, DiploidHaplotype) - Method in class picard.fingerprint.HaplotypeBlock
-
Gets the expected genotype of the provided SNP given the provided haplotype of this haplotype block.
- getSnpManifest() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getSnpRefAllele() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getSnps() - Method in class picard.fingerprint.HaplotypeBlock
-
Returns an unmodifiable, unordered, collection of all SNPs in this haplotype block.
- getSNPSubstitutionType(VariantContext) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Returns the type of the substitution (transition vs transversion) represented by this variant.
- getSoftEnd() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Calculates the reference coordinate for the end of the read taking into account soft clips but not hard clips.
- getSoftEnd() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getSoftEnd(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Calculates the reference coordinate for the end of the read taking into account soft clips but not hard clips.
- getSoftStart() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Calculates the reference coordinate for the beginning of the read taking into account soft clips but not hard clips.
- getSoftStart() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getSoftStart(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Calculates the reference coordinate for the beginning of the read taking into account soft clips but not hard clips.
- getSolePredecessor() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- getSolePredecessor() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- getSolePredecessor() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- getSoleSuccessor() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- getSoleSuccessor() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- getSoleSuccessor() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- getSolexaQualityCharFromFourQualities(String[], int, FormatUtil) - Static method in class picard.util.IlluminaUtil
-
Get a Solexa ASCII quality value from an array of strings that are integer qualities in this order: [cycle-1-A, cycle-1-C, cycle-1-G, cycle-1-T, cycle-2-A, ...].
- getSomaticClusteringModel() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- getSortedAnnotationNames() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- getSortedLabels() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- getSortedSampleSet(Map<String, VCFHeader>, GATKVariantContextUtils.GenotypeMergeType) - Static method in class org.broadinstitute.hellbender.utils.variant.VcfUtils
- getSource() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker.DictSource
- getSource() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- getSource() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeterResults
- getSource() - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Returns the reader source name.
- getSource() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getSource() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getSource() - Method in class picard.fingerprint.Fingerprint
- getSourceContig() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- getSources() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Get the set of source vertices of this graph NOTE: We return a LinkedHashSet here in order to preserve the determinism in the output order of VertexSet(), which is deterministic in output due to the underlying sets all being LinkedHashSets.
- getSourceSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getSourceSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getSourceStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getSourceStrand() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getSourceVersion() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getSourceVersion() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getSpan() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Get the raw span of this assembly region (excluding the padding)
- getSpan() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionBounds
- getSpan() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionStatistics
- getSpan() - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
-
Get the span of this activity profile, which is from the start of the first state to the stop of the last
- getSpanningInterval(List<? extends Locatable>) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
getSpanningInterval returns interval that covers all of the locations passed in.
- getSpanningIntervals(List<? extends Locatable>, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Get a single interval per contig that includes all of the specified intervals (This is used to improve GenomicsDB performance for exomes)
- getSpanningIterator(Iterator<Tuple2<K, V>>) - Static method in class org.broadinstitute.hellbender.utils.spark.SparkUtils
-
An iterator that groups values having the same key into iterable collections.
- getSparkContext(String, Map<String, String>, String) - Static method in class org.broadinstitute.hellbender.engine.spark.SparkContextFactory
-
Get a
JavaSparkContext. - getSparkMaster() - Method in class org.broadinstitute.hellbender.engine.spark.SparkCommandLineArgumentCollection
- getSparkProperties() - Method in class org.broadinstitute.hellbender.engine.spark.SparkCommandLineArgumentCollection
- getSparkVerbosity(Log.LogLevel) - Method in class org.broadinstitute.hellbender.engine.spark.SparkCommandLineArgumentCollection
-
Returns the Spark log level for the argument set.
- getSpecies() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getSpecies() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getSpecificity(GenotypeConcordanceScheme, GenotypeConcordanceStates.TruthState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the specificity defined by the scheme across the subset of truth states.
- getSplicesForTesting() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager
-
For testing purposes only
- getSplitBy(GATKRead, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.readersplitters.ReaderSplitter
-
Returns the value from this record for this splitter.
- getSplitBy(GATKRead, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.readersplitters.ReadGroupSplitter
- getSplitByFunction() - Method in class org.broadinstitute.hellbender.tools.readersplitters.LibraryNameSplitter
- getSplitByFunction() - Method in class org.broadinstitute.hellbender.tools.readersplitters.ReadGroupIdSplitter
- getSplitByFunction() - Method in class org.broadinstitute.hellbender.tools.readersplitters.ReadGroupSplitter
- getSplitByFunction() - Method in class org.broadinstitute.hellbender.tools.readersplitters.SampleNameSplitter
- getSpliteratorForDrivingVariants() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalker
- getSpliteratorForDrivingVariants() - Method in class org.broadinstitute.hellbender.engine.VariantLocusWalker
- getSpliteratorForDrivingVariants() - Method in class org.broadinstitute.hellbender.engine.VariantWalker
- getSpliteratorForDrivingVariants() - Method in class org.broadinstitute.hellbender.engine.VariantWalkerBase
-
Return a spliterator to be used to iterate over the elements of the driving variants.
- getSplitReads() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
- getSplitReadTemplateNames() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
- getSplitsBy(SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.readersplitters.ReaderSplitter
-
Returns the values from the header that will be used to split the reader.
- getSplitsBy(SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.readersplitters.ReadGroupSplitter
- getStandardBQSRReadFilterList() - Static method in class org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator
-
Return the full list of raw read filters used for BQSR contexts, including WellFormed.
- getStandardCovariateClassNames() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList
-
Returns the list of simple class names of standard covariates.
- getStandardEvaluatorNames() - Static method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getStandardHaplotypeCallerAnnotationGroups() - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- getStandardizedCopyRatios() - Method in class org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisedCopyRatioResult
- getStandardMutect2AnnotationGroups() - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- getStandardStratificationNames() - Static method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getStandardUsagePreamble() - Method in class picard.cmdline.CommandLineProgram
- getStandardUsagePreamble(Class<?>) - Static method in class picard.cmdline.CommandLineProgram
-
A typical command line program will call this to get the beginning of the usage message, and then typically append a description of the program, like this: public String USAGE = getStandardUsagePreamble(getClass()) + "Frobnicate the freebozle."
- getStart() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval
- getStart() - Method in class org.broadinstitute.hellbender.engine.AlignmentContext
- getStart() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
- getStart() - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
- getStart() - Method in interface org.broadinstitute.hellbender.engine.Shard
- getStart() - Method in class org.broadinstitute.hellbender.engine.ShardBoundary
- getStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
- getStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AnnotatedInterval
- getStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatio
- getStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatioSegment
- getStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
- getStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntervalCopyNumberGenotypingData
- getStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LegacySegment
- getStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LinearCopyRatio
- getStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment
- getStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount
- getStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval
- getStart() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocus
- getStart() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getStart() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.PathPart
- getStart() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartContig
- getStart() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartGap
- getStart() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.Mapping
-
Returns the primary interval start position, or
SAMRecord.NO_ALIGNMENT_STARTif unmapped. - getStart() - Method in class org.broadinstitute.hellbender.tools.sv.BafEvidence
- getStart() - Method in class org.broadinstitute.hellbender.tools.sv.DepthEvidence
- getStart() - Method in class org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence
- getStart() - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepth
- getStart() - Method in class org.broadinstitute.hellbender.tools.sv.SplitReadEvidence
- getStart() - Method in class org.broadinstitute.hellbender.tools.walkers.consensus.ReadsWithSameUMI
- getStart() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.MinorAlleleFractionRecord
- getStart() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- getStart() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- getStart() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getStart() - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
- getStart() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature
- getStart() - Method in class org.broadinstitute.hellbender.utils.codecs.table.TableFeature
- getStart() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
- getStart() - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- getStart() - Method in class org.broadinstitute.hellbender.utils.haplotype.FlowBasedHaplotype
- getStart() - Method in class org.broadinstitute.hellbender.utils.IndexRange
- getStart() - Method in class org.broadinstitute.hellbender.utils.read.Fragment
- getStart() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getStart() - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
-
Gets the 1-based start position of the interval on the contig.
- getStart() - Method in class org.broadinstitute.hellbender.utils.SVInterval
- getStart() - Method in class org.broadinstitute.hellbender.utils.variant.MinimalVariant
- getStart() - Method in class org.broadinstitute.hellbender.utils.variant.VariantContextVariantAdapter
- getStart() - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- getStartCodon() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfExonFeature
- getStartColumn() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
-
Do not call before
XsvLocatableTableCodec.readActualHeader(LineIterator)or exception will be thrown.. - getStartColumnName() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalHeader
- getStartingVC() - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- getStartInterval(SAMSequenceDictionary, int) - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocus
- getStartLocation() - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- getStartLocation() - Method in class org.broadinstitute.hellbender.utils.SVInterval
- getStartPosition() - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- getStartPositionInTranscript(Locatable, List<? extends Locatable>, Strand) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Gets the position describing where the given allele and variant lie inside the given transcript using transcript-based coordinates.
- getStartPositions() - Method in class org.broadinstitute.hellbender.utils.haplotype.EventMap
-
Get the starting positions of events in this event map
- getStartStrand() - Method in class org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence
- getStateList() - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
-
Get the list of activity profile results in this object
- getStates() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- getStatesForKey(int) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- getStatistic() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.MutectStats
- getStatus() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult
- getStatusSummary(boolean) - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessOutput
-
Construct a summary message for process output.
- getStd() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.InfoConcordanceRecord
- getStderr() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessOutput
- getStderrSettings() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- getStdinSettings() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- getStdout() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessOutput
- getStdoutSettings() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- getStop() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.PathPart
- getStop() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartContig
- getStop() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartGap
- getStop() - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- getStopCodon() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfExonFeature
- getStopLocation() - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- getStopPosition() - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- getStrand() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getStrand() - Method in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedAllele
- getStrand() - Method in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedReferenceBases
- getStrand() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval
- getStrand() - Method in class org.broadinstitute.hellbender.tools.sv.SplitReadEvidence
- getStrand() - Method in class org.broadinstitute.hellbender.tools.walkers.consensus.MoleculeID
- getStrand() - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
-
Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively
- getStrand() - Method in interface org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqTranscript
-
Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively
- getStrandA() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getStrandB() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getStrandCorrectedAllele(Allele, Strand) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Get the strand-corrected (reverse complemented)
Allelefor the givenAlleleandStrand. - getStrandCounts(Genotype) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest
- getStrandCountsFromLikelihoodMap(VariantContext, AlleleLikelihoods<GATKRead, Allele>, ReducibleAnnotationData<List<Integer>>, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils
-
Allocate and fill a Nx2 strand contingency table where N is the number of alleles.
- getStrandedOffset(boolean, int, int) - Static method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ContextCovariate
-
Helper method: computes the correct offset to use in computations of covariate values.
- getStrandedUnclippedEndForFlow(GATKRead, SAMFileHeader, MarkDuplicatesSparkArgumentCollection) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- getStrandedUnclippedStart(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Returns the read's unclipped start if the read is on the forward strand, or the read's unclipped end if the read is on the reverse strand.
- getStrandedUnclippedStartForFlow(GATKRead, SAMFileHeader, MarkDuplicatesSparkArgumentCollection) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- getStrandOfRead(GATKRead) - Static method in class org.broadinstitute.hellbender.tools.walkers.consensus.MoleculeID
-
Extracts the strand portion of the
SAMTag.MIfield of the read - getStrandSwitch() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- getStratifierClasses() - Static method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getStratifiers() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- getStratManager() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getStratsAndStatesForKey(int) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- getStratsAndStatesStringForKey(int) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- getStream() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- getStream() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Writer
- getStreamLocations() - Method in class org.broadinstitute.hellbender.utils.runtime.InputStreamSettings
- getStreamLocations() - Method in class org.broadinstitute.hellbender.utils.runtime.OutputStreamSettings
- getStructuralVariantLength() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVContext
-
Returns the absolute structural variant length as recorded in the SVLEN annotation.
- getSubsequenceAt(String, long, long) - Method in class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
-
Gets the subsequence of the contig in the range [start,stop] Uses the sequence cache if possible, or updates the cache to handle the request.
- getSubset(SimpleInterval) - Method in class org.broadinstitute.hellbender.utils.reference.ReferenceBases
-
getSubset returns only the bases of the interval passed in.
- getSubsetOfVariantContext(VariantContext, String) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
-
Subset a VariantContext to a single sample
- getSubsetOfVariantContext(VariantContext, Set<String>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
-
Subset a VariantContext to a set of samples
- getSuccessorCount() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- getSuccessorCount() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- getSuccessorCount() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- getSuccessorMask() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- getSuccessorMask() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- getSuccessorMask() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- getSuccessors() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- getSuccessors() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- getSuccessors() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- getSuccessorVal(int) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Kmer
- getSuffix() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex
-
Get the suffix byte of this DeBruijnVertex The suffix byte is simply the last byte of the kmer sequence, so if this is holding sequence ACT getSuffix would return T
- getSuffix() - Method in interface picard.sam.SamErrorMetric.BaseCalculator
-
The suffix that pertains to the implementation of aggregation
- getSuffix() - Method in class picard.sam.SamErrorMetric.BaseErrorAggregation
- getSuffix() - Method in class picard.sam.SamErrorMetric.IndelErrorCalculator
-
The suffix that pertains to the implementation of aggregation
- getSuffix() - Method in class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
-
The suffix that pertains to the implementation of aggregation
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.BinnedReadCycleStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CigarOperatorsInReadStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CollectionStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.ConsensusStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellTileStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellYStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.GCContentStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelLengthStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymerStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.MismatchesInReadStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.NsInReadStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.PairStratifier
- getSuffix() - Method in interface picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.SimpleErrorCalculator
-
The suffix that pertains to the implementation of aggregation
- getSuffixString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex
-
Get the string representation of the suffix of this DeBruijnVertex
- getSuggestedAlternateCommand(Set<Class<?>>, String) - Method in class org.broadinstitute.hellbender.Main
-
When a command does not match any known command, searches for similar commands, using the same method as GIT *
- getSum() - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the sum of all pairs of tuples defined by the truth state set and call state set.
- getSum(Set<GenotypeConcordanceStates.TruthState>, Set<GenotypeConcordanceStates.CallState>) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the sum of all pairs of tuples defined by the truth state set and call state set.
- getSummaryLine() - Method in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter
- getSummaryLine() - Method in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter
- getSummaryLineForLevel(int) - Method in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter.CountingAndReadFilter
- getSummaryLineForLevel(int) - Method in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter
- getSummaryLineForLevel(int) - Method in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter.CountingAndVariantFilter
- getSummaryLineForLevel(int) - Method in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter
- getSuperCategoryMap() - Static method in class picard.util.help.HelpConstants
- getSuperCategoryProperty(String) - Static method in class org.broadinstitute.hellbender.utils.help.HelpConstants
-
Given a group name, return a supercategory string for use by the online doc system to determine which supercateogry the group is in.
- getSuperCategoryProperty(String) - Static method in class picard.util.help.HelpConstants
-
Given a group name, return a supercategory string for use by the online doc system to determine which supercateogry the group is in.
- getSupplementaryIntervals() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.Mapping
- getSupportedFuncotationFields() - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
- getSupportedFuncotationFields() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory
- getSupportedFuncotationFields() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
- getSupportedFuncotationFields() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory
- getSupportedFuncotationFields() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.LocatableXsvFuncotationFactory
- getSupportedFuncotationFields() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory
- getSupportedFuncotationFieldsForSegments() - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
- getSupportedFuncotationFieldsForSegments() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
- getSupportedOptions() - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLDoclet
- getSupportInformation() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- getSupportingContigIds() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVContext
-
Returns the ids of the assembled contig that support this context's structural variant.
- getSupportLowerBound() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BetaBinomialDistribution
- getSupportUpperBound() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BetaBinomialDistribution
- getSVLength() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- getSVLocatableComparator(SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
-
Gets a comparator for objects implementing
SVLocatable. - getSVSegments(VariantContext, GATKSVVCFConstants.StructuralVariantAnnotationType, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Get list of SVSegments (type and interval) to annotate as one variant for a given VCF record For simple variants, the list will contain one element representing the SV.
- getSVType(VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Get SV type for variant from ALT field of VCF
- getSymbAltAlleleLine(String) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFHeaderLines
- getSymbAltAlleleLines() - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFHeaderLines
- getSymbolicAlleleSymbols(Allele) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKSVVariantContextUtils
-
Parses allele for the base type string, e.g.
- getTabixFormat() - Method in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceCodec
- getTabixFormat() - Method in class org.broadinstitute.hellbender.utils.codecs.copynumber.SimpleCountCodec
- getTabixFormat() - Method in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceCodec
- getTabixFormat() - Method in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceCodec
- getTabixFormat() - Method in class org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec
- getTabixFormat() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupCodec
- getTabixFormat() - Method in class org.broadinstitute.hellbender.utils.codecs.SiteDepthCodec
- getTabixFormat() - Method in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceCodec
- getTable(int) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
- getTable(String) - Method in class org.broadinstitute.hellbender.utils.report.GATKReport
-
Return a table with a given name
- getTableDescription() - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
- getTableForCovariate(Covariate) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
- getTableFromSamples(GenotypesContext, int) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest
-
Create the contingency table by retrieving the per-sample strand bias annotation and adding them together
- getTableName() - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
- getTables() - Method in class org.broadinstitute.hellbender.utils.report.GATKReport
- getTag() - Method in class org.broadinstitute.hellbender.engine.GATKPath
- getTagAttributes() - Method in class org.broadinstitute.hellbender.engine.GATKPath
- getTagFilterPrefix() - Method in class org.broadinstitute.hellbender.utils.help.GATKHelpDocWorkUnitHandler
- getTagFilterPrefix() - Method in class picard.util.help.PicardHelpDocWorkUnitHandler
- getTags() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- getTailAlignment() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
- getTailAlignment() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- getTarget() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager.SelectionMetric
- getTarget() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager.TruthSensitivityMetric
- getTargetPartitionSize() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Returns the size of each input partition (in bytes) that is used to determine the recommended number of reducers for running a processing pipeline.
- getTargetTerritory() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord
- getTechnicalArtifactProbabilities() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorProbabilities
- getTempFilePath(String, String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Get a temporary file path based on the prefix and extension provided.
- getTemplateName() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
- getTemplateName(DocWorkUnit) - Method in class org.broadinstitute.hellbender.utils.help.GATKHelpDocWorkUnitHandler
- getTemplateName(DocWorkUnit) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLWorkUnitHandler
- getTemplateName(DocWorkUnit) - Method in class picard.util.help.PicardHelpDocWorkUnitHandler
- getTemplateSize() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
- getTestSparkContext() - Static method in class org.broadinstitute.hellbender.engine.spark.SparkContextFactory
-
Get the test
JavaSparkContextif it has been registered, otherwise returns null. - getTestSparkContext(Map<String, String>) - Static method in class org.broadinstitute.hellbender.engine.spark.SparkContextFactory
-
Get the test
JavaSparkContextif it has been registered, otherwise returns null. - getTheoreticalFPP(long) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter
- getTheta() - Method in class picard.arrays.illumina.InfiniumTransformation
- getThetaIlmn() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getThreadingGraph() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult
- getThreadLocal() - Static method in class org.broadinstitute.hellbender.utils.runtime.ProcessController
-
Returns a thread local ProcessController.
- getThreshold() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
-
Maximum probability that a potential variant is not a true somatic mutation.
- getThreshold() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ThresholdCalculator
- getThreshold(double) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager.SelectionMetric
- getThreshold(double) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager.TruthSensitivityMetric
- getThresholdForSelectingAdaptersToKeep() - Method in class picard.util.AdapterMarker
- getTies() - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU.TestStatistic
- getTile() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- getTile() - Method in class picard.illumina.parser.CbclData
- getTile() - Method in class picard.illumina.parser.ClusterData
- getTile() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
- getTile() - Method in interface picard.sam.util.PhysicalLocation
- getTile() - Method in class picard.sam.util.PhysicalLocationInt
- getTiledFiles(File, Pattern) - Static method in class picard.illumina.BasecallsConverter
-
Applies an lane and tile based regex to return all files matching that regex for each tile.
- getTiledFiles(File, Pattern) - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Return all files that match pattern of the given file type in the given base directory
- getTileFromReadName(String) - Static method in class picard.util.IlluminaUtil
-
Parse the tile # from the read name.
- getTileInfo() - Method in class picard.illumina.parser.readers.BaseBclReader.CycleData
- getTileNum() - Method in class picard.illumina.parser.readers.BaseBclReader.TileData
- getTileNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
- getTileNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- getTileNumber() - Method in class picard.illumina.parser.Tile
-
Returns the number/name of this tile.
- getTileOfNextCluster() - Method in class picard.illumina.parser.MultiTileParser
- getTileOfNextCluster() - Method in class picard.illumina.parser.MultiTileBclParser
-
Returns the tile of the next cluster that will be returned by PerTilePerCycleParser and therefore should be called before next() if you want to know the tile for the data returned by next()
- getTileOfNextCluster() - Method in class picard.illumina.parser.PerTileParser
-
Return the tile of the NEXT ILLUMINA_DATA object to be returned by the method next.
- getTiles() - Method in class picard.illumina.parser.MultiTileBclFileUtil
- getTiles() - Method in class picard.illumina.parser.MultiTileFileUtil
- getTiles() - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Return a list of all tiles available for this file format and run
- getTiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
Discover all files of this type in expectedBase that match pattern and construct a list of tiles available based on these files.
- getTiles() - Method in class picard.illumina.parser.TileIndex
- getTileTemplateRead() - Method in class picard.illumina.parser.TilePhasingValue
- getToCoverage() - Method in class org.broadinstitute.hellbender.utils.locusiterator.LIBSDownsamplingInfo
- getToMarkQueueMinimumDistance() - Method in class picard.sam.markduplicates.util.MarkQueue
-
Returns the minimum genomic distance such that we can be assured that all duplicates have been considered.
- getToolDeprecationInfo(String) - Static method in class org.broadinstitute.hellbender.cmdline.DeprecatedToolsRegistry
-
Utility method to pull up the version number at which a tool was deprecated and the suggested replacement, if any
- getToolDeprecationMessage(String) - Method in class org.broadinstitute.hellbender.Main
-
Get deprecation message for a tool
- getToolkitName() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- getToolkitName(Class<?>) - Static method in class org.broadinstitute.hellbender.utils.runtime.RuntimeUtils
- getToolkitShortName() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- getToolLogger() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData
- getToolName() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns the name of this tool.
- getToolReturnCode() - Method in exception org.broadinstitute.hellbender.exceptions.PicardNonZeroExitException
- getToolStatusWarning(boolean) - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
-
If this tool is either Experimental or Beta, return a warning message advising against use in production envirogetnment.
- getToolVersion() - Method in class org.broadinstitute.hellbender.tools.funcotator.OutputRenderer
- getTopGenomicSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getTopGenomicSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getTotal() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
- getTotalBaseQuality() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.LibraryRawStatistics
- getTotalCount() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- getTotalCount() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.Datum
- getTotalCoverage() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
- getTotalCycles() - Method in class picard.illumina.parser.ReadStructure.Substructure
- getTotalDepth() - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepth
- getTotalExonLength() - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
-
Returns a count of the total number of reference bases spanned by gene summary.
- getTotalInserts() - Method in class org.broadinstitute.hellbender.metrics.PerUnitInsertSizeMetricsCollector
- getTotalInserts() - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
- getTotalLength() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
- getTotalLoci() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
- getTotalMeanCoverage() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
- getTotalObs() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the total number of observations of any allele.
- getTotalObs() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
Gets the total number of observations presented at this locus.
- getTotalObs() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- getTotalObservations() - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.CDF
- getTotalObservations() - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram
- getTotalOutputCycles() - Method in class picard.illumina.parser.OutputMapping
- getTotalReadCount() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
- getTotalReads() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- getTotals() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
- getTrailingDeletionBasesRemoved() - Method in class org.broadinstitute.hellbender.utils.read.CigarBuilder
-
Counts the number of trailing deletion bases that were removed in the last call to make().
- getTrailingDeletionBasesRemoved() - Method in class org.broadinstitute.hellbender.utils.read.CigarBuilder.Result
- getTrainingData() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- getTrancheIndex() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- getTrancheIndex() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VQSLODTranche
- getTrancheString(T) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- getTranscriptAlleleStart() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- getTranscriptAlleleStartPosition(VariantContext, List<? extends Locatable>, Strand) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Get the position (1-based, inclusive) of the given
VariantContextstart relative to the transcript it appears in. - getTranscriptCodingSequence() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
-
Return the
ReferenceSequencecontaining the coding region for the transcript of thisSequenceComparison. - getTranscriptCoordinate(int) - Method in class picard.annotation.Gene.Transcript
-
Given a coordinate on the genome (same chromosome) give the corresponding coordinate in the transcript.
- getTranscriptEndPos() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getTranscriptExonNumber() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getTranscriptFuncotations(FuncotationMap) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsUtils
-
Munge a FuncotationMap into a stream of sets of pairs of funcotation name / funcotation value.
- getTranscriptId() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getTranscriptId() - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
-
Returns id of the transcript (RefSeq NM_* id)
- getTranscriptId() - Method in interface org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqTranscript
-
Returns id of the transcript (RefSeq NM_* id)
- getTranscriptIdWithoutVersionNumber(String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Removes the transcript ID version number from the given transcript ID (if it exists).
- getTranscriptIntervalTree() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine.GTFIntervalTreesContainer
- getTranscriptionStartSite(GencodeGtfTranscriptFeature) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate
-
Get transcription start site from GTF transcript: first (5') base of transcript
- getTranscriptionStartSiteTree() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine.GTFIntervalTreesContainer
- getTranscriptLength() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getTranscriptList() - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
-
Get the list of transcripts, in order.
- getTranscriptName() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getTranscripts() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfGeneFeature
- getTranscriptStartPos() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getTranscriptStatus() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getTranscriptStrand() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getTranscriptType() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getTranscriptUniqueGeneName() - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
-
Returns a uniquified name of the Gene and TranscriptID
- getTransformedReadStream(ReadFilter) - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns a stream over the reads, which are: 1.
- getTransformedVariantStream(Spliterator<VariantContext>, VariantTransformer, CountingVariantFilter, VariantTransformer) - Method in class org.broadinstitute.hellbender.engine.VariantWalkerBase
-
Returns a stream over the variants returned by source, which are: 1.
- getTransformedVariantStream(CountingVariantFilter) - Method in class org.broadinstitute.hellbender.engine.VariantWalkerBase
-
Returns a stream over the variants, which are: 1.
- getTransientAttribute(Object) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
This is used to access a transient attribute store provided by the underlying implementation.
- getTransientAttribute(Object) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
-
This is used to access the transient attribute store in the underlying SAMRecord.
- getTraversalIntervals() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns the list of intervals to iterate, either limited to the user-supplied intervals or the entire reference genome if none were specified.
- getTraversalIntervals() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getTraversalParameters(SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
Returns the full set of traversal parameters specified on the command line, including the parsed intervals and a flag indicating whether unmapped records were requested.
- getTrimmedEnd() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- getTrimmedStart() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- getTrios() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation
-
Computes the trios from the provided pedigree file
- getTrios() - Method in class org.broadinstitute.hellbender.utils.samples.SampleDB
-
Returns all the trios present in the db.
- getTrios(boolean) - Method in class org.broadinstitute.hellbender.utils.samples.SampleDB
-
Returns all the trios present in the sample database.
- getTrueKey() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.InfoConcordanceRecord
- getTrueNegativeCount() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
- getTruePositives() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceSummaryRecord
- getTrueU() - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU.TestStatistic
- getTruth() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval
- getTruthHeader() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- getTruthIfPresentElseEval() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval
- getTruthSensitivity() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- getTruthState(Genotype) - Method in class org.broadinstitute.hellbender.tools.sv.concordance.SVConcordanceAnnotator
- getTumor() - Method in class org.broadinstitute.hellbender.tools.funcotator.metadata.TumorNormalPair
- getTumorAltCount() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.NormalArtifactRecord
- getTumorDepth() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.NormalArtifactRecord
- getTumorLogOdds() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.Datum
- getTumorLogOdds(VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
-
Get the (Natural) log odds of variants from the log-10 odds in a VariantContext object
- getTumorSeqAllele2() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getType() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationKey
- getType() - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
- getType() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory
- getType() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
- getType() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory
- getType() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.LocatableXsvFuncotationFactory
- getType() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory
- getType() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- getType() - Method in interface org.broadinstitute.hellbender.tools.sv.SVLocatable
- getType() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase
- getType() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.NormalArtifactRecord
- getType() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.EmptyFragment
- getType() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.FlowModeFragment
- getType() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Fragment
- getType() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord
- getType() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair
- getType() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Passthrough
- getTypeInferredFromSimpleChimera() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- getTypeSpecificAttributes() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- getU() - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU.Result
- getU() - Method in class org.broadinstitute.hellbender.utils.svd.SimpleSVD
- getU() - Method in interface org.broadinstitute.hellbender.utils.svd.SVD
-
Get the U matrix of a Singular Value Decomposition U has the property that V.transpose * V = I Note that U need not be square.
- getU1() - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU.TestStatistic
- getU2() - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU.TestStatistic
- getUcscGenomeVersion() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- getUnaccountedForAnnotations(List<DataSourceFuncotationFactory>, Map<String, String>) - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine
-
Creates a
LinkedHashMapof annotations in the givenannotationMapthat do not occur in the givendataSourceFactories. - getUnambiguousReads() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- getUnclippedEnd() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Returns the alignment end (1-based, inclusive) adjusted for clipped bases.
- getUnclippedEnd() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getUnclippedStart() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Returns the alignment start (1-based, inclusive) adjusted for clipped bases.
- getUnclippedStart() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- getUnfilteredBaseQHistogram() - Method in class picard.analysis.AbstractWgsMetricsCollector
- getUnfilteredDepthHistogram() - Method in class picard.analysis.AbstractWgsMetricsCollector
- getUnfilteredReads() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Loads the reads into a
JavaRDDusing the intervals specified, and returns them without applying any filtering. - getUniqueFalseNegativeCount() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
- getUniqueNameSuffix() - Static method in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
Return a disambiguating name suffix to be used by the multiple collectors to decorate output names, which are provided by the user in the form of a base name that needs to be disambiguated for each individual collector.
- getUniqueNameSuffix() - Static method in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
-
Return a disambiguating name suffix to be used by the multiple collectors to decorate output names, which are provided by the user in the form of a base name that needs to be disambiguated for each individual collector.
- getUniquenessValue() - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- getUniqueNormalizationIds() - Method in class picard.arrays.illumina.IlluminaBPMFile
- getUniqueReadThreadingGraph(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Returns a read-threading graph in the assembly set that has a particular kmerSize.
- getUniqueTrueNegativeCount() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
- getUnknownCommandMessage(Set<Class<?>>, String) - Method in class org.broadinstitute.hellbender.Main
-
When a command does not match any known command, searches for a deprecation message, if any, or for similar commands.
- getUnmappedBoth() - Method in class picard.sam.util.SamComparison
- getUnmappedLeft() - Method in class picard.sam.util.SamComparison
- getUnmappedRight() - Method in class picard.sam.util.SamComparison
- getUnpairedReads() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPairedUnpairedSplitterSpark
- getUnsupportedBuilds() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- getUpdatedGenotypes(VariantContext, Genotype, Genotype, Genotype, ArrayList<Genotype>) - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.FamilyLikelihoods
-
Applies the trio genotype combination to the given trio.
- getUpdateMethod() - Method in class org.broadinstitute.hellbender.utils.mcmc.ParameterizedModel
- getUri() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetResponse.Block
- getUsage() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- getUserDisabledAnnotationNames() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKVariantAnnotationArgumentCollection
- getUserDisabledAnnotationNames() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationArgumentCollection
-
Returns the disabled annotation names.
- getUserDisabledReadFilterNames() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKReadFilterArgumentCollection
-
Returns the set of filters disabled by the user.
- getUserDisabledReadFilterNames() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterArgumentCollection
-
Returns the disabled read filter names.
- getUserEnabledAnnotationGroups() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKVariantAnnotationArgumentCollection
- getUserEnabledAnnotationGroups() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationArgumentCollection
-
Returns the enabled annotation.
- getUserEnabledAnnotationNames() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKVariantAnnotationArgumentCollection
- getUserEnabledAnnotationNames() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationArgumentCollection
-
Returns the enabled annotation.
- getUserEnabledReadFilterNames() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKReadFilterArgumentCollection
-
Returns the list with the read filters provided by the user, preserving the order.
- getUserEnabledReadFilterNames() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterArgumentCollection
-
Returns the enabled filter names.
- getUserSuppliedIntervals() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Expose a read-only version of the raw user-supplied intervals.
- getUtil(IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.IlluminaFileUtil
-
Given a file type, get the Parameterized File Util object associated with it
- getUtrs() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature
- getV() - Method in class org.broadinstitute.hellbender.utils.svd.SimpleSVD
- getV() - Method in interface org.broadinstitute.hellbender.utils.svd.SVD
-
Get the V matrix of a Singular Value Decomposition.
- getValidatedMetadata(AbstractRecordCollection<METADATA, ?>...) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
-
For all non-null inputs, validate that all metadata are identical and return the metadata.
- getValidatedSequenceDictionary(AbstractLocatableCollection<?, ?>...) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
-
For all non-null inputs, validate that all sequence dictionaries match (using
CopyNumberArgumentValidationUtils.isSameDictionary(htsjdk.samtools.SAMSequenceDictionary, htsjdk.samtools.SAMSequenceDictionary)) and return the sequence dictionary; otherwise, emit a warning. - getValidationAltCount() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- getValidationRefCount() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- getValidationStringency() - Method in class picard.fingerprint.FingerprintChecker
- getValue() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerAndInterval
- getValue() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval
- getValue() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.KmerAndCount
- getValue() - Method in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils.IndexPair
- getValue() - Method in class org.broadinstitute.hellbender.tools.sv.BafEvidence
- getValue() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.MutectStats
- getValue() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.OptionalField
- getValue() - Method in class org.broadinstitute.hellbender.utils.KV
- getValue() - Method in class org.broadinstitute.hellbender.utils.mcmc.Parameter
- getValue() - Method in interface org.broadinstitute.hellbender.utils.SVIntervalTree.Entry
- getValue(int) - Method in class org.broadinstitute.hellbender.utils.codecs.table.TableFeature
-
Gets the value associated with the ith column (first column is 0).
- getValue(AnnotationKey<T>) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationMap
- getValueCounts() - Method in class org.broadinstitute.hellbender.utils.CompressedDataList
- getValueFormat() - Method in class org.broadinstitute.hellbender.utils.report.GATKReportColumnFormat
- getValueForRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.BaseQuality
- getValueForRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.FragmentLength
- getValueForRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.MappingQuality
- getValueForRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.PerAlleleAnnotation
- getValueForRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosition
- getValueFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
- getValues() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
-
Get the data from this
XsvTableFeature. - getValues(Collection<FeatureInput<T>>) - Method in class org.broadinstitute.hellbender.engine.FeatureContext
-
Gets all Features from the sources represented by the provided FeatureInput arguments that overlap this FeatureContext's query interval.
- getValues(Collection<FeatureInput<T>>, int) - Method in class org.broadinstitute.hellbender.engine.FeatureContext
-
Gets all Features from the sources represented by the provided FeatureInput arguments that overlap this FeatureContext's query interval, AND that start at the specified start position.
- getValues(FeatureInput<T>) - Method in class org.broadinstitute.hellbender.engine.FeatureContext
-
Gets all Features from the source represented by the provided FeatureInput argument that overlap this FeatureContext's query interval.
- getValues(FeatureInput<T>, int) - Method in class org.broadinstitute.hellbender.engine.FeatureContext
-
Gets all Features from the source represented by the provided FeatureInput argument that overlap this FeatureContext's query interval AND that start at the specified start position.
- getValues(FeatureInput<T>, int, int) - Method in class org.broadinstitute.hellbender.engine.FeatureContext
-
Gets all Features from the source represented by the provided FeatureInput argument that overlap this FeatureContext's query interval as expanded by the specified number of leading/trailing bases.
- getValues(FeatureInput<T>, Locatable) - Method in class org.broadinstitute.hellbender.engine.FeatureContext
-
Gets all Features from the source represented by the provided FeatureInput argument that overlap the given interval.
- getValuesOfInterest(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.flow.FlowBasedTPAttributeSymetricReadFilter
- getValuesOfInterest(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.flow.FlowBasedTPAttributeValidReadFilter
- getValuesOfInterest(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.flow.HmerQualitySymetricReadFilter
- getValuesTo(int) - Method in class org.broadinstitute.hellbender.utils.codecs.table.TableFeature
-
Gets all the values from the first column (0) to the last one specified (exclusive).
- getValuesWithoutLocationColumns() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
-
Get the data from this
XsvTableFeaturewithout the columns that contain location information. - getVar(int, int) - Static method in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- getVarFamilyCalledCount() - Method in class org.broadinstitute.hellbender.utils.samples.MendelianViolation
- getVarianceVector() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- getVariant() - Method in class org.broadinstitute.hellbender.engine.spark.VariantWalkerContext
- getVariantBuilder(SVCallRecord) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
-
Create a builder for a variant from an
SVCallRecordfor VCF interoperability - getVariantCallingSubsetApplied() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Returns the location used for subsetting.
- getVariantChromosome() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- getVariantClassification() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getVariantContexts() - Method in class org.broadinstitute.hellbender.utils.haplotype.EventMap
-
Get the variant contexts in order of start position in this event map
- getVariantContextsFromActiveHaplotypes(int, List<Haplotype>, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
-
Returns the list of events discovered in assembled haplotypes that are active at this location.
- getVariantContextsFromGivenAlleles(int, List<VariantContext>, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
-
Returns the list of given alleles active at this location.
- getVariantEvalArgs() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- getVariantEvaluators() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.EvaluationContext
-
Returns a sorted set of VariantEvaluators
- getVariantRegion() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer.Result
-
Returns the trimmed variant containing region
- getVariantRegion(SimpleInterval, SimpleInterval) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer.Result
-
Returns the trimmed variant containing a specific region.
- getVariants(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.VariantWalkerSpark
-
Loads variants and the corresponding reads, reference and features into a
JavaRDDfor the intervals specified. - getVariantSequenceDictionaries() - Method in class org.broadinstitute.hellbender.engine.FeatureManager
-
Returns the list of sequence dictionaries retrieved from the VCF headers of variant Feature inputs.
- getVariantsForFeature(FeatureInput<VariantContext>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.VariantEvalContext
- getVariantShardsFromInterval(Locatable) - Static method in class org.broadinstitute.hellbender.engine.VariantShard
-
getVariantShardsFromInterval calculates *all* shards overlapping location.
- getVariantStart() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- getVariantStop() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- getVariantType() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- getVariantType() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceSummaryRecord
- getVariantType() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.InfoConcordanceRecord
- getVariantType(VariantContext) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.VariantType
- getVariantTypeFlat() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- getVariantTypeFromOrdinal(int) - Static method in enum class picard.util.VariantType
-
Gets the enum for a given ordinal
- getVariationEvents(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Returns a sorted set of variant events that best explain the haplotypes found by the assembly across kmerSizes.
- getVc() - Method in class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger.VCWithNewAlleles
- getVCFAnnotationDescriptions() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
-
Returns the set of descriptions to be added to the VCFHeader line (for all annotations in this engine).
- getVCFAnnotationDescriptions(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
-
Returns the set of descriptions to be added to the VCFHeader line (for all annotations in this engine).
- getVCFForSample(String) - Method in class org.broadinstitute.hellbender.tools.genomicsdb.SampleNameMap
- getVCFForSampleAsPath(String) - Method in class org.broadinstitute.hellbender.tools.genomicsdb.SampleNameMap
- getVCFHeaderLines() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
-
Get the VCF header lines to include when emitting reference confidence values via
ReferenceConfidenceModel.calculateRefConfidence(org.broadinstitute.hellbender.utils.haplotype.Haplotype, java.util.Collection<org.broadinstitute.hellbender.utils.haplotype.Haplotype>, org.broadinstitute.hellbender.utils.SimpleInterval, org.broadinstitute.hellbender.engine.AssemblyRegion, org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods<org.broadinstitute.hellbender.utils.read.GATKRead, org.broadinstitute.hellbender.utils.haplotype.Haplotype>, org.broadinstitute.hellbender.tools.walkers.genotyper.PloidyModel, java.util.List<htsjdk.variant.variantcontext.VariantContext>). - getVCFIndexForSample(String) - Method in class org.broadinstitute.hellbender.tools.genomicsdb.SampleNameMap
- getVCFIndexForSampleAsPath(String) - Method in class org.broadinstitute.hellbender.tools.genomicsdb.SampleNameMap
- getVcfKey() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.BaseQuality
- getVcfKey() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.FragmentLength
- getVcfKey() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.MappingQuality
- getVcfKey() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.PerAlleleAnnotation
- getVcfKey() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosition
- getVcfOutputEnd() - Method in class org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFBlockCombiner
- getVcfOutputEnd() - Method in class org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFWriter
-
Return the position of the end of the variant contexts already output by the writer
- getVerbosity() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- getVersion() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- getVersion() - Method in class org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals
- getVersion() - Method in interface org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals
-
Returns the PoN version.
- getVersion() - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
- getVersion() - Method in class org.broadinstitute.hellbender.tools.sv.SVFeaturesHeader
- getVersion() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- getVersion() - Method in class org.broadinstitute.hellbender.utils.report.GATKReport
- getVersion() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getVersion() - Method in class picard.arrays.illumina.InfiniumTransformation
- getVersion() - Method in class picard.cmdline.CommandLineProgram
- getVersion() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
- getVersion(Class<?>) - Static method in class org.broadinstitute.hellbender.utils.runtime.RuntimeUtils
- getVertices() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
-
Get the list of vertices in this path in order defined by the edges of the path
- getViolationsCount() - Method in class org.broadinstitute.hellbender.utils.samples.MendelianViolation
- getWeight() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
- getWidth() - Method in class org.broadinstitute.hellbender.utils.report.GATKReportColumnFormat
- getWindow() - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
-
Get the full expanded window of bases spanned by this context, including any extra bases of requested context around the current interval.
- getWindow() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.ClusteringParameters
- getWordCount() - Method in class picard.util.AbstractInputParser
- getWordStarts(String) - Static method in class org.broadinstitute.hellbender.utils.text.TextFormattingUtils
-
Returns the word starting positions within line, excluding the first position 0.
- getWrapped() - Method in class org.broadinstitute.hellbender.utils.UniqueIDWrapper
- getWriter(Path) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.InfoConcordanceRecord
-
Get a table writer
- getWriter(GATKPath) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceSummaryRecord
- getX() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- getX() - Method in class picard.illumina.parser.ClusterData
- getX() - Method in interface picard.sam.util.PhysicalLocation
- getX() - Method in class picard.sam.util.PhysicalLocationInt
- getXCoordinate() - Method in class picard.illumina.parser.CbclData
- getY() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- getY() - Method in class picard.illumina.parser.ClusterData
- getY() - Method in interface picard.sam.util.PhysicalLocation
- getY() - Method in class picard.sam.util.PhysicalLocationInt
- getYCoordinate() - Method in class picard.illumina.parser.CbclData
- getZ() - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU.Result
- getZeroBasedTileNumber() - Method in class picard.illumina.parser.TileIndex.TileIndexRecord
- getZeroInitializedEnumMap(Class<T>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
- getZishScore(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics
- getZishScore(String, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- gfaFile - Variable in class org.broadinstitute.hellbender.tools.LocalAssembler
- GG - Enum constant in enum class picard.fingerprint.DiploidGenotype
- GIBBS - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterizedModel.UpdateMethod
- GibbsBuilder(S2, T2) - Constructor for class org.broadinstitute.hellbender.utils.mcmc.ParameterizedModel.GibbsBuilder
-
Constructor for
ParameterizedModel.GibbsBuilder. - GibbsSampler<V extends Enum<V> & ParameterEnum,
S extends ParameterizedState<V>, T extends DataCollection> - Class in org.broadinstitute.hellbender.utils.mcmc -
Implements Gibbs sampling of a multivariate probability density function.
- GibbsSampler(int, ParameterizedModel<V, S, T>) - Constructor for class org.broadinstitute.hellbender.utils.mcmc.GibbsSampler
-
Constructs a GibbsSampler given the total number of samples (including burn-in) and a
ParameterizedModel. - givenDragstrParams(DragstrParams, int, int, double, double) - Static method in class org.broadinstitute.hellbender.utils.genotyper.GenotypePriorCalculator
-
Composes a calculator based on Dragstr Parameters.
- givenHetToHomRatio(double, double, double, double) - Static method in class org.broadinstitute.hellbender.utils.genotyper.GenotypePriorCalculator
-
Calculate priors based on fix heterozygosities (per event type) and het to hom-var prior ratio.
- GLOBAL_PSI_SCALE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineContigPloidyModelArgumentCollection
- globalPriorIndel - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
-
Prior indel pseudocounts for Dirichlet distribution of allele frequencies.
- globalPriorSnp - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
-
Prior SNP pseudocounts for Dirichlet distribution of allele frequencies.
- globalQScorePrior - Variable in class org.broadinstitute.hellbender.tools.ApplyBQSRUniqueArgumentCollection
-
If specified, the value of this argument will be used as a flat prior for all mismatching quality scores instead of the reported quality score (assigned by the sequencer).
- GLUTAMIC_ACID - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- GLUTAMINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- GLYCINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- GMMFromTables(GATKReportTable, GATKReportTable, GATKReportTable, int, int) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator
-
Rebuild a Gaussian Mixture Model from gaussian means and co-variates stored in a GATKReportTables
- GnarlyGenotyper - Class in org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper
-
Perform "quick and dirty" joint genotyping on one or more samples pre-called with HaplotypeCaller
- GnarlyGenotyper() - Constructor for class org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyper
- GnarlyGenotyperEngine - Class in org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper
-
Guts of the GnarlyGenotyper
- GnarlyGenotyperEngine(boolean, int, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyperEngine
- gnomad - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations.AlleleFrequencyDataSource
- gold_standard_matching_rate - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- goldStandard - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
-
Some analyses want to count overlap not with dbSNP (which is in general very open) but actually want to itemize their overlap specifically with a set of gold standard sites such as HapMap, OMNI, or the gold standard indels.
- GOOD_CIGAR - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- GoodAndBadMappings(List<AlignmentInterval>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig.GoodAndBadMappings
- GoodAndBadMappings(List<AlignmentInterval>, List<AlignmentInterval>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig.GoodAndBadMappings
- GoodAndBadMappings(List<AlignmentInterval>, List<AlignmentInterval>, AlignmentInterval) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig.GoodAndBadMappings
- GoodCigarReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.GoodCigarReadFilter
- goodNonCanonicalMappingSATag - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera
- gop(int, int) - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParams
-
Returns the GOP for a specific period and repeat length in Phred scale.
- GOP_TABLE_NAME - Static variable in class org.broadinstitute.hellbender.utils.dragstr.DragstrParamUtils
- GOP_VALUES_ARGUMENT_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- gp - Variable in class org.broadinstitute.hellbender.utils.dragstr.DragstrParamsBuilder
- gp(int, int) - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParamsBuilder
- GP_VALUES_ARGUMENT_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- GQ_BAND_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- GQ_BAND_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- GQ_MEAN_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- GQ_STDEV_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- grabCount() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.KmerAndCount
- granularity - Variable in class org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndex
- graph - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotypeFinder
- Graph() - Constructor for class picard.util.GraphUtils.Graph
- GRAPH_OUTPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- GraphBasedKBestHaplotypeFinder<V extends BaseVertex,
E extends BaseEdge> - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs -
Efficient algorithm to obtain the list of best haplotypes given the
instance. - GraphBasedKBestHaplotypeFinder(BaseGraph<V, E>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.GraphBasedKBestHaplotypeFinder
-
Constructor for the default case of all sources and sinks
- GraphBasedKBestHaplotypeFinder(BaseGraph<V, E>, Set<V>, Set<V>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.GraphBasedKBestHaplotypeFinder
-
Constructs a new best haplotypes finder.
- GraphBasedKBestHaplotypeFinder(BaseGraph<V, E>, V, V) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.GraphBasedKBestHaplotypeFinder
-
Constructor for the special case of a single source and sink
- graphEquals(BaseGraph<T, E>, BaseGraph<T, E>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Semi-lenient comparison of two graphs, truing true if g1 and g2 have similar structure By similar this means that both graphs have the same number of vertices, where each vertex can find a vertex in the other graph that's seqEqual to it.
- graphOutput - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
This argument is meant for debugging and is not immediately useful for normal analysis use.
- GraphUtils - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
-
Utility functions used in the graphs package
- GraphUtils - Class in picard.util
-
Created by farjoun on 11/2/16.
- GraphUtils() - Constructor for class picard.util.GraphUtils
- GraphUtils.Graph<Node extends Comparable<Node>> - Class in picard.util
- GREATER - Enum constant in enum class org.broadinstitute.hellbender.engine.filters.ReadTagValueFilter.Operator
- GREATER_OR_EQUAL - Enum constant in enum class org.broadinstitute.hellbender.engine.filters.ReadTagValueFilter.Operator
- GREEN - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
-
The green intensity value for the control.
- GroundTruthReadsBuilder - Class in org.broadinstitute.hellbender.tools.walkers.groundtruth
-
An internal tool to produce a flexible and robust ground truth set for base calling training.
- GroundTruthReadsBuilder() - Constructor for class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- GroupAlignmentSummaryMetricsPerUnitMetricCollector(String, String, String) - Constructor for class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
- groupEvidence(Function<EVIDENCE, U>, Function<List<EVIDENCE>, NEW_EVIDENCE_TYPE>) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Group evidence into lists of evidence -- for example group by read name to force read pairs to support a single haplotype.
- groupIntervalsByContig(List<SimpleInterval>) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Accepts a sorted List of intervals, and returns a List of Lists of intervals grouped by contig, one List per contig.
- GSALIB - Enum constant in enum class org.broadinstitute.hellbender.utils.R.RScriptLibrary
- GT - Enum constant in enum class picard.fingerprint.DiploidGenotype
- GT_FILTERED - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- GT_FILTERED - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- GT_FILTERED_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- GTA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- GTC_CALL_RATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The call rate as determined by Autocall/IAAP (and stored in the GTC File)
- GTC_CALL_RATE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- GTC_CALL_RATE_DETAIL - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- GtcToVcf - Class in picard.arrays
-
Class to convert an Illumina GTC file into a VCF file.
- GtcToVcf() - Constructor for class picard.arrays.GtcToVcf
- GTF_FILE_EXTENSION - Static variable in class org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec
- GTF_FILE_TYPE_STRING - Static variable in class org.broadinstitute.hellbender.utils.codecs.gtf.EnsemblGtfCodec
- GTF_FILE_TYPE_STRING - Static variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfCodec
- GTFIntervalTreesContainer(SVIntervalTree<GencodeGtfTranscriptFeature>, SVIntervalTree<String>, SVIntervalTree<String>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine.GTFIntervalTreesContainer
- gtfSourceFileType - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
-
The source file type from which the data in this
GencodeGtfFeatureBaseDataoriginated. - GtoA - Enum constant in enum class picard.analysis.artifacts.Transition
- GtoC - Enum constant in enum class picard.analysis.artifacts.Transition
- GtoG - Enum constant in enum class picard.analysis.artifacts.Transition
- GtoT - Enum constant in enum class picard.analysis.artifacts.Transition
- GTZ - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- GUANINE - Static variable in enum class org.broadinstitute.hellbender.utils.Nucleotide
- gunzip(File, File) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Un-gzips the input file to the output file.
- gunzipToTempIfNeeded(File) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Un-gzips the input file to a output file but only if the file's name ends with '.gz'.
- GVCF - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceMode
-
Reference model emitted with condensed non-variant blocks, i.e.
- GVCF_BLOCK - Static variable in class org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter
- GVCF_FILE_EXTENSION - Static variable in class org.broadinstitute.hellbender.tools.IndexFeatureFile
- GVCF_INPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
- GVCF_VALIDATE - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants
- GVCFBlock - Class in org.broadinstitute.hellbender.utils.variant.writers
- GVCFBlock(VariantContext, int, int) - Constructor for class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- GVCFBlockCombiner - Class in org.broadinstitute.hellbender.utils.variant.writers
-
Combines variants into GVCF blocks.
- GVCFBlockCombiner(List<? extends Number>, boolean) - Constructor for class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlockCombiner
- GVCFBlockCombiningIterator - Class in org.broadinstitute.hellbender.utils.variant.writers
-
Turns an iterator of
VariantContextinto one which combines GVCF blocks. - GVCFBlockCombiningIterator(Iterator<VariantContext>, List<Number>, int) - Constructor for class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlockCombiningIterator
- GVCFGQBands - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper
- GVCFGQBands - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
-
When HC is run in reference confidence mode with banding compression enabled (-ERC GVCF), homozygous-reference sites are compressed into bands of similar genotype quality (GQ) that are emitted as a single VCF record.
- GVCFGQBands - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
When Mutect2 is run in reference confidence mode with banding compression enabled (-ERC GVCF), homozygous-reference sites are compressed into bands of similar tumor LOD (TLOD) that are emitted as a single VCF record.
- GVCFGQBands - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- GvcfMetricAccumulator - Class in picard.vcf
-
An accumulator for collecting metrics about a single-sample GVCF.
- GvcfMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets) - Constructor for class picard.vcf.GvcfMetricAccumulator
- GVCFWriter - Class in org.broadinstitute.hellbender.utils.variant.writers
-
Genome-wide VCF writer Merges blocks based on GQ
- GVCFWriter(VariantContextWriter, List<? extends Number>) - Constructor for class org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter
- GVCFWriter(VariantContextWriter, List<? extends Number>, boolean) - Constructor for class org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter
-
Create a new GVCF writer Should be a non-empty list of boundaries.
H
- H - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier.AlnModType.ModTypeString
- H - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- hadoopPathExists(JavaSparkContext, URI) - Static method in class org.broadinstitute.hellbender.utils.spark.SparkUtils
-
Determine if the
targetPathexists. - HALF_OF_DEFAULT_PCR_SNV_ERROR_QUAL - Static variable in class org.broadinstitute.hellbender.utils.fragments.FragmentUtils
- HAMMING - Enum constant in enum class picard.illumina.DistanceMetric
- hammingDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
- handleAdditionalRecords(SAMRecord, Map<SAMReadGroupRecord, List<FastqWriter>>, SAMRecord, SAMRecord) - Method in class picard.sam.SamToFastq
- handleAdditionalRecords(SAMRecord, Map<SAMReadGroupRecord, List<FastqWriter>>, SAMRecord, SAMRecord) - Method in class picard.sam.SamToFastqWithTags
- handleChunk(List<ReadEndsForMarkDuplicates>) - Method in class picard.sam.markduplicates.MarkDuplicates
- handleNonUserException(Exception) - Method in class org.broadinstitute.hellbender.Main
-
Handle any exception that does not come from the user.
- handleResult(Object) - Method in class org.broadinstitute.hellbender.Main
-
Handle the result returned for a tool.
- handleStorageException(StorageException) - Method in class org.broadinstitute.hellbender.Main
-
Handle any exception that does not come from the user.
- handleUserException(Exception) - Method in class org.broadinstitute.hellbender.Main
-
Handle an exception that was likely caused by user error.
- haplotype() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotype
- Haplotype - Class in org.broadinstitute.hellbender.utils.haplotype
- Haplotype(byte[]) - Constructor for class org.broadinstitute.hellbender.utils.haplotype.Haplotype
-
Create a new non-ref haplotype
- Haplotype(byte[], boolean) - Constructor for class org.broadinstitute.hellbender.utils.haplotype.Haplotype
-
Main constructor
- Haplotype(byte[], boolean, int, Cigar) - Constructor for class org.broadinstitute.hellbender.utils.haplotype.Haplotype
-
Create a new haplotype with bases Requires bases.length == cigar.getReadLength()
- Haplotype(byte[], Locatable) - Constructor for class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- HAPLOTYPE_ALIGNMENT_TIEBREAKING_PRIORITY - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- HAPLOTYPE_CALLER_PHASING_GT_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- HAPLOTYPE_CALLER_PHASING_ID_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- HAPLOTYPE_COMPLEXITY_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- HAPLOTYPE_DEBUG_HISTOGRAM_OUTPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- HAPLOTYPE_DOMINANCE_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- HAPLOTYPE_EQUIVALENCE_COUNTS_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- HAPLOTYPE_MAP - Variable in class picard.fingerprint.CalculateFingerprintMetrics
- HAPLOTYPE_MAP - Variable in class picard.fingerprint.CheckFingerprint
- HAPLOTYPE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
- HAPLOTYPE_MAP - Variable in class picard.fingerprint.ExtractFingerprint
- HAPLOTYPE_MAP - Variable in class picard.fingerprint.IdentifyContaminant
- HAPLOTYPE_SCORE_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- HAPLOTYPE_TAG - Static variable in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
- HaplotypeBAMDestination - Class in org.broadinstitute.hellbender.utils.haplotype
-
Utility class that allows easy creation of destinations for the HaplotypeBAMWriters
- HaplotypeBAMDestination(SAMFileHeader, Optional<String>) - Constructor for class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMDestination
-
Create a new HaplotypeBAMDestination
- haplotypeBAMWriter - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- HaplotypeBAMWriter - Class in org.broadinstitute.hellbender.utils.haplotype
-
A BAMWriter that aligns reads to haplotypes and emits their best alignments to a destination.
- HaplotypeBAMWriter(HaplotypeBAMWriter.WriterType, Path, boolean, boolean, SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter
-
Create a new HaplotypeBAMWriter of type "type" for writing SAMRecords to an output file
- HaplotypeBAMWriter(HaplotypeBAMWriter.WriterType, HaplotypeBAMDestination) - Constructor for class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter
-
Create a new HaplotypeBAMWriter of type "type" for writing SAMRecords to and output destination
- HaplotypeBAMWriter.WriterType - Enum Class in org.broadinstitute.hellbender.utils.haplotype
-
Possible modes for writing haplotypes to BAMs
- HaplotypeBasedVariantRecaller - Class in org.broadinstitute.hellbender.tools.walkers.variantrecalling
-
Calculate likelihood matrix for each Allele in VCF against a set of Reads limited by a set of Haplotypes
- HaplotypeBasedVariantRecaller() - Constructor for class org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeBasedVariantRecaller
- HaplotypeBasedVariantRecallerArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.variantrecalling
-
Set of arguments for the
HaplotypeBasedVariantRecaller - HaplotypeBasedVariantRecallerArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeBasedVariantRecallerArgumentCollection
- HaplotypeBlock - Class in picard.fingerprint
-
Represents information about a group of SNPs that form a haplotype in perfect LD with one another.
- HaplotypeBlock(double) - Constructor for class picard.fingerprint.HaplotypeBlock
-
Constructs a haplotype block with the provided minor allele frequency.
- HaplotypeCaller - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Call germline SNPs and indels via local re-assembly of haplotypes
- HaplotypeCaller() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
- HaplotypeCallerArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Set of arguments for the
HaplotypeCallerEngine - HaplotypeCallerArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- HaplotypeCallerArgumentCollection.FlowMode - Enum Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
the different flow modes, in terms of their parameters and their values NOTE: a parameter value ending with /o is optional - meaning it will not fail the process if it is not existent on the target parameters collection.
- HaplotypeCallerEngine - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
The core engine for the HaplotypeCaller that does all of the actual work of the tool.
- HaplotypeCallerEngine(HaplotypeCallerArgumentCollection, AssemblyRegionArgumentCollection, boolean, boolean, SAMFileHeader, CachingIndexedFastaSequenceFile, VariantAnnotatorEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
-
Create and initialize a new HaplotypeCallerEngine given a collection of HaplotypeCaller arguments, a reads header, and a reference file
- HaplotypeCallerGenotypingDebugger - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
A short helper class that manages a singleton debug stream for HaplotypeCaller genotyping information that is useful for debugging.
- HaplotypeCallerGenotypingDebugger() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingDebugger
- HaplotypeCallerGenotypingEngine - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
HaplotypeCaller's genotyping strategy implementation.
- HaplotypeCallerGenotypingEngine(HaplotypeCallerArgumentCollection, SampleList, boolean, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine
- HaplotypeCallerReadThreadingAssemblerArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
- HaplotypeCallerReadThreadingAssemblerArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerReadThreadingAssemblerArgumentCollection
- HaplotypeCallerSpark - Class in org.broadinstitute.hellbender.tools
-
******************************************************************************** * This tool DOES NOT match the output of HaplotypeCaller.
- HaplotypeCallerSpark() - Constructor for class org.broadinstitute.hellbender.tools.HaplotypeCallerSpark
- HaplotypeComparator() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampUtils.HaplotypeComparator
- HaplotypeFilteringAnnotation - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Set of annotations meant to be reflective of HaplotypeFiltering operations that were applied in FlowBased HaplotypeCaller.
- HaplotypeFilteringAnnotation() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.HaplotypeFilteringAnnotation
- haplotypeHistogramOutput - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
This argument is meant for debugging and is not immediately useful for normal analysis use.
- HaplotypeMap - Class in picard.fingerprint
-
A collection of metadata about Haplotype Blocks including multiple in memory "indices" of the data to make it easy to query the correct HaplotypeBlock or Snp by snp names, positions etc.
- HaplotypeMap(SAMFileHeader) - Constructor for class picard.fingerprint.HaplotypeMap
-
Constructs an empty HaplotypeMap using the provided SAMFileHeader's sequence dictionary.
- HaplotypeMap(File) - Constructor for class picard.fingerprint.HaplotypeMap
- HaplotypeMap(Collection<HaplotypeBlock>) - Constructor for class picard.fingerprint.HaplotypeMap
-
since this constructor doesn't initialize the HaplotypeMap "properly", it should be used carefully!
- haplotypeOutputPaddingSize - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- HaplotypeProbabilities - Class in picard.fingerprint
-
Abstract class for storing and calculating various likelihoods and probabilities for haplotype alleles given evidence.
- HaplotypeProbabilities(HaplotypeBlock) - Constructor for class picard.fingerprint.HaplotypeProbabilities
- HaplotypeProbabilities.Genotype - Enum Class in picard.fingerprint
-
Log10(P(evidence| haplotype)) for the 3 different possible haplotypes {aa, ab, bb}
- HaplotypeProbabilitiesFromContaminatorSequence - Class in picard.fingerprint
-
Represents the probability of the underlying haplotype of the contaminating sample given the data.
- HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeBlock, double) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
- HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeProbabilitiesFromContaminatorSequence) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
- HaplotypeProbabilitiesFromGenotype - Class in picard.fingerprint
-
Represents a set of HaplotypeProbabilities that were derived from a single SNP genotype at a point in time.
- HaplotypeProbabilitiesFromGenotype(HaplotypeProbabilitiesFromGenotype) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
- HaplotypeProbabilitiesFromGenotype(Snp, HaplotypeBlock, double, double, double) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
- HaplotypeProbabilitiesFromGenotypeLikelihoods - Class in picard.fingerprint
-
Represents the likelihood of the HaplotypeBlock given the GenotypeLikelihoods (GL field from a VCF, which is actually a log10-likelihood) for each of the SNPs in that block.
- HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeBlock) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
- HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeProbabilitiesFromGenotypeLikelihoods) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
- HaplotypeProbabilitiesFromSequence - Class in picard.fingerprint
-
Represents the probability of the underlying haplotype given the data.
- HaplotypeProbabilitiesFromSequence(HaplotypeBlock) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- HaplotypeProbabilitiesFromSequence(HaplotypeProbabilitiesFromSequence) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- HaplotypeProbabilityOfNormalGivenTumor - Class in picard.fingerprint
-
A wrapper class for any HaplotypeProbabilities instance that will assume that the given evidence is that of a tumor sample and provide an hp for the normal sample that tumor came from.
- HaplotypeProbabilityOfNormalGivenTumor(HaplotypeProbabilities, double) - Constructor for class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- HaplotypeProbabilityOfNormalGivenTumor(HaplotypeProbabilityOfNormalGivenTumor) - Constructor for class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- haplotypeReadMatching(FlowBasedHaplotype, FlowBasedRead) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
-
Aligns single read to a single haplotype.
- HaplotypeRegionWalker - Class in org.broadinstitute.hellbender.tools.walkers.variantrecalling
-
a service class for HaplotypeBasedVariableRecaller that reads a SAM/BAM file, interprets the reads as haplotypes and called a provided consumer with the 'best' haplotypes found for a given query location.
- HAPLOTYPES - Variable in class picard.fingerprint.FingerprintMetrics
-
Number of haplotypes examined
- HAPLOTYPES_BEFORE_FILTERING_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- HAPLOTYPES_CONFIDENTLY_CHECKED - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The subset of genotyped haplotypes for which there was sufficient sequence data to confidently genotype the haplotype.
- HAPLOTYPES_CONFIDENTLY_MATCHING - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The subset of confidently checked haplotypes that match the expected genotypes.
- HAPLOTYPES_FILTERED_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- HAPLOTYPES_WITH_EVIDENCE - Variable in class picard.fingerprint.FingerprintMetrics
-
Number of haplotypes that had evidence in the source file
- HAPLOTYPES_WITH_GENOTYPES - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The number of haplotypes that had expected genotypes to compare to.
- haplotypesBamFile - Variable in class org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeBasedVariantRecallerArgumentCollection
-
This argument specifies a BAM file with Haplotypes to limit reads on
- hapStartIndex - Variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- HARD_CLIP_OVERLAPPING_READS - Variable in class picard.sam.MergeBamAlignment
- HARD_CLIPPED_TAGS - Static variable in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- HardAlleleFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
-
Base class for Hard filters that are applied at the allele level
- HardAlleleFilter() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.HardAlleleFilter
- HARDCLIP_BASES - Enum constant in enum class org.broadinstitute.hellbender.utils.clipping.ClippingRepresentation
-
WARNING: THIS OPTION IS STILL UNDER DEVELOPMENT AND IS NOT SUPPORTED.
- hardClipAdaptorSequence(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
- hardClipAttributes(int, int, int) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Clip key attributes that may change after a hard clipping operation
- hardClipAttributes(int, int, int) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
-
Clip attributes that change after a hard clipping operation The method clips string or array attributes that are part of a pre-set list originating from FlowBasedRead (a white-list), that are at the same length as the sequence.
- hardClipBothEndsByReferenceCoordinates(GATKRead, int, int) - Static method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
- hardClipByReferenceCoordinates(int, int) - Method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
- hardClipByReferenceCoordinatesLeftTail(GATKRead, int) - Static method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
- hardClipByReferenceCoordinatesRightTail(GATKRead, int) - Static method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
- hardClipLowQualEnds(GATKRead, byte) - Static method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
- hardClipSoftClippedBases(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
- hardClipSoftClippedBases(GATKRead, int) - Static method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
- hardClipToRegion(GATKRead, int, int) - Static method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
-
Hard clip the read to the variable region (from refStart to refStop)
- hardClipUncertainBases(GATKRead, SAMFileHeader, FlowBasedArgumentCollection) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
-
Hard clips uncertain flows (currently four first flows read that often generate noisy base calls
- hardClipUncertainBases(GATKRead, String, FlowBasedArgumentCollection) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
-
Hard clips uncertain flows (currently four first flows read that often generate noisy base calls
- HardFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- HardFilter() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.HardFilter
- HardThresholdingOutputStream - Class in org.broadinstitute.hellbender.utils.io
-
An output stream which stops at the threshold instead of potentially triggering early.
- HardThresholdingOutputStream(int) - Constructor for class org.broadinstitute.hellbender.utils.io.HardThresholdingOutputStream
- HardwareFeatureException(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.HardwareFeatureException
- HardwareFeatureException(String, Exception) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.HardwareFeatureException
- harmonizeAltAlleles(List<Allele>, List<Genotype>) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
- HAS_MATCHING_BASES_AND_QUALS - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- HAS_READ_GROUP - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- hasAccession(String) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
- hasAmbiguousSequence() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
-
Checks whether the vertex sequence is ambiguous or not.
- hasAnnotation(String) - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval
- hasApplicableEnd() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType
- hasApplicableEnd() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType
- hasApplicableEnd() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- hasApplicableLength() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType
- hasApplicableLength() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType
- hasApplicableLength() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- hasAttribute(Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData
- hasAttribute(String) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Check whether this read has a particular attribute
- hasAttribute(String) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- hasBackingDataSource() - Method in class org.broadinstitute.hellbender.engine.FeatureContext
-
Determines whether this FeatureContext has a backing source of Features.
- hasBackingDataSource() - Method in class org.broadinstitute.hellbender.engine.ReadsContext
-
Does this context have a backing source of reads data?
- hasBackingDataSource() - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
-
Determines whether this ReferenceContext has a backing reference data source.
- hasBAQTag(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.baq.BAQ
-
Returns true if the read has a BAQ tag, or false otherwise
- hasBaseIndelQualities(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
- hasBaseQualities() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Indicates whether there is any base-qualities.
- hasBases() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Indicates whether there are any bases.
- hasBeenOverhangClipped() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.SplitRead
- hasBothParents() - Method in class picard.pedigree.PedFile.PedTrio
-
True if this record has paternal and maternal ids, otherwise false.
- hasCbcls(File, int) - Static method in class picard.illumina.parser.IlluminaFileUtil
- hasChimericAlignments() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
-
After fine tuning, a contig may have no, or only one, good alignment left.
- hasColumn(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- hasColumn(String) - Method in class picard.util.TabbedTextFileWithHeaderParser
- hasCoverage() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Returns true if any base in the range has coverage of > 0
- hasCRAMFileContents(File) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Validate that a file has CRAM contents by checking that it has a valid CRAM file header (no matter what the extension).
- hasCRAMFileContents(Path) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Validate that a file has CRAM contents by checking that it has a valid CRAM file header (no matter what the extension).
- hasCycles() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Checks for the presence of directed cycles in the graph.
- hasDistalTargets(ReadMetadata, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.DiscordantReadPairEvidence
- hasDistalTargets(ReadMetadata, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
-
Returns true if this piece of evidence specifies a possible distal target for the breakpoint.
- hasDistalTargets(ReadMetadata, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SplitRead
- hasDuplicationAnnotation() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications
-
To be overridden as appropriate.
- hasDuplicationAnnotation() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- hasDuplicationAnnotation() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- hasEquallyGoodAlnConfigurations() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- hasError() - Method in class picard.util.ThreadPoolExecutorWithExceptions
- hasEval() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval
- hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns true if evidence has been added, false if the probabilities are just the priors.
- hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- hasEvidence() - Method in class picard.fingerprint.CappedHaplotypeProbabilities
- hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- hasFeatures() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Are sources of Features available?
- hasField(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- hasField(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
- hasField(String) - Method in interface org.broadinstitute.hellbender.tools.funcotator.Funcotation
- hasFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.Downsampler
-
Are there items that have survived the downsampling process waiting to be retrieved?
- hasFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.FractionalDownsampler
- hasFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.LevelingDownsampler
- hasFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.MutectDownsampler
- hasFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.PassThroughDownsampler
- hasFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.PositionalDownsampler
- hasFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.ReservoirDownsampler
- hasFinalizedItems() - Method in interface org.broadinstitute.hellbender.utils.iterators.PushPullTransformer
-
Are there items that have survived the transformation process waiting to be retrieved?
- hasFinalizedItems() - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlockCombiner
- hasFixedQual() - Method in class org.broadinstitute.hellbender.utils.recalibration.QualQuantizer.QualInterval
- HasGenomeLocation - Interface in org.broadinstitute.hellbender.utils
-
Indicates that this object has a genomic location and provides a systematic interface to get it.
- hasGoodMQ() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
-
Idea is to keep mapped contig that either has at least two alignments over
AlignedContig.ALIGNMENT_MQ_THRESHOLD, or in the case of a single alignment, it must be MQ >AlignedContig.ALIGNMENT_MQ_THRESHOLD. - hashCode() - Method in class org.broadinstitute.hellbender.engine.FeatureInput
-
FeatureInputs will be hashed by the engine, so make an effort to produce a reasonable hash code
- hashCode() - Method in class org.broadinstitute.hellbender.engine.GATKPath
- hashCode() - Method in class org.broadinstitute.hellbender.engine.ReadContextData
- hashCode() - Method in class org.broadinstitute.hellbender.engine.ReadlessAssemblyRegion
- hashCode() - Method in class org.broadinstitute.hellbender.engine.ReferenceShard
- hashCode() - Method in class org.broadinstitute.hellbender.engine.ShardBoundary
- hashCode() - Method in class org.broadinstitute.hellbender.engine.VariantShard
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractRecordCollection
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AnnotatedIntervalCollection
-
Columns, encoder, and decoder are not used.
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleLocatableMetadata
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleLocatableMetadata
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleMetadata
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AnnotatedInterval
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationKey
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationMap
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledCopyRatioSegment
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledLegacySegment
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyNumberPosteriorDistribution
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatio
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatioSegment
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CoveragePerContig
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntervalCopyNumberGenotypingData
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LegacySegment
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LinearCopyRatio
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.gcnv.IntegerCopyNumberState
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval
- hashCode() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection
- hashCode() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocus
- hashCode() - Method in class org.broadinstitute.hellbender.tools.FlagStat.FlagStatus
- hashCode() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- hashCode() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
- hashCode() - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
- hashCode() - Method in class org.broadinstitute.hellbender.tools.funcotator.metadata.TumorNormalPair
- hashCode() - Method in class org.broadinstitute.hellbender.tools.funcotator.metadata.VcfFuncotationMetadata
- hashCode() - Method in class org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo
- hashCode() - Method in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedAllele
- hashCode() - Method in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedReferenceBases
- hashCode() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Kmer
- hashCode() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.TransitPairCount
- hashCode() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- hashCode() - Method in class org.broadinstitute.hellbender.tools.reference.ReferencePair
- hashCode() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableEntry
- hashCode() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableRow
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerBloomFilter
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedAssembly
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig.GoodAndBadMappings
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.InvertedDuplicationBreakpointComplications
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantCanonicalRepresentation
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInducingAssemblyContig
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera.DistancesBetweenAlignmentsOnRefAndOnRead
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.DiscordantReadPairEvidence
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SplitRead
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.TemplateSizeAnomaly
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.WeirdTemplateSize
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistribution
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervals
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVLocation
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.MDElement
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchSetSpark
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter
- hashCode() - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- hashCode() - Method in class org.broadinstitute.hellbender.tools.sv.BafEvidence
- hashCode() - Method in class org.broadinstitute.hellbender.tools.sv.DepthEvidence
- hashCode() - Method in class org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence
- hashCode() - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepth
- hashCode() - Method in class org.broadinstitute.hellbender.tools.sv.SplitReadEvidence
- hashCode() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType
- hashCode() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
- hashCode() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleAndContext
- hashCode() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
-
necessary to override here so that graph.containsVertex() works the same way as vertex.equals() as one might expect
- hashCode() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.InverseAllele
- hashCode() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqVertex
- hashCode() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.Kmer
- hashCode() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LocationAndAlleles
- hashCode() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex
- hashCode() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.Splice
- hashCode() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine.SVSegment
- hashCode() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfExonFeature
- hashCode() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- hashCode() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.OptionalField
- hashCode() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
- hashCode() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfGeneFeature
- hashCode() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature
- hashCode() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
- hashCode() - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchSet
- hashCode() - Method in class org.broadinstitute.hellbender.utils.collections.IndexedSet
- hashCode() - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParams
- hashCode() - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- hashCode() - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- hashCode() - Method in class org.broadinstitute.hellbender.utils.IndexRange
- hashCode() - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Insert
-
Must be overrided in agreement with equals.
- hashCode() - Method in class org.broadinstitute.hellbender.utils.KV
- hashCode() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.ReadsKey.KeyForFragment
- hashCode() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.ReadsKey.KeyForPair
- hashCode() - Method in class org.broadinstitute.hellbender.utils.read.PrimaryAlignmentKey
- hashCode() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- hashCode() - Method in class org.broadinstitute.hellbender.utils.reference.ReferenceBases
- hashCode() - Method in class org.broadinstitute.hellbender.utils.samples.Sample
- hashCode() - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
- hashCode() - Method in class org.broadinstitute.hellbender.utils.SVInterval
- hashCode() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree.OverlapIterator
- hashCode() - Method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
- hashCode() - Method in class org.broadinstitute.hellbender.utils.variant.MinimalVariant
- hashCode() - Method in class org.broadinstitute.hellbender.utils.variant.VariantContextVariantAdapter
- hashCode() - Method in class picard.annotation.Gene.Transcript
- hashCode() - Method in class picard.fingerprint.FingerprintIdDetails
- hashCode() - Method in class picard.fingerprint.HaplotypeBlock
- hashCode() - Method in class picard.fingerprint.Snp
- hashCode() - Method in class picard.illumina.parser.Range
- hashCode() - Method in class picard.illumina.parser.ReadDescriptor
- hashCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
- hashCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- hashCode() - Method in class picard.illumina.parser.ReadStructure
- hashCode() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
- hashCode() - Method in class picard.sam.util.Pair
-
Basic hashcode function.
- hashCode() - Method in class picard.sam.util.PrimaryAlignmentKey
- hashCode() - Method in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
- hasHeader() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- hashKeyForPassthroughRead(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.markduplicates.ReadsKey
-
Makes a hash key for the read.
- hashMapCapacity(int) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
-
return a good initialCapacity for a HashMap that will hold a given number of elements
- hashToIndex(Object) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerSet
- hashToIndex(Object) - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
- hasIncompletePictureFromTwoAlignments(AlignmentInterval, AlignmentInterval) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
-
This predicate tests if an assembly contig with two (picked) alignments has the full event, or breakpoint assembled.
- hasInfoAnnotation(String) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
- hasInsertAt(int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Element
- hasInsertAt(int, int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- hasInsertedSequence() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- hasJunctionTreeEvidence() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JTBestHaplotype
- hasLocation() - Method in interface picard.sam.util.PhysicalLocation
-
Default implementation of a method to check whether real location data has been set.
- hasMessage() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessControllerAckResult
- hasMoltenField() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.AnalysisModuleScanner
- hasMultipleKmerSizes() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Indicates whether there are more than one kmerSize in the set.
- hasNext() - Method in class org.broadinstitute.hellbender.engine.ActivityProfileStateIterator
- hasNext() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionFromActivityProfileStateIterator
- hasNext() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionIterator
- hasNext() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker.MergingIterator
- hasNext() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointDensityFilter
- hasNext() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.PairedStrandedIntervalTreeIterator
- hasNext() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.PairedStrandedIntervalTreeOverlapperIterator
- hasNext() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- hasNext() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils.IteratorFilter
- hasNext() - Method in class org.broadinstitute.hellbender.tools.spark.utils.FlatMapGluer
- hasNext() - Method in interface org.broadinstitute.hellbender.tools.spark.utils.LongIterator
- hasNext() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence.BAFSiteIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.BaseUtils.HmerIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.bigquery.StorageAPIAvroReader
- hasNext() - Method in class org.broadinstitute.hellbender.utils.BinaryTableReader
- hasNext() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- hasNext() - Method in class org.broadinstitute.hellbender.utils.iterators.AllLocusIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.iterators.ByteArrayIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.iterators.CloseAtEndIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.iterators.IntervalLocusIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.iterators.IntervalOverlappingIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.iterators.PushToPullIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.iterators.ReadFilteringIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.iterators.SAMRecordToReadIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.iterators.ShardedIntervalIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState
-
Is there another pileup available?
- hasNext() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator
-
override the hasNext, to incorportate our limiting factor
- hasNext() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.MultiHitAlignedReadIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree.OverlapIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree.ValuesIterator
- hasNext() - Method in class org.broadinstitute.hellbender.utils.text.XReadLines
- hasNext() - Method in class picard.illumina.parser.MultiTileParser
- hasNext() - Method in class picard.illumina.parser.MultiTileBclParser
- hasNext() - Method in class picard.illumina.parser.PerTileParser
- hasNext() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
Return true if the file has more elements to return, false otherwise
- hasNext() - Method in class picard.illumina.parser.readers.BarcodeFileReader
- hasNext() - Method in class picard.illumina.parser.readers.BclReader
- hasNext() - Method in class picard.illumina.parser.readers.CbclReader
- hasNext() - Method in class picard.illumina.parser.readers.ClocsFileReader
- hasNext() - Method in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader
- hasNext() - Method in class picard.illumina.parser.readers.FilterFileReader
- hasNext() - Method in class picard.illumina.parser.readers.LocsFileReader
- hasNext() - Method in class picard.illumina.parser.readers.PosFileReader
- hasNext() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
- hasNext() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- hasNext() - Method in class picard.util.AsyncIterator
- hasNext() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- hasNext() - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
- hasNext() - Method in class picard.vcf.ByIntervalListVariantContextIterator
- hasNext() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
- hasNext() - Method in class picard.vcf.PairedVariantSubContextIterator
- hasNext() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
- hasNode(int) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- hasNoEvidence() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph.ThreadingNode
- hasNonDiagonalElements() - Method in class org.broadinstitute.hellbender.tools.validation.CompareMatrix
- hasOverlapper(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Check the tree against a probe interval to see if there's an overlapping interval.
- hasPendingItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.Downsampler
-
Are there items stored in this downsampler that it doesn't yet know whether they will ultimately survive the downsampling process?
- hasPendingItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.FractionalDownsampler
- hasPendingItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.LevelingDownsampler
- hasPendingItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.MutectDownsampler
- hasPendingItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.PassThroughDownsampler
- hasPendingItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.PositionalDownsampler
- hasPendingItems() - Method in class org.broadinstitute.hellbender.utils.downsampling.ReservoirDownsampler
- hasPileupBeenDownsampled() - Method in class org.broadinstitute.hellbender.engine.AlignmentContext
-
Returns true if any reads have been filtered out of the pileup due to excess DoC.
- hasRateFactor() - Method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.PCRErrorModel
- HasReadGroupReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.HasReadGroupReadFilter
- hasReads() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Are sources of reads available?
- hasReads() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Are sources of reads available?
- hasReference() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Is a source of reference data available?
- hasReference() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Is a source of reference data available?
- hasRegion(Locatable) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OnRampBase
- hasSampleBarcode() - Method in class picard.illumina.parser.ReadStructure
- hasSampleOverlap(SVCallRecord, SVCallRecord, double) - Static method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterLinkage
-
Returns true if there is sufficient fractional carrier sample overlap in the two records.
- hasSampleSetOverlap(Set<String>, Set<String>, double) - Static method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterLinkage
-
Checks for minimum fractional sample overlap of the two sets.
- hasSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_BaseQualityRankSumTest
- hasSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_MappingQualityRankSumTest
- hasSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth
- hasSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_ReadPosRankSumTest
- hasSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality
- hasSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
- hasSecondaryRawKeys() - Method in interface org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation
- hasSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RawGtCount
- hasSecondaryRawKeys() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
- hasSequenceInfo() - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- hasStoppingEvidence(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JTBestHaplotype
- hasSupplementalHits() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
-
True if either the first or second of pair has supplementary alignments, otherwise false.
- hasTruth() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval
- hasUserSuppliedIntervals() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Are sources of intervals available?
- hasUserSuppliedIntervals() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Are sources of intervals available?
- hasUserSuppliedName() - Method in class org.broadinstitute.hellbender.engine.FeatureInput
- hasWebDocumentation(Class<?>) - Static method in class picard.cmdline.CommandLineProgram
-
Determine if a class has web documentation based on its package name
- hasWellDefinedFragmentSize(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Can the adaptor sequence of read be reliably removed from the read based on the alignment of read and its mate?
- HAVANA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.AnnotationSource
- hcArgs - Variable in class org.broadinstitute.hellbender.tools.HaplotypeCallerSpark
- hcArgs - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- hcArgs - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- HDF5 - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts.Format
- HDF5SimpleCountCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
Helper class for
SimpleCountCollectionused to read/write HDF5. - HDF5SVDReadCountPanelOfNormals - Class in org.broadinstitute.hellbender.tools.copynumber.denoising
-
Represents the SVD panel of normals to be created by
CreateReadCountPanelOfNormals. - HDF5Utils - Class in org.broadinstitute.hellbender.tools.copynumber.utils
-
TODO move into hdf5-java-bindings
- HDFS_PREFIX - Static variable in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
- HDFS_SCHEME - Static variable in class org.broadinstitute.hellbender.engine.GATKPath
- HDFS_SCHEME - Static variable in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
- header - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetClass
- header - Variable in class org.broadinstitute.hellbender.utils.codecs.table.TableCodec
- header - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- header - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
- HEADER - Variable in class picard.sam.ReplaceSamHeader
- HEADER - Variable in class picard.vcf.FixVcfHeader
- HEADER_FIELD_EQUAL_CHR - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils
- HEADER_FIELD_LIST_SEPARATOR_STR - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils
- HEADER_FIELD_SEPARATOR_CHR - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils
- HEADER_FIELD_SEPARATOR_REGEXP - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils
- HEADER_LISTED_FIELD_DELIMITER - Static variable in class org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer
-
The delimiter in the header for the list of fields that each funcotation has.
- HEADER_NAMES - Static variable in class picard.arrays.illumina.IlluminaManifest
- HEADER_ONLY - Variable in class picard.sam.ViewSam
- HEADER_PREFIX_CHR - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils
- headerlessReadAdapter(SAMRecord) - Static method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
-
Produces a SAMRecordToGATKReadAdapter wrapping the provided SAMRecord, and nulls out the header in the encapsulated read.
- HeaderlessSAMRecordCoordinateComparator - Class in org.broadinstitute.hellbender.utils.read
-
A comparator for headerless SAMRecords that exactly matches the ordering of the
SAMRecordCoordinateComparator - HeaderlessSAMRecordCoordinateComparator(SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.utils.read.HeaderlessSAMRecordCoordinateComparator
- headerLines() - Method in class picard.vcf.filter.AlleleBalanceFilter
- headerLines() - Method in class picard.vcf.filter.FisherStrandFilter
- headerLines() - Method in class picard.vcf.filter.QdFilter
- headerLines() - Method in interface picard.vcf.filter.VariantFilter
-
Return VCF header lines that define filters that may be applied by the VariantFilter.
- HeaderMissingReadGroup(GATKRead) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.HeaderMissingReadGroup
- headerWarningFile - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- height() - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- HELICOS - Enum constant in enum class org.broadinstitute.hellbender.utils.NGSPlatform
- HelpConstants - Class in org.broadinstitute.hellbender.utils.help
- HelpConstants - Class in picard.util.help
- HET_ALLELE12 - Enum constant in enum class picard.fingerprint.HaplotypeProbabilities.Genotype
- HET_ALLELIC_COUNTS_FILE_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.ModelSegments
- HET_AS_HOM - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
num of hets, observed as homs with LOD > threshold
- HET_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
-
The Chi-squared pvalue for the number of HETs and HOMs relative to the expected counts (2x2 table)
- HET_CROSS_ENTROPY_LOD - Variable in class picard.fingerprint.FingerprintMetrics
-
The categorical cross entropy of the counts of HETs and HOMs relative to the expected counts (big is bad)
- HET_DEL_QS_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- HET_GENOTYPE_FOR_PHASING - Static variable in class picard.fingerprint.HaplotypeMap
- HET_HOMVAR_RATIO - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
(count of hets)/(count of homozygous non-ref) for this sample
- HET_HOMVAR_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
-
(count of hets)/(count of homozygous non-ref) for this sample
- HET_PCT - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
100 * (count of hets) / (total calls) for this sample
- HET_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The ppv (positive predictive value) for all heterozygous variants (PPV is the TP / (TP + FP))
- HET_PPV_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- HET_REF_VAR1 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HET_REF_VAR1 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- HET_REF_VAR1_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- HET_REF_VAR2 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HET_REF_VAR3 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HET_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The sensitivity for all heterozygous variants (Sensitivity is TP / (TP + FN))
- HET_SENSITIVITY_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- HET_SNP_Q - Variable in class picard.analysis.directed.PanelMetricsBase
-
The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
- HET_SNP_Q - Variable in class picard.analysis.WgsMetrics
-
The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
- HET_SNP_SENSITIVITY - Variable in class picard.analysis.directed.PanelMetricsBase
-
The theoretical HET SNP sensitivity.
- HET_SNP_SENSITIVITY - Variable in class picard.analysis.WgsMetrics
-
The theoretical HET SNP sensitivity.
- HET_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The specificity for all heterozygous variants cannot be calculated
- HET_SPECIFICITY_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- HET_TO_HOM_RATIO_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- HET_VAR1_VAR2 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HET_VAR1_VAR2 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- HET_VAR1_VAR2_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- HET_VAR1_VAR3 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HET_VAR3_VAR4 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- hetAltDepthDistribution(int) - Static method in class picard.analysis.TheoreticalSensitivity
- HeterogeneousPloidyModel - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
-
General heterogeneous ploidy model.
- HeterogeneousPloidyModel(SampleList, int[]) - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.HeterogeneousPloidyModel
- heterozygosity - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- HeterozygosityCalculator - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
A class containing utility methods used in the calculation of annotations related to cohort heterozygosity, e.g.
- HeterozygosityCalculator(VariantContext) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.HeterozygosityCalculator
-
Create a new HeterozygosityUtils -- a new class should be instantiated for each VariantContext to store data for that VC
- heterozygosityPerBp - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- heterozygosityStandardDeviation - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
-
The standard deviation of the distribution of alt allele fractions.
- HetHet_Het - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- HetHet_HomRef - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- HetHet_HomVar - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- HetHet_inheritedRef - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- HetHet_inheritedVar - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- hetHomRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- hetSNPSensitivity(double[], double[], int, double) - Static method in class picard.analysis.TheoreticalSensitivity
- hetSNPSensitivity(double[], double[], int, double, boolean) - Static method in class picard.analysis.TheoreticalSensitivity
- HG_TO_NCBI - Static variable in class picard.arrays.illumina.IlluminaManifest
- HG17 - Static variable in class picard.arrays.illumina.IlluminaManifest
- HG18 - Static variable in class picard.arrays.illumina.IlluminaManifest
- hg19 - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations.Reference
- HG19 - Static variable in class picard.arrays.illumina.IlluminaManifest
- HG19_MITOCHONDRIAL_CONTIG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorConstants
-
Name of the Mitochondrial contig for the HG19 human reference.
- hg38 - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations.Reference
- HG38_MITOCHONDRIAL_CONTIG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorConstants
-
Name of the Mitochondrial contig for the HG38 human reference.
- HI_CONF_DENOVO_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- hierarchicalBayesianQualityEstimate(double, RecalDatum, RecalDatum, RecalDatum...) - Static method in class org.broadinstitute.hellbender.transformers.BQSRReadTransformer
- HIGH_COVERAGE_RATIO_THRESHOLD_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination
- HIGH_QUALITY_SOFT_CLIPS - Enum constant in enum class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState.Type
- highConfidenceRegion - Variable in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- highCoverageIntervalsFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- highDepthCoverageFactor - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- highDepthCoveragePeakFactor - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- highQualityDepthHistogram - Variable in class picard.analysis.WgsMetrics
-
Count of sites with a given depth of coverage.
- highQualityDepthHistogramArray - Variable in class picard.analysis.AbstractWgsMetricsCollector
-
Count of sites with a given depth of coverage.
- HISTIDINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- Histogram - Class in org.broadinstitute.hellbender.utils
-
Class used for storing a list of doubles as a run length encoded histogram that compresses the data into bins spaced at defined intervals.
- Histogram() - Constructor for class org.broadinstitute.hellbender.utils.Histogram
-
Create an empty histogram object with a default bin size of 0.1
- Histogram(Double) - Constructor for class org.broadinstitute.hellbender.utils.Histogram
-
Create an empty histogram object with a with a specified bin size
- Histogram_FILE - Variable in class picard.analysis.CollectInsertSizeMetrics
- HISTOGRAM_FILE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
- Histogram_R_SCRIPT - Static variable in class picard.analysis.CollectInsertSizeMetrics
- HISTOGRAM_WIDTH - Variable in class picard.analysis.CollectInsertSizeMetrics
- histogramGenerator - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- histogramPlotFile - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetricsArgumentCollection
- histogramWidth - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetricsArgumentCollection
- HITS_TAG - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScorer
- HitsForInsert - Class in org.broadinstitute.hellbender.utils.read.mergealignment
-
Holds all the hits (alignments) for a read or read pair.
- HitsForInsert() - Constructor for class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
- HitsForInsert.NumPrimaryAlignmentState - Enum Class in org.broadinstitute.hellbender.utils.read.mergealignment
- HMER_QUALITY_SYMETRIC_READ_FILTER - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- HmerIndelLength - Class in org.broadinstitute.hellbender.tools.walkers.annotator.flow
-
Flow Annotation: length of the hmer indel, if so
- HmerIndelLength() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.flow.HmerIndelLength
- HmerIndelNuc - Class in org.broadinstitute.hellbender.tools.walkers.annotator.flow
-
Flow Annotation: nucleotide of the hmer indel, if so
- HmerIndelNuc() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.flow.HmerIndelNuc
- HmerIterator(byte[]) - Constructor for class org.broadinstitute.hellbender.utils.BaseUtils.HmerIterator
- HmerMotifs - Class in org.broadinstitute.hellbender.tools.walkers.annotator.flow
-
Flow Annotation: motifs to the left and right of the indel
- HmerMotifs() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.flow.HmerMotifs
- HmerQualitySymetricReadFilter - Class in org.broadinstitute.hellbender.engine.filters.flow
-
A read filter to test if the quality values for each hmer in a flow based read form a polindrome (as they should)
- HmerQualitySymetricReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.flow.HmerQualitySymetricReadFilter
- HMM_BASE_QUALITIES_TAG - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine
- hmm_glocal(byte[], byte[], int, int, byte[], int[], byte[]) - Method in class org.broadinstitute.hellbender.utils.baq.BAQ
- HOM_ALLELE1 - Enum constant in enum class picard.fingerprint.HaplotypeProbabilities.Genotype
- HOM_ALLELE2 - Enum constant in enum class picard.fingerprint.HaplotypeProbabilities.Genotype
- HOM_ALT - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel
- HOM_AS_HET - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
num of homs, observed as hets with LOD > threshold
- HOM_AS_OTHER_HOM - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
num of homs, observed as other homs with LOD > threshold
- HOM_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
-
The Chi-squared pvalue for
FingerprintMetrics.NUM_HOM_ALLELE1andFingerprintMetrics.NUM_HOM_ALLELE2relative to the expected counts (2x2 table) - HOM_CROSS_ENTROPY_LOD - Variable in class picard.fingerprint.FingerprintMetrics
-
The categorical cross entropy of
FingerprintMetrics.NUM_HOM_ALLELE1andFingerprintMetrics.NUM_HOM_ALLELE2relative to the expected counts (big is bad) - HOM_DEL_QS_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- HOM_REF - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- HOM_REF - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HOM_REF - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- HOM_REF - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel
- HOM_REF_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- HOM_REF_GENOTYPE_INDEX - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator
- HOM_VAR - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- HOM_VAR1 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HOM_VAR1 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- HOM_VAR1_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- HOM_VAR2 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HOM_VAR3 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HOMO - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.Genus
-
Humans
- HomogeneousPloidyModel - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
-
PloidyModelimplementation tailored to work with a homogeneous constant ploidy across samples and positions. - HomogeneousPloidyModel(SampleList, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.HomogeneousPloidyModel
-
Constructs a homogeneous ploidy model given the sample list and ploidy.
- HOMOLOGY - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- HOMOLOGY_LENGTH - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- homologyForwardStrandRep - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications
-
'+' strand representations of micro-homology, inserted sequence and duplicated sequence on the reference.
- homoPolymerLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies a base onto the length of the homopolymer preceding it (in the read direction).
- homopolymerStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies a base onto the make up (repeating base and following reference base) and length of the homopolymer from whence it came.
- HomoSapiensConstants - Class in org.broadinstitute.hellbender.utils.variant
-
Homo sapiens genome constants.
- homozygousAlleleList(Allele, int) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Returns a homozygous call allele list given the only allele and the ploidy.
- HomRefHet_inheritedRef - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- HomRefHet_inheritedVar - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- HomRefHomRef_HomRef - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- HomRefHomVAR_Het - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- HOMVAR_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The ppv (positive predictive value) for all homozygous variants (PPV is the TP / (TP + FP))
- HOMVAR_PPV_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- HOMVAR_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The sensitivity for all homozygous variants (Sensitivity is TP / (TP + FN))
- HOMVAR_SENSITIVITY_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- HOMVAR_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The specificity for all homozygous variants cannot be calculated.
- HOMVAR_SPECIFICITY_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- HomVarHet_inheritedRef - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- HomVarHet_inheritedVar - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- HomVarHomVar_HomVar - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- HOPSCOTCH_SET_EXTENSION - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerUtils
- HopscotchCollection<T> - Class in org.broadinstitute.hellbender.utils.collections
-
Multiset implementation that provides low memory overhead with a high load factor by using the hopscotch algorithm.
- HopscotchCollection() - Constructor for class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
-
make a small HopscotchCollection
- HopscotchCollection(int) - Constructor for class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
-
make a HopscotchCollection for a specified capacity (or good guess)
- HopscotchCollection(Collection<? extends T>) - Constructor for class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
-
make a HopscotchCollection from a collection
- HopscotchCollectionSpark<T> - Class in org.broadinstitute.hellbender.tools.spark.utils
- HopscotchCollectionSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchCollectionSpark
-
make a small HopscotchCollectionSpark
- HopscotchCollectionSpark(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchCollectionSpark
-
make a HopscotchCollectionSpark for a specified capacity (or good guess)
- HopscotchCollectionSpark(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchCollectionSpark
- HopscotchCollectionSpark(Collection<? extends T>) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchCollectionSpark
-
make a HopscotchCollectionSpark from a collection
- HopscotchCollectionSpark.Serializer<T> - Class in org.broadinstitute.hellbender.tools.spark.utils
- HopscotchMap<K,
V, T extends Map.Entry<K, V>> - Class in org.broadinstitute.hellbender.utils.collections -
A uniquely keyed map with O(1) operations.
- HopscotchMap() - Constructor for class org.broadinstitute.hellbender.utils.collections.HopscotchMap
- HopscotchMap(int) - Constructor for class org.broadinstitute.hellbender.utils.collections.HopscotchMap
- HopscotchMap(Collection<? extends T>) - Constructor for class org.broadinstitute.hellbender.utils.collections.HopscotchMap
- HopscotchMapSpark<K,
V, T extends Map.Entry<K, V>> - Class in org.broadinstitute.hellbender.tools.spark.utils -
A uniquely keyed map with O(1) operations.
- HopscotchMapSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMapSpark
- HopscotchMapSpark(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMapSpark
- HopscotchMapSpark(Collection<? extends T>) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMapSpark
- HopscotchMapSpark.Serializer - Class in org.broadinstitute.hellbender.tools.spark.utils
- HopscotchMultiMap<K,
V, T extends Map.Entry<K, V>> - Class in org.broadinstitute.hellbender.utils.collections -
A map that can contain multiple values for a given key.
- HopscotchMultiMap() - Constructor for class org.broadinstitute.hellbender.utils.collections.HopscotchMultiMap
- HopscotchMultiMap(int) - Constructor for class org.broadinstitute.hellbender.utils.collections.HopscotchMultiMap
- HopscotchMultiMap(Collection<? extends T>) - Constructor for class org.broadinstitute.hellbender.utils.collections.HopscotchMultiMap
- HopscotchMultiMapSpark<K,
V, T extends Map.Entry<K, V>> - Class in org.broadinstitute.hellbender.tools.spark.utils -
A map that can contain multiple values for a given key.
- HopscotchMultiMapSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMultiMapSpark
- HopscotchMultiMapSpark(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMultiMapSpark
- HopscotchMultiMapSpark(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMultiMapSpark
- HopscotchMultiMapSpark(Collection<? extends T>) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMultiMapSpark
- HopscotchMultiMapSpark.Serializer - Class in org.broadinstitute.hellbender.tools.spark.utils
- HopscotchSet<T> - Class in org.broadinstitute.hellbender.utils.collections
-
Implements Set by imposing a unique-element constraint on HopscotchCollection.
- HopscotchSet() - Constructor for class org.broadinstitute.hellbender.utils.collections.HopscotchSet
- HopscotchSet(int) - Constructor for class org.broadinstitute.hellbender.utils.collections.HopscotchSet
- HopscotchSet(Collection<? extends T>) - Constructor for class org.broadinstitute.hellbender.utils.collections.HopscotchSet
- HopscotchSetSpark<T> - Class in org.broadinstitute.hellbender.tools.spark.utils
-
Implements Set by imposing a unique-element constraint on HopscotchCollection.
- HopscotchSetSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchSetSpark
- HopscotchSetSpark(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchSetSpark
- HopscotchSetSpark(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchSetSpark
- HopscotchSetSpark(Collection<? extends T>) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchSetSpark
- HopscotchSetSpark.Serializer - Class in org.broadinstitute.hellbender.tools.spark.utils
- HopscotchUniqueMultiMap<K,
V, T extends Map.Entry<K, V>> - Class in org.broadinstitute.hellbender.utils.collections -
A map that can contain multiple values for a given key, but distinct entries.
- HopscotchUniqueMultiMap() - Constructor for class org.broadinstitute.hellbender.utils.collections.HopscotchUniqueMultiMap
- HopscotchUniqueMultiMap(int) - Constructor for class org.broadinstitute.hellbender.utils.collections.HopscotchUniqueMultiMap
- HopscotchUniqueMultiMap(Collection<? extends T>) - Constructor for class org.broadinstitute.hellbender.utils.collections.HopscotchUniqueMultiMap
- HopscotchUniqueMultiMapSpark<K,
V, T extends Map.Entry<K, V>> - Class in org.broadinstitute.hellbender.tools.spark.utils -
A map that can contain multiple values for a given key, but distinct entries.
- HopscotchUniqueMultiMapSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchUniqueMultiMapSpark
- HopscotchUniqueMultiMapSpark(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchUniqueMultiMapSpark
- HopscotchUniqueMultiMapSpark(Collection<? extends T>) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchUniqueMultiMapSpark
- HopscotchUniqueMultiMapSpark.Serializer - Class in org.broadinstitute.hellbender.tools.spark.utils
- HOST_KMER_COUNT_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- HOST_MIN_IDENTITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- HOST_MIN_IDENTITY_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- HOST_READS_FILTERED - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterMetrics
-
The number of subtracted reads identified as host
- HostAlignmentReadFilter - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Filters out reads above a threshold identity (number of matches less deletions), given in bases.
- HostAlignmentReadFilter(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.HostAlignmentReadFilter
- HostAlignmentReadFilter(int, Set<String>) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.HostAlignmentReadFilter
- HOSTILE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.PCRErrorModel
-
a most aggressive model will be applied that sacrifices true positives in order to remove more false positives
- hostKmerThresh - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
-
Controls the stringency of read filtering based on host k-mer matching.
- HOUR_IN_MS - Static variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- HQ_MAPPINGS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- HS_LIBRARY_SIZE - Variable in class picard.analysis.directed.HsMetrics
-
The estimated number of unique molecules in the selected part of the library.
- HS_PENALTY_100X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 100X.
- HS_PENALTY_10X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 10X.
- HS_PENALTY_20X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 20X.
- HS_PENALTY_30X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 30X.
- HS_PENALTY_40X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 40X.
- HS_PENALTY_50X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 50X.
- HsMetricCollector - Class in picard.analysis.directed
-
Calculates HS metrics for a given SAM or BAM file.
- HsMetricCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, boolean, boolean, int, int) - Constructor for class picard.analysis.directed.HsMetricCollector
- HsMetricCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, int, int) - Constructor for class picard.analysis.directed.HsMetricCollector
- HsMetrics - Class in picard.analysis.directed
-
Metrics generated by CollectHsMetrics for the analysis of target-capture sequencing experiments.
- HsMetrics() - Constructor for class picard.analysis.directed.HsMetrics
- HtsgetClass - Enum Class in org.broadinstitute.hellbender.tools.htsgetreader
-
Classes of data that can be requested in an htsget request as defined by the spec
- HtsgetErrorResponse - Class in org.broadinstitute.hellbender.tools.htsgetreader
-
Class allowing deserialization from json htsget error response
- HtsgetErrorResponse() - Constructor for class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetErrorResponse
- HtsgetFormat - Enum Class in org.broadinstitute.hellbender.tools.htsgetreader
-
Formats currently supported by htsget as defined by spec
- HtsgetReader - Class in org.broadinstitute.hellbender.tools
-
A tool that downloads a file hosted on an htsget server to a local file
- HtsgetReader() - Constructor for class org.broadinstitute.hellbender.tools.HtsgetReader
- HtsgetRequestBuilder - Class in org.broadinstitute.hellbender.tools.htsgetreader
-
Builder for an htsget request that allows converting the request to a URI after validating that it is properly formed
- HtsgetRequestBuilder(URI, String) - Constructor for class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- HtsgetRequestField - Enum Class in org.broadinstitute.hellbender.tools.htsgetreader
-
Fields which can be used to filter a htsget request as defined by the spec
- HtsgetResponse - Class in org.broadinstitute.hellbender.tools.htsgetreader
-
Class allowing deserialization from json htsget response
- HtsgetResponse() - Constructor for class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetResponse
- HtsgetResponse.Block - Class in org.broadinstitute.hellbender.tools.htsgetreader
- htsjdk.samtools - package htsjdk.samtools
- HTTP_PREFIX - Static variable in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
- HTTPS_PREFIX - Static variable in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
- HttpUtils - Class in org.broadinstitute.hellbender.utils
- HUGE_FRAGMENT_LENGTH - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- HYBRID - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection.CopyNumberPosteriorExpectationMode
- HybridADVIArgumentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.arguments
- HybridADVIArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- HybridADVIArgumentCollection.HybridADVIArgument - Enum Class in org.broadinstitute.hellbender.tools.copynumber.arguments
- HYPERPARAMETERS_JSON_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
I
- ID - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
-
The ID of this entry
- ID_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord
- ID_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.HtsgetReader
- IDENTICAL - Enum constant in enum class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.SequenceDictionaryCompatibility
- identicalBySequence(List<Haplotype>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LongHomopolymerHaplotypeCollapsingEngine
-
Given that collapsing and uncollapsing of a set of different (by sequence) haplotypes may result in duplicate haplotype, this method is a helper designed to re-index a result set of haplotypes and arrange them into group of distinct haplotypes.
- identifyContaminant(Path, double) - Method in class picard.fingerprint.FingerprintChecker
-
Generates a per-sample Fingerprint for the contaminant in the supplied SAM file.
- IdentifyContaminant - Class in picard.fingerprint
-
Program to create a fingerprint for the contaminating sample when the level of contamination is both known and uniform in the genome.
- IdentifyContaminant() - Constructor for class picard.fingerprint.IdentifyContaminant
- identity() - Static method in interface org.broadinstitute.hellbender.transformers.ReadTransformer
- identity() - Static method in interface org.broadinstitute.hellbender.transformers.VariantTransformer
- IDENTITY_FUNCTION - Static variable in class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceWindowFunctions
-
A function for requesting only reference bases that directly overlap each read.
- IDENTITY_MARGIN_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- IDENTITY_MARGIN_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- identityFunction() - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Returns a function that always returns its input argument.
- identityMargin - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
-
For reads having multiple alignments, the best hit is always counted as long as it is above the identity score threshold.
- IDS - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants.ValidationType
-
Checks whether the variant IDs exists, only relevant if the user indicates a DBSNP vcf file (see
ValidateVariants.dbsnp). - idToClusterMap - Variable in class org.broadinstitute.hellbender.tools.sv.concordance.ClosestSVFinder
- idx - Variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- IG_C_GENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- IG_C_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- IG_D_GENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- IG_J_GENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- IG_J_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- IG_LV_GENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- IG_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- IG_V_GENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- IG_V_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- IGC - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- IGNORE - Variable in class picard.sam.ValidateSamFile
- IGNORE_ALIGNMENT_CONTIGS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- IGNORE_ALIGNMENT_CONTIGS_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- IGNORE_ALL_FILTERS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
- IGNORE_FILTER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
- IGNORE_FILTER_STATUS - Variable in class picard.vcf.GenotypeConcordance
- IGNORE_HISTOGRAM_DIFFERENCES - Variable in class picard.analysis.CompareMetrics
- IGNORE_ITR_ARTIFACTS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- IGNORE_MISSING_MATES - Variable in class picard.sam.FixMateInformation
- IGNORE_READ_GROUPS - Variable in class picard.fingerprint.CheckFingerprint
- IGNORE_SAFETY_CHECKS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.GatherVcfsCloud
- IGNORE_SEQUENCE - Variable in class picard.analysis.CollectMultipleMetrics
- IGNORE_SEQUENCE - Variable in class picard.analysis.CollectRnaSeqMetrics
- IGNORE_UNEXPECTED_BARCODES - Variable in class picard.illumina.IlluminaBasecallsToFastq
- IGNORE_UNEXPECTED_BARCODES - Variable in class picard.illumina.IlluminaBasecallsToSam
- IGNORE_VARIANTS_THAT_START_OUTSIDE_INTERVAL - Static variable in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
- IGNORE_WARNINGS - Variable in class picard.sam.ValidateSamFile
- ignoreAC0Sites() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- ignoreAlignment(SAMRecord) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
- ignoreAlignment(SAMRecord) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.SamAlignmentMerger
-
For now, we only ignore those alignments that have more than
maxGapsinsertions or deletions. - ignoreAlignment(SAMRecord) - Method in class picard.sam.AbstractAlignmentMerger
- ignoreAlignment(SAMRecord) - Method in class picard.sam.SamAlignmentMerger
-
For now, we ignore only those alignments that have more than
SamAlignmentMerger.maxGapsinsertions or deletions. - ignoreCrossContigID(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- IGNORED_READS - Variable in class picard.analysis.RnaSeqMetrics
-
Number of primary alignments that are mapped to a sequence specified on command-line as IGNORED_SEQUENCE.
- ignoreExceptions - Variable in class org.broadinstitute.hellbender.utils.runtime.ScriptExecutor
- ignoreInputSamples - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
-
When this flag is set, only the AC and AN calculated from external sources will be used, and the calculation will not use the discovered allele frequency in the callset whose posteriors are being calculated.
- ignoreInputSamplesForMissingResources - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
-
Don't add input sample ACs for variants not seen in the supporting panel.
- ignoreIntervalsOutsideStart - Variable in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
-
this option has no effect unless intervals are specified.
- ignoreLastModificationTime - Variable in class org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates
-
If true, it won't show a warning if the last-modification time of the before and after input files suggest that they have been reversed.
- ignoreOverlaps - Variable in class org.broadinstitute.hellbender.tools.walkers.qc.CheckPileup
- ignoreSafetyChecks - Variable in class org.broadinstitute.hellbender.tools.GatherVcfsCloud
- ignoreUnexpectedBarcodes - Variable in class picard.illumina.BasecallsConverter
- IGR - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Intergenic region.
- IGV_HEADER_DELIMITER - Static variable in class org.broadinstitute.hellbender.utils.codecs.table.TableCodec
- IGVUtils - Class in org.broadinstitute.hellbender.utils
-
Utilities for interacting with IGV-specific formats.
- ILLUMINA - Enum constant in enum class org.broadinstitute.hellbender.utils.NGSPlatform
- ILLUMINA - Enum constant in enum class picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
- ILLUMINA_ALLEGED_MINIMUM_QUALITY - Static variable in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
- ILLUMINA_BEAD_POOL_MANIFEST_FILE - Variable in class picard.arrays.GtcToVcf
- ILLUMINA_BEAD_POOL_MANIFEST_FILE - Variable in class picard.arrays.illumina.CompareGtcFiles
- ILLUMINA_BUILD - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ILLUMINA_CHR - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ILLUMINA_FLAGGED - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Flagged by Illumina as a bad assay
- ILLUMINA_FLAGGED_BAD_CHR - Static variable in class picard.arrays.illumina.IlluminaManifestRecord
- ILLUMINA_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- ILLUMINA_POS - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ILLUMINA_STRAND - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ILLUMINA_STRAND_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- IlluminaAdapterPair - Enum Class in org.broadinstitute.hellbender.utils.illumina
-
Describes adapters used on each pair of strands
- IlluminaAdpcFileWriter - Class in picard.arrays.illumina
-
A class to encompass writing an Illumina adpc.bin file.
- IlluminaAdpcFileWriter(File) - Constructor for class picard.arrays.illumina.IlluminaAdpcFileWriter
- IlluminaAdpcFileWriter.Record - Class in picard.arrays.illumina
- IlluminaBasecallingMetrics - Class in picard.illumina
-
Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis.
- IlluminaBasecallingMetrics() - Constructor for class picard.illumina.IlluminaBasecallingMetrics
- IlluminaBasecallsToFastq - Class in picard.illumina
- IlluminaBasecallsToFastq() - Constructor for class picard.illumina.IlluminaBasecallsToFastq
- IlluminaBasecallsToFastq.ReadNameFormat - Enum Class in picard.illumina
-
Simple switch to control the read name format to emit.
- IlluminaBasecallsToSam - Class in picard.illumina
-
IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into SAM, BAM or CRAM file format.
- IlluminaBasecallsToSam() - Constructor for class picard.illumina.IlluminaBasecallsToSam
- IlluminaBPMFile - Class in picard.arrays.illumina
-
A class to parse the contents of an Illumina Bead Pool Manifest (BPM) file A BPM file contains metadata (including the alleles, mapping and normalization information) on an Illumina Genotyping Array Each type of genotyping array has a specific BPM .
- IlluminaBPMFile(File) - Constructor for class picard.arrays.illumina.IlluminaBPMFile
- IlluminaBPMLocusEntry - Class in picard.arrays.illumina
-
A simple class to represent a locus entry in an Illumina Bead Pool Manifest (BPM) file
- IlluminaBPMLocusEntry() - Constructor for class picard.arrays.illumina.IlluminaBPMLocusEntry
- IlluminaDataProviderFactory - Class in picard.illumina.parser
-
IlluminaDataProviderFactory accepts options for parsing Illumina data files for a lane and creates an IlluminaDataProvider, an iterator over the ClusterData for that lane, which utilizes these options.
- IlluminaDataProviderFactory(File, int, ReadStructure, BclQualityEvaluationStrategy, Set<IlluminaDataType>) - Constructor for class picard.illumina.parser.IlluminaDataProviderFactory
-
Create factory with the specified options, one that favors using QSeqs over all other files
- IlluminaDataProviderFactory(File, File, int, ReadStructure, BclQualityEvaluationStrategy, Set<IlluminaDataType>) - Constructor for class picard.illumina.parser.IlluminaDataProviderFactory
-
Create factory with the specified options, one that favors using QSeqs over all other files
- IlluminaDataType - Enum Class in picard.illumina.parser
-
List of data types of interest when parsing Illumina data.
- IlluminaFileUtil - Class in picard.illumina.parser
-
General utils for dealing with IlluminaFiles as well as utils for specific, support formats.
- IlluminaFileUtil(File, int) - Constructor for class picard.illumina.parser.IlluminaFileUtil
- IlluminaFileUtil(File, File, int) - Constructor for class picard.illumina.parser.IlluminaFileUtil
- IlluminaFileUtil.SupportedIlluminaFormat - Enum Class in picard.illumina.parser
- IlluminaGenotype - Enum Class in picard.arrays.illumina
- IlluminaLaneMetrics - Class in picard.illumina
-
Embodies characteristics that describe a lane.
- IlluminaLaneMetrics() - Constructor for class picard.illumina.IlluminaLaneMetrics
- IlluminaLaneMetricsCollector() - Constructor for class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
- IlluminaLaneTileCode(int, int, int) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
- IlluminaManifest - Class in picard.arrays.illumina
-
A class to represent an Illumina Manifest file.
- IlluminaManifest(File) - Constructor for class picard.arrays.illumina.IlluminaManifest
- IlluminaManifest(File, int) - Constructor for class picard.arrays.illumina.IlluminaManifest
- IlluminaManifestRecord - Class in picard.arrays.illumina
-
A class to represent a record (line) from an Illumina Manifest [Assay] entry
- IlluminaManifestRecord.IlluminaStrand - Enum Class in picard.arrays.illumina
- IlluminaMetricsCode - Enum Class in picard.illumina.parser
-
Illumina's TileMetricsOut.bin file codes various metrics, both concrete (all density id's are code 100) or as a base code (e.g.
- IlluminaPhasingMetrics - Class in picard.illumina
-
Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.
- IlluminaPhasingMetrics() - Constructor for class picard.illumina.IlluminaPhasingMetrics
- IlluminaReadNameEncoder - Class in picard.fastq
-
A read name encoder following the encoding initially produced by picard fastq writers.
- IlluminaReadNameEncoder(String) - Constructor for class picard.fastq.IlluminaReadNameEncoder
- IlluminaTileMetrics(int, int, int, float) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- IlluminaTileMetrics(ByteBuffer, TileMetricsOutReader.TileMetricsVersion) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- IlluminaUtil - Class in picard.util
-
Misc utilities for working with Illumina specific files and data
- IlluminaUtil() - Constructor for class picard.util.IlluminaUtil
- IlluminaUtil.IlluminaAdapterPair - Enum Class in picard.util
-
Describes adapters used on each pair of strands
- IMAGING_DATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The date that this sample was imaged
- IMAGING_DATE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- IMPRECISE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- ImpreciseDeletion(EvidenceTargetLink, int, ReadMetadata, ReferenceMultiSparkSource) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.ImpreciseDeletion
- ImpreciseVariantDetector - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- ImpreciseVariantDetector() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.ImpreciseVariantDetector
- impreciseVariantEvidenceThreshold - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- IMPROPER - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
- impute(GATKRead) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.DragstrPairHMMInputScoreImputator
- impute(GATKRead) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NonSymmetricalPairHMMInputScoreImputator
- impute(GATKRead) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.StandardPairHMMInputScoreImputator
- impute(GATKRead) - Method in interface org.broadinstitute.hellbender.utils.pairhmm.PairHMMInputScoreImputator
-
Given a read returns an score imputation that in turn can be queried for the pair-HMM match, insertion, deletion scores at each position of the read.
- IMPUTE_ZEROS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormals
- in - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- in - Variable in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- IN_FRAME_DEL - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Deletion that keeps the sequence in frame (i.e.
- IN_FRAME_INS - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Insertion that keeps the sequence in frame (i.e.
- IN_PON_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- INBREEDING_COEFFICIENT_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- InbreedingCoeff - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Likelihood-based test for the consanguinuity among samples
- InbreedingCoeff() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff
- InbreedingCoeff(Set<String>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff
- InbreedingCoeff(GATKPath) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff
- INCLUDE_BARCODE_QUALITY - Variable in class picard.illumina.IlluminaBasecallsToSam
- INCLUDE_BC_IN_RG_TAG - Variable in class picard.illumina.IlluminaBasecallsToSam
- INCLUDE_BQ_HISTOGRAM - Variable in class picard.analysis.CollectWgsMetrics
- INCLUDE_DUPLICATES - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- INCLUDE_DUPLICATES - Variable in class picard.analysis.CollectInsertSizeMetrics
- INCLUDE_FILTERED - Variable in class picard.util.IntervalListTools
- INCLUDE_FILTERED - Variable in class picard.vcf.VcfToIntervalList
- INCLUDE_FILTERED_SHORT_NAME - Static variable in class picard.vcf.VcfToIntervalList
- INCLUDE_INDELS - Variable in class picard.analysis.directed.CollectTargetedMetrics
- INCLUDE_NO_CALLS - Variable in class picard.analysis.QualityScoreDistribution
- INCLUDE_NON_PF_READS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- INCLUDE_NON_PF_READS - Variable in class picard.analysis.CollectOxoGMetrics
- INCLUDE_NON_PF_READS - Variable in class picard.fastq.BamToBfq
- INCLUDE_NON_PF_READS - Variable in class picard.illumina.IlluminaBasecallsToFastq
- INCLUDE_NON_PF_READS - Variable in class picard.illumina.IlluminaBasecallsToSam
- INCLUDE_NON_PF_READS - Variable in class picard.sam.SamToFastq
- INCLUDE_NON_PRIMARY_ALIGNMENTS - Variable in class picard.sam.SamToFastq
- INCLUDE_SECONDARY_ALIGNMENTS - Variable in class picard.analysis.CollectQualityYieldMetrics
- INCLUDE_SECONDARY_ALIGNMENTS - Variable in class picard.sam.MergeBamAlignment
- INCLUDE_SUPPLEMENTAL_ALIGNMENTS - Variable in class picard.analysis.CollectQualityYieldMetrics
- INCLUDE_UNPAIRED - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- INCLUDE_UNPAIRED - Variable in class picard.analysis.CollectMultipleMetrics
- includeAligned - Enum constant in enum class picard.sam.FilterSamReads.Filter
- includeDeletions() - Method in class org.broadinstitute.hellbender.engine.LocusWalker
-
Does this tool require deletions in the AlignmentContext? Tools that don't should override to return
false. - includeDeletions() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage
- includeDupReads - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
include duplicate read?
- includeJavascript - Enum constant in enum class picard.sam.FilterSamReads.Filter
- includeMappingLocation - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- includeNoCalls - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityScoreDistributionSpark
- includeNonPfReads - Variable in class picard.illumina.BasecallsConverter
- includeNs() - Method in class org.broadinstitute.hellbender.engine.LocusWalker
-
Does this tool require Ns in the AlignmentContext? Tools that do should override to return
true. - includeNs() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage
- includePairedIntervals - Enum constant in enum class picard.sam.FilterSamReads.Filter
- includePluginClass(Class<?>) - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
- includePluginClass(Class<?>) - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
- includeReadList - Enum constant in enum class picard.sam.FilterSamReads.Filter
- includeRefAllele() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.BaseQuality
- includeRefAllele() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.FragmentLength
- includeRefAllele() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.MappingQuality
- includeRefAllele() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.PerAlleleAnnotation
- includes(byte) - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Checks whether this nucleotide code encloses all possible nucleotides for another code.
- includes(Nucleotide) - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Checks whether this nucleotide code encloses all possible nucleotides for another code.
- includeSuppAlign - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- includeSupplementalAlignments - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
- includeTagValues - Enum constant in enum class picard.sam.FilterSamReads.Filter
- incMultiplicity(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge
-
Increase the multiplicity of this edge by incr
- incMultiplicity(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MultiSampleEdge
- incNAdapterClippedBases(int) - Method in class org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- incNQClippedBases(int) - Method in class org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- incNRangeClippedBases(int) - Method in class org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- incomingEdgeOf(V) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Get the incoming edge of v.
- incomingVerticesOf(V) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Get the set of vertices connected to v by incoming edges NOTE: We return a LinkedHashSet here in order to preserve the determinism in the output order of VertexSet(), which is deterministic in output due to the underlying sets all being LinkedHashSets.
- INCOMPARABLE_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- IncompatibleRecalibrationTableParameters(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.IncompatibleRecalibrationTableParameters
- IncompatibleSequenceDictionaries(String, String, SAMSequenceDictionary, String, SAMSequenceDictionary) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.IncompatibleSequenceDictionaries
- INCOMPLETE - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments.ReasonForAlignmentClassificationFailure
- INCONCLUSIVE - Enum constant in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
- INCORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
Number of aligned reads that are mapped to the incorrect strand.
- increase() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Updates the genotype counts to match the next genotype according to the canonical ordering of PLs.
- increase(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Increases the allele counts a number of times.
- increment(boolean) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- increment(int) - Method in class picard.analysis.CounterManager.Counter
-
Increments value corresponding to reference sequence index
- increment(long, double) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- increment(Object, String) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Increment the value for a given position in the table.
- increment(String, Nucleotide, ReadOrientation, int) - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.DepthOneHistograms
- increment(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Increments a count for the truth/call state tuple.
- increment(GenotypeConcordanceStates.TruthAndCallStates, double) - Method in class picard.vcf.GenotypeConcordanceCounts
- INCREMENTAL_WORKSPACE_ARG_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- incrementDatumOrPutIfNecessary2keys(NestedIntegerArray<RecalDatum>, byte, double, int, int) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
-
Increments the RecalDatum at the specified position in the specified table, or put a new item there if there isn't already one.
- incrementDatumOrPutIfNecessary3keys(NestedIntegerArray<RecalDatum>, byte, double, int, int, int) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
-
Increments the RecalDatum at the specified position in the specified table, or put a new item there if there isn't already one.
- incrementDatumOrPutIfNecessary4keys(NestedIntegerArray<RecalDatum>, byte, double, int, int, int, int) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
-
Increments the RecalDatum at the specified position in the specified table, or put a new item there if there isn't already one.
- incrementFalseNegative() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
- incrementNumberOfDiscardedItems(int) - Method in class org.broadinstitute.hellbender.utils.downsampling.Downsampler
-
Increments the number of discarded items by the given value.
- incrementNumMismatches(double) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- incrementNumObservations(long) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- incrementReadCount() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Increments the # of reads mapping to this target.
- incrementTrueNegative() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
- incrementUniqueFalseNegative() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
- incrementUniqueTrueNegative() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
- incSeqClippedBases(String, int) - Method in class org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- INDEL - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary.Type
- INDEL - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary.Type
- INDEL - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.VariantType
- INDEL_CALIBRATION_SENSITIVITY_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- INDEL_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord
- INDEL_CONFLICT - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Both insertion and deletion sequence found in reference.
- INDEL_CONTINUATION_QUAL - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- INDEL_EXTENSION_ERROR - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Deprecated.- but used in existing extended manifest files.
- INDEL_FPR_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord
- indel_het_to_hom_ratio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- INDEL_HETEROZYGOSITY - Static variable in class org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants
-
Standard heterozygous rate for INDEL variation.
- INDEL_INFORMATIVE_BASES_CACHE_ATTRIBUTE_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
- INDEL_NOT_FOUND - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Neither insertion nor deletion sequence found in reference.
- indel_novelty_rate - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- INDEL_OUTPUT - Variable in class picard.vcf.SplitVcfs
- INDEL_PADDING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- INDEL_SEQ_MISMATCH - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Deprecated.- but used in existing extended manifest files.
- INDEL_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- INDEL_START_QUAL - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- INDEL_START_TOLERANCE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- indelClassify(VariantContext, FlowAnnotatorBase.LocalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- IndelClassify - Class in org.broadinstitute.hellbender.tools.walkers.annotator.flow
-
Flow Annotation: indel class: ins, del, NA
- IndelClassify() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.flow.IndelClassify
- indelCounter - Variable in class picard.vcf.GenotypeConcordance
- IndelDPPerSample - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- IndelErrorCalculator - Class in picard.sam.SamErrorMetric
-
A calculator that estimates the error rate of the bases it observes for indels only.
- IndelErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.IndelErrorCalculator
- IndelErrorMetric - Class in picard.sam.SamErrorMetric
-
Metric to be used for InDel errors
- IndelErrorMetric() - Constructor for class picard.sam.SamErrorMetric.IndelErrorMetric
- IndelErrorMetric(String, long, long, long, long, long) - Constructor for class picard.sam.SamErrorMetric.IndelErrorMetric
- indelHeterozygosity - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
-
This argument informs the prior probability of having an indel at a site.
- indelHeterozygosity - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine
- indelLength(VariantContext, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel
- IndelLength - Class in org.broadinstitute.hellbender.tools.walkers.annotator.flow
-
Flow Annotation: length of indel
- IndelLength() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.flow.IndelLength
- IndelLengthHistogram - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
-
Simple utility for histogramming indel lengths Based on code from chartl
- IndelLengthHistogram(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelLengthHistogram
- indelLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into the number of bases in an insertion
- IndelLengthStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.IndelLengthStratifier
- indelNoveltyRate - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- IndelNoveltyRate - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- indelPaddingForGenotyping - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
-
Parameters that control genotyping regions
- indelRate - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- indelRatePerBp - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- indelRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MetricsCollection
- indelRatioLociBased - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MetricsCollection
- indels - Variable in class org.broadinstitute.hellbender.utils.variant.DbSnpBitSetUtil.DbSnpBitSets
- indels - Variable in class picard.util.DbSnpBitSetUtil.DbSnpBitSets
- INDELS_CONTEXT_SIZE - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
-
The context covariate will use a context of this size to calculate its covariate value for base insertions and deletions.
- indelsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratify by Indels in the read cigars.
- IndelsInReadStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
- IndelSize - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies the eval RODs by the indel size Indel sizes are stratified from sizes -100 to +100.
- IndelSize(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.IndelSize
- indelSizeToEliminateInRefModel - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
-
This parameter determines the maximum size of an indel considered as potentially segregating in the reference model.
- IndelSummary - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
- IndelSummary(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- indelThreshold - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- indelToMatch - Static variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Position in the transition probability array for the Indel-to-Match transition.
- INDEPENDENT_MATES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- independentMates - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- IndependentReplicateMetric - Class in picard.analysis.replicates
-
A class to store information relevant for biological rate estimation
- IndependentReplicateMetric() - Constructor for class picard.analysis.replicates.IndependentReplicateMetric
- independentReplicationRateFromBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
- independentReplicationRateFromTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The biological duplication rate (as a fraction of the duplicates sets) calculated from tripleton sets.
- independentReplicationRateFromUmi - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
Given the UMIs one can estimate the rate of biological duplication directly, as this would be the rate of having different UMIs in all duplicate sets.
- IndependentSampleGenotypesModel - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
-
This class delegates genotyping to allele count- and ploidy-dependent
GenotypeLikelihoodCalculators under the assumption that sample genotypes are independent conditional on their population frequencies. - IndependentSampleGenotypesModel() - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.IndependentSampleGenotypesModel
- IndependentSampleGenotypesModel(int, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.IndependentSampleGenotypesModel
-
Initialize model with given maximum allele count and ploidy for caching
- index() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Returns the index of this genotype allele count within all possible genotypes with the same ploidy.
- index() - Method in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.TableDataHeaderFields
- index() - Method in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.TableNameHeaderFields
- INDEX - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.utils.segmentation.KernelSegmenter.ChangepointSortOrder
- INDEX_VALIDATION_STRINGENCY - Variable in class picard.sam.ValidateSamFile
- indexByClass(Class<? extends Covariate>) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList
-
Returns the index of the covariate by class name or -1 if not found.
- INDEXED - Enum constant in enum class org.broadinstitute.hellbender.utils.illumina.IlluminaAdapterPair
- INDEXED - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- IndexedAlleleList<A extends htsjdk.variant.variantcontext.Allele> - Class in org.broadinstitute.hellbender.utils.genotyper
-
Allele list implementation using an indexed-set.
- IndexedAlleleList() - Constructor for class org.broadinstitute.hellbender.utils.genotyper.IndexedAlleleList
-
Constructs a new empty allele-list
- IndexedAlleleList(A...) - Constructor for class org.broadinstitute.hellbender.utils.genotyper.IndexedAlleleList
-
Constructs a new allele-list from an array of alleles.
- IndexedAlleleList(Collection<A>) - Constructor for class org.broadinstitute.hellbender.utils.genotyper.IndexedAlleleList
-
Constructs a new allele-list from a collection of alleles.
- IndexedSampleList - Class in org.broadinstitute.hellbender.utils.genotyper
-
Simple implementation of a sample-list using an indexed-set.
- IndexedSampleList() - Constructor for class org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList
-
Constructs an empty sample-list.
- IndexedSampleList(String...) - Constructor for class org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList
-
Constructs a sample-list from an array of samples.
- IndexedSampleList(Collection<String>) - Constructor for class org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList
-
Constructs a sample-list from a collection of samples.
- IndexedSet<E> - Class in org.broadinstitute.hellbender.utils.collections
-
Set where each element can be reference by a unique integer index that runs from 0 to the size of the set - 1.
- IndexedSet(int) - Constructor for class org.broadinstitute.hellbender.utils.collections.IndexedSet
-
Creates an empty indexed set indicating the expected number of elements.
- IndexedSet(E...) - Constructor for class org.broadinstitute.hellbender.utils.collections.IndexedSet
-
Creates a new sample list from a existing array of elements.
- IndexedSet(Collection<E>) - Constructor for class org.broadinstitute.hellbender.utils.collections.IndexedSet
-
Creates a new sample list from a existing collection of elements.
- IndexEntry(DataInputStream) - Constructor for class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.IndexEntry
- IndexEntry(SVInterval, long) - Constructor for class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.IndexEntry
- IndexFeatureFile - Class in org.broadinstitute.hellbender.tools
-
This tool creates an index file for the various kinds of feature-containing files supported by GATK (such as VCF and BED files).
- IndexFeatureFile() - Constructor for class org.broadinstitute.hellbender.tools.IndexFeatureFile
- indexImageFile - Variable in class org.broadinstitute.hellbender.tools.spark.bwa.BwaArgumentCollection
-
The BWA-MEM index image file name that you've distributed to each executor.
- indexImageFile - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
-
This file should be generated using BwaMemIndexImageCreator.
- indexOf(Object) - Method in class org.broadinstitute.hellbender.utils.collections.IndexedSet
-
Returns the index of an object.
- indexOf(String) - Method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Returns the index of a column by its name.
- indexOfAllele(Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingData
- indexOfAllele(Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingLikelihoods
- indexOfAllele(Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix
- indexOfAllele(Allele) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Returns the index of an allele within the likelihood collection.
- indexOfAllele(Allele) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.ActualPermutation
- indexOfAllele(Allele) - Method in interface org.broadinstitute.hellbender.utils.genotyper.AlleleList
-
Returns the index of the given Allele in this AlleleList.
- indexOfAllele(Allele) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.NonPermutation
- indexOfAllele(Allele) - Method in class org.broadinstitute.hellbender.utils.genotyper.IndexedAlleleList
- indexOfAllele(Allele) - Method in interface org.broadinstitute.hellbender.utils.genotyper.LikelihoodMatrix
-
Queries the index of an allele in the matrix.
- indexOfEvidence(EVIDENCE) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix
- indexOfEvidence(EVIDENCE) - Method in interface org.broadinstitute.hellbender.utils.genotyper.LikelihoodMatrix
-
Queries the index of a unit of evidence in the matrix.
- indexOfMax(double[]) - Static method in class picard.util.MathUtil
-
Returns the index of the largest element in the array.
- indexOfMax(long[]) - Static method in class picard.util.MathUtil
-
Returns the index of the largest element in the array.
- indexOfMin(double[]) - Static method in class picard.util.MathUtil
-
Returns the index of the smallest element in the array.
- indexOfMin(int[]) - Static method in class picard.util.MathUtil
-
Returns the index of the smallest element in the array.
- indexOfReference() - Method in interface org.broadinstitute.hellbender.utils.genotyper.AlleleList
-
Resolves the index of the reference allele in an allele-list.
- indexOfSample(String) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingData
- indexOfSample(String) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingLikelihoods
- indexOfSample(String) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.HeterogeneousPloidyModel
- indexOfSample(String) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.HomogeneousPloidyModel
- indexOfSample(String) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Returns the index of a sample within the likelihood collection.
- indexOfSample(String) - Method in class org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList
- indexOfSample(String) - Method in interface org.broadinstitute.hellbender.utils.genotyper.SampleList
-
Returns the index of an object.
- IndexRange - Class in org.broadinstitute.hellbender.utils
-
Represents 0-based integer index range.
- IndexRange(int, int) - Constructor for class org.broadinstitute.hellbender.utils.IndexRange
-
Creates a new range given its
fromandtoindices. - IndexUtils - Class in org.broadinstitute.hellbender.utils
- indicesAvailable() - Method in class org.broadinstitute.hellbender.engine.ReadsPathDataSource
-
Are indices available for all files?
- indicesSpecified() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.SampleNameMap
- INDIVIDUAL_ID - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.PedReader.Field
- IndividualAlignmentSummaryMetricsCollector(AlignmentSummaryMetrics.Category, String, String, String) - Constructor for class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- inferArtifactName() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
Label the artifacts corresponding to known error modes.
- inferArtifactName() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
Label the artifacts corresponding to known error modes.
- INFERRED_EXON_COMBINATION - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Transcript model contains all possible in-frame exons supported by homology, experimental evidence or conservation, but
- INFERRED_TRANSCRIPT_MODEL - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Transcript model is not supported by a single piece of transcript evidence.
- INFERRED_UMI_ENTROPY - Variable in class picard.sam.markduplicates.UmiMetrics
-
Entropy (in base 4) of the inferred UMI sequences, indicating the effective number of bases in the inferred UMIs.
- INFERRED_UNIQUE_UMIS - Variable in class picard.sam.markduplicates.UmiMetrics
-
Number of different inferred UMI sequences derived
- inferSimpleTypeFromNovelAdjacency(NovelAdjacencyAndAltHaplotype, BasicReference) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.ContigChimericAlignmentIterativeInterpreter
- inferStructuralVariantType(VariantContext) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
-
Returns the SV class according to the SVTYPE field if available, else the alternate alleles.
- InfiniumDataFile - Class in picard.arrays.illumina
-
A class to provide methods for accessing Illumina Infinium Data Files.
- InfiniumEGTFile - Class in picard.arrays.illumina
-
A class to parse the contents of an Illumina Infinium cluster (EGT) file A cluster file contains information about the clustering information used in mapping red / green intensity information to genotype calls
- InfiniumEGTFile(File) - Constructor for class picard.arrays.illumina.InfiniumEGTFile
- InfiniumFileTOC - Class in picard.arrays.illumina
-
A class to encapsulate the table of contents for an Illumina Infinium Data Files.
- InfiniumFileTOC() - Constructor for class picard.arrays.illumina.InfiniumFileTOC
- InfiniumGTCFile - Class in picard.arrays.illumina
-
A class to parse the contents of an Illumina Infinium genotype (GTC) file A GTC file is the output of Illumina's genotype calling software (either Autocall or Autoconvert) and contains genotype calls, confidence scores, basecalls and raw intensities for all calls made on the chip.
- InfiniumGTCFile(File, File) - Constructor for class picard.arrays.illumina.InfiniumGTCFile
-
Creates an InfiniumGTCFile object and parses the given input file.
- InfiniumGTCRecord - Class in picard.arrays.illumina
- InfiniumGTCRecord(String) - Constructor for class picard.arrays.illumina.InfiniumGTCRecord
- InfiniumNormalizationManifest - Class in picard.arrays.illumina
-
A class to parse the contents of an Illumina Infinium Normalization Manifest file An Illumina Infinium Normalization Manifest file contains a subset of the information contained in the Illumina Manifest file in addition to the normalization ID which is needed for normalizating intensities in GtcToVcf
- InfiniumNormalizationManifest(File) - Constructor for class picard.arrays.illumina.InfiniumNormalizationManifest
- InfiniumTransformation - Class in picard.arrays.illumina
- InfiniumTransformation() - Constructor for class picard.arrays.illumina.InfiniumTransformation
- InfiniumVcfFields - Class in picard.arrays.illumina
-
A class to store fields that are specific to a VCF generated from an Illumina GTC file.
- InfiniumVcfFields() - Constructor for class picard.arrays.illumina.InfiniumVcfFields
- InfiniumVcfFields.GENOTYPE_VALUES - Enum Class in picard.arrays.illumina
- info - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase
- INFO - Variable in class picard.fingerprint.FingerprintMetrics
-
Additional information about the fingerprint
- InfoConcordanceReader(Path) - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.InfoConcordanceRecord.InfoConcordanceReader
- InfoConcordanceRecord - Class in org.broadinstitute.hellbender.tools.walkers.validation
-
Keeps track of concordance between two info fields.
- InfoConcordanceRecord(VariantContext.Type, String, String, double, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.InfoConcordanceRecord
-
Record keeps track of concordance between values from INFO-field keys of a VCF.
- InfoConcordanceRecord.InfoConcordanceReader - Class in org.broadinstitute.hellbender.tools.walkers.validation
-
Table reading class for InfoConcordanceRecords
- InfoConcordanceRecord.InfoConcordanceWriter - Class in org.broadinstitute.hellbender.tools.walkers.validation
-
Table writing class for InfoConcordanceRecords
- InfoFieldAnnotation - Interface in org.broadinstitute.hellbender.tools.walkers.annotator
-
Annotations relevant to the INFO field of the variant file (ie annotations for sites).
- informativeReadOverlapMargin - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- INIT_ARD_REL_UNEXPLAINED_VARIANCE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
- INITIAL_MAF_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel
- INITIAL_QSCORE - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedHMMEngine
- INITIAL_TEMPERATURE - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- INITIAL_TEMPERATURE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- INITIAL_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- INITIAL_TUMOR_LOG_10_ODDS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- INITIAL_TUMOR_LOG_10_ODDS_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- initialErrorRateForPruning - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
Initial base error rate guess for the probabilistic adaptive pruning model.
- initialize() - Method in class picard.illumina.parser.MultiTileBclParser
- initialize() - Method in enum class picard.nio.PathProvider
- initialize(int, int) - Method in class org.broadinstitute.hellbender.utils.pairhmm.FlowBasedPairHMM
- initialize(int, int) - Method in class org.broadinstitute.hellbender.utils.pairhmm.Log10PairHMM
-
Initialize this PairHMM, making it suitable to run against a read and haplotype with given lengths Note: Do not worry about padding, just provide the true max length of the read and haplotype.
- initialize(int, int) - Method in class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM
-
Initialize this PairHMM, making it suitable to run against a read and haplotype with given lengths Note: Do not worry about padding, just provide the true max length of the read and haplotype.
- initialize(int, int) - Method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
-
Initialize this PairHMM, making it suitable to run against a read and haplotype with given lengths Note: Do not worry about padding, just provide the true max length of the read and haplotype.
- initialize(ReferenceSequenceFile) - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.Splice
- initialize(String) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingDebugger
- initialize(List<Haplotype>, Map<String, List<GATKRead>>, int, int) - Method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
-
Initialize this PairHMM, making it suitable to run against a read and haplotype with given lengths This function is used by the JNI implementations to transfer all data once to the native code
- initialize(List<Haplotype>, Map<String, List<GATKRead>>, int, int) - Method in class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM
-
Initialize this PairHMM, making it suitable to run against a read and haplotype with given lengths This function is used by the JNI implementations to transfer all data once to the native code
- initialize(InsertSizeMetricsArgumentCollection, SAMFileHeader) - Method in class org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollector
- initialize(InsertSizeMetricsArgumentCollection, SAMFileHeader, List<Header>) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectInsertSizeMetricsSpark
- initialize(InsertSizeMetricsArgumentCollection, SAMFileHeader, List<Header>) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.InsertSizeMetricsCollectorSpark
-
Initialize the collector with input arguments;
- initialize(QualityYieldMetricsArgumentCollection, SAMFileHeader, List<Header>) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark
- initialize(QualityYieldMetricsArgumentCollection, SAMFileHeader, List<Header>) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityYieldMetricsCollectorSpark
-
Initialize the collector with input arguments;
- initialize(ExampleMultiMetricsArgumentCollection, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollector
- initialize(ExampleMultiMetricsArgumentCollection, SAMFileHeader, List<Header>) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleCollectMultiMetricsSpark
-
Initialize the collector with it's input arguments.
- initialize(ExampleMultiMetricsArgumentCollection, SAMFileHeader, List<Header>) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollectorSpark
-
Initialize the collector with input arguments.
- initialize(ExampleSingleMetricsArgumentCollection, SAMFileHeader, List<Header>) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleCollectSingleMetricsSpark
-
Initialize the collector with it's input arguments.
- initialize(ExampleSingleMetricsArgumentCollection, SAMFileHeader, List<Header>) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetricsCollectorSpark
-
Initialize the collector with input arguments;
- initialize(T, SAMFileHeader, List<Header>) - Method in interface org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSpark
-
Give the collector's input arguments to the collector (if the collector is being driven by a standalone tool.
- initialize(T, SAMFileHeader, List<Header>) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSparkTool
- initializeAdditionalWriters() - Method in class picard.sam.SamToFastq
- initializeAdditionalWriters() - Method in class picard.sam.SamToFastqWithTags
- initializeAnnotationOverrides(LinkedHashMap<String, String>) - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
Set values in
DataSourceFuncotationFactory.annotationOverrideMapbased on the given annotation override values and whether or not thisDataSourceFuncotationFactorysupports those annotations. - initializeConfigurationsFromCommandLineArgs(String[], String) - Method in class org.broadinstitute.hellbender.utils.config.ConfigFactory
-
Get the configuration filename from the command-line (if it exists) and create a configuration for it.
- initializeConfigurationsFromCommandLineArgs(String[], String, Class<? extends T>) - Method in class org.broadinstitute.hellbender.utils.config.ConfigFactory
-
Get the configuration from filename the command-line (if it exists) and create a configuration for it of the given type.
- initialized - Variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- initializeDefaultMapWithKeys() - Method in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRenderer
-
Initializes
MafOutputRenderer.defaultMapwith the default keys for the columns in a MAF file. - initializeDrivingVariants() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalker
- initializeDrivingVariants() - Method in class org.broadinstitute.hellbender.engine.VariantLocusWalker
- initializeDrivingVariants() - Method in class org.broadinstitute.hellbender.engine.VariantWalker
- initializeDrivingVariants() - Method in class org.broadinstitute.hellbender.engine.VariantWalkerBase
-
Process the feature inputs that represent the primary driving source(s) of variants for this tool, and perform any necessary header and sequence dictionary validation.
- initializeDrivingVariants() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval
- initializeEvaluationObjects(boolean, List<String>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
-
Initialize required, standard and user-specified evaluation objects
- initializeIntervals() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
-
Loads our intervals using the best available sequence dictionary (as returned by
GenomicsDBImport.getBestAvailableSequenceDictionary()) to parse/verify them. - initializeLog10Priors(byte[], byte[], byte[], int) - Method in class org.broadinstitute.hellbender.utils.pairhmm.Log10PairHMM
-
Initializes the matrix that holds all the constants related to the editing distance between the read and the haplotype.
- initializeLog10Probabilities(byte[], byte[], byte[]) - Method in class org.broadinstitute.hellbender.utils.pairhmm.Log10PairHMM
-
Initializes the matrix that holds all the constants related to quality scores.
- initializeNewRawAnnotationData(List<Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
-
Initializing a AlleleSpecificAnnotationData<CompressedDataList
> object for annotateRawData() to be used for the per-read data generated by calculateRawData(). - initializeProgressMeter(String) - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Helper method to initialize the progress meter without exposing engine level arguements.
- initializeShardHeader() - Method in class org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter
-
Initializes shard header depending on which header function (set or write) was used
- initializeStats(boolean, Map<DoCOutputType.Partition, List<String>>) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoveragePartitionedDataStore
- initializeStratificationObjects(boolean, List<String>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
-
Initialize required, standard and user-specified stratification objects
- initialLogPriorOfVariantVersusArtifact - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- initialPosteriorThreshold - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- initiateCopy() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
-
Initiate the copy from
NioFileCopierWithProgressMeter.sourcetoNioFileCopierWithProgressMeter.dest. - initiateScheme() - Method in class picard.vcf.GA4GHScheme
- initiateScheme() - Method in class picard.vcf.GA4GHSchemeWithMissingAsHomRef
- initiateScheme() - Method in class picard.vcf.GenotypeConcordanceScheme
- initStreamWriter(Function<T, ByteArrayOutputStream>) - Method in class org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor
-
Obtain a stream writer that serializes and writes batches of items of type
Ton a background thread. - injectSystemPropertiesFromConfig(T) - Method in class org.broadinstitute.hellbender.utils.config.ConfigFactory
-
Injects system properties from the given configuration file.
- inPlaceCombine(RecalibrationTables, RecalibrationTables) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
-
Combines the right table into the left table, in-place (without making a copy)
- input - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.CountVariantsSpark
- INPUT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
- INPUT - Variable in class picard.analysis.CollectMultipleMetrics
- INPUT - Variable in class picard.analysis.CollectOxoGMetrics
- INPUT - Variable in class picard.analysis.CollectRrbsMetrics
- INPUT - Variable in class picard.analysis.CollectWgsMetrics
- INPUT - Variable in class picard.analysis.CompareMetrics
- INPUT - Variable in class picard.analysis.directed.CollectTargetedMetrics
- INPUT - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- INPUT - Variable in class picard.analysis.SinglePassSamProgram
- INPUT - Variable in class picard.annotation.SortGff
- INPUT - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
- INPUT - Variable in class picard.arrays.CombineGenotypingArrayVcfs
- INPUT - Variable in class picard.arrays.CreateBafRegressMetricsFile
- INPUT - Variable in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
- INPUT - Variable in class picard.arrays.GtcToVcf
- INPUT - Variable in class picard.arrays.illumina.BpmToNormalizationManifestCsv
- INPUT - Variable in class picard.arrays.illumina.CompareGtcFiles
- INPUT - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- INPUT - Variable in class picard.fastq.BamToBfq
- INPUT - Variable in class picard.fingerprint.CalculateFingerprintMetrics
- INPUT - Variable in class picard.fingerprint.CheckFingerprint
- INPUT - Variable in class picard.fingerprint.ClusterCrosscheckMetrics
- INPUT - Variable in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
- INPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
- INPUT - Variable in class picard.fingerprint.ExtractFingerprint
- INPUT - Variable in class picard.fingerprint.IdentifyContaminant
- INPUT - Variable in class picard.fingerprint.LiftOverHaplotypeMap
- INPUT - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
- INPUT - Variable in class picard.illumina.MarkIlluminaAdapters
- INPUT - Variable in class picard.reference.NonNFastaSize
- INPUT - Variable in class picard.reference.NormalizeFasta
- INPUT - Variable in class picard.sam.AddCommentsToBam
- INPUT - Variable in class picard.sam.AddOATag
- INPUT - Variable in class picard.sam.AddOrReplaceReadGroups
- INPUT - Variable in class picard.sam.BamIndexStats
- INPUT - Variable in class picard.sam.BuildBamIndex
- INPUT - Variable in class picard.sam.CalculateReadGroupChecksum
- INPUT - Variable in class picard.sam.CheckTerminatorBlock
- INPUT - Variable in class picard.sam.CleanSam
- INPUT - Variable in class picard.sam.DownsampleSam
- INPUT - Variable in class picard.sam.FilterSamReads
- INPUT - Variable in class picard.sam.FixMateInformation
- INPUT - Variable in class picard.sam.GatherBamFiles
- INPUT - Variable in class picard.sam.markduplicates.CheckDuplicateMarking
- INPUT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- INPUT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- INPUT - Variable in class picard.sam.MergeSamFiles
- INPUT - Variable in class picard.sam.PositionBasedDownsampleSam
- INPUT - Variable in class picard.sam.ReorderSam
- INPUT - Variable in class picard.sam.ReplaceSamHeader
- INPUT - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- INPUT - Variable in class picard.sam.RevertSam
- INPUT - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- INPUT - Variable in class picard.sam.SamFormatConverter
- INPUT - Variable in class picard.sam.SamToFastq
- INPUT - Variable in class picard.sam.SetNmMdAndUqTags
- INPUT - Variable in class picard.sam.SortSam
- INPUT - Variable in class picard.sam.SplitSamByLibrary
- INPUT - Variable in class picard.sam.SplitSamByNumberOfReads
- INPUT - Variable in class picard.sam.ValidateSamFile
- INPUT - Variable in class picard.sam.ViewSam
- INPUT - Variable in class picard.util.AccumulateQualityYieldMetrics
- INPUT - Variable in class picard.util.BedToIntervalList
- INPUT - Variable in class picard.util.IntervalListToBed
- INPUT - Variable in class picard.util.IntervalListTools
- INPUT - Variable in class picard.util.LiftOverIntervalList
- INPUT - Variable in class picard.vcf.AccumulateVariantCallingMetrics
- INPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
- INPUT - Variable in class picard.vcf.filter.FilterVcf
- INPUT - Variable in class picard.vcf.FixVcfHeader
- INPUT - Variable in class picard.vcf.GatherVcfs
- INPUT - Variable in class picard.vcf.LiftoverVcf
- INPUT - Variable in class picard.vcf.MakeSitesOnlyVcf
- INPUT - Variable in class picard.vcf.MakeVcfSampleNameMap
- INPUT - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- INPUT - Variable in class picard.vcf.MergeVcfs
- INPUT - Variable in class picard.vcf.RenameSampleInVcf
- INPUT - Variable in class picard.vcf.SortVcf
- INPUT - Variable in class picard.vcf.SplitVcfs
- INPUT - Variable in class picard.vcf.UpdateVcfSequenceDictionary
- INPUT - Variable in class picard.vcf.VcfFormatConverter
- INPUT - Variable in class picard.vcf.VcfToIntervalList
- INPUT_2_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark
- INPUT_2_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark
- INPUT_ARGNAME - Static variable in class org.broadinstitute.hellbender.tools.sv.CondenseDepthEvidence
- INPUT_ARGNAME - Static variable in class org.broadinstitute.hellbender.tools.sv.PrintReadCounts
- INPUT_BASE - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- INPUT_CALL_HEADER - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEvents
- INPUT_GCS_PATH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.ParallelCopyGCSDirectoryIntoHDFSSpark
- INPUT_GLOB - Static variable in class org.broadinstitute.hellbender.tools.spark.ParallelCopyGCSDirectoryIntoHDFSSpark
- INPUT_GLOB_ALL_FILES - Static variable in class org.broadinstitute.hellbender.tools.spark.ParallelCopyGCSDirectoryIntoHDFSSpark
- INPUT_INDEX_COMPANION - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- INPUT_INDEX_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
- INPUT_INTERVALS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- INPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- INPUT_MODEL_INTERVAL_FILE - Static variable in class org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy
- INPUT_MODEL_INTERVAL_FILE - Static variable in class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller
- INPUT_PARAMS_FILE - Variable in class picard.illumina.ExtractBarcodesProgram
- INPUT_SAMPLE_FILE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
- INPUT_SAMPLE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
- INPUT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- INPUT_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- input2 - Variable in class org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark
- inputBam - Variable in class org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndex
- inputPaired - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSpark
- inputReadStructure - Variable in class picard.illumina.ExtractBarcodesProgram
-
The read structure of the actual Illumina Run, i.e.
- inputReports - Variable in class org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReports
- inputReports - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.GatherTranches
- inputs - Variable in class org.broadinstitute.hellbender.tools.GatherVcfsCloud
- InputStreamSettings - Class in org.broadinstitute.hellbender.utils.runtime
-
Settings that define text to write to the process stdin.
- InputStreamSettings() - Constructor for class org.broadinstitute.hellbender.utils.runtime.InputStreamSettings
- inputUnpaired - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSpark
- inRange(double, double, double, String) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Checks that the input is within range and returns the same value or throws an
IllegalArgumentException - inRange(int, int, int, String) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Checks that the input int value is within range and returns the same value or throws an
IllegalArgumentException - inRange(long, double, double, String) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Checks that the input is within range and returns the same value or throws an
IllegalArgumentException - inRange(long, long, long, String) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Checks that the input is within range and returns the same value or throws an
IllegalArgumentException - inRange(DoubleRange, double, String) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Validates the value of a parameter.
- inRange(IntRange, int, String) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Validates the value of a parameter.
- INS - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantType
- INS - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.SupportedType
- INS - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.StructuralVariantAnnotationType
- INS_iDEL - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.ComplexVariantSubtype
- insertAllele(Allele, Allele, int) - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- insertAt(int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Element
- insertAt(int, int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- insertBasesAt(int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Element
- insertBasesAt(int, int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- INSERTED_SEQUENCE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- INSERTED_SEQUENCE_LENGTH - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- INSERTED_SEQUENCE_MAPPINGS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- insertedSequenceForwardStrandRep - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications
- insertion - Enum constant in enum class org.broadinstitute.hellbender.utils.variant.DbSnpVariantType
- insertion - Enum constant in enum class picard.util.VariantType
- Insertion(String, int, int, String, Allele, Allele, int, Map<String, Object>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.Insertion
- Insertion(NovelAdjacencyAndAltHaplotype, BasicReference) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.Insertion
- INSERTION - Enum constant in enum class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner.State
- INSERTION_ASSUMED_LENGTH_FOR_OVERLAP - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- insertion_to_deletion_ratio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- insertion_to_deletion_ratio_for_large_indels - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- insertionDeletionRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- insertionMappings - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera
- insertionMatrix - Variable in class org.broadinstitute.hellbender.utils.pairhmm.FlowBasedPairHMM
- insertionMatrix - Variable in class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM
- INSERTIONS_DEFAULT_QUALITY - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
-
A default base qualities to use as a prior (reported quality) in the insertion covariate model.
- INSERTIONS_Q - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
-
The (phred) rate of insertions.
- insertionsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratify by Insertions in the read cigars.
- insertionToInsertion - Static variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Position in the transition probability array for the Insertion-to-Insertion transition.
- insertLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into the read-pairs estimated insert-length, as long as it isn't larger than 10x the length of the read
- insertQualsAt(int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Element
- insertQualsAt(int, int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- inserts() - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Element
- inserts(int, int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Element
- insertSize(int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Element
- InsertSizeDistribution - Class in org.broadinstitute.hellbender.tools.spark.sv
-
Holds the information characterizing and insert size distribution.
- InsertSizeDistribution(String) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistribution
- InsertSizeDistributionShape - Enum Class in org.broadinstitute.hellbender.tools.spark.sv
-
Supported insert size distributions shapes.
- InsertSizeMetrics - Class in org.broadinstitute.hellbender.metrics
-
Metrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually written to a file with the extension ".insertSizeMetrics".
- InsertSizeMetrics - Class in picard.analysis
-
Metrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually written to a file with the extension ".insert_size_metrics".
- InsertSizeMetrics() - Constructor for class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
- InsertSizeMetrics() - Constructor for class picard.analysis.InsertSizeMetrics
- InsertSizeMetricsArgumentCollection - Class in org.broadinstitute.hellbender.metrics
-
ArgumentCollection for InsertSizeMetrics collectors.
- InsertSizeMetricsArgumentCollection() - Constructor for class org.broadinstitute.hellbender.metrics.InsertSizeMetricsArgumentCollection
- InsertSizeMetricsCollector - Class in org.broadinstitute.hellbender.metrics
-
Collects InsertSizeMetrics on the specified accumulationLevels
- InsertSizeMetricsCollector - Class in picard.analysis.directed
-
Collects InsertSizeMetrics on the specified accumulationLevels using
- InsertSizeMetricsCollector() - Constructor for class org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollector
- InsertSizeMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, double, Integer, Integer, double, boolean) - Constructor for class picard.analysis.directed.InsertSizeMetricsCollector
- InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector - Class in picard.analysis.directed
-
A Collector for individual InsertSizeMetrics for a given SAMPLE or SAMPLE/LIBRARY or SAMPLE/LIBRARY/READ_GROUP (depending on aggregation levels)
- InsertSizeMetricsCollectorSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines.metrics
-
Worker class to collect insert size metrics, add metrics to file, and provides accessors to stats of groups of different level.
- InsertSizeMetricsCollectorSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.InsertSizeMetricsCollectorSpark
- insOpenPenalties() - Method in interface org.broadinstitute.hellbender.utils.pairhmm.PairHMMInputScoreImputation
- INSTANCE - Static variable in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils.TransientFieldPhysicalLocationComparator
- instanceMain(String[]) - Method in class org.broadinstitute.hellbender.cmdline.CommandLineArgumentValidator
-
Entry point to run command line argument validation only.
- instanceMain(String[]) - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- instanceMain(String[]) - Method in class org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram
- instanceMain(String[]) - Method in class org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor
-
Entry point for Picard tools that are called from GATK.
- instanceMain(String[]) - Method in class org.broadinstitute.hellbender.Main
-
This method is not intended to be used outside of the GATK framework and tests.
- instanceMain(String[]) - Method in class picard.cmdline.CommandLineProgram
- instanceMain(String[]) - Method in class picard.cmdline.PicardCommandLine
-
For testing
- instanceMain(String[], List<String>, String) - Method in class picard.cmdline.PicardCommandLine
-
The main method.
- instanceMain(String[], List<String>, List<Class<? extends CommandLineProgram>>, String) - Method in class org.broadinstitute.hellbender.Main
-
The main method.
- instanceMainPostParseArgs() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- instanceMainWithExit(String[]) - Method in class picard.cmdline.CommandLineProgram
- INT_EXON_DUP - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- int1() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark.IntPair
- int2() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark.IntPair
- IntBiConsumer - Interface in org.broadinstitute.hellbender.utils.functional
-
Created by davidben on 8/19/16.
- Integer - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportDataType
-
Used for int, byte, short, and long values.
- IntegerCopyNumberSegment - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
-
A genotyped integer copy-number segment.
- IntegerCopyNumberSegment(SimpleInterval, IntegerCopyNumberState, IntegerCopyNumberState, int, double, double, double, double) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
- IntegerCopyNumberSegmentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
Represents a collection of
IntegerCopyNumberSegmentfor a sample. - IntegerCopyNumberSegmentCollection(File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.IntegerCopyNumberSegmentCollection
- IntegerCopyNumberSegmentCollection(SampleLocatableMetadata, List<IntegerCopyNumberSegment>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.IntegerCopyNumberSegmentCollection
- IntegerCopyNumberState - Class in org.broadinstitute.hellbender.tools.copynumber.gcnv
-
This class represents integer copy number states.
- IntegerCopyNumberState(int) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.gcnv.IntegerCopyNumberState
- integrate(DoubleUnaryOperator, double, double, int) - Static method in class org.broadinstitute.hellbender.utils.IntegrationUtils
- integrate2d(ToDoubleBiFunction<Double, Double>, double, double, int, double, double, int) - Static method in class org.broadinstitute.hellbender.utils.IntegrationUtils
- IntegrationUtils - Class in org.broadinstitute.hellbender.utils
-
Created by tsato on 5/1/17.
- IntegrationUtils() - Constructor for class org.broadinstitute.hellbender.utils.IntegrationUtils
- INTENSITY_ONLY_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- IntensityChannel - Enum Class in picard.illumina.parser
-
The channels in a FourChannelIntensityData object, and the channels produced by a ClusterIntensityFileReader, for cases in which it is desirable to handle these abstractly rather than having the specific names in the source code.
- INTER_CHR_NO_SS_WITH_LEFT_MATE_FIRST_IN_PARTNER - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.SupportedType
- INTER_CHR_NO_SS_WITH_LEFT_MATE_FIRST_IN_PARTNER - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera
- INTER_CHR_NO_SS_WITH_LEFT_MATE_SECOND_IN_PARTNER - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.SupportedType
- INTER_CHR_NO_SS_WITH_LEFT_MATE_SECOND_IN_PARTNER - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera
- INTER_CHR_STRAND_SWITCH_33 - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.SupportedType
- INTER_CHR_STRAND_SWITCH_33 - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera
- INTER_CHR_STRAND_SWITCH_55 - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.SupportedType
- INTER_CHR_STRAND_SWITCH_55 - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera
- INTERAL_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta
- InterChromosomeBreakend(String, int, String, Allele, Allele, Map<String, Object>, boolean) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.InterChromosomeBreakend
- INTERGENIC - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- INTERGENIC - Enum constant in enum class picard.annotation.LocusFunction
- INTERGENIC - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- INTERGENIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Number of bases in primary alignments that do not align to any gene.
- INTERGENIC_CONSERVED - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- INTERLEAVE - Variable in class picard.sam.SamToFastq
- INTEROP_SUBDIRECTORY_NAME - Static variable in class picard.illumina.parser.TileMetricsUtil
-
The path to the directory containing the tile metrics file relative to the basecalling directory.
- interruptAndShutdownExecutors(ThreadPoolExecutorWithExceptions...) - Method in class picard.illumina.BasecallsConverter
- intersect(byte, byte) - Static method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Checks whether two nucleotides intersect given their byte encodings.
- intersect(Locatable) - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
-
Returns the intersection of the two intervals.
- intersect(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- intersect(Nucleotide) - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns the nucleotide code that include all and only the nucleotides that are included by this another code.
- intersect(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVInterval
-
Returns
nullif the two intervals don't overlap as judged bySVInterval.overlaps(SVInterval). - INTERSECT - Enum constant in enum class picard.util.IntervalListTools.Action
- INTERSECT_INTERVALS - Variable in class picard.vcf.GenotypeConcordance
- INTERSECTION - Enum constant in enum class org.broadinstitute.hellbender.utils.IntervalSetRule
-
Take the intersection of intervals (the subset that overlaps all intervals specified)
- interval - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Aggregation
- interval - Variable in class org.broadinstitute.hellbender.engine.ShardBoundary
- INTERVAL - Enum constant in enum class org.broadinstitute.hellbender.utils.variant.GATKVCFIndexType
- INTERVAL_CONTIG_NAMES_SUB_PATH - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils
- INTERVAL_COUNT - Enum constant in enum class picard.util.IntervalList.IntervalListScatterMode
-
A scatter by interval **count** which attempts to fill each resulting interval list with the same number of intervals, disregarding the base count.
- INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER - Enum constant in enum class picard.util.IntervalList.IntervalListScatterMode
-
A scatter by interval **count** which attempts to fill each resulting interval list with approximately equal numbers of intervals, disregarding the base count.
- INTERVAL_EXCLUSION_PADDING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
- INTERVAL_FILE_EXTENSION_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- INTERVAL_FILE_PREFIX_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- INTERVAL_GC_CONTENT_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- INTERVAL_ITERATOR - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- INTERVAL_LEFT_BOUND_INDEX - Static variable in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- INTERVAL_LIST - Variable in class picard.reference.ExtractSequences
- INTERVAL_LIST - Variable in class picard.sam.AddOATag
- INTERVAL_LIST - Variable in class picard.sam.FilterSamReads
- INTERVAL_LIST - Variable in class picard.sam.ViewSam
- INTERVAL_LIST_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVNamingConstants
- INTERVAL_LIST_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- INTERVAL_LIST_SIZE_WARNING_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- INTERVAL_MATRIX_SUB_PATH - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils
- INTERVAL_MERGING_RULE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
- INTERVAL_NUMBER_OF_DIGITS_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- INTERVAL_PADDING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
- INTERVAL_PSI_SCALE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
- INTERVAL_RIGHT_BOUND_INDEX - Static variable in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- INTERVAL_SET_RULE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
- INTERVAL_SUBDIVISION - Enum constant in enum class picard.util.IntervalList.IntervalListScatterMode
-
A simple scatter approach in which all output intervals have size equal to the total base count of the source list divide by the scatter count (except for possible variance in the final interval list).
- INTERVAL_VARIANT_ID_FIELD_SEPARATOR - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- IntervalAlignmentContextIterator - Class in org.broadinstitute.hellbender.utils.locusiterator
-
For special cases where we want to emit AlignmentContexts regardless of whether we have an overlap with a given interval.
- IntervalAlignmentContextIterator(Iterator<AlignmentContext>, IntervalLocusIterator, SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator
-
Note: Typically, if you are calling this from a walker tool, you want to use
AlignmentContextIteratorBuilder - intervalArgumentCollection - Variable in class org.broadinstitute.hellbender.engine.GATKTool
- intervalArgumentCollection - Variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- intervalArgumentCollection - Variable in class org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy
- intervalArgumentCollection - Variable in class org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
- intervalArgumentCollection - Variable in class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller
- intervalArgumentCollection - Variable in class picard.analysis.CollectWgsMetrics
- IntervalArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
Intended to be used as an @ArgumentCollection for specifying intervals at the command line.
- IntervalArgumentCollection - Interface in picard.cmdline.argumentcollections
-
Base interface for an interval argument collection.
- IntervalArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
- IntervalCopyNumberGenotypingData - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
-
The bundle of integer copy-number posterior distribution and baseline integer copy-number state for an interval.
- IntervalCopyNumberGenotypingData(SimpleInterval, CopyNumberPosteriorDistribution, IntegerCopyNumberState) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntervalCopyNumberGenotypingData
- IntervalCoverageFinder - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
Class to find the coverage of the intervals.
- IntervalCoverageFinder(ReadMetadata, List<SVInterval>, Iterator<GATKRead>, SVReadFilter) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.IntervalCoverageFinder
- intervalExclusionPadding - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
Use this to add padding to the intervals specified using -XL.
- intervalFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- intervalIsOnDictionaryContig(SimpleInterval, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Determines whether the provided interval is within the bounds of its assigned contig according to the provided dictionary
- IntervalListScatter - Class in picard.util.IntervalList
- IntervalListScatter(IntervalListScatterer, IntervalList, int) - Constructor for class picard.util.IntervalList.IntervalListScatter
- IntervalListScatterer - Interface in picard.util.IntervalList
-
An interface for a class that scatters IntervalLists.
- IntervalListScattererByBaseCount - Class in picard.util.IntervalList
-
a Baseclass for scatterers that scatter by uniqued base count.
- IntervalListScattererByBaseCount() - Constructor for class picard.util.IntervalList.IntervalListScattererByBaseCount
- IntervalListScattererByIntervalCount - Class in picard.util.IntervalList
-
Scatters
IntervalListby interval count so that resultingIntervalList's have the same number of intervals in them. - IntervalListScattererByIntervalCount() - Constructor for class picard.util.IntervalList.IntervalListScattererByIntervalCount
- IntervalListScattererByIntervalCountWithDistributedRemainder - Class in picard.util.IntervalList
-
Scatters
IntervalListby into `interval count` shards so that resultingIntervalList's have approximately same number of intervals in them. - IntervalListScattererByIntervalCountWithDistributedRemainder() - Constructor for class picard.util.IntervalList.IntervalListScattererByIntervalCountWithDistributedRemainder
- IntervalListScattererWithoutSubdivision - Class in picard.util.IntervalList
-
A BaseCount Scatterer that avoid breaking-up intervals.
- IntervalListScattererWithoutSubdivision() - Constructor for class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
- IntervalListScattererWithoutSubdivisionWithOverflow - Class in picard.util.IntervalList
-
Like
IntervalListScattererWithoutSubdivisionbut will overflow current list if the projected size of the remaining lists is bigger than the "ideal". - IntervalListScattererWithoutSubdivisionWithOverflow() - Constructor for class picard.util.IntervalList.IntervalListScattererWithoutSubdivisionWithOverflow
- IntervalListScattererWithSubdivision - Class in picard.util.IntervalList
-
An IntervalListScatterer that attempts to place the same number of (uniquified) bases in each output interval list.
- IntervalListScattererWithSubdivision() - Constructor for class picard.util.IntervalList.IntervalListScattererWithSubdivision
- IntervalListScatterMode - Enum Class in picard.util.IntervalList
-
An enum to control the creation of the various IntervalListScatter objects
- IntervalListToBed - Class in picard.util
-
Trivially simple command line program to convert an IntervalList file to a BED file.
- IntervalListToBed() - Constructor for class picard.util.IntervalListToBed
- IntervalListTools - Class in picard.util
-
Performs various
IntervalListmanipulations. - IntervalListTools() - Constructor for class picard.util.IntervalListTools
- IntervalListTools.Action - Enum Class in picard.util
- IntervalLocusIterator - Class in org.broadinstitute.hellbender.utils.iterators
-
Returns a SimpleInterval for each locus in a set of intervals.
- IntervalLocusIterator(Iterator<SimpleInterval>) - Constructor for class org.broadinstitute.hellbender.utils.iterators.IntervalLocusIterator
- intervalMergingRule - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
By default, the program merges abutting intervals (i.e.
- IntervalMergingRule - Enum Class in org.broadinstitute.hellbender.utils
-
a class we use to determine the merging rules for intervals passed to the GATK
- intervalOnlyAssembly - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- IntervalOverlappingIterator<T extends htsjdk.samtools.util.Locatable> - Class in org.broadinstitute.hellbender.utils.iterators
-
Wraps an iterator of
Locatablewith a list of sorted intervals to return only the objects which overlaps with them - IntervalOverlappingIterator(Iterator<T>, List<SimpleInterval>, SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.utils.iterators.IntervalOverlappingIterator
-
Wraps an iterator to be filtered by a sorted list of intervals
- IntervalOverlapReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
A simple read filter that allows for the user to specify intervals at the filtering stage.
- IntervalOverlapReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.IntervalOverlapReadFilter
-
Default constructor.
- IntervalOverlapReadFilter(List<String>) - Constructor for class org.broadinstitute.hellbender.engine.filters.IntervalOverlapReadFilter
-
Constructor with provided intervals.
- intervalPadding - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
Use this to add padding to the intervals specified using -L.
- intervalPadding - Variable in class org.broadinstitute.hellbender.tools.walkers.PairWalker
- IntervalPileup - Interface in org.broadinstitute.hellbender.utils
- IntervalPileup.Element - Interface in org.broadinstitute.hellbender.utils
- IntervalPileup.Insert - Interface in org.broadinstitute.hellbender.utils
- intervals - Variable in class picard.analysis.AbstractWgsMetricsCollector
- intervals - Variable in class picard.analysis.WgsMetrics
-
The intervals over which this metric was computed.
- INTERVALS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- INTERVALS - Variable in class picard.analysis.CollectMultipleMetrics
- INTERVALS - Variable in class picard.analysis.CollectOxoGMetrics
- INTERVALS - Variable in class picard.analysis.CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
- INTERVALS - Variable in class picard.analysis.CollectWgsMetrics
- INTERVALS - Variable in class picard.reference.NonNFastaSize
- INTERVALS - Variable in class picard.sam.MergeSamFiles
- INTERVALS - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- INTERVALS - Variable in class picard.vcf.GenotypeConcordance
- INTERVALS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- INTERVALS_PATH - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- INTERVALS_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- intervalSetRule - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
By default, the program will take the UNION of all intervals specified using -L and/or -XL.
- IntervalSetRule - Enum Class in org.broadinstitute.hellbender.utils
-
set operators for combining lists of intervals
- intervalsFile - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
-
File containing tribble-readable features for the IntervalStratificiation
- intervalSize(List<GenomeLoc>) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
- IntervalsManipulationProgramGroup - Class in picard.cmdline.programgroups
-
Tools that process genomic intervals in various formats.
- IntervalsManipulationProgramGroup() - Constructor for class picard.cmdline.programgroups.IntervalsManipulationProgramGroup
- intervalsSpecified() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
Have any intervals been specified for inclusion or exclusion
- IntervalStratification - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies the variants by whether they overlap an interval in the set provided on the command line.
- IntervalStratification(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.IntervalStratification
- intervalStrings - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalIntervalArgumentCollection
- intervalStrings - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredIntervalArgumentCollection
- intervalStrings - Variable in class org.broadinstitute.hellbender.engine.filters.IntervalOverlapReadFilter
- IntervalUtils - Class in org.broadinstitute.hellbender.utils
-
Parse text representations of interval strings that can appear in GATK-based applications.
- IntervalUtils() - Constructor for class org.broadinstitute.hellbender.utils.IntervalUtils
- IntervalUtils.IntervalBreakpointType - Enum Class in org.broadinstitute.hellbender.utils
-
An enum to classify breakpoints whether the breakpoint is the start or end of a region.
- IntervalWalker - Class in org.broadinstitute.hellbender.engine
-
An IntervalWalker is a tool that processes a single interval at a time, with the ability to query optional overlapping sources of reads, reference data, and/or variants/features.
- IntervalWalker() - Constructor for class org.broadinstitute.hellbender.engine.IntervalWalker
- IntervalWalkerContext - Class in org.broadinstitute.hellbender.engine.spark
-
Encapsulates a
SimpleIntervalwith the reads that overlap it (theReadsContextand itsReferenceContextandFeatureContext. - IntervalWalkerContext(SimpleInterval, ReadsContext, ReferenceContext, FeatureContext) - Constructor for class org.broadinstitute.hellbender.engine.spark.IntervalWalkerContext
- IntervalWalkerSpark - Class in org.broadinstitute.hellbender.engine.spark
-
A Spark version of
IntervalWalker. - IntervalWalkerSpark() - Constructor for class org.broadinstitute.hellbender.engine.spark.IntervalWalkerSpark
- intervalWeight(Interval) - Method in interface picard.util.IntervalList.IntervalListScatterer
-
A method that defines the "weight" of an interval list for the purpose of scattering.
- intervalWeight(Interval) - Method in class picard.util.IntervalList.IntervalListScattererByBaseCount
- intervalWeight(Interval) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
- IntHistogram - Class in org.broadinstitute.hellbender.tools.spark.utils
-
Histogram of observations on a compact set of non-negative integer values.
- IntHistogram(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram
- IntHistogram.CDF - Class in org.broadinstitute.hellbender.tools.spark.utils
- IntHistogram.CDF.Serializer - Class in org.broadinstitute.hellbender.tools.spark.utils
- IntHistogram.Serializer - Class in org.broadinstitute.hellbender.tools.spark.utils
- IntPair(int, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark.IntPair
- INTRA_CHR_REF_ORDER_SWAP - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.SupportedType
- INTRA_CHR_REF_ORDER_SWAP - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera
- INTRA_CHR_STRAND_SWITCH_33 - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.SupportedType
- INTRA_CHR_STRAND_SWITCH_33 - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera
- INTRA_CHR_STRAND_SWITCH_55 - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.SupportedType
- INTRA_CHR_STRAND_SWITCH_55 - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera
- IntraChromosomalStrandSwitch33BreakEnd(String, int, String, Allele, Allele, Map<String, Object>, boolean) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.IntraChromosomalStrandSwitch33BreakEnd
- IntraChromosomalStrandSwitch55BreakEnd(String, int, String, Allele, Allele, Map<String, Object>, boolean) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.IntraChromosomalStrandSwitch55BreakEnd
- IntraChromosomeRefOrderSwap(String, int, String, Allele, Allele, Map<String, Object>, boolean) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.IntraChromosomeRefOrderSwap
- INTRAGENIC - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- INTRON - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Variant lies between exons within the bounds of the chosen transcript.
- INTRON - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- INTRON_CONSERVED - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- INTRONIC - Enum constant in enum class picard.annotation.LocusFunction
- INTRONIC - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- INTRONIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Number of bases in primary alignments that align to an intronic base for some gene, and not a coding or UTR base.
- IntToDoubleBiFunction - Interface in org.broadinstitute.hellbender.utils.functional
-
Created by davidben on 8/19/16.
- IntToDoubleFunctionCache - Class in org.broadinstitute.hellbender.utils
-
A helper class to maintain a cache of an int to double function defined on n = 0, 1, 2.
- IntToDoubleFunctionCache() - Constructor for class org.broadinstitute.hellbender.utils.IntToDoubleFunctionCache
- INV - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.SupportedType
- INV - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.StructuralVariantAnnotationType
- INV_LOG_10 - Static variable in class org.broadinstitute.hellbender.utils.MathUtils
- INV_LOG_2 - Static variable in class org.broadinstitute.hellbender.utils.MathUtils
- INV_LOG_2 - Static variable in class org.broadinstitute.hellbender.utils.param.ParamUtils
- INV_SPAN - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- INV33 - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- INV55 - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- INVALID - Static variable in enum class org.broadinstitute.hellbender.utils.Nucleotide
- INVALID_ATTRIBUTES - Static variable in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- INVALID_ELEMENT_FROM_READ - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.RankSumTest
- INVALID_TABLE_NAME_REGEX - Static variable in class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
REGEX that matches any table with an invalid name
- INVALIDATE_PREVIOUS_FILTERS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- INVdel - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.ComplexVariantSubtype
- INVdup - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.ComplexVariantSubtype
- InverseAllele - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
-
Utility class for defining a "not" allele concept that is used to score haplotypes that are not supporting the allele.
- inverseRate(long, long) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
- Inversion(String, int, int, String, Allele, Allele, int, Map<String, Object>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.Inversion
- Inversion(NovelAdjacencyAndAltHaplotype, int, BasicReference) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.Inversion
- INVERT - Variable in class picard.util.IntervalListTools
- INVERT_GT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- INVERT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- INVERT_SOFT_CLIP_RATIO_FILTER - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- invertCigar(Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
Inverts the order of the operators in the cigar.
- invertFilterExpression - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
-
Invert the selection criteria for --filter-expression
- invertGenotypeFilterExpression - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
-
Invert the selection criteria for --genotype-filter-expression
- IO_SIZE - Variable in class picard.util.FifoBuffer
- ION_TORRENT - Enum constant in enum class org.broadinstitute.hellbender.utils.NGSPlatform
- IOUtils - Class in org.broadinstitute.hellbender.utils.io
- IOUtils() - Constructor for class org.broadinstitute.hellbender.utils.io.IOUtils
- IS_BISULFITE_SEQUENCE - Variable in class picard.sam.MergeBamAlignment
- IS_BISULFITE_SEQUENCE - Variable in class picard.sam.SetNmMdAndUqTags
- IS_BISULFITE_SEQUENCED - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
- IS_BISULFITE_SEQUENCED - Variable in class picard.analysis.CollectGcBiasMetrics
- IS_BISULFITE_SEQUENCED - Variable in class picard.sam.ValidateSamFile
- IS_HOST_ALIGNED_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- IS_MIXED - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- IS_MIXED - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- IS_MIXED_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- IS_SINGLETON_KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- IS_ZCALLED - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
Whether the sample was zcalled
- isAbleToValidateGenotype(Genotype, Allele) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicSomaticShortMutationValidator
- isAbove(NioFileCopierWithProgressMeter.Verbosity) - Method in enum class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter.Verbosity
- isAcceptableFeatureType(Class<? extends Feature>) - Method in class org.broadinstitute.hellbender.engine.FeatureWalker
-
Returns whether the given class of features is acceptable for this walker.
- isAcceptableFeatureType(Class<? extends Feature>) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleFeatureWalker
- isAcceptableFeatureType(Class<? extends Feature>) - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotateSegments
- isAcceptableFeatureType(Class<? extends Feature>) - Method in class org.broadinstitute.hellbender.tools.sv.CondenseDepthEvidence
- isAcceptableFeatureType(Class<? extends Feature>) - Method in class org.broadinstitute.hellbender.tools.sv.PrintReadCounts
- isActive() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Does this region represent an active region (all isActiveProbs above threshold) or an inactive region (all isActiveProbs below threshold)?
- isActive() - Method in class org.broadinstitute.hellbender.engine.ReadlessAssemblyRegion
- isActive(AlignmentContext, ReferenceContext, FeatureContext) - Method in interface org.broadinstitute.hellbender.engine.AssemblyRegionEvaluator
-
Given a pileup over a single locus, returns an ActivityProfileState containing the probability (0.0 to 1.0) that the locus is an "active" site.
- isActive(AlignmentContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
-
Given a pileup, returns an ActivityProfileState containing the probability (0.0 to 1.0) that it's an "active" site.
- isActive(AlignmentContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- isActiveProb() - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState
- isActualFlowOrderRequired() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.CycleSkipStatus
- isActualFlowOrderRequired() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- isAdapter(SAMRecord) - Method in class picard.analysis.AdapterUtility
-
Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
- isAdapterClipped(SAMRecord) - Static method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- isAdapterClippedWithQ(SAMRecord) - Static method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- isAdapterSequence(byte[]) - Method in class picard.analysis.AdapterUtility
-
Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
- isAdapterSequence(byte[], boolean) - Method in class picard.analysis.AdapterUtility
-
Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
- isAdditionalCovariateTable(NestedIntegerArray<RecalDatum>) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
- isAfter(Locatable, Locatable, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Tests whether the first Locatable starts after the end of the second Locatable
- isAfterDeletionEnd() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Is the current element immediately after a deletion, but itself not a deletion? Suppose we are aligning a read with cigar 1M2D3M.
- isAfterInsertion() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Does an insertion occur immediately before the current position on the genome?
- isAfterSoftClip() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Does a soft-clipping event occur immediately before the current position on the genome?
- isAlleleInList(Allele, Allele, Allele, List<Allele>) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Does an allele match any in a list of alleles? We don't assume that ref1/alt1 are in their minimal representation
- isAlleleSpecific(InfoFieldAnnotation) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils
-
Helper function to determine if an annotation is allele-specific
- isAllRegularBases(byte[]) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
-
Returns true iff all bases are 'regular'
BaseUtils.isRegularBase(byte). - isAltAfterAssembly(PileupElement, byte) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
- isAltAllele(Allele) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
- isAltBeforeAssembly(PileupElement, byte) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
- isAltGenotype(Genotype) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
- isAmbiguous() - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Checks whether the nucleotide refer to an ambiguous base.
- isAmbiguous() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- isAntiTraining - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrainingSet
- isAppendFile() - Method in class org.broadinstitute.hellbender.utils.runtime.OutputStreamSettings
- isArtifact(VariantContext, Mutect2FilteringEngine) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ClusteredEventsFilter
- isArtifact(VariantContext, Mutect2FilteringEngine) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FragmentLengthFilter
- isArtifact(VariantContext, Mutect2FilteringEngine) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.HardFilter
- isArtifact(VariantContext, Mutect2FilteringEngine) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MultiallelicFilter
- isArtifact(VariantContext, Mutect2FilteringEngine) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NRatioFilter
- isArtifact(VariantContext, Mutect2FilteringEngine) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.PanelOfNormalsFilter
- isAvailable - Variable in enum class picard.nio.PathProvider
- isBaseClipped() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- isBaseInsideAdaptor(GATKRead, long) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
is this base inside the adaptor of the read? There are two cases to treat here: 1) Read is in the negative strand => Adaptor boundary is on the left tail 2) Read is in the positive strand => Adaptor boundary is on the right tail Note: We return false to all reads that are UNMAPPED or have an weird big insert size (probably due to mismapping or bigger event)
- isBefore(Locatable, Locatable, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Tests whether the first Locatable ends before the start of the second Locatable
- isBefore(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
Tests whether this contig is completely before contig 'that'.
- isBeforeDeletionStart() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Is the current element immediately before a deletion, but itself not a deletion? Suppose we are aligning a read with cigar 3M2D1M.
- isBeforeInsertion() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Does an insertion occur immediately after the current position on the genome?
- isBeforeSoftClip() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Does a soft-clipping event occur immediately after the current position on the genome?
- isBetaFeature() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- isBetween(GenomeLoc, GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- isBlank(byte[]) - Method in class picard.util.AbstractInputParser
-
Determines whether a given line is a comment
- isBlockGzipped(File) - Static method in class picard.illumina.parser.readers.BclReader
- isBufferEmpty() - Method in class org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFBlockCombiner
- isBufferTruncated() - Method in class org.broadinstitute.hellbender.utils.runtime.CapturedStreamOutput
- isBufferTruncated() - Method in class org.broadinstitute.hellbender.utils.runtime.StreamOutput
-
Returns true if the buffer was truncated.
- isCalledAndDiploidWithLikelihoodsOrWithGQ(Genotype) - Static method in class org.broadinstitute.hellbender.utils.GenotypeUtils
-
Returns true if the genotype is a diploid genotype with likelihoods.
- isCandidateForFatInsertion() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
-
For replacement, one could have a case where the sequence being replaced (i.e.
- isCanonical() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- isCanonical() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- isCanonical() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- isCanonical() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Kmer
- isCanonical(long) - Static method in class org.broadinstitute.hellbender.tools.LocalAssembler.Kmer
- isChimeric(SAMRecord, int, Set<SamPairUtil.PairOrientation>) - Static method in class picard.analysis.ChimeraUtil
-
Checks whether the given read is part of a chimeric pair.
- isChimeric(SAMRecord, SAMRecord, int, Set<SamPairUtil.PairOrientation>) - Static method in class picard.analysis.ChimeraUtil
-
Checks whether the given read is part of a chimeric pair.
- isClipOverlappingReads() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
- isClipOverlappingReads() - Method in class picard.sam.AbstractAlignmentMerger
- isClosed() - Method in class org.broadinstitute.hellbender.utils.AutoCloseableReference
-
Checks whether this reference has already been closed.
- isClosed() - Method in class picard.util.CircularByteBuffer
-
Returns true if the buffer is closed, false otherwise.
- isClusterRecord() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- isCnvType(StructuralVariantType) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKSVVariantContextUtils
-
Determines whether a given SV type represents a CNV.
- isCnvType(GATKSVVCFConstants.StructuralVariantAnnotationType) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKSVVariantContextUtils
-
Determines whether a given SV type represents a CNV.
- isCollapsed() - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- isComment(byte[]) - Method in class picard.util.AbstractInputParser
-
Determines whether a given line is a comment
- isCommentLine(String[]) - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Checks whether a line is a comment line or not.
- isComplexIndel(Allele, Allele) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
This method should only be run on variants that are known to be indels.
- isConsensus - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrainingSet
- isContaminant(HitsForInsert) - Method in class picard.sam.AbstractAlignmentMerger
- isContaminant(HitsForInsert) - Method in class picard.sam.SamAlignmentMerger
-
Criteria for contaminant reads: 1.
- isContiguous(VariantContext) - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
-
Allow overlapping input blocks, as in the case where shards are split with duplicate boundary events
- isCopyComplete() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- isCycleMember() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- isCycleMember() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- isCycleMember() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- isDbSnpSite(String, int) - Method in class org.broadinstitute.hellbender.utils.variant.DbSnpBitSetUtil
-
Returns true if there is a dbSnp entry at pos in sequenceName, otherwise false
- isDbSnpSite(String, int) - Method in class picard.util.DbSnpBitSetUtil
-
Returns true if there is a dbSnp entry at pos in sequenceName, otherwise false
- isDebug() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- isDebugGraphTransformations() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- isDeletion() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Is this element a deletion w.r.t.
- isDeletion(Allele, Allele) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Determines whether the given reference and alternate alleles constitute a deletion mutation.
- isDeletion(String, String) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Determines whether the given reference and alternate alleles constitute a deletion mutation.
- isDelimiter(byte) - Method in class picard.util.AbstractInputParser
-
Determines whether a given character is a delimiter
- isDelimiter(byte) - Method in class picard.util.CsvInputParser
-
Determines whether a given character is a delimiter
- isDelimiter(byte) - Method in class picard.util.TabbedInputParser
-
Determines whether a given character is a delimiter
- isDependentArgumentAllowed(Class<?>) - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
- isDependentArgumentAllowed(Class<?>) - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
- isDepthOnly() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- isDestFileValid() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeterResults
-
Returns whether the downloaded file is valid by comparing the
NioFileCopierWithProgressMeterResults.checksumandNioFileCopierWithProgressMeterResults.expectedChecksumvalues. - isDifferentByKSStatistic(IntHistogram, float) - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.CDF
-
Using the Kolmogorov-Smirnov statistic for two samples: Is the specified histogram significantly different from the CDF? This is what we use in production code: It minimizes the number of comparisons, and quits as soon as it finds a significant K-S stat (rather than finding the max).
- isDiploidWithLikelihoods(Genotype) - Static method in class org.broadinstitute.hellbender.utils.GenotypeUtils
-
Returns true if the genotype is a diploid genotype with likelihoods.
- isDisabledFilter(String) - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
-
Determine if a particular ReadFilter was disabled on the command line, either directly of by disabling all tool defaults.
- isDisjointFrom(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVInterval
- isDistantMate(GATKRead) - Static method in class org.broadinstitute.hellbender.tools.PrintDistantMates
- isDoingExactLog10Calculations() - Method in class org.broadinstitute.hellbender.utils.pairhmm.Log10PairHMM
-
Is this HMM using exact log calculations?
- isDone(B) - Method in class org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec
- isDone(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec
- isDone(BlockCompressedIntervalStream.Reader<F>) - Method in class org.broadinstitute.hellbender.utils.codecs.AbstractBCICodec
- isDupContraction() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- isDupe() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- isDuplicate() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- isDuplicate() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- isDuplicateMarked() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.ReadPair
- isEligibleForPrefetching(Path) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
- isEligibleForPrefetching(GATKPath) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
- isEmpty() - Method in class org.broadinstitute.hellbender.engine.FeatureManager
-
Does this manager have no sources of Features to query?
- isEmpty() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableEntry
- isEmpty() - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- isEmpty() - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter
- isEmpty() - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- isEmpty() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine
-
Returns true if there are any active or finalized clusters.
- isEmpty() - Method in class org.broadinstitute.hellbender.tools.walkers.consensus.ReadsWithSameUMI
- isEmpty() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
-
Does this vertex have an empty sequence? That is, is it a dummy node that's only present for structural reasons but doesn't actually contribute to the sequence of the graph?
- isEmpty() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- isEmpty() - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
-
Is this profile empty? (ie., does it contain no ActivityProfileStates?)
- isEmpty() - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
- isEmpty() - Method in class org.broadinstitute.hellbender.utils.CompressedDataList
- isEmpty() - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
determine if the collection is empty
- isEmpty() - Method in class org.broadinstitute.hellbender.utils.Histogram
- isEmpty() - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
- isEmpty() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- isEmpty() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport
- isEmpty() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
- isEmpty() - Method in class picard.illumina.parser.ReadStructure.Substructure
- isEmpty() - Method in class picard.sam.markduplicates.util.MarkQueue
- isEmpty(SAMRecord) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
- isEnabled() - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingDebugger
- isEnoughValidationReads() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- isEvidence(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter
- isEvidenceUpstreamOfBreakpoint() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
-
If true: the evidence suggests a breakpoint at a reference location upstream of the interval's start coordinate If false: the evidence suggests a breakpoint downstream of the interval's end coordinate
- isEvidenceUpstreamOfBreakpoint() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
- isExpected() - Method in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
- isExperimentalFeature() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- isF1R2(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
- isF2R1(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
- isFail() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- isFeatureFile(Path) - Static method in class org.broadinstitute.hellbender.engine.FeatureManager
- isFileUrl(String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
- isFinalized() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
- isFinite(double, String) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Checks that the input is not infinity nor NaN or throws an
IllegalArgumentException - isFirstOfPair() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- isFirstOfPair() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- isFlow(SAMRecord) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- isFlow(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- isFlowEnabled() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- isForwardStrand() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.Mapping
- isFrameshift(int, int, int) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Determines whether the given reference and alternate alleles constitute a frameshift mutation.
- isFrameshift(Allele, Allele) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Determines whether the given reference and alternate alleles constitute a frameshift mutation.
- isFrameshift(String, String) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Determines whether the given reference and alternate alleles constitute a frameshift mutation.
- isFuncotationInTranscriptList(GencodeFuncotation, Set<String>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Determines whether the given
funcotationhas a transcript ID that is in the givenacceptableTranscripts. - isGap() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.PathPart
- isGap() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartContig
- isGap() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartGap
- isGatkIntervalFile(String) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Check if string argument was intended as a file Accepted file extensions: .bed .list, .picard, .interval_list, .intervals.
- isGatkIntervalFile(String, boolean) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Check if string argument was intended as a file Accepted file extensions are defined in
IntervalUtils.GATK_INTERVAL_FILE_EXTENSIONS - isGcsUrl(String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
- isGcsUrl(GATKPath) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Return true if this
GATKPathrepresents a gcs URI. - isGencodeFuncotation(Funcotation) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
- isGenomicsDBPath(String) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Check if a given path represents GenomicsDB URI.
- isGenomicsDBPath(GATKPath) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Check if a given GATKPath represents a GenomicsDB URI.
- isGood(Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
A good Cigar object obeys the following rules: - is valid as per SAM spec
Cigar.isValid(String, long). - isGzipped(File) - Static method in class picard.illumina.parser.readers.BclReader
- isHadoopUrl(String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Returns true if the given path is a HDFS (Hadoop filesystem) URL.
- isHadoopURL() - Method in class org.broadinstitute.hellbender.engine.GATKPath
-
Returns true if this is a HDFS (Hadoop filesystem) URL.
- isHDF5File(Path) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Given a Path, determine if it is an HDF5 file without requiring that we're on a platform that supports HDF5 (let the caller decide if a return value of false is fatal).
- isHeaderLine(String[]) - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Determines whether a line is a repetition of the header.
- isHeterozygous() - Method in enum class picard.fingerprint.DiploidGenotype
- isHigherPriorityThan(SnpEffUtil.EffectFunctionalClass) - Method in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectFunctionalClass
- isHmerIndel(VariantContext, FlowAnnotatorBase.LocalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- isHomogeneous() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.HeterogeneousPloidyModel
- isHomogeneous() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.HomogeneousPloidyModel
- isHomogeneous() - Method in interface org.broadinstitute.hellbender.tools.walkers.genotyper.PloidyModel
-
Checks whether the ploidy is homogeneous across all samples.
- isHomomozygous() - Method in enum class picard.fingerprint.DiploidGenotype
- isHomRefBlock(VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
-
determine if a VC is a homRef block, i.e.
- isHttpUrl(String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
- isImpreciseDeletion() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
- isIndel() - Method in interface org.broadinstitute.hellbender.utils.variant.GATKVariant
- isIndel() - Method in class org.broadinstitute.hellbender.utils.variant.MinimalVariant
- isIndel() - Method in class org.broadinstitute.hellbender.utils.variant.VariantContextVariantAdapter
- isIndel() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- isIndel(Allele, Allele) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Determines whether the given reference and alternate alleles constitute an insertion or deletion mutation.
- isIndel(String, String) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Determines whether the given reference and alternate alleles constitute an insertion or deletion mutation.
- isIndelBetweenCodons(int, int, String, Strand) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Checks to see whether a given indel location occurs on a codon boundary.
- isIndexed() - Method in class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
-
A
CachingIndexedFastaSequenceFileis always indexed. - isInextensible() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- isInformative() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods.BestAllele
- isInformative(double[]) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- isInFrameWithEndOfRegion(int, int) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Calculates whether the given
startPosition(1-based, inclusive) is in frame relative to the end of the region. - isInsertion(Allele, Allele) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Determines whether the given reference and alternate alleles constitute an insertion mutation.
- isInsertion(String, String) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Determines whether the given reference and alternate alleles constitute an insertion mutation.
- isInsideDeletion(Cigar, int) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Is the offset inside a deletion?
- isInsideRead(GATKRead, int) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Is a base inside a read?
- isIntensityOnly() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- isIntrachromosomal() - Method in interface org.broadinstitute.hellbender.tools.sv.SVLocatable
- isKeepAlignerProperPairFlags() - Method in class picard.sam.AbstractAlignmentMerger
- isKeepValid() - Method in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- isKept(int) - Method in interface org.broadinstitute.hellbender.utils.collections.Permutation
-
Given an index of the original list, return whether this index is found at any position of the permuted list.
- isKept(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.ActualPermutation
- isKept(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.NonPermutation
- isKnown - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrainingSet
- isKnown(String) - Static method in enum class org.broadinstitute.hellbender.utils.NGSPlatform
-
checks whether or not the requested platform is listed in the set (and is not unknown)
- isLabelFlat(String) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- isLeftEdge() - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
-
Is this the left edge state? I.e., one that is before or after the current read?
- isLeftOverhang(GenomeLoc, GenomeLoc) - Static method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager
-
Is this a proper overhang on the left side of the read?
- isLegacyPicardStyle(String[]) - Static method in class picard.cmdline.CommandLineSyntaxTranslater
- isLinearChainStart(SeqVertex) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqGraph
-
Is source vertex potentially a start of a linear chain of vertices? We are a start of a zip chain if our out degree is 1 and either the the vertex has no incoming connections or 2 or more (we must start a chain) or we have exactly one incoming vertex and that one has out-degree > 1 (i.e., source's incoming vertex couldn't be a start itself
- isLowQualityGraph() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
- isLowQualityGraph() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
- isLowQualityGraph() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
-
Does the graph not have enough complexity? We define low complexity as a situation where the number of non-unique kmers is more than 20% of the total number of kmers.
- isMapped() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.Mapping
- isMapped(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter
- isMappedPrimary(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter
- isMappedToPrimaryContig(GATKRead, ReadMetadata) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter
- isMarked() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- isMarked() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- isMarked() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- isMatch() - Method in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
- isMatched() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
- isMergeEvals() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- isMissing(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns true if EITHER the truth or call state is MISSING.
- isNaturalLog() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
- isNBase(byte) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
- isNegativeOrZero(double, String) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Checks that the input is positive or zero and returns the same value or throws an
IllegalArgumentException - isNegativeStrand(GencodeGtfTranscriptFeature) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate
-
Check if strand of transcript from GTF is negative
- isNeitherIncompleteNorSimpleTranslocation() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera
- isNewBlock(long, long) - Static method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream
- isNextToSoftClip() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Does a soft-clipping event occur immediately before or after the current position on the genome?
- isNonEmpty(Collection<?>) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Checks that a
Collectionis notnulland that it is not empty. - isNonPermuted() - Method in interface org.broadinstitute.hellbender.utils.collections.Permutation
-
Checks whether this is a trivial permutation where the resulting element list is the same as original.
- isNonPermuted() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.ActualPermutation
- isNonPermuted() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.NonPermutation
- isNonPrimary(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
- isNonRefAllele(Allele) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
- isNormal(Genotype) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- isNotFailure() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse
- isNucleotide(byte) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
-
Returns true iff the base represented by the byte is a nucleotide base (ACGT).
- ISOLATION_FOREST_HYPERPARAMETERS_JSON - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
- ISOLATION_FOREST_PYTHON_SCRIPT - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
- ISOLEUCINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- isOpticalDuplicate - Variable in class picard.sam.markduplicates.util.ReadEnds
-
A *transient* flag marking this read end as being an optical duplicate.
- isOutOfNoiseFloor() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- isOverwriteExisting() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- isPaired() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- isPaired() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
- isPaired() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- isPaired() - Method in class picard.sam.markduplicates.util.ReadEnds
- isPaired() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
- isPartial() - Method in interface org.broadinstitute.hellbender.utils.collections.Permutation
-
Checks whether this permutation is a partial one of the original list.
- isPartial() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.ActualPermutation
- isPartial() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.NonPermutation
- isPast(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
Tests whether this contig is completely after contig 'that'.
- isPerformDownsampling() - Method in class org.broadinstitute.hellbender.utils.locusiterator.LIBSDownsamplingInfo
- isPf() - Method in class picard.illumina.parser.CbclData
- isPf() - Method in class picard.illumina.parser.ClusterData
- isPhasing(IlluminaMetricsCode) - Static method in enum class picard.illumina.parser.IlluminaMetricsCode
- isPopulateOaTag() - Method in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- isPositionInFrame(int) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Gets whether the given position is in-frame.
- isPositive(double, String) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Checks that the input is greater than zero and returns the same value or throws an
IllegalArgumentException - isPositive(int, String) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Checks that the input
intvalue is greater than zero and returns the same value or throws anIllegalArgumentException - isPositive(long, String) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Checks that the input is greater than zero and returns the same value or throws an
IllegalArgumentException - isPositiveAck() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessControllerAckResult
- isPositiveOrZero(double, String) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Checks that the input is positive or zero and returns the same value or throws an
IllegalArgumentException - isPositiveOrZero(int, String) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Checks that the input is positive or zero and returns the same value or throws an
IllegalArgumentException - isPositiveOrZero(long, String) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Checks that the input is positive or zero and returns the same value or throws an
IllegalArgumentException - isPredecessor(LocalAssembler.Contig) - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- isPreservingCase() - Method in class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
-
Is this CachingIndexedFastaReader keeping the original case of bases in the fasta, or is everything being made upper case?
- isPrimaryLine(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter
- isProperlyPaired() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- isProperlyPaired() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- isProperlyPolymorphic(VariantContext) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Determines whether the provided VariantContext has real alternate alleles.
- isQualityClipped(SAMRecord) - Static method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- isQualityScoreTable(NestedIntegerArray<RecalDatum>) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
- isQueryable() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- isQueryableByInterval() - Method in interface org.broadinstitute.hellbender.engine.ReadsDataSource
- isQueryableByInterval() - Method in class org.broadinstitute.hellbender.engine.ReadsPathDataSource
- isRC() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- isRead1ReverseStrand() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.EmptyFragment
- isRead1ReverseStrand() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.FlowModeFragment
- isRead1ReverseStrand() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Fragment
- isRead1ReverseStrand() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair
- isRead1ReverseStrand() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.PairedEnds
- isReadGroupTable(NestedIntegerArray<RecalDatum>) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
- isReadNameGroupedBam(SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Interrogates the header to determine if the bam is expected to be sorted such that reads with the same name appear in order.
- isReadsRequired() - Method in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.TensorType
- isReciprocalOverlap(SimpleInterval, SimpleInterval, double) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Determine whether the two intervals specified overlap each other by at least the threshold proportion specified.
- isRecoverDanglingBranches() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- isRedirectErrorStream() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- isRef() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge
-
Does this edge indicate a path through the reference graph?
- isReference() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotype
- isReferenceNode(V) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
- isRefSink(V) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
- isRefSource(V) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
- isRefStrandDefinedInManifest() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- isRegularBase(byte) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
-
Returns true iff the base represented by the byte is a 'regular' base (ACGT or *).
- isRemoteStorageUrl(String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Returns true if the given path is a GCS, HDFS (Hadoop filesystem), or Http(s) URL.
- isRepeatAllele(Allele, Allele, String) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Helper function for isTandemRepeat that checks that allele matches somewhere on the reference
- isRequestedReducibleRawKey(String) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
-
Method which checks if a key is a raw key of the requested reducible annotations
- isReservedTag(String) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
- isReservedTag(String) - Method in class picard.sam.AbstractAlignmentMerger
- isResetMappingInformation() - Method in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- isReverseStrand() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- isReverseStrand() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- isRightAlign(String) - Static method in class org.broadinstitute.hellbender.utils.report.GATKReportColumn
-
Check if the value can be right aligned.
- isRightEdge() - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
-
Are we on the right edge? I.e., is the current state off the right of the alignment?
- isRightOverhang(GenomeLoc, GenomeLoc) - Static method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager
-
Is this a proper overhang on the right side of the read?
- isSameBlock(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
- isSameDictionary(SAMSequenceDictionary, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
-
Compares two non-null sequence dictionaries using sequence index, name, and length only.
- isSameFormat(GATKReport) - Method in class org.broadinstitute.hellbender.utils.report.GATKReport
-
Returns whether or not the two reports have the same format, from columns, to tables, to reports, and everything in between.
- isSameFormat(GATKReportTable) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Returns whether or not the two tables have the same format including columns and everything in between.
- isSampleContaminationPresent() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection
-
Returns true if there is some sample contamination present, false otherwise.
- isSecondaryAlignment() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- isSecondaryAlignment() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- isSecondOfPair() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- isSecondOfPair() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- isSegmentVariantContext(VariantContext, int) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Determine whether a given variant context represents a segment.
- isSequenceDictionaryFromIndex(SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.IndexUtils
-
Determine if
sequenceDictionaryhas the form of a dictionary created from an index file byIndexUtils.createSequenceDictionaryFromFeatureIndex(java.nio.file.Path)). - isSequenceDictionaryUsingB37Reference(SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Returns if the given
SAMSequenceDictionaryis for the B37 Human Genome Reference. - isSilent() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- isSimpleCNV() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- isSingleEndReadKnownFragment(SAMRecord) - Static method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
-
This method is used to generate the following two metrics: UNPAIRED_DUPS_WITH_TLEN UNPAIRED_DUPS_WITHOUT_TLEN It will return true if and only if the read is single ended and the exact fragment length is known (i.e.
- isSink(V) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
- isSiteLowHeteroplasmy(VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MTLowHeteroplasmyFilterTool
- isSkipBlankLines() - Method in class picard.util.AbstractInputParser
- isSnp() - Method in interface org.broadinstitute.hellbender.utils.variant.GATKVariant
- isSnp() - Method in class org.broadinstitute.hellbender.utils.variant.MinimalVariant
- isSnp() - Method in class org.broadinstitute.hellbender.utils.variant.VariantContextVariantAdapter
- isSnp() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- isSoloTranscript() - Method in class picard.annotation.Gene.Transcript
- isSource(V) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
- isSpanningDeletion(Allele) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- isSpanningDeletionOnly(VariantContext) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- isSpecialFile(File) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Returns true if the file is a special file.
- isStandard() - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Checks whether the nucleotide refers to a concrete (rather than ambiguous) base.
- isStop() - Method in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- isSubsettingToSpecificSamples() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- isSubTypeOf(SnpEffUtil.EffectType, SnpEffUtil.EffectType) - Static method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil
- isSuccessor(LocalAssembler.Contig) - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- isSupplementaryAlignment() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- isSupplementaryAlignment() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- isSupportConnected() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BetaBinomialDistribution
- isSupportingSegmentFuncotation() - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
- isSupportingSegmentFuncotation() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
- isSymbolic() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.InverseAllele
- isSymbolicEnd() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph.ThreadingNode
- isSymmetricallyNormalizeAllelesToReference() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
- isTandemRepeat(VariantContext, byte[]) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Returns true iff VC is an non-complex indel where every allele represents an expansion or contraction of a series of identical bases in the reference.
- isTemplateLenTestable(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter
- isTestable(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
- isTheUpstreamMate() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType
- isThreadingStart(Kmer, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Checks whether a kmer can be the threading start based on the current threading start location policy.
- isThreadingStart(Kmer, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
-
Checks whether a kmer can be the threading start based on the current threading start location policy.
- isThreadingStart(Kmer, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
-
Checks whether a kmer can be the threading start based on the current threading start location policy.
- isTraining - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrainingSet
- isTransition(byte, byte) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
- isTransition(VariantContext) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
If this is a BiAllelic SNP, is it a transition?
- isTreatGroupedDelimitersAsOne() - Method in class picard.util.AbstractInputParser
- isTruth - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrainingSet
- isTumor(Genotype) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- isTwoBit(GATKPath) - Static method in class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceTwoBitSparkSource
- isUnmapped() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
- isUnmapped() - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
Return true if this GenomeLoc represents the UNMAPPED location
- isUnmapped() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- isUnmapped() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- isUnmapped(GenomeLoc) - Static method in class org.broadinstitute.hellbender.utils.GenomeLoc
- isUnmappedGenomeLocString(String) - Static method in class org.broadinstitute.hellbender.utils.GenomeLocParser
- isUnmixedMnpIgnoringNonRef(VariantContext) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Returns true if the context represents a MNP.
- isUnplaced() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Does the read have a position assigned to it for sorting purposes.
- isUnplaced() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- isUpstreamOf(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVInterval
-
Returns false if the two intervals overlap as judged by
SVInterval.overlaps(SVInterval) - isUsableBaseForAnnotation(PileupElement) - Static method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Can the base in this pileup element be used in comparative tests?
- isUsableRead(GATKRead) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.OrientationBiasReadCounts
- isUsableRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_ReadPosRankSumTest
- isUsableRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.RankSumTest
-
Can the read be used in comparative tests between ref / alt bases?
- isUsableRead(GATKRead, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosRankSumTest
- isValid() - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Whether this nucleotide code is valid or not.
- isValid() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- isValid(String, int, int) - Static method in class org.broadinstitute.hellbender.utils.SimpleInterval
-
Test that these are valid values for constructing a SimpleInterval: contig cannot be null start must be >= 1 end must be >= start
- isValidArrayOffsetAndRangeLength(int, int, int, String) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Checks that a range in an array specified using the first element index/offset and the length of the range is valid.
- isValidated() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
- isValidBase(byte) - Static method in enum class picard.fingerprint.DiploidGenotype
- isValidGenomeLoc(String, int, int) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
- isValidGenomeLoc(String, int, int, boolean) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
Would a genome loc created with the given parameters be valid w.r.t.
- isValidLength(int) - Method in class org.broadinstitute.hellbender.utils.IndexRange
-
Checks whether this range is valid for a collection or array of a given size.
- isValidLog10Probability(double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- isValidLog10ProbabilityVector(double[], int, boolean) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Check that the log10 prob vector vector is well formed
- isValidPair(SVCallRecord, SVCallRecord) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.ClusteringParameters
- isValidProbability(double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- isVar(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns true if EITHER the truth or call state is a VAR.
- isVariantFile(File) - Static method in class picard.vcf.VcfUtils
-
Checks if the suffix is one of those that are allowed for the various formats that contain variants (currently vcf and bcf)
- isVariationPresent() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer.Result
-
Checks whether there is any variation present in the target region.
- isVariationPresent() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Checks whether there is any variation present in the assembly result set.
- isViolation(Genotype, Genotype, Genotype) - Static method in class org.broadinstitute.hellbender.utils.samples.MendelianViolation
-
Evaluate the genotypes of mom, dad, and child to detect Mendelian violations
- isViolation(Sample, Sample, Sample, VariantContext) - Method in class org.broadinstitute.hellbender.utils.samples.MendelianViolation
-
Tests whether there is a mendelian violation between the supplied samples.
- isWasPoorlyRecovered() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JTBestHaplotype
- isWGT - Variable in class picard.arrays.illumina.InfiniumEGTFile
- isWithinInterval(Locatable) - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
- isXnp(Allele, Allele) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Determines whether the given reference and alternate alleles constitute a polymorphism in one or more nucleotides (XNP).
- isXnp(String, String) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Determines whether the given reference and alternate alleles constitute a polymorphism in one or more nucleotides (XNP).
- iterateOnGenotypes(VariantContext, List<Allele>, Map<Allele, Integer>, int[], boolean, int[]) - Method in class org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyperEngine
-
Remove the NON_REF allele from the genotypes, updating PLs, ADs, and GT calls
- iterator - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
- iterator() - Method in class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Gets an iterator over all Features in this data source, restricting traversal to Features overlapping our intervals if intervals were provided via
FeatureDataSource.setIntervalsForTraversal(List) - iterator() - Method in class org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard
- iterator() - Method in class org.broadinstitute.hellbender.engine.MultiVariantDataSource
-
Gets an iterator over all variants in this data source, restricting traversal to variants overlapping our intervals if intervals were provided via
MultiVariantDataSource.setIntervalsForTraversal(List)Calling this method invalidates (closes) any previous iterator obtained from this method. - iterator() - Method in class org.broadinstitute.hellbender.engine.ReadsContext
-
Get an iterator over the reads in this context.
- iterator() - Method in class org.broadinstitute.hellbender.engine.ReadsPathDataSource
-
Iterate over all reads in this data source.
- iterator() - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
-
Get an iterator over the reference bases in this context.
- iterator() - Method in class org.broadinstitute.hellbender.engine.ReferenceFileSource
-
Start an iteration over the entire reference.
- iterator() - Method in class org.broadinstitute.hellbender.engine.ReferenceMemorySource
-
Start an iteration over the entire reference.
- iterator() - Method in class org.broadinstitute.hellbender.engine.ShardBoundaryShard
- iterator() - Method in class org.broadinstitute.hellbender.engine.ShardToMultiIntervalShardAdapter
- iterator() - Method in class org.broadinstitute.hellbender.tools.DownsampleableSparkReadShard
- iterator() - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
- iterator() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet
- iterator() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.IntervalCoverageFinder
- iterator() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerCleaner
- iterator() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadsForQNamesFinder
- iterator() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree
- iterator() - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- iterator() - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- iterator() - Method in class org.broadinstitute.hellbender.utils.bigquery.StorageAPIAvroReader
- iterator() - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
- iterator() - Method in class org.broadinstitute.hellbender.utils.collections.IndexedSet
- iterator() - Method in class org.broadinstitute.hellbender.utils.CompressedDataList
- iterator() - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
get an iterator over this collection
- iterator() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- iterator() - Method in class org.broadinstitute.hellbender.utils.iterators.PushToPullIterator
- iterator() - Method in class org.broadinstitute.hellbender.utils.iterators.ReadFilteringIterator
- iterator() - Method in class org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator
- iterator() - Method in class org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator
- iterator() - Method in class org.broadinstitute.hellbender.utils.iterators.SAMRecordToReadIterator
- iterator() - Method in class org.broadinstitute.hellbender.utils.nio.PathLineIterator
- iterator() - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
The best way to access PileupElements where you only care about the bases and quals in the pileup.
- iterator() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
-
return this iterator, for the iterable interface
- iterator() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList
-
Returns a new iterator over all covariates in this list.
- iterator() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
- iterator() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Return an iterator over the entire tree.
- iterator() - Method in class org.broadinstitute.hellbender.utils.text.XReadLines
-
I'm an iterator too...
- iterator() - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Returns an iterator on the remaining records in the input.
- iterator() - Method in class picard.annotation.Gene
- iterator() - Method in class picard.arrays.illumina.IlluminaManifest
- iterator() - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- iterator() - Method in class picard.illumina.parser.ReadStructure.Substructure
- iterator() - Method in class picard.illumina.parser.TileIndex
- iterator() - Method in class picard.util.AbstractInputParser
- iterator() - Method in class picard.util.IntervalList.IntervalListScatter
- iterator() - Method in class picard.util.TabbedTextFileWithHeaderParser
-
Creates the iterator object.
- iterator(SimpleInterval) - Method in class org.broadinstitute.hellbender.engine.ReadsContext
-
Get an iterator over the reads of the backing data source over a given interval.
- iterator(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Return an iterator over all intervals greater than or equal to the specified interval.
- IteratorFilter(Iterator<T>, Predicate<T>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils.IteratorFilter
- iterators() - Method in class picard.vcf.processor.VariantIteratorProducer
-
Renders the embodied regions of the VCF files in the form of
CloseableIterators overVariantContexts. - Iterators - Class in picard.util
- Iterators() - Constructor for class picard.util.Iterators
- iteratorSize(Iterator<T>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
-
count the number of items available from an iterator
- iteratorSize(LongIterator) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
- IUPAC_NUCLEOTIDE_CODES - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- IUPACReadTransformer - Class in org.broadinstitute.hellbender.transformers
-
A read transformer to convert IUPAC bases (i.e.
- IUPACReadTransformer() - Constructor for class org.broadinstitute.hellbender.transformers.IUPACReadTransformer
- IUPACReadTransformer(boolean) - Constructor for class org.broadinstitute.hellbender.transformers.IUPACReadTransformer
J
- JAVA - Enum constant in enum class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner.Implementation
-
use the pure java implementation of Smith-Waterman, works on all hardware
- JAVA_BGMM - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsModelBackend
- JAVA_DEFAULT_HASH_LOAD_FACTOR - Static variable in class org.broadinstitute.hellbender.utils.Utils
- JAVASCRIPT_FILE - Variable in class picard.sam.FilterSamReads
- JAVASCRIPT_FILE - Variable in class picard.vcf.filter.FilterVcf
- JexlExpression - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies the eval RODs by user-supplied JEXL expressions https://gatk.broadinstitute.org/hc/en-us/articles/360035891011-JEXL-filtering-expressions for more details
- JexlExpression(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.JexlExpression
- JexlExpressionReadTagValueFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads that the attributes of meet a given set of jexl expressions
- JexlExpressionReadTagValueFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.JexlExpressionReadTagValueFilter
- JexlExpressionReadTagValueFilter(String) - Constructor for class org.broadinstitute.hellbender.engine.filters.JexlExpressionReadTagValueFilter
- JexlExpressionReadTagValueFilter(List<String>) - Constructor for class org.broadinstitute.hellbender.engine.filters.JexlExpressionReadTagValueFilter
- join(CharSequence, Object...) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Returns a string of the values in an
Objectarray joined by a separator. - join(String, double[]) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Returns a string of the values in joined by separator, such as A,B,C
- join(String, int[]) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Returns a string of the values in ints joined by separator, such as A,B,C
- join(String, Collection<T>) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Returns a string of the form elt1.toString() [sep elt2.toString() ...
- join(JavaRDD<GATKRead>, List<String>) - Static method in class org.broadinstitute.hellbender.utils.spark.JoinReadsWithVariants
-
Joins each read of an RDD
with overlapping variants from a list of variants files. - join(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVInterval
- JoinReadsWithVariants - Class in org.broadinstitute.hellbender.utils.spark
-
Joins an RDD of GATKReads to variant data by copying the variants files to every node, using Spark's file copying mechanism.
- JOINT_ALIGNMENT_COUNT_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- JOINT_LIKELIHOOD_TAG_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- JOINT_POSTERIOR_TAG_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- JointGermlineCNVSegmentation - Class in org.broadinstitute.hellbender.tools.walkers.sv
-
Merge GCNV segments VCFs This tool takes in segmented VCFs produced by
PostprocessGermlineCNVCalls. - JointGermlineCNVSegmentation() - Constructor for class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- JTBestHaplotype<V extends BaseVertex,
E extends BaseEdge> - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs -
A best haplotype object for being used with junction trees.
- JTBestHaplotype(JTBestHaplotype<V, E>, List<E>, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JTBestHaplotype
- JTBestHaplotype(V, BaseGraph<V, E>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JTBestHaplotype
- JUDGMENT_HEADER_LINE - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- JUDGMENT_INFO_FIELD_KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- JumboGenotypeAnnotation - Interface in org.broadinstitute.hellbender.tools.walkers.annotator
-
FORMAT annotations that look at more inputs than regular annotations
- JumboInfoAnnotation - Interface in org.broadinstitute.hellbender.tools.walkers.annotator
-
INFO annotations that look at more inputs than regular annotations
- JUMP_DUPLICATE_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of outward-facing pairs that are duplicates
- JUMP_DUPLICATE_PCT - Variable in class picard.analysis.JumpingLibraryMetrics
-
The fraction of outward-facing pairs that are marked as duplicates
- JUMP_LIBRARY_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
-
The estimated library size for outward-facing pairs
- JUMP_MEAN_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
-
The mean insert size for outward-facing pairs
- JUMP_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of outward-facing pairs in the SAM file
- JUMP_SIZE - Variable in class picard.sam.MergeBamAlignment
-
Deprecated.
- JUMP_STDEV_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
-
The standard deviation on the insert size for outward-facing pairs
- JumpingLibraryMetrics - Class in picard.analysis
-
High level metrics about the presence of outward- and inward-facing pairs within a SAM file generated with a jumping library, produced by the CollectJumpingLibraryMetrics program and usually stored in a file with the extension ".jump_metrics".
- JumpingLibraryMetrics() - Constructor for class picard.analysis.JumpingLibraryMetrics
- JunctionTreeKBestHaplotypeFinder<V extends BaseVertex,
E extends BaseEdge> - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs - JunctionTreeKBestHaplotypeFinder(BaseGraph<V, E>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
-
Constructor for the default case of all sources and sinks
- JunctionTreeKBestHaplotypeFinder(BaseGraph<V, E>, Set<V>, Set<V>, int, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
- JunctionTreeKBestHaplotypeFinder(BaseGraph<V, E>, V, V) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
-
Constructor for the special case of a single source and sink
- JunctionTreeKBestHaplotypeFinder(BaseGraph<V, E>, V, V, int, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
-
Constructor for the special case of a single source and sink
- JunctionTreeLinkedDeBruijnGraph - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
-
Experimental version of the ReadThreadingGraph with support for threading reads to generate JunctionTrees for resolving connectivity information at longer ranges.
- JunctionTreeLinkedDeBruijnGraph(int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
- JunctionTreeLinkedDeBruijnGraph.ThreadingNode - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
- JunctionTreeLinkedDeBruijnGraph.ThreadingTree - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
-
Class for storing a junction tree.
- JUST_ASSEMBLED_REFERENCE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult.Status
-
Assembly succeeded, but graph degenerated into just the reference sequence
- JUST_DETERMINE_ACTIVE_REGIONS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- justDetermineActiveRegions - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
-
This argument is intended for benchmarking and scalability testing.
K
- K - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- K_BEST_HAPLOTYPE_COMPARATOR - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.GraphBasedKBestHaplotypeFinder
- K_MEANS_PLUS_PLUS - Enum constant in enum class org.broadinstitute.hellbender.utils.clustering.BayesianGaussianMixtureModeller.InitMethod
- kAdvance - Variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- KB_TO_BYTES - Static variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- KBestHaplotype<V extends BaseVertex,
E extends BaseEdge> - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs -
Represents a result from a K-best haplotype search.
- KBestHaplotype(KBestHaplotype<V, E>, E, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotype
- KBestHaplotype(KBestHaplotype<V, E>, List<E>, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotype
- KBestHaplotype(V, BaseGraph<V, E>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotype
- KBestHaplotypeFinder<V extends BaseVertex,
E extends BaseEdge> - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs -
A common interface for the different KBestHaplotypeFinder implementations to conform to
- KBestHaplotypeFinder(Set<V>, Set<V>, BaseGraph<V, E>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotypeFinder
- KEEP_ALIGNMENT_INFORMATION - Static variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- KEEP_ALL_ALTS_ARG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- KEEP_COMBINED_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- KEEP_COMBINED_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- KEEP_FIRST_DUPLICATE - Variable in class picard.sam.RevertSam
- KEEP_FIRST_DUPLICATE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- KEEP_IF_ALL_UNFILTERED - Enum constant in enum class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.FilteredRecordMergeType
-
Requires all records present at site to be unfiltered.
- KEEP_IF_ANY_UNFILTERED - Enum constant in enum class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.FilteredRecordMergeType
-
Union - leaves the record if any record is unfiltered.
- KEEP_INTERVAL_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- KEEP_ORIGINAL_AC_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
- KEEP_READ_GROUP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- KEEP_REVERSE_STRAND_ONLY_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- KEEP_RG_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- KEEP_SPECIFIED_RAW_COMBINED_ANNOTATION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsAnnotationArgumentCollection
- KEEP_SPECIFIED_RAW_COMBINED_ANNOTATION_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsAnnotationArgumentCollection
- KEEP_UNCONDITIONAL - Enum constant in enum class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.FilteredRecordMergeType
-
If any record is present at this site (regardless of possibly being filtered), then all such records are kept and the filters are reset.
- keepAlignmentInformation - Variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- keepAllAlts - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- keepBoundaryFlows - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- keepCombined - Variable in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
-
If specified, keep all the combined raw annotations (e.g.
- keepCycles() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.GraphBasedKBestHaplotypeFinder
- keepCycles() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
- keepCycles() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotypeFinder
- keepDuplicateInformation - Variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- keepFirstDuplicate - Variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- keepNegatives - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
keep negatives?
- keepOnlyReverse - Variable in class org.broadinstitute.hellbender.engine.filters.ReadStrandFilter
- keepPriorInCount - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.AllelePseudoDepth
- keepRG - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- keepSitesWithAC0 - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- keepSpecifiedCombined - Variable in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsAnnotationArgumentCollection
-
Keep only the specific combined raw annotations specified.
- keepSupplementaryAlignments - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
keep supplementary alignments?
- KERNEL_APPROXIMATION_DIMENSION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- KERNEL_SCALING_ALLELE_FRACTION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- KERNEL_SEGMENTER_DIMENSION - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationSegmenter
- KERNEL_SEGMENTER_LINEAR_COST - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationSegmenter
- KERNEL_SEGMENTER_LOG_LINEAR_COST - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationSegmenter
- KERNEL_VARIANCE_ALLELE_FRACTION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- KERNEL_VARIANCE_COPY_RATIO_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- kernelApproximationDimension - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- kernelScalingAlleleFraction - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- KernelSegmenter<DATA> - Class in org.broadinstitute.hellbender.tools.copynumber.utils.segmentation
-
Segments data (i.e., finds multiple changepoints) using a method based on the kernel-segmentation algorithm described in https://hal.inria.fr/hal-01413230/document, which gives a framework to quickly calculate the cost of a segment given a low-rank approximation to a specified kernel.
- KernelSegmenter(List<DATA>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.utils.segmentation.KernelSegmenter
- KernelSegmenter.ChangepointSortOrder - Enum Class in org.broadinstitute.hellbender.tools.copynumber.utils.segmentation
- kernelVarianceAlleleFraction - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- kernelVarianceCopyRatio - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- KETO - Static variable in enum class org.broadinstitute.hellbender.utils.Nucleotide
- key - Variable in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.EmptyFragment
- key - Variable in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.FlowModeFragment
- key - Variable in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Fragment
- key - Variable in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair
- key() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.EmptyFragment
- key() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.FlowModeFragment
- key() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Fragment
- key() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord
- key() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair
- key() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Passthrough
- KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityHistogram
- KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.OriginalAlignment
- KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.UniqueAltReadCount
- KEY - Variable in class picard.analysis.CompareMetrics
- KEY - Variable in class picard.analysis.CompareMetrics.MetricComparisonDifferences
- keyAsString(int[]) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedKeyCodec
-
Prints the key as character-encoded string
- keyForRead(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.markduplicates.ReadsKey
-
Makes a unique key for the read.
- keyFromContext(String) - Static method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ContextCovariate
- keyFromCycle(int, int) - Static method in class org.broadinstitute.hellbender.utils.recalibration.covariates.CycleCovariate
-
Encodes the cycle number as a key.
- keyFromValue(Object) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ContextCovariate
- keyFromValue(Object) - Method in interface org.broadinstitute.hellbender.utils.recalibration.covariates.Covariate
-
Converts an Object key into a long key using only the lowest numberOfBits() bits Only necessary for on-the-fly recalibration when you have the object, but need to store it in memory in long format.
- keyFromValue(Object) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.CycleCovariate
- keyFromValue(Object) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.QualityScoreCovariate
- keyFromValue(Object) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadGroupCovariate
- keyNames - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.ChromosomeCounts
- keys - Variable in class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray.Leaf
- keySet() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
- keySet() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- keySet() - Method in class org.broadinstitute.hellbender.utils.mcmc.ParameterizedState
-
Returns a Set of the keys of the
Parameterobjects that are held internally as values of the parameter map. - klDivergance(double[], double[]) - Static method in class picard.util.MathUtil
-
Calculate the KL divergence from measured to distribution // https://en.wikipedia.org/wiki/Kullback%E2%80%93Leibler_divergence
- KMASK - Static variable in class org.broadinstitute.hellbender.tools.LocalAssembler.Kmer
- Kmer - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Fast wrapper for byte[] kmers This objects has several important features that make it better than using a raw byte[] for a kmer: -- Can create kmer from a range of a larger byte[], allowing us to avoid Array.copyOfRange -- Fast equals and hashcode methods -- can get actual byte[] of the kmer, even if it's from a larger byte[], and this operation only does the work of that operation once, updating its internal state
- Kmer(byte[]) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.Kmer
-
Create a new kmer using all bases in kmer
- Kmer(byte[], int, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.Kmer
-
Create a new kmer backed by the bases in bases, spanning start -> start + length Under no circumstances can bases be modified anywhere in the client code.
- Kmer(long) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.Kmer
- Kmer(String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.Kmer
-
Create a new kmer based on the string kmer This is not a good method to use for performance
- KMER_FILE_PATH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- KMER_LENGTH_FOR_READ_ERROR_CORRECTION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- KMER_MASK_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
- KMER_MASK_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
- KMER_SIZE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- KMER_SIZE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
- KMER_SIZE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- KMER_SIZE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- KMER_SIZE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
- KMER_SPACING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
- KMER_SPACING_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
- KmerAdjacency(long) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- KmerAdjacencyImpl(long) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- KmerAdjacencyRC(LocalAssembler.KmerAdjacencyImpl) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- KmerAndCount - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
-
A <Kmer,count> pair.
- KmerAndCount(SVKmerLong) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.KmerAndCount
- KmerAndCount(SVKmerLong, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.KmerAndCount
- KmerAndCount.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- KmerAndInterval - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
A <Kmer,IntervalId> pair.
- KmerAndInterval(SVKmer, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerAndInterval
- KmerAndInterval.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- KmerCleaner - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
Eliminates dups, and removes over-represented kmers.
- KmerCleaner(Iterator<Tuple2<KmerAndInterval, Integer>>, int, int, int, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerCleaner
- KmerCounter - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
Iterates over reads, kmerizing them, and counting up just the kmers that appear in a passed-in set.
- KmerCounter(int, int, HopscotchUniqueMultiMapSpark<SVKmer, Integer, KmerAndInterval>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerCounter
- KMerCounter - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
generic utility class that counts kmers Basically you add kmers to the counter, and it tells you how many occurrences of each kmer it's seen.
- KMerCounter(int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.KMerCounter
-
Create a new kmer counter
- kmerFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- kmerFilePath - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- kmerize(byte[], byte[], byte, LocalAssembler.KmerSet<LocalAssembler.KmerAdjacency>) - Static method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
-
Transform a read's calls into KmerAdjacencies, and add them to a KmerSet.
- kmerize(String, int, LocalAssembler.KmerSet<LocalAssembler.KmerAdjacency>) - Static method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
-
Kmerize a String.
- kmerLengthForReadErrorCorrection - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
Enabling this argument may cause fundamental problems with the assembly graph itself.
- kmerMaskString - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
-
K-mer masking allows mismatches to occur at one or more specified positions.
- KmerSearchableGraph<V extends BaseVertex,
E extends BaseEdge> - Interface in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs -
Common interface for those graphs that implement vertex by kmer look-up.
- KmerSet(int) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.KmerSet
- kmerSize - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
-
Reducing the k-mer length will increase the number of host reads subtracted in the filtering phase of the pipeline, but it may also increase the number of non-host (i.e.
- kmerSize - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
- kmerSize() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerBloomFilter
- kmerSize() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet
- kmerSizes - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
Multiple kmer sizes can be specified, using e.g.
- kmerSpacing - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
-
The k-mer set size can be reduced by only storing k-mers starting at every n bases in the reference.
- kmersToIgnoreFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
-
This is a path to a file of kmers that appear too frequently in the reference to be usable as probes to localize reads.
- kmerToVertexMap - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
A map from kmers -> their corresponding vertex in the graph
- KNOWN - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.GeneTranscriptStatus
- KNOWN_NCRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- KNOWN_SITES_ARG_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator
- knownCNVsFile - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
-
File containing tribble-readable features containing known CNVs.
- knownIndelsComplete - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- knownIndelsPartial - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- knownNames - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
-
List of feature tracks to be used for specifying "known" variants other than dbSNP.
- knownPlatformsString() - Static method in enum class org.broadinstitute.hellbender.utils.NGSPlatform
-
Get a human-readable list of platform names
- knownSNPsComplete - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- knownSNPsPartial - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- knownSubInterfaces(Class<?>) - Static method in class org.broadinstitute.hellbender.utils.ClassUtils
-
Finds all subinterfaces of the given interface (in the same package).
- knownSubInterfaceSimpleNames(Class<?>) - Static method in class org.broadinstitute.hellbender.utils.ClassUtils
-
Finds sub-interfaces of the given interface (in the same package) and returns their simple names.
- knownVariants - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark
- knownVariants - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- KS_SIGNIFICANCE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
- kSize - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- kSize - Variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- KSIZE - Static variable in class org.broadinstitute.hellbender.tools.LocalAssembler.Kmer
- KSWindowFinder - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- KSWindowFinder(ReadMetadata, SVReadFilter) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
- KV<K,
V> - Class in org.broadinstitute.hellbender.utils -
replacement for dataflow Key-Value class, don't use this anywhere new
L
- LabeledVariantAnnotationsData - Class in org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data
-
Represents a collection of
LabeledVariantAnnotationsDatumas a list of lists of datums. - LabeledVariantAnnotationsData(Collection<String>, Collection<String>, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- LabeledVariantAnnotationsData(Collection<String>, Collection<String>, boolean, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- LabeledVariantAnnotationsWalker - Class in org.broadinstitute.hellbender.tools.walkers.vqsr.scalable
-
Base walker for both
ExtractVariantAnnotationsandScoreVariantAnnotations, which enforces identical variant-extraction behavior in both tools viaLabeledVariantAnnotationsWalker.extractVariantMetadata(htsjdk.variant.variantcontext.VariantContext, org.broadinstitute.hellbender.engine.FeatureContext, boolean). - LabeledVariantAnnotationsWalker() - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
- LABELS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.CombineSegmentBreakpoints
- LABELS_PATH - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- LABELS_SNP_PATH - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- lane - Variable in class picard.illumina.parser.BaseIlluminaDataProvider
- lane - Variable in class picard.illumina.parser.ParameterizedFileUtil
- lane - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
-
The lane, which is determined from the file name
- LANE - Variable in class picard.fastq.BamToBfq
- LANE - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
- LANE - Variable in class picard.illumina.ExtractBarcodesProgram
- LANE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The lane for which the metrics were calculated.
- LANE - Variable in class picard.illumina.IlluminaLaneMetrics
-
This lane's number.
- LANE - Variable in class picard.illumina.IlluminaPhasingMetrics
-
Illumina flowcell lane number
- LANE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- LANE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- laneFactories - Variable in class picard.illumina.BasecallsConverter
- laneIsSet() - Method in class picard.illumina.parser.ClusterData
- LanePhasingMetricsCollector - Class in picard.illumina
-
Helper class used to transform tile data for a lane into a collection of IlluminaPhasingMetrics
- LanePhasingMetricsCollector(Collection<Tile>, boolean) - Constructor for class picard.illumina.LanePhasingMetricsCollector
-
Constructor takes a lane's collection of Tiles and calculates the median phasing/prephasing for the first and second (if available) reads
- LANES - Variable in class picard.illumina.CheckIlluminaDirectory
- laneTileCode - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
- LARGE_INDEL_SIZE_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- LARGE_RUNTIME_RESOURCES_PATH - Static variable in class org.broadinstitute.hellbender.utils.io.Resource
-
Path to the directory for large runtime system resources
- LargeLongHopscotchSet - Class in org.broadinstitute.hellbender.tools.spark.utils
-
Set of longs that is larger than the max Java array size ( ~ 2^31 ~ 2 billion) and therefore cannot fit into a single LongHopscotchSet.
- LargeLongHopscotchSet(long) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- LargeLongHopscotchSet(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- LargeLongHopscotchSet.Serializer - Class in org.broadinstitute.hellbender.tools.spark.utils
- last - Variable in class org.broadinstitute.hellbender.utils.SVIntervalTree.OverlapIterator
- lastBase() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer
- lastBase() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
- lastBase() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
- lastIndexOf(byte[], byte[]) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Find the last occurrence of the query sequence in the reference sequence Returns the index of the last occurrence or -1 if the query sequence is not found
- lastProgressTime_ns - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- lastProgressValue - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- lastTrimer() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer
- lastTrimer() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
- lastTrimer() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
- LATEST_REPORT_VERSION - Static variable in class org.broadinstitute.hellbender.utils.report.GATKReport
- launchProcess(ProcessSettings) - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase
-
Executes a command line program with the settings and waits for it to return, processing the output on a background thread.
- Leaf(int[], T) - Constructor for class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray.Leaf
- learn(List<Datum>, double[]) - Method in interface org.broadinstitute.hellbender.tools.walkers.mutect.clustering.AlleleFractionCluster
- learn(List<Datum>, double[]) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BetaBinomialCluster
- learn(List<Datum>, double[]) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BinomialCluster
- learnAndClearAccumulatedData() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel
- LEARNING_RATE - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- LEARNING_RATE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- learnParameters() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteredHaplotypeFilter
- learnParameters() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2Filter
- learnParameters() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
-
Refine model parameters based on data acquired in a non-final pass of
FilterMutectCalls - learnParameters() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter
- learnParametersAndClearAccumulatedData() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2Filter
- learnPriorForArtifactStates() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelEngine
- LearnReadOrientationModel - Class in org.broadinstitute.hellbender.tools.walkers.readorientation
-
Learn the prior probability of read orientation artifact from the output of
CollectF1R2CountsofMutect2Details of the model may be found in docs/mutect/mutect.pdf. - LearnReadOrientationModel() - Constructor for class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel
- LearnReadOrientationModelEngine - Class in org.broadinstitute.hellbender.tools.walkers.readorientation
- LearnReadOrientationModelEngine(Histogram<Integer>, List<Histogram<Integer>>, List<AltSiteRecord>, double, int, int, Logger) - Constructor for class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelEngine
-
Contract: the reference contexts must be combined with its reverse complements prior to instantiating this class
- learnThreshold() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- LEFT - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportColumnFormat.Alignment
- LEFT - Enum constant in enum class org.broadinstitute.hellbender.utils.Tail
- LEFT_FILE - Variable in class picard.fingerprint.CrosscheckMetric
-
The LEFT file from which the fingerprint was obtained.
- LEFT_FILE - Variable in class picard.sam.SamComparisonMetric
-
Left file used in comparison
- LEFT_GROUP_VALUE - Variable in class picard.fingerprint.CrosscheckMetric
-
The LEFT group value.
- LEFT_LANE - Variable in class picard.fingerprint.CrosscheckMetric
-
The LEFT lane.
- LEFT_LIBRARY - Variable in class picard.fingerprint.CrosscheckMetric
-
The LEFT library identifier.
- LEFT_MOLECULAR_BARCODE_SEQUENCE - Variable in class picard.fingerprint.CrosscheckMetric
-
The LEFT molecular (sample) barcode.
- LEFT_PRIMER - Variable in class picard.util.BaitDesigner
- LEFT_RUN_BARCODE - Variable in class picard.fingerprint.CrosscheckMetric
-
The LEFT run barcode (PU field) expected to look like : D047KACXX110901.1.ACCAACTG.
- LEFT_SAMPLE - Variable in class picard.fingerprint.CrosscheckMetric
-
The LEFT sample identifier.
- leftAlignAndTrim(VariantContext, ReferenceContext, int, boolean) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Main routine workhorse for
LeftAlignAndTrimVariants. - LeftAlignAndTrimVariants - Class in org.broadinstitute.hellbender.tools.walkers.variantutils
-
Left-align indels in a variant callset
- LeftAlignAndTrimVariants() - Constructor for class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
- leftAlignIndels(Cigar, byte[], byte[], int) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Takes the alignment of the read sequence
readSeqto the reference sequencerefSeqstarting at 0-based positionreadStarton therefand specified by itscigar. - LeftAlignIndels - Class in org.broadinstitute.hellbender.tools
-
Left-aligns indels in read data
- LeftAlignIndels() - Constructor for class org.broadinstitute.hellbender.tools.LeftAlignIndels
- leftAlignVariant(VariantContextBuilder, int, int, List<Allele>, ReferenceSequence) - Static method in class picard.util.LiftoverUtils
-
Normalizes and left aligns a
VariantContextBuilder. - leftMedianDeviation(int) - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.CDF
- leftVariantContext - Variable in class picard.vcf.PairedVariantSubContextIterator.VcfTuple
- LEGACY_SEG_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- LEGACY_SEG_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- LEGACY_SEGMENTS_FILE_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegments
- LegacySegment - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
- LegacySegment(String, SimpleInterval, int, double) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.LegacySegment
- LegacySegmentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
Represents a CBS-style segmentation to enable IGV-compatible plotting.
- LegacySegmentCollection(SampleLocatableMetadata, List<LegacySegment>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.LegacySegmentCollection
- legalSizes - Static variable in class org.broadinstitute.hellbender.utils.collections.SetSizeUtils
-
Largest prime numbers less than each half power of 2 from 2^8 to 2^31 Note the last size is the greatest prime that is an allowable Java array size (<=2^31-3)
- length - Variable in class picard.illumina.parser.Range
- length - Variable in class picard.illumina.parser.ReadDescriptor
- length() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.SequenceRC
- length() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer.ASCIICharSequence
- length() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
-
Get the length of this sequence
- length() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
-
Length of the path in edges.
- length() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.Kmer
-
The length of this kmer
- length() - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Insert
- length() - Method in class picard.annotation.Gene.Transcript
- length() - Method in class picard.illumina.parser.ReadStructure.Substructure
- LENGTH_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
- leniantHammingDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
-
Deprecated.
- LENIENT_DUP - Variable in class picard.sam.util.SAMComparisonArgumentCollection
- LENIENT_HAMMING - Enum constant in enum class picard.illumina.DistanceMetric
- LENIENT_HEADER - Variable in class picard.sam.util.SAMComparisonArgumentCollection
- LENIENT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- LENIENT_LOW_MQ_ALIGNMENT - Variable in class picard.sam.util.SAMComparisonArgumentCollection
- LENIENT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- LENIENT_UNKNOWN_MQ_ALIGNMENT - Variable in class picard.sam.util.SAMComparisonArgumentCollection
- lenientHammingDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
-
Similar to Hamming distance but this version doesn't penalize matching bases with low quality for the read.
- lenientVCFProcessing - Variable in class org.broadinstitute.hellbender.engine.GATKTool
- LESS - Enum constant in enum class org.broadinstitute.hellbender.engine.filters.ReadTagValueFilter.Operator
- LESS_OR_EQUAL - Enum constant in enum class org.broadinstitute.hellbender.engine.filters.ReadTagValueFilter.Operator
- LEUCINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- LevelingDownsampler<T extends List<E>,
E> - Class in org.broadinstitute.hellbender.utils.downsampling -
Leveling Downsampler: Given a set of Lists of arbitrary items and a target size, removes items from the Lists in an even fashion until the total size of all Lists is <= the target size.
- LevelingDownsampler(long) - Constructor for class org.broadinstitute.hellbender.utils.downsampling.LevelingDownsampler
-
Construct a LevelingDownsampler Uses the default minElementsPerStack of 1
- LevelingDownsampler(long, int) - Constructor for class org.broadinstitute.hellbender.utils.downsampling.LevelingDownsampler
-
Construct a LevelingDownsampler
- levelToLog4jLevel(Log.LogLevel) - Static method in class org.broadinstitute.hellbender.utils.LoggingUtils
-
Converts a picard log level to a log4j log level.
- LEXICOGRAPHICAL_ORDER_COMPARATOR - Static variable in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Lexicographical (contig) order comparator.
- LexicographicallySortedSequenceDictionary(String, SAMSequenceDictionary) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.LexicographicallySortedSequenceDictionary
- lhs - Variable in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter.CountingAndReadFilter
- lhs - Variable in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter.CountingAndVariantFilter
- lhs - Variable in class org.broadinstitute.hellbender.engine.filters.ReadFilter.ReadFilterBinOp
- library - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Partition
- LIBRARY - Enum constant in enum class org.broadinstitute.hellbender.metrics.MetricAccumulationLevel
- LIBRARY - Enum constant in enum class picard.analysis.MetricAccumulationLevel
- LIBRARY - Enum constant in enum class picard.fingerprint.CrosscheckMetric.DataType
- LIBRARY - Enum constant in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateType
- LIBRARY - Variable in class org.broadinstitute.hellbender.metrics.MultiLevelMetrics
-
The library to which these metrics apply.
- LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The name of the library being assayed.
- LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The name of the library being assayed.
- LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The name of the library being assayed.
- LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The name of the library being assayed.
- LIBRARY - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The name of the library being assayed.
- LIBRARY - Variable in class picard.metrics.MultilevelMetrics
-
The library to which these metrics apply.
- LIBRARY - Variable in class picard.sam.DuplicationMetrics
-
The library on which the duplicate marking was performed.
- LIBRARY - Variable in class picard.sam.markduplicates.UmiMetrics
-
Library that was used to generate UMI data.
- LIBRARY_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- LIBRARY_NAME - Variable in class org.broadinstitute.hellbender.tools.SplitReads
- LIBRARY_NAME - Variable in class picard.illumina.BarcodeMetric
-
The name of the library
- LIBRARY_NAME - Variable in class picard.illumina.IlluminaBasecallsToSam
- LIBRARY_NAME - Variable in class picard.sam.FastqToSam
- LIBRARY_NAME - Variable in class picard.sam.RevertSam
- LIBRARY_NAME_ARG - Static variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- LIBRARY_NAME_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
-
Column header for the library name.
- LIBRARY_NAME_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.SplitReads
- LIBRARY_NAME_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.SplitReads
- LIBRARY_NAME_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- LIBRARY_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToSam
- libraryId - Variable in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- libraryId - Variable in class picard.sam.markduplicates.util.ReadEnds
- libraryIdGenerator - Variable in class picard.sam.markduplicates.MarkDuplicates
- LibraryIdGenerator - Class in org.broadinstitute.hellbender.utils.read.markduplicates
-
A class to generate library Ids and keep duplication metrics by library IDs.
- LibraryIdGenerator - Class in picard.sam.markduplicates.util
-
A class to generate library Ids and keep duplication metrics by library IDs.
- LibraryIdGenerator(SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator
- LibraryIdGenerator(SAMFileHeader) - Constructor for class picard.sam.markduplicates.util.LibraryIdGenerator
- LibraryIdGenerator(SAMFileHeader, boolean) - Constructor for class picard.sam.markduplicates.util.LibraryIdGenerator
- libraryName - Variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- LibraryNameSplitter - Class in org.broadinstitute.hellbender.tools.readersplitters
-
Splits readers by library name.
- LibraryNameSplitter() - Constructor for class org.broadinstitute.hellbender.tools.readersplitters.LibraryNameSplitter
- LibraryRawStatistics(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.LibraryRawStatistics
- LibraryReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads from the specified library.
- LibraryReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.LibraryReadFilter
- LibraryReadFilter(SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.engine.filters.LibraryReadFilter
- LibraryStatistics - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
statistics of fragment length distributions
- LibraryStatistics(IntHistogram.CDF, long, long, long, long) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics
- LibraryStatistics.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- libraryToHistoPairMap - Variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
- libraryToKeep - Variable in class org.broadinstitute.hellbender.engine.filters.LibraryReadFilter
- LIBSDownsamplingInfo - Class in org.broadinstitute.hellbender.utils.locusiterator
-
Simple wrapper about the information LIBS needs about downsampling
- LIBSDownsamplingInfo(boolean, int) - Constructor for class org.broadinstitute.hellbender.utils.locusiterator.LIBSDownsamplingInfo
- LIFTOVER_FAILED - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
- LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS - Static variable in class picard.fingerprint.LiftOverHaplotypeMap
- LIFTOVER_MIN_MATCH - Variable in class picard.vcf.LiftoverVcf
- LiftOverHaplotypeMap - Class in picard.fingerprint
-
Liftover SNPs in HaplotypeMaps from one reference to another
- LiftOverHaplotypeMap() - Constructor for class picard.fingerprint.LiftOverHaplotypeMap
- LiftOverIntervalList - Class in picard.util
-
This tool adjusts the coordinates in an interval list on one reference to its homologous interval list on another reference, based on a chain file that describes the correspondence between the two references.
- LiftOverIntervalList() - Constructor for class picard.util.LiftOverIntervalList
- LiftoverUtils - Class in picard.util
- LiftoverUtils() - Constructor for class picard.util.LiftoverUtils
- LiftoverVcf - Class in picard.vcf
-
Summary
- LiftoverVcf() - Constructor for class picard.vcf.LiftoverVcf
- liftSimpleVariantContext(VariantContext, Interval) - Static method in class picard.util.LiftoverUtils
- liftVariant(VariantContext, Interval, ReferenceSequence, boolean, boolean) - Static method in class picard.util.LiftoverUtils
-
This will take an input VariantContext and lift to the provided interval.
- likelihood - Variable in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods.BestAllele
-
If allele != null, the indicates the likelihood of the evidence.
- LIKELIHOOD_CALCULATION_ENGINE_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- LIKELIHOOD_RANK_SUM_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- likelihoodArgs - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- likelihoodArgs - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- likelihoodCalculationEngine - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- LikelihoodEngineArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Set of arguments related to
ReadLikelihoodCalculationEngineimplementations - LikelihoodEngineArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- likelihoodEngineImplementation - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- LikelihoodMatrix<EVIDENCE,
A extends htsjdk.variant.variantcontext.Allele> - Interface in org.broadinstitute.hellbender.utils.genotyper -
Likelihood matrix between a set of alleles and evidence.
- LikelihoodRankSumTest - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Rank Sum Test of per-read likelihoods of REF versus ALT reads
- LikelihoodRankSumTest() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.LikelihoodRankSumTest
- limitingProcessedRegionsTo(IntervalList) - Method in class picard.vcf.processor.VariantProcessor.Builder
- limitScore - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
maximum value for delta in score
- LINCRNA - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Variant lies on one of the lincRNAs.
- LINCRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- LINE_DELIMITER - Static variable in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- LINE_LENGTH - Variable in class picard.reference.ExtractSequences
- LINE_LENGTH - Variable in class picard.reference.NormalizeFasta
- LINE_WIDTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker
- LINE_WIDTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta
- LINEAR - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection.StratifyingScale
- LINEAR - Enum constant in enum class org.broadinstitute.hellbender.utils.variant.GATKVCFIndexType
- LinearCopyRatio - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
-
Represents a value of copy ratio in linear space generated by
GermlineCNVCallerwith the corresponding interval. - LinearCopyRatio(SimpleInterval, double) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.LinearCopyRatio
- LinearCopyRatioCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
Collection of copy ratios in linear space generated by
GermlineCNVCallerwith their corresponding intervals - LinearCopyRatioCollection(File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.LinearCopyRatioCollection
- LinearCopyRatioCollection(SampleLocatableMetadata, List<LinearCopyRatio>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.LinearCopyRatioCollection
- LineIteratorReader - Class in org.broadinstitute.hellbender.utils.codecs
-
A reader wrapper around a LineIterator.
- LineIteratorReader(LineIterator) - Constructor for class org.broadinstitute.hellbender.utils.codecs.LineIteratorReader
- LINK - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- LINK_LOCS - Variable in class picard.illumina.CheckIlluminaDirectory
-
Deprecated.It is no longer necessary to create locs file symlinks.
- LINKED_DE_BRUIJN_GRAPH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- LIST - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval
-
Note that the --list argument requires a fully resolved and correct command-line to work.
- LIST_DELIMITER - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils
- listFromPrimitives(int[]) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Simple wrapper for sticking elements of a int[] array into a List
- listModulesAndExit() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval
-
List all of the available evaluation modules, then exit successfully
- listWeight(IntervalList) - Method in interface picard.util.IntervalList.IntervalListScatterer
-
A method that defines the "weight" of an interval for the purpose of scattering.
- listWeight(IntervalList) - Method in class picard.util.IntervalList.IntervalListScattererByBaseCount
- listWeight(IntervalList) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
- LL_EXPECTED_SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The Log Likelihood of the sequence data given the expected sample's genotypes.
- LL_RANDOM_SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The Log Likelihood of the sequence data given a random sample from the human population.
- LLK - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
-
The log likelihood
- LLK0 - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
-
The log likelihood 0
- LmmFilter - Class in org.broadinstitute.hellbender.tools.funcotator.filtrationRules
-
FuncotationFiltermatching variants which: Have been flagged by LMM as important for loss of function. - LmmFilter() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.LmmFilter
- LNCRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- LO_CONF_DENOVO_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- load(InputStream) - Static method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusUtils.BinaryTableIndex
- load(String) - Static method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusUtils.BinaryTableIndex
- LOAD_FACTOR - Static variable in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
- loadBQSRScriptResource() - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
-
Retrieve the BQSR.R script
- loadCNVCalls(String, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.CNVInputReader
-
Loads an external cnv call list and returns the results in an SVIntervalTree.
- loadContaminationFile(File, double, Set<String>, Logger) - Static method in class org.broadinstitute.hellbender.utils.downsampling.AlleleBiasedDownsamplingUtils
-
Create sample-contamination maps from file.
- loadFastaDictionary(File) - Static method in class org.broadinstitute.hellbender.utils.reference.ReferenceUtils
-
Given a fasta dictionary file, returns its sequence dictionary
- loadFastaDictionary(InputStream) - Static method in class org.broadinstitute.hellbender.utils.reference.ReferenceUtils
-
Given an InputStream connected to a fasta dictionary, returns its sequence dictionary Note: does not close the InputStream it's passed
- loadFastaDictionary(GATKPath) - Static method in class org.broadinstitute.hellbender.utils.reference.ReferenceUtils
-
Given a fasta dictionary file, returns its sequence dictionary
- loadFingerprints(Path, Path, boolean, String) - Method in class picard.fingerprint.FingerprintChecker
-
Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
- loadFingerprintsFromIndexedVcf(Path, String) - Method in class picard.fingerprint.FingerprintChecker
-
Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
- loadFingerprintsFromNonIndexedVcf(Path, String) - Method in class picard.fingerprint.FingerprintChecker
-
Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
- loadFingerprintsFromQueriableReader(VCFFileReader, String, Path) - Method in class picard.fingerprint.FingerprintChecker
-
Loads genotypes from the supplied reader into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
- loadFingerprintsFromVariantContexts(Iterable<VariantContext>, String, Path) - Method in class picard.fingerprint.FingerprintChecker
-
Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
- loadIndex(Path) - Static method in class org.broadinstitute.hellbender.utils.IndexUtils
-
Loads and returns the index of the feature file or null if there is no index.
- loadIntervals(List<String>, IntervalSetRule, IntervalMergingRule, int, GenomeLocParser) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
- loadIntervalsNonMerging(List<String>, int, GenomeLocParser) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Method that takes a list of interval strings in the command line format and parses them into GenomicLoc objects without attempting to perform any sort of interval merging whatsover regardless of overlap between the intervals.
- loadLibraryFromClasspath(String) - Static method in class org.broadinstitute.hellbender.utils.NativeUtils
-
Loads a native library stored on our classpath by extracting it to a temporary location and invoking
System.load(java.lang.String)on it - loadPropertiesFile(String, Class<?>) - Static method in class picard.util.PropertyUtils
-
Attempt to load a Properties object from an on-disk properties file.
- loadRefFlat(File, SAMSequenceDictionary) - Static method in class picard.annotation.GeneAnnotationReader
- loadTabixIndex(Path) - Static method in class org.broadinstitute.hellbender.utils.IndexUtils
-
Try to load the tabix index from disk, checking for out of date indexes and old versions
- loadTribbleIndex(Path) - Static method in class org.broadinstitute.hellbender.utils.IndexUtils
-
Load a Tribble .idx index from disk, checking for out of date indexes and old versions
- loc - Variable in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.Splice
- LocalAssembler - Class in org.broadinstitute.hellbender.tools
- LocalAssembler() - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler
- LocalAssembler.AssemblyTooComplexException - Exception in org.broadinstitute.hellbender.tools
-
Something to throw when we have too many Contigs or Traversals to proceed with assembly.
- LocalAssembler.Contig - Interface in org.broadinstitute.hellbender.tools
-
An unbranched sequence of Kmers.
- LocalAssembler.ContigEndKmer - Class in org.broadinstitute.hellbender.tools
-
Initial or final Kmer in a Contig.
- LocalAssembler.ContigImpl - Class in org.broadinstitute.hellbender.tools
-
Simple implementation of Contig interface.
- LocalAssembler.ContigListRC - Class in org.broadinstitute.hellbender.tools
-
A list of Contigs that presents a reverse-complemented view of a List of Contigs.
- LocalAssembler.ContigOrientation - Enum Class in org.broadinstitute.hellbender.tools
- LocalAssembler.ContigRCImpl - Class in org.broadinstitute.hellbender.tools
-
Implementation of Contig for the reverse-complement of some other Contig.
- LocalAssembler.Kmer - Class in org.broadinstitute.hellbender.tools
-
fixed-size, immutable kmer.
- LocalAssembler.KmerAdjacency - Class in org.broadinstitute.hellbender.tools
-
A Kmer that remembers its predecessors and successors, and the number of times it's been observed in the assembly's input set of reads.
- LocalAssembler.KmerAdjacencyImpl - Class in org.broadinstitute.hellbender.tools
-
Class to implement KmerAdjacency for canonical Kmers.
- LocalAssembler.KmerAdjacencyRC - Class in org.broadinstitute.hellbender.tools
-
Class to implement KmerAdjacency for Kmers that are the reverse-complement of a canonical Kmer.
- LocalAssembler.KmerSet<KMER extends LocalAssembler.Kmer> - Class in org.broadinstitute.hellbender.tools
-
Set of Kmers.
- LocalAssembler.Path - Class in org.broadinstitute.hellbender.tools
-
A path through the assembly graph for something (probably a read).
- LocalAssembler.PathBuilder - Class in org.broadinstitute.hellbender.tools
-
A helper class for Path building.
- LocalAssembler.PathPart - Interface in org.broadinstitute.hellbender.tools
-
A single-Contig portion of a path across the assembly graph.
- LocalAssembler.PathPartContig - Class in org.broadinstitute.hellbender.tools
-
A part of a path that is present as a sub-sequence of some Contig.
- LocalAssembler.PathPartGap - Class in org.broadinstitute.hellbender.tools
-
A part of a path that isn't present in the graph.
- LocalAssembler.SequenceRC - Class in org.broadinstitute.hellbender.tools
-
A CharSequence that is a view of the reverse-complement of another sequence.
- LocalAssembler.TransitPairCount - Class in org.broadinstitute.hellbender.tools
-
A count of the number of read Paths that cross through some Contig from some previous Contig to some subsequent Contig.
- LocalAssembler.Traversal - Class in org.broadinstitute.hellbender.tools
-
A list of Contigs through the assembly graph.
- LocalAssembler.TraversalEndpointComparator - Class in org.broadinstitute.hellbender.tools
- LocalAssembler.TraversalSet - Class in org.broadinstitute.hellbender.tools
-
Set of traversals.
- LocalAssembler.WalkData - Class in org.broadinstitute.hellbender.tools
-
Per-Contig storage for depth-first graph walking.
- LocalAssembler.WalkDataFactory - Class in org.broadinstitute.hellbender.tools
- LocalContext(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase.LocalContext
- LOCATABLE - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.Metadata.Type
- LOCATABLE_XSV - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.DataSourceType
-
This value indicates a simple arbitrary separated value (XSV) file that can be annotated on records via matching by gene location.
- LocatableFuncotationCreator - Class in org.broadinstitute.hellbender.tools.funcotator.dataSources
-
Implements fields for use in known locatables.
- LocatableFuncotationCreator() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.LocatableFuncotationCreator
- LocatableMetadata - Interface in org.broadinstitute.hellbender.tools.copynumber.formats.metadata
-
Interface for marking objects that contain metadata associated with a collection of locatables.
- locatableToString(Locatable) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
- locatableToSVInterval(Locatable, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
-
Converts locatable (uses 1-based, closed intervals) to SVInterval (1-based half-open).
- LocatableXsvFuncotationFactory - Class in org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv
-
Factory for creating
TableFuncotations by handling `Separated Value` files with arbitrary delimiters (e.g. - LocatableXsvFuncotationFactory(String, String, LinkedHashMap<String, String>, FeatureInput<? extends Feature>) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.LocatableXsvFuncotationFactory
-
Create a
LocatableXsvFuncotationFactory. - LocatableXsvFuncotationFactory(String, String, LinkedHashMap<String, String>, FeatureInput<? extends Feature>, boolean) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.LocatableXsvFuncotationFactory
-
Create a
LocatableXsvFuncotationFactory. - LocatableXsvFuncotationFactory(String, String, LinkedHashMap<String, String>, FeatureInput<? extends Feature>, boolean, int) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.LocatableXsvFuncotationFactory
-
Create a
LocatableXsvFuncotationFactory. - LOCATION_BIN_SIZE - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- LocationAndAlleles - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
This class exists to allow VariantContext objects to be compared based only on their location and set of alleles, providing a more liberal equals method so that VariantContext objects can be placed into a Set which retains only VCs that have non-redundant location and Allele lists.
- LocationAndAlleles(int, List<Allele>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LocationAndAlleles
- LocationTranslationException - Exception in org.broadinstitute.hellbender.tools.walkers.groundtruth
- Locs - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- LocsFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- LocsFileFaker() - Constructor for class picard.illumina.parser.fakers.LocsFileFaker
- LocsFileReader - Class in picard.illumina.parser.readers
-
The locs file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
- LocsFileReader(File) - Constructor for class picard.illumina.parser.readers.LocsFileReader
- LocsFileReader(File, int, int) - Constructor for class picard.illumina.parser.readers.LocsFileReader
- locus - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Aggregation
- LOCUS_ACCUMULATION_CAP - Variable in class picard.analysis.CollectWgsMetrics
- LOCUS_DEPTH_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAF
- LOCUS_MAX_READS - Variable in class picard.fingerprint.ExtractFingerprint
- LOCUS_MAX_READS - Variable in class picard.fingerprint.IdentifyContaminant
- LocusFunction - Enum Class in picard.annotation
-
Describes the behavior of a locus relative to a gene.
- LocusIteratorByState - Class in org.broadinstitute.hellbender.utils.locusiterator
-
Iterator that traverses a SAM File, accumulating information on a per-locus basis Produces AlignmentContext objects, that contain ReadPileups of PileupElements.
- LocusIteratorByState(Iterator<GATKRead>, DownsamplingMethod, Collection<String>, SAMFileHeader, boolean) - Constructor for class org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState
-
Create a new LocusIteratorByState
- LocusIteratorByState(Iterator<GATKRead>, DownsamplingMethod, Collection<String>, SAMFileHeader, boolean, boolean) - Constructor for class org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState
-
Create a new LocusIteratorByState
- LocusIteratorByState(Iterator<GATKRead>, LIBSDownsamplingInfo, Collection<String>, SAMFileHeader, boolean) - Constructor for class org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState
-
Create a new LocusIteratorByState
- LocusIteratorByState(Iterator<GATKRead>, LIBSDownsamplingInfo, Collection<String>, SAMFileHeader, boolean, boolean) - Constructor for class org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState
-
Create a new LocusIteratorByState
- locusLevel - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
- locusReader() - Method in class org.broadinstitute.hellbender.utils.dragstr.STRTableFile
-
Return a loci reader across the whole genome.
- locusReader(SimpleInterval) - Method in class org.broadinstitute.hellbender.utils.dragstr.STRTableFile
-
Return a loci reader for a given interval in the genome.
- LocusWalker - Class in org.broadinstitute.hellbender.engine
-
A LocusWalker is a tool that processes reads that overlap a single position in a reference at a time from one or multiple sources of reads, with optional contextual information from a reference and/or sets of variants/Features.
- LocusWalker() - Constructor for class org.broadinstitute.hellbender.engine.LocusWalker
- LocusWalkerByInterval - Class in org.broadinstitute.hellbender.engine
-
An implementation of
LocusWalkerthat supports arbitrary interval side inputs. - LocusWalkerByInterval() - Constructor for class org.broadinstitute.hellbender.engine.LocusWalkerByInterval
- LocusWalkerContext - Class in org.broadinstitute.hellbender.engine.spark
- LocusWalkerContext(AlignmentContext, ReferenceContext, FeatureContext) - Constructor for class org.broadinstitute.hellbender.engine.spark.LocusWalkerContext
- LocusWalkerSpark - Class in org.broadinstitute.hellbender.engine.spark
-
A Spark version of
LocusWalker. - LocusWalkerSpark() - Constructor for class org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark
- LOD - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The LOD score for OBSERVED_GENOTYPE vs.
- LOD_BAND_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- LOD_BAND_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- LOD_EXPECTED_SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The LOD for Expected Sample vs.
- LOD_SCORE - Variable in class picard.fingerprint.CrosscheckMetric
-
The resulting LOD score comparing LEFT and RIGHT data.
- LOD_SCORE_NORMAL_TUMOR - Variable in class picard.fingerprint.CrosscheckMetric
-
The resulting LOD score comparing LEFT as normal and RIGHT as tumor.
- LOD_SCORE_TUMOR_NORMAL - Variable in class picard.fingerprint.CrosscheckMetric
-
The resulting LOD score comparing LEFT as tumor and RIGHT as normal.
- LOD_SELF_CHECK - Variable in class picard.fingerprint.FingerprintMetrics
-
The fingerprinting LOD score this sample gets when compared to itself (big is good)
- LOD_THRESHOLD - Variable in class picard.fingerprint.ClusterCrosscheckMetrics
- LOD_THRESHOLD - Variable in class picard.fingerprint.CrosscheckFingerprints
- LOF - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- LofFilter - Class in org.broadinstitute.hellbender.tools.funcotator.filtrationRules
-
FuncotationFiltermatching variants which: Are classified as FRAME_SHIFT_*, NONSENSE, START_CODON_DEL, or SPLICE_SITE Occur on a gene where loss of function is a disease mechanism Have a max MAF of 1% across sub-populations of ExAC or gnomAD - LofFilter(FilterFuncotations.Reference, FilterFuncotations.AlleleFrequencyDataSource) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.LofFilter
-
Build a new Loss of Function filter using the ExAC or gnomAD datasoure
- log - Static variable in class picard.illumina.SortedBasecallsConverter
- log - Static variable in class picard.util.LiftoverUtils
- log(String...) - Method in class org.broadinstitute.hellbender.utils.runtime.ProgressLogger
-
Log a message to whatever logger is being used
- LOG - Static variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- LOG - Static variable in class picard.vcf.VcfFormatConverter
- LOG - Static variable in class picard.vcf.VcfToIntervalList
- LOG_10 - Static variable in class org.broadinstitute.hellbender.utils.MathUtils
- LOG_10_INFORMATIVE_THRESHOLD - Static variable in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
- LOG_10_MATH - Static variable in class picard.util.MathUtil
- LOG_2 - Static variable in class org.broadinstitute.hellbender.utils.MathUtils
- LOG_2_MATH - Static variable in class picard.util.MathUtil
- LOG_4_BASE_E - Static variable in class picard.util.MathUtil
-
Constant to convert between the natural base e and 4.0.
- LOG_ARTIFACT_VERSUS_VARIANT_PRIOR_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- LOG_EMISSION_SAMPLES_PER_ROUND - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- LOG_EMISSION_SAMPLES_PER_ROUND_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- LOG_EMISSION_SAMPLING_MEDIAN_REL_ERROR - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- LOG_EMISSION_SAMPLING_MEDIAN_REL_ERROR_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- LOG_EMISSION_SAMPLING_ROUNDS - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- LOG_EMISSION_SAMPLING_ROUNDS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- LOG_FAILED_INTERVALS - Variable in class picard.vcf.LiftoverVcf
- LOG_INDEL_PRIOR_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- LOG_MEAN_BIAS_STANDARD_DEVIATION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
- LOG_NORMAL - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistributionShape
-
The insert size distribution follows a log-normal; i.e.
- LOG_ODDS_THRESHOLD - Variable in class picard.analysis.TheoreticalSensitivityMetrics
-
Log-likelihood ratio is used as a threshold to distinguish a positive site with a given allele fraction from HOM_REF.
- LOG_ONE_HALF - Static variable in class org.broadinstitute.hellbender.utils.NaturalLogUtils
- LOG_ONE_THIRD - Static variable in class org.broadinstitute.hellbender.utils.MathUtils
- LOG_ONE_THIRD - Static variable in class org.broadinstitute.hellbender.utils.NaturalLogUtils
- LOG_PROB_TO_PHRED_MULTIPLIER - Static variable in class org.broadinstitute.hellbender.utils.QualityUtils
- LOG_SNV_PRIOR_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
-
Parameters
- log10(int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- log10_1p(double) - Static method in class picard.util.MathUtil
-
this function mimics the behavior of log_1p but resulting in log _base 10_ of (1+x) instead of natural log of 1+x
- LOG10_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
-
The log10 of the Chi-squared pvalue
- LOG10_E - Static variable in class org.broadinstitute.hellbender.utils.MathUtils
- LOG10_HET_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
-
The log10 of the Chi-squared pvalue for the number of HETs and HOMs
- LOG10_HOM_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
-
The log10 of the Chi-squared pvalue for
FingerprintMetrics.NUM_HOM_ALLELE1andFingerprintMetrics.NUM_HOM_ALLELE2 - LOG10_ONE_HALF - Static variable in class org.broadinstitute.hellbender.utils.MathUtils
- LOG10_ONE_THIRD - Static variable in class org.broadinstitute.hellbender.utils.MathUtils
- LOG10_P_OF_ZERO - Static variable in class org.broadinstitute.hellbender.utils.MathUtils
-
The smallest log10 value we'll emit from normalizeFromLog10 and other functions where the real-space value is 0.0.
- LOG10_PVAL - Variable in class picard.arrays.BafRegressMetrics
-
The log p-value of the estimate
- log10BinomialCoefficient(int, int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- log10BinomialProbability(int, int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- log10BinomialProbability(int, int, double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
binomial Probability(int, int, double) with log applied to result
- Log10Cache - Class in org.broadinstitute.hellbender.utils
- Log10Cache() - Constructor for class org.broadinstitute.hellbender.utils.Log10Cache
- log10CombinationCount() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Gets the log10 combination count, computing it if uninitialized.
- log10Factorial(int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- Log10FactorialCache - Class in org.broadinstitute.hellbender.utils
-
Wrapper class so that the log10Factorial array is only calculated if it's used
- Log10FactorialCache() - Constructor for class org.broadinstitute.hellbender.utils.Log10FactorialCache
- log10Gamma(double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Calculates the log10 of the gamma function for x.
- log10MeanWeights() - Method in class org.broadinstitute.hellbender.utils.Dirichlet
- log10MinTrueLikelihood(double, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
-
Calculate minimal likelihood that reasonably matching read can get.
- log10MinTrueLikelihood(double, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedHMMEngine
-
Calculate minimal likelihood that reasonably matching read can get.
- log10MinTrueLikelihood(double, boolean) - Method in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
-
Standard read disqulification threshold algorithm
- log10MultinomialCoefficient(int, int[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Calculates the log10 of the multinomial coefficient.
- log10OneMinusPow10(double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Calculates
log10(1-10^a)without losing precision. - log10OneMinusX(double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Compute in a numerically correct way the quantity log10(1-x) Uses the approximation log10(1-x) = log10(1/x - 1) + log10(x) to avoid very quick underflow in 1-x when x is very small log10(1-x) = log10( x * (1-x) / x ) = log10(x) + log10( (1-x) / x) = log10(x) + log10(1/x - 1)
- Log10PairHMM - Class in org.broadinstitute.hellbender.utils.pairhmm
-
Util class for performing the pair HMM for global alignment.
- Log10PairHMM(boolean) - Constructor for class org.broadinstitute.hellbender.utils.pairhmm.Log10PairHMM
-
Create an uninitialized PairHMM
- log10ProbOnlyRefAlleleExists() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculationResult
- log10ProbVariantPresent() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculationResult
- log10QempLikelihood(double, long, long) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- log10QempPrior(double, double) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- log10sumLog10(double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- log10sumLog10(double[], int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- log10sumLog10(double[], int, int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- log10SumLog10(double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- log10SumLog10(double[], int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- log10SumLog10(double[], int, int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- log10SumLog10(double, double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- log10SumLog10(double, double, double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Do the log-sum trick for three double values.
- log10ToLog(double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- log1mexp(double) - Static method in class org.broadinstitute.hellbender.utils.NaturalLogUtils
-
Calculates
log(1-exp(a))without losing precision. - log2(double) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
log the value in base 2
- LOG2_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- LOG2_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- LOGARITHMIC - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection.StratifyingScale
- logb(double, double) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
log the value in base b
- logConfigFields(T) - Static method in class org.broadinstitute.hellbender.utils.config.ConfigFactory
-
Logs all the parameters in the given
Configobject atLevel.DEBUG - logConfigFields(T, Log.LogLevel) - Static method in class org.broadinstitute.hellbender.utils.config.ConfigFactory
-
Logs all the parameters in the given
Configobject at the givenLog.LogLevel - logCovariatesUsed() - Method in class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
- logDirichletNormalization(double...) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticLikelihoodsEngine
- logEvidence(RealMatrix, double[]) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticLikelihoodsEngine
- logFinalPairedReads(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterEmptyLogger
- logFinalPairedReads(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterFileLogger
- logFinalPairedReads(JavaRDD<GATKRead>) - Method in interface org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterLogger
- logger - Variable in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- logger - Variable in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
- logger - Variable in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
- logger - Static variable in class org.broadinstitute.hellbender.cmdline.ModeArgumentUtils
- logger - Static variable in class org.broadinstitute.hellbender.engine.FeatureInput
- logger - Static variable in class org.broadinstitute.hellbender.engine.ProgressMeter
- logger - Variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVSegmentVariantComposer
- logger - Static variable in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
Standard Logger.
- logger - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory
-
Standard Logger.
- logger - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
Standard Logger.
- logger - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory
-
Standard Logger.
- logger - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
-
Standard Logger.
- logger - Static variable in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
- logger - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.ContainsKmerReadFilter
- logger - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBuildReferenceTaxonomyUtils
- logger - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPairedUnpairedSplitterSpark
- logger - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- logger - Variable in class org.broadinstitute.hellbender.tools.sv.concordance.SVConcordanceAnnotator
- logger - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation
- logger - Static variable in class org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator
- logger - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination
- logger - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
- logger - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleFiltering
- logger - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.OccurrenceMatrix
- logger - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase
- logger - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampUtils
- logger - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
- logger - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel
- logger - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine
- logger - Static variable in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager
- logger - Static variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- logger - Static variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- logger - Static variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- logger - Static variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.IntervalStratification
- logger - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrainingSet
- logger - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager
- logger - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- logger - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorEngine
- logger - Static variable in class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
- logger - Static variable in class org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator
- logger - Static variable in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentContextIteratorBuilder
- logger - Static variable in class org.broadinstitute.hellbender.utils.MannWhitneyU
- logger - Static variable in class org.broadinstitute.hellbender.utils.pairhmm.FlowBasedPairHMM
- logger - Static variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- logger - Static variable in class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
- logger - Static variable in interface org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner
- LoggingUtils - Class in org.broadinstitute.hellbender.utils
-
Logging utilities.
- LoggingUtils() - Constructor for class org.broadinstitute.hellbender.utils.LoggingUtils
- logIndelPrior - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- logItemizedWarning(Logger, Collection<?>, String) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSUtils
-
Prints warning message followed by a list of relevant items
- LOGLESS_CACHING - Enum constant in enum class org.broadinstitute.hellbender.utils.pairhmm.PairHMM.Implementation
- LoglessPairHMM - Class in org.broadinstitute.hellbender.utils.pairhmm
- LoglessPairHMM() - Constructor for class org.broadinstitute.hellbender.utils.pairhmm.LoglessPairHMM
- logLikelihood(int, int) - Method in interface org.broadinstitute.hellbender.tools.walkers.mutect.clustering.AlleleFractionCluster
- logLikelihood(int, int) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BetaBinomialCluster
- logLikelihood(int, int) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BinomialCluster
- logLikelihoodGivenSomatic(int, int) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel
-
emission likelihood of given allele counts given that a variant is somatic, which is the weighted sum of cluster likelihoods
- logLikelihoodRatio(int, int, double) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- logLikelihoodRatio(int, List<Byte>) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- logLikelihoodRatio(int, List<Byte>, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- logLikelihoodRatio(int, List<Byte>, int, Optional<BetaDistributionShape>) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
-
this implements the isActive() algorithm described in docs/mutect/mutect.pdf the multiplicative factor is for the special case where we pass a singleton list of alt quals and want to duplicate that alt qual over multiple reads
- logLikelihoodsToProbs(double[]) - Static method in class picard.util.MathUtil
-
Deprecated.
- logMemoryStats(Log) - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- logPrimaryReads(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterEmptyLogger
- logPrimaryReads(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterFileLogger
- logPrimaryReads(JavaRDD<GATKRead>) - Method in interface org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterLogger
- logProbability(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistribution
- logProbability(int) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BetaBinomialDistribution
- logProbToPhred(double) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Convert a log-probability to a phred-scaled value ( log(0.001) => 30 )
- logProgress(double, long, double) - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- logProgressSimple(double, long, double) - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- logProgressVerbose(double, long, double) - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- logReadCounts(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreFileLogger
- logReadCounts(JavaRDD<GATKRead>) - Method in interface org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreLogger
- logReads(String, String, Collection<GATKRead>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampUtils
- logReadsAfterDeduplication(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterEmptyLogger
- logReadsAfterDeduplication(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterFileLogger
- logReadsAfterDeduplication(JavaRDD<GATKRead>) - Method in interface org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterLogger
- logReadsAfterHostFilter(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterEmptyLogger
- logReadsAfterHostFilter(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterFileLogger
- logReadsAfterHostFilter(JavaRDD<GATKRead>) - Method in interface org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterLogger
- logReadsAfterPrealignedHostFilter(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterEmptyLogger
- logReadsAfterPrealignedHostFilter(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterFileLogger
- logReadsAfterPrealignedHostFilter(JavaRDD<GATKRead>) - Method in interface org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterLogger
- logReadsAfterQualityFilter(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterEmptyLogger
- logReadsAfterQualityFilter(JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterFileLogger
- logReadsAfterQualityFilter(JavaRDD<GATKRead>) - Method in interface org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterLogger
- logResultDataPretty(TableResult, Logger) - Static method in class org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils
-
Creates a
Stringcontaining the given results in a pretty ascii-art table. - logRRatio - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- logSNVPrior - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- logSumExp(double...) - Static method in class org.broadinstitute.hellbender.utils.NaturalLogUtils
-
Computes $\log(\sum_i e^{a_i})$ trying to avoid underflow issues by using the log-sum-exp trick.
- logSumLog(double, double) - Static method in class org.broadinstitute.hellbender.utils.NaturalLogUtils
- logToLog10(double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Converts LN to LOG10
- LONG_HOMOPOLYMER - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
- LONG_HOMOPOLYMER - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- LONG_INDEL_LENGTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- longArrayCollectionSize(Collection<long[]>) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerUtils
-
Returns the total number of longs in the Collection
- longArrayCollectionToBloomFilter(Collection<long[]>, long, double) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerUtils
-
Converts a Collection of Lists of Longs's into a Bloom filter
- longArrayCollectionToSet(Collection<long[]>, long) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerUtils
-
Converts a Collection of Lists of Longs's into a Hopscotch set
- LongBloomFilter - Class in org.broadinstitute.hellbender.tools.spark.utils
-
Bloom filter for primitive longs.
- LongBloomFilter(long, double) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter
- LongBloomFilter(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter
- LongBloomFilter.Serializer - Class in org.broadinstitute.hellbender.tools.spark.utils
- longHash(long) - Static method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- LongHomopolymerHaplotypeCollapsingEngine - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Utility class, useful for flow based applications, implementing a workaround for long homopolymers handling.
- LongHomopolymerHaplotypeCollapsingEngine(int, boolean, byte[], Locatable, Logger, boolean, SmithWatermanAligner, SWParameters) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LongHomopolymerHaplotypeCollapsingEngine
- LongHopscotchSet - Class in org.broadinstitute.hellbender.tools.spark.utils
-
This class is based on the HopscotchCollection and HopscotchSet classes for storing Objects.
- LongHopscotchSet() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
-
make a small LongHopscotchSet
- LongHopscotchSet(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
-
make a LongHopscotchSet for a specified minimum capacity
- LongHopscotchSet(long[]) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
-
make a LongHopscotchSet containing an initial array of values
- LongHopscotchSet(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- LongHopscotchSet.Serializer - Class in org.broadinstitute.hellbender.tools.spark.utils
- longIndelLength - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- LongIterator - Interface in org.broadinstitute.hellbender.tools.spark.utils
-
Iterator-like interface for collections of primitive long's
- longLaneStr(int) - Static method in class picard.illumina.parser.IlluminaFileUtil
- LOOKAHEAD_CACHE_IN_BP_DEFAULT_VALUE - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- LOOKAHEAD_CACHE_IN_BP_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- lookaheadFeatureCachingInBp - Variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
- LOSS_OF_HET_RATE - Variable in class picard.fingerprint.CrosscheckFingerprints
- LOST - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapTargetStatus
-
Gene or transcript exists in source and target genome, however source was not mapped.
- LOW_COUNT_FILTER_COUNT_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
- LOW_COUNT_FILTER_PERCENTAGE_OF_SAMPLES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
- LOW_COVERAGE_RATIO_THRESHOLD_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination
- LOW_DP - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- LOW_DP - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- LOW_DP_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- LOW_GQ - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- LOW_GQ - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- LOW_GQ_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- LOW_HET_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- LOW_HET_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MTLowHeteroplasmyFilterTool
- LOW_MQ_THRESHOLD - Variable in class picard.sam.util.SAMComparisonArgumentCollection
- LOW_QS_SCORE_FILTER_KEY - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- LOW_QUAL_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- LOW_QUAL_TAIL - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
-
Reads with low quality bases on either tail (beginning or end) will not be considered in the context.
- LOW_QUALITY_OR_LOW_COMPLEXITY_READS_FILTERED - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterMetrics
-
The number of reads filtered because they were low-quality or low-complexity
- LOW_SCORE_FILTER_NAME_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- LOW_SEQUENCE_QUALITY - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Transcript supported by transcript evidence that, while ampping best-in-genome, shows regions of poor sequence quality.
- LOW_VQSLOD_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSR
- lowQualVariantToGQ0HomRef(VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
-
"reblock" a variant by converting its genotype to homRef, changing PLs, adding reblock END tags and other attributes
- LowWeightChainPruner<V extends BaseVertex,
E extends BaseEdge> - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs -
Prune all chains from this graph where all edges in the path have multiplicity < pruneFactor For A -[1]> B -[1]> C -[1]> D would be removed with pruneFactor 2 but A -[1]> B -[2]> C -[1]> D would not be because the linear chain includes an edge with weight >= 2
- LowWeightChainPruner(int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.LowWeightChainPruner
- LRR - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- LRUCache<K,
V> - Class in org.broadinstitute.hellbender.utils -
An LRU cache implemented as an extension to LinkedHashMap
- LRUCache(int) - Constructor for class org.broadinstitute.hellbender.utils.LRUCache
- LS454 - Enum constant in enum class org.broadinstitute.hellbender.utils.NGSPlatform
- LUMP_PROBS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- lumpProbs - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- LYSINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
M
- M - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- M - Enum constant in enum class picard.illumina.parser.ReadType
- M2_CENTER_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3
- M2_FILTERS_HEADER_LINE - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3
- M2_FILTERS_KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3
- M2ArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.mutect
- M2ArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- M2ArgumentCollection.FlowMode - Enum Class in org.broadinstitute.hellbender.tools.walkers.mutect
-
the different flow modes, in terms of their parameters and their values NOTE: a parameter value ending with /o is optional - meaning it will not fail the process if it is not existent on the target parameters collection.
- M2FiltersArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- M2FiltersArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- MACHINE_NAME - Variable in class picard.illumina.IlluminaBasecallsToFastq
- MACRO_LNCRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- MAD_COVERAGE - Variable in class picard.analysis.WgsMetrics
-
The median absolute deviation of coverage of the genome after all filters are applied.
- MAD_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The median absolute deviation of the distribution of all read lengths.
- MAF - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.OutputFormatType
- MAF_DBSNP_VAL_STATUS_DELIMITER - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.CustomMafFuncotationCreator
- MAF_DBSNP_VAL_STATUS_FIELD - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.CustomMafFuncotationCreator
- MAF_STEP_SIZE - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel
- MAF_TO_SWITCH_TO_HOM_REF - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel
- MAF_TO_SWITCH_TO_UNSCRUPULOUS_HOM_REF - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel
- MafOutputRenderer - Class in org.broadinstitute.hellbender.tools.funcotator.mafOutput
-
A Funcotator output renderer for writing to MAF files.
- MafOutputRenderer(Path, List<DataSourceFuncotationFactory>, VCFHeader, LinkedHashMap<String, String>, LinkedHashMap<String, String>, Set<String>, String, Set<String>, String) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRenderer
-
Create a
MafOutputRenderer. - MafOutputRendererConstants - Class in org.broadinstitute.hellbender.tools.funcotator.mafOutput
-
Class to hold all the constants required for the
MafOutputRenderer. - MafOutputRendererConstants() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- mafTransform(String, String, String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRenderer
-
Transforms a given
valueto the equivalent MAF-valid value based on the givenkey. - mafTransformInvert(String, String, String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRenderer
-
Transforms a given
valuefrom a MAF-valid value to a general-purpose value based on the givenkey. - MAGIC_STRING - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.Serializer
-
Placed at the beginning of each standalone serialization of the meta-data identifies file that most likely are valid serializations.
- main(String[]) - Static method in class org.broadinstitute.hellbender.CommandLineArgumentValidatorMain
- main(String[]) - Static method in class org.broadinstitute.hellbender.Main
-
The entry point to GATK from commandline.
- main(String[]) - Static method in class picard.cmdline.PicardCommandLine
-
Override this if you want to include different java packages to search for classes that extend CommandLineProgram.
- main(String[]) - Static method in class picard.sam.DuplicationMetrics
- main(String[]) - Static method in class picard.Test
- Main - Class in org.broadinstitute.hellbender
-
This is the main class of Hellbender and is the way of executing individual command line programs.
- Main() - Constructor for class org.broadinstitute.hellbender.Main
- mainEntry(String[]) - Method in class org.broadinstitute.hellbender.Main
-
The entry point to the toolkit from commandline: it uses
Main.instanceMain(String[])to run the command line program and handle the returned object withMain.handleResult(Object), and exit with 0. - mainSourceFileAsFeatureInput - Variable in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
The backing data store as a FeatureInput to leverage tribble querying.
- make() - Method in class org.broadinstitute.hellbender.utils.read.CigarBuilder
- make() - Method in enum class picard.util.IntervalList.IntervalListScatterMode
-
Create the scatterer
- make(boolean) - Method in class org.broadinstitute.hellbender.utils.read.CigarBuilder
- make(double, double, double) - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParamsBuilder
- make(int, long, byte, short, long) - Static method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocus
- make(String...) - Static method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
- make(DoubleSequence) - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParamsBuilder
- makeAllReadCollector() - Method in class org.broadinstitute.hellbender.metrics.MultiLevelCollector
- makeAllReadCollector() - Method in class org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector
-
These are exposed here (rather than being encapsulated in the Distributor subclasses below in order to provide subclasses with an explicit point to add initialization (specific to accumulation level) for a PerUnitMetricCollector it is creating.
- makeAllReadCollector() - Method in class picard.analysis.directed.TargetMetricsCollector
- makeAllReadCollector() - Method in class picard.metrics.MultiLevelCollector
- makeAndRecordDeletionsRemovedResult() - Method in class org.broadinstitute.hellbender.utils.read.CigarBuilder
-
Return a Result object containing the output of make() as well as the number of leading and trailing deletion bases removed relative to the cigar elements that were add()ed.
- makeAnnotatedCall(byte[], SimpleInterval, FeatureContext, SAMFileHeader, VariantContext, int, AlleleLikelihoods<GATKRead, Allele>, VariantContext, VariantAnnotatorEngine, AlleleLikelihoods<GATKRead, Haplotype>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine
- makeApproximateDiploidLog10LikelihoodsFromGQ(Genotype, int) - Static method in class org.broadinstitute.hellbender.utils.GenotypeUtils
-
Make approximate likelihoods for a diploid genotype without PLs.
- makeArg(SAMRecord, ReferenceSequence) - Method in class org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollector
- makeArg(SAMRecord, ReferenceSequence) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelCollector
- makeArg(SAMRecord, ReferenceSequence) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector
-
Convert the current SAMRecord and the ReferenceSequence for that record into an ARGTYPE object.
- makeArg(SAMRecord, ReferenceSequence) - Method in class org.broadinstitute.hellbender.metrics.SAMRecordAndReferenceMultiLevelCollector
- makeArg(SAMRecord, ReferenceSequence) - Method in class org.broadinstitute.hellbender.metrics.SAMRecordMultiLevelCollector
- makeArg(SAMRecord, ReferenceSequence) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollector
-
Process the record and create a collector args object to hold the results of any calculation for re-use across multiple levels.
- makeArg(SAMRecord, ReferenceSequence) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
- makeArg(SAMRecord, ReferenceSequence) - Method in class picard.analysis.GcBiasMetricsCollector
- makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.MultiLevelCollector
- makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.SAMRecordAndReferenceMultiLevelCollector
- makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.SAMRecordMultiLevelCollector
- makeBAMFile(File) - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
-
Write the reads from this builder to output, creating an index as well
- makeBarcodeRegex(int) - Static method in class picard.illumina.parser.ParameterizedFileUtil
- makeBiallelicList(Allele, Allele, int, int) - Static method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
-
Creates list for biallelic sites with the specified number of each allele.
- makeBlock(VariantContext, VariantContext) - Method in class org.broadinstitute.hellbender.utils.haplotype.EventMap
-
Create a block substitution out of two variant contexts that start at the same position vc1 can be SNP, and vc2 can then be either a insertion or deletion.
- makeCalculator(GenotypeCalculationArgumentCollection) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator
- makeCalculator(DragstrParams, int, int, int, double, double) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator
- makeCalls() - Method in class org.broadinstitute.hellbender.tools.copynumber.caller.SimpleCopyRatioCaller
- makeChildCollector(String, String, String) - Method in class org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollector
- makeChildCollector(String, String, String) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelCollector
-
Construct a PerUnitMetricCollector with the given arguments.
- makeChildCollector(String, String, String) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector
-
Construct a PerUnitMetricCollector with the given arguments.
- makeChildCollector(String, String, String) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollector
-
Make an PerUnitExampleMultiMetricsCollector with the given arguments
- makeChildCollector(String, String, String) - Method in class picard.analysis.AlignmentSummaryMetricsCollector
- makeChildCollector(String, String, String) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
-
Make an InsertSizeCollector with the given arguments
- makeChildCollector(String, String, String) - Method in class picard.analysis.directed.RnaSeqMetricsCollector
- makeChildCollector(String, String, String) - Method in class picard.analysis.directed.TargetMetricsCollector
- makeChildCollector(String, String, String) - Method in class picard.analysis.GcBiasMetricsCollector
- makeChildCollector(String, String, String) - Method in class picard.analysis.RrbsMetricsCollector
- makeChildCollector(String, String, String) - Method in class picard.metrics.MultiLevelCollector
-
Construct a PerUnitMetricCollector with the given arguments.
- makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) - Method in class picard.analysis.directed.CollectHsMetrics
- makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) - Method in class picard.analysis.directed.CollectTargetedMetrics
-
A factory method for the TargetMetricsCollector to use this time.
- makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
- makeCombinedAnnotationString(List<Allele>, Map<Allele, Histogram>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
- makeCycleFileParser(List<File>) - Method in class picard.illumina.parser.MultiTileBclParser
- makeCycleFileParser(List<File>, PerTileCycleParser.CycleFilesParser<BclData>) - Method in class picard.illumina.parser.MultiTileBclParser
- makeDataProvider() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
- makeDataProvider(Integer) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
- makeDataProvider(List<Integer>) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Call this method to create a ClusterData iterator over the specified tiles.
- makeEvalVariantFilter() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- makeEvalVariantFilter() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance
- makeEvalVariantFilter() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3
- makeEvalVariantFilter() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance
- makeExceptionMsg() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
Create a string that will be included in any NoSuchElementException thrown by the next() method
- makeExceptionMsg() - Method in class picard.illumina.parser.readers.ClocsFileReader
- makeExceptionMsg() - Method in class picard.illumina.parser.readers.LocsFileReader
- makeExceptionMsg() - Method in class picard.illumina.parser.readers.PosFileReader
- makeFeatureInterval(T) - Method in class org.broadinstitute.hellbender.engine.FeatureWalker
-
This method can be overridden if you need to customize the interval for a given feature.
- makeFeatureInterval(T) - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotateSegments
- makeFilePathAbsolute(String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Changes relative local file paths to be absolute file paths.
- makeFilteredPileup(Predicate<PileupElement>) - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Make a new pileup consisting of elements of this pileup that satisfy the predicate.
- makeFromAlleles(String, String, int, List<String>) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
For testing purposes only.
- makeGenotypeAllelesFromCopyNumber(int, int, Allele) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKSVVariantContextUtils
-
Build the list of called alleles based on reference and called copy numbers For CNVs only, i.e.
- makeGenotypeCall(int, GenotypeBuilder, GenotypeAssignmentMethod, double[], List<Allele>, List<Allele>, GenotypePriorCalculator) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Add the genotype call (GT) field to GenotypeBuilder using the requested
GenotypeAssignmentMethod - makeGenotypeCall(int, GenotypeBuilder, GenotypeAssignmentMethod, double[], List<Allele>, GenotypePriorCalculator) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- makeGenotypeCall(GenotypeBuilder, double[], List<Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyperEngine
-
For a genotype with likelihoods that has a no-call GT, determine the most likely genotype from PLs and set it We use a GenotypeLikelihoodCalculator to convert from the best PL index to the indexes of the alleles for that genotype so we can set the GenotypeBuilder with the alleles
- makeGenotypeCalls - Variable in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
-
By default CombineGVCFs reverts all genotypes to no-calls, but calls can be made if specified
- makeIgnoredSequenceIndicesSet(SAMFileHeader, Set<String>) - Static method in class picard.analysis.directed.RnaSeqMetricsCollector
- makeIndexableSourceFromStream(InputStream) - Method in class org.broadinstitute.hellbender.utils.codecs.AbstractBCICodec
- makeIndexableSourceFromStream(InputStream) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec
- makeIndexableSourceFromStream(InputStream) - Method in class org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec
- makeInstance(String, String, File, File, Set<MetricAccumulationLevel>, File, File, File, Set<String>) - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
- makeInstance(String, String, File, File, Set<MetricAccumulationLevel>, File, File, File, Set<String>, boolean) - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
-
By default, this method calls the
CollectMultipleMetrics.ProgramInterface.makeInstance(String, String, File, File, Set, File, File, File, Set)method without 'includeUnpaired' parameter. - makeInstanceOf(Class<T>) - Static method in class org.broadinstitute.hellbender.utils.ClassUtils
-
Create objects of a concrete class.
- makeInstancesOfSubclasses(Class<? extends T>, Package) - Static method in class org.broadinstitute.hellbender.utils.ClassUtils
-
Finds and creates objects of all concrete subclasses of the given class in the package.
- makeInterpretation(JavaRDD<AssemblyContigWithFineTunedAlignments>, SvDiscoveryInputMetaData) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInterpreter
- makeInterpretation(JavaRDD<AssemblyContigWithFineTunedAlignments>, SvDiscoveryInputMetaData) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyInterpreter
- makeIntervalArgumentCollection() - Method in class picard.analysis.CollectWgsMetrics
- makeIntoFlowBased(SAMReadGroupRecord) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- makeIntoFlowBased(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- makeItSo(FastqReader, FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
-
Handles the FastqToSam execution on the FastqReader(s).
- makeItSo(File, File, boolean, long, Collection<SinglePassSamProgram>) - Static method in class picard.analysis.SinglePassSamProgram
- makeKernel(int, double) - Static method in class org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile
- makeLaneTileRegex(String, int) - Static method in class picard.illumina.parser.ParameterizedFileUtil
-
Return a regex string for finding Lane and Tile given a file extension pattern
- makeLibraryCollector(SAMReadGroupRecord) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelCollector
- makeLibraryCollector(SAMReadGroupRecord) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector
- makeLibraryCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
- makeLocationString(String, int, String, int) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- makeLocationString(NovelAdjacencyAndAltHaplotype) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- makeMergedVariantContext(List<VariantContext>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- makeNewHMM(PairHMMNativeArguments) - Method in enum class org.broadinstitute.hellbender.utils.pairhmm.PairHMM.Implementation
- makeOneBpInterval(String, int) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
-
Given chromosome name and requested position (1-based coordinate system), return a 1 bp long interval that spans only the requested base.
- makeOREdge(Collection<BaseEdge>, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge
-
Create a new BaseEdge with the given multiplicity.
- makeOverlapDetector(File, SAMFileHeader, File, Log) - Static method in class picard.analysis.directed.RnaSeqMetricsCollector
- makePermutations(List<T>, int, boolean) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Make all combinations of N size of objects if objects = [A, B, C] if N = 1 => [[A], [B], [C]] if N = 2 => [[A, A], [B, A], [C, A], [A, B], [B, B], [C, B], [A, C], [B, C], [C, C]]
- makePhredBinaryFromSolexaQualityAscii_1_3(String) - Static method in class picard.util.IlluminaUtil
-
Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
- makePhredBinaryFromSolexaQualityAscii_1_3(String, int, int) - Static method in class picard.util.IlluminaUtil
-
Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
- makePileupElement() - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
-
Create a new PileupElement based on the current state of this element Must not be a left or right edge
- makePloidyLengthAlleleList(int, Allele) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- makePostReadFilterTransformer() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns the post-filter read transformer (simple or composite) that will be applied to the reads after filtering.
- makePostReadFilterTransformer() - Method in class org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR
-
Returns the BQSR post-transformer.
- makePostReadFilterTransformer() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
- makePostReadFilterTransformer() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- makePostReadFilterTransformer() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads
- makePostVariantFilterTransformer() - Method in class org.broadinstitute.hellbender.engine.VariantWalkerBase
-
Returns the post-filter variant transformer (simple or composite) that will be applied to the variants after filtering.
- makePostVariantFilterTransformer() - Method in class org.broadinstitute.hellbender.tools.funcotator.Funcotator
- makePreReadFilterTransformer() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns the pre-filter read transformer (simple or composite) that will be applied to the reads before filtering.
- makePreReadFilterTransformer() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
- makePreReadFilterTransformer() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads
- makePreVariantFilterTransformer() - Method in class org.broadinstitute.hellbender.engine.VariantWalkerBase
-
Returns the pre-filter variant transformer (simple or composite) that will be applied to the variants before filtering.
- makePrintStreamMaybeGzipped(GATKPath) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Makes a print stream for a file, gzipping on the fly if the file's name ends with '.gz'.
- makePriorPseudocounts(int) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine
- makeQualityScoreTable() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
-
Allocate a new quality score table, based on requested parameters in this set of tables, without any data in it.
- makeRawAnnotationString(List<Allele>, Map<Allele, Double>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
- makeRawAnnotationString(List<Allele>, Map<Allele, List<Integer>>) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils
-
Helper method to output raw allele-specific strand counts as a string
- makeReaderMaybeGzipped(InputStream, boolean) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
makes a reader for an inputStream wrapping it in an appropriate unzipper if necessary
- makeReaderMaybeGzipped(Path) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Makes a reader for a file, unzipping if the file's name ends with '.gz'.
- makeReadFilter() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns a read filter (simple or composite) that can be applied to reads.
- makeReadFilter() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Returns a read filter (simple or composite) that can be applied to the reads returned from
GATKSparkTool.getReads(). - makeReadFilter(SAMFileHeader) - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Like
GATKSparkTool.makeReadFilter()but with the ability to pass a different SAMFileHeader. - makeReadFilter(SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeBasedVariantRecaller
- makeReadGroupCollector(SAMReadGroupRecord) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelCollector
- makeReadGroupCollector(SAMReadGroupRecord) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector
- makeReadGroupCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
- makeReads() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
-
Create a read stream based on the parameters.
- makeReadThreadingAssembler() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerReadThreadingAssemblerArgumentCollection
- makeReadThreadingAssembler() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.MutectReadThreadingAssemblerArgumentCollection
- makeReadThreadingAssembler() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- makeReducedAnnotationString(VariantContext, Map<Allele, Double>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
- makeReferenceArgumentCollection() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
- makeReferenceArgumentCollection() - Method in class picard.analysis.CollectRrbsMetrics
- makeReferenceArgumentCollection() - Method in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- makeReferenceArgumentCollection() - Method in class picard.cmdline.CommandLineProgram
- makeReferenceArgumentCollection() - Method in class picard.sam.CreateSequenceDictionary
- makeReferenceArgumentCollection() - Method in class picard.sam.DownsampleSam
- makeReferenceArgumentCollection() - Method in class picard.util.ScatterIntervalsByNs
- makeReferenceArgumentCollection() - Method in class picard.vcf.LiftoverVcf
- makeReferenceConfidenceVariantContext(int, byte[], String, int, ReadPileup, Locatable, int, boolean, List<VariantContext>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
- makeSampleCollector(SAMReadGroupRecord) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelCollector
- makeSampleCollector(SAMReadGroupRecord) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector
- makeSampleCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
- makeSamReaderFactory() - Method in class org.broadinstitute.hellbender.engine.GATKTool
- makeSeekable(List<File>, BclQualityEvaluationStrategy, int[]) - Static method in class picard.illumina.parser.readers.BclReader
- makeSequenceDictionary(File) - Method in class picard.sam.CreateSequenceDictionary
-
Read all the sequences from the given reference file, and convert into SAMSequenceRecords
- makeSink(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceBCICodec
- makeSink(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceCodec
- makeSink(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceBCICodec
- makeSink(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceCodec
- makeSink(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceBCICodec
- makeSink(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceCodec
- makeSink(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in interface org.broadinstitute.hellbender.utils.codecs.FeatureOutputCodec
-
Create a consumer of features.
- makeSink(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.SiteDepthBCICodec
- makeSink(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.SiteDepthCodec
- makeSink(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceBCICodec
- makeSink(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceCodec
- MakeSitesOnlyVcf - Class in picard.vcf
-
Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.
- MakeSitesOnlyVcf() - Constructor for class picard.vcf.MakeSitesOnlyVcf
- makeSortingCollection() - Static method in class picard.util.SequenceDictionaryUtils
- makeSortMerger(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceBCICodec
- makeSortMerger(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceCodec
- makeSortMerger(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceBCICodec
- makeSortMerger(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceCodec
- makeSortMerger(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceBCICodec
- makeSortMerger(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceCodec
- makeSortMerger(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in interface org.broadinstitute.hellbender.utils.codecs.FeatureOutputCodec
-
Get an object that wraps the usual FeatureSink that post-processes the interval-ordered stream of features.
- makeSortMerger(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.SiteDepthBCICodec
- makeSortMerger(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.SiteDepthCodec
- makeSortMerger(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceBCICodec
- makeSortMerger(GATKPath, SAMSequenceDictionary, List<String>, int) - Method in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceCodec
- makeSourceFromStream(InputStream) - Method in class org.broadinstitute.hellbender.utils.codecs.AbstractBCICodec
- makeSourceFromStream(InputStream) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec
- makeSourceFromStream(InputStream) - Method in class org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec
- makeStandardHCReadFilters() - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- makeStandardHCReadTransformer() - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- makeStandardMutect2PostFilterReadTransformer(Path, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- makeStandardMutect2ReadFilters() - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- makeTemporaryBAMFile() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
-
Make an indexed BAM file contains the reads in the builder, marking it for deleteOnExit()
- makeTileIterator(File) - Method in class picard.illumina.parser.PerTileParser
-
Factory method for the iterator of each tile
- makeTileIterator(File) - Method in class picard.illumina.parser.PosParser
-
Make an CloseableIterator
based on the given file and fileType specified at construction. - makeTruthVariantFilter() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- makeTruthVariantFilter() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVConcordance
- makeTruthVariantFilter() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- makeTruthVariantFilter() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance
- makeTruthVariantFilter() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3
- makeTruthVariantFilter() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance
- makeValueObjectForAnnotation(double) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.FisherStrand
- makeValueObjectForAnnotation(int[][]) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.FisherStrand
- makeVariantAnnotations() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Returns a list of annotations that can be applied to VariantContexts.
- makeVariantAnnotations() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- makeVariantAnnotations() - Method in class org.broadinstitute.hellbender.tools.HaplotypeCallerSpark
- makeVariantAnnotations() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- makeVariantAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
-
If we are in reference confidence mode we want to filter the annotations as there are certain annotations in the standard HaplotypeCaller set which are no longer relevant, thus we filter them out before constructing the VariantAnnotationEngine because the user args will have been parsed by that point.
- makeVariantAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- makeVariantFilter() - Method in class org.broadinstitute.hellbender.engine.spark.VariantWalkerSpark
-
Returns the variant filter (simple or composite) that will be applied to the variants before calling
VariantWalkerSpark.getVariants(org.apache.spark.api.java.JavaSparkContext). - makeVariantFilter() - Method in class org.broadinstitute.hellbender.engine.VariantWalkerBase
-
Returns the variant filter (simple or composite) that will be applied to the variants before calling
#apply. - makeVariantFilter() - Method in class org.broadinstitute.hellbender.tools.funcotator.Funcotator
- makeVariantFilter() - Method in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- makeVariantFilter() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
-
Create filters for variant types, ids, and genomic intervals.
- makeVariantFilter() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants
- makeVariantFilter(boolean) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine
- makeVCFHeader(SAMSequenceDictionary, Set<VCFHeaderLine>) - Method in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper
- makeVCFHeader(SAMSequenceDictionary, Set<VCFHeaderLine>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
-
Create a VCF header.
- MakeVcfSampleNameMap - Class in picard.vcf
-
Creates a TSV from sample name to VCF/GVCF path, with one line per input.
- MakeVcfSampleNameMap() - Constructor for class picard.vcf.MakeVcfSampleNameMap
- makeVCFWriter(GATKPath, SAMSequenceDictionary, boolean, boolean, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper
- makeVCFWriter(GATKPath, SAMSequenceDictionary, boolean, boolean, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
-
Create a VCF or GVCF writer as appropriate, given our arguments
- makeVectorTable(String, String, List<String>, double[], String, String) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator
- makeZippedInputStream(InputStream) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
creates an input stream from a zipped stream
- Male - Enum constant in enum class picard.pedigree.Sex
- MALE - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.Sex
- MALE_CHROMS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- MalformedBAM(File, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MalformedBAM
- MalformedBAM(String, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MalformedBAM
- MalformedBAM(GATKRead, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MalformedBAM
- MalformedFile(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MalformedFile
- MalformedFile(Path, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MalformedFile
- MalformedFile(Path, String, Exception) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MalformedFile
- MalformedFile(GATKPath, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MalformedFile
- MalformedFile(GATKPath, String, Exception) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MalformedFile
- MalformedGenomeLoc(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MalformedGenomeLoc
- MalformedGenomeLoc(String, Exception) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MalformedGenomeLoc
- MalformedRead(String, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MalformedRead
- MalformedRead(GATKRead, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MalformedRead
- MANDATORY_PROPERTIES - Static variable in class org.broadinstitute.hellbender.engine.spark.SparkContextFactory
-
GATK will not run without these properties They will always be set unless explicitly overridden with
StandardArgumentDefinitions.SPARK_PROPERTY_NAME - MANE_PLUS_CLINICAL - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
the transcript belongs to the MANE Select Plus Clinical data set.
- MANE_SELECT - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
the transcript belongs to the MANE Select data set.
- MANIFEST_FILE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- MANIFEST_FILE_HEADER_NAMES - Static variable in class picard.arrays.illumina.IlluminaManifest
- MANIFEST_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- manifestFileParser - Variable in class picard.arrays.illumina.IlluminaManifest
- manifestName - Variable in class picard.arrays.illumina.InfiniumEGTFile
- MannWhitneyU - Class in org.broadinstitute.hellbender.utils
-
Imported with changes from Picard private.
- MannWhitneyU() - Constructor for class org.broadinstitute.hellbender.utils.MannWhitneyU
- MannWhitneyU.RankedData - Class in org.broadinstitute.hellbender.utils
-
The ranked data in one list and a list of the number of ties.
- MannWhitneyU.Result - Class in org.broadinstitute.hellbender.utils
-
The results of performing a rank sum test.
- MannWhitneyU.TestStatistic - Class in org.broadinstitute.hellbender.utils
-
The values of U1, U2 and the transformed number of ties needed for the calculation of sigma in the normal approximation.
- MannWhitneyU.TestType - Enum Class in org.broadinstitute.hellbender.utils
-
A variable that indicates if the test is one sided or two sided and if it's one sided which group is the dominator in the null hypothesis.
- manualAnnotations - Variable in class org.broadinstitute.hellbender.tools.funcotator.OutputRenderer
-
LinkedHashMapof manually specified annotations to add to each output in addition to annotations provided toOutputRenderer.write(VariantContext, FuncotationMap). - MANUALLY_ANNOTATED - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.LocusLevel
-
Manually annotated locus
- MAP - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection.CopyNumberPosteriorExpectationMode
- MAP_FILE - Variable in class picard.arrays.MergePedIntoVcf
- MAP_INFO_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- MAP_NAME_VALUE_DELIMITER - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- MAP_QUAL_RANK_SUM_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- mapMappingQualityToPhredLikelihoodScore(int) - Static method in class org.broadinstitute.hellbender.transformers.DRAGENMappingQualityReadTransformer
- MAPPABILITY - Static variable in class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.CopyNumberAnnotations
- MAPPABILITY_TRACK_PATH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervals
- MAPPED - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- MAPPED_READS - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreMetrics
-
The number of non-host reads mapped to a pathogen
- mappedAndUnmappedReadIterator(int, int, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
create an iterator containing the specified read piles
- MappedFeature(GATKRead, FlowFeatureMapperArgumentCollection.MappingFeatureEnum, byte[], byte[], int, int, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper.MappedFeature
- MappedReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.MappedReadFilter
- mappedReadIterator(int, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
-
create an iterator containing the specified read piles
- Mapping(String) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.Mapping
- Mapping(GATKRead) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.Mapping
- MAPPING_ERROR_RATE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineContigPloidyModelArgumentCollection
- MAPPING_ERROR_RATE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
- MAPPING_QUALITIES - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- MAPPING_QUALITY_AVAILABLE - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- MAPPING_QUALITY_DEPTH_DEPRECATED - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- MAPPING_QUALITY_NOT_ZERO - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- MAPPING_QUALITY_THRESHOLD_FOR_GENOTYPING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- MAPPING_QUALITY_UNAVAILABLE - Static variable in class org.broadinstitute.hellbender.utils.QualityUtils
- MAPPING_QUALITY_ZERO_BY_SAMPLE_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- mappingFeature - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
kind of feature we are mapping (looking for)
- MappingQuality - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Median mapping quality of reads supporting each alt allele.
- MappingQuality() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.MappingQuality
- MappingQualityAvailableReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.MappingQualityAvailableReadFilter
- MappingQualityFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- MappingQualityFilter(double, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MappingQualityFilter
- MappingQualityNotZeroReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.MappingQualityNotZeroReadFilter
- MappingQualityRankSumTest - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Rank Sum Test for mapping qualities of REF versus ALT reads
- MappingQualityRankSumTest() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.MappingQualityRankSumTest
- MappingQualityReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads with mapping qualities within a specified range.
- MappingQualityReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.MappingQualityReadFilter
- MappingQualityReadFilter(int) - Constructor for class org.broadinstitute.hellbender.engine.filters.MappingQualityReadFilter
- MappingQualityReadFilter(int, Integer) - Constructor for class org.broadinstitute.hellbender.engine.filters.MappingQualityReadFilter
- MappingQualityReadTransformer - Class in org.broadinstitute.hellbender.transformers
-
A read transformer to modify the mapping quality of reads with MQ=255 to reads with MQ=60
- MappingQualityReadTransformer(int, int) - Constructor for class org.broadinstitute.hellbender.transformers.MappingQualityReadTransformer
- mappingQualityStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into the mapping-quality of the read under consideration
- mappingQualityThreshold - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- MappingQualityZero - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Count of all reads with MAPQ = 0 across all samples
- MappingQualityZero() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.MappingQualityZero
- MAPPINGS_DIFFER - Enum constant in enum class picard.sam.util.SamComparison.AlignmentComparison
- MAPPINGS_DIFFER - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records which are mapped in both files but do not meet criteria to be counted in MAPPINGS_MATCH.
- MAPPINGS_MATCH - Enum constant in enum class picard.sam.util.SamComparison.AlignmentComparison
- MAPPINGS_MATCH - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records for which mappings match in files.
- MAPQ - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestField
- mapQual - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
Mapping quality,
SAMRecord.NO_MAPPING_QUALITYif unspecified. - mapQualTieBreaker - Static variable in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
- mapToDouble(IntToDoubleFunction) - Method in class org.broadinstitute.hellbender.utils.IndexRange
-
Apply an int -> double function to this range, producing a double[]
- mapToInteger(IntUnaryOperator) - Method in class org.broadinstitute.hellbender.utils.IndexRange
-
Apply an int -> int function to this range, producing an int[]
- marginalize(Map<B, List<A>>) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Perform marginalization from an allele set to another (smaller one) taking the maximum value for each evidence in the original allele subset.
- mark(JavaRDD<GATKRead>, SAMFileHeader, MarkDuplicatesScoringStrategy, OpticalDuplicateFinder, int, boolean, MarkDuplicates.DuplicateTaggingPolicy, MarkDuplicatesSparkArgumentCollection) - Static method in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
-
Main method for marking duplicates, takes an JavaRDD of GATKRead and an associated SAMFileHeader with corresponding sorting information and returns a new JavaRDD\<GATKRead\> in which all read templates have been marked as duplicates NOTE: This method expects the incoming reads to be grouped by read name (queryname sorted/querygrouped) and for this to be explicitly be set in the the provided header.
- mark(JavaRDD<GATKRead>, SAMFileHeader, OpticalDuplicateFinder, MarkDuplicatesSparkArgumentCollection, int) - Static method in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- markDuplicateFragments(List<ReadEndsForMarkDuplicates>, boolean) - Method in class picard.sam.markduplicates.MarkDuplicates
-
Takes a list of ReadEndsForMarkDuplicates objects and removes from it all objects that should not be marked as duplicates.
- MarkDuplicates - Class in picard.sam.markduplicates
-
A better duplication marking algorithm that handles all cases including clipped and gapped alignments.
- MarkDuplicates() - Constructor for class picard.sam.markduplicates.MarkDuplicates
- MarkDuplicates.DuplicateTaggingPolicy - Enum Class in picard.sam.markduplicates
-
Enum used to control how duplicates are flagged in the DT optional tag on each read.
- MarkDuplicates.DuplicateType - Enum Class in picard.sam.markduplicates
-
Enum for the possible values that a duplicate read can be tagged with in the DT attribute.
- MarkDuplicatesForFlowArgumentCollection - Class in picard.sam.markduplicates
- MarkDuplicatesForFlowArgumentCollection() - Constructor for class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- MarkDuplicatesForFlowHelper - Class in picard.sam.markduplicates
-
MarkDuplicates calculation helper class for flow based mode The class extends the behavior of MarkDuplicates which contains the complete code for the non-flow based mode.
- MarkDuplicatesForFlowHelper(MarkDuplicates) - Constructor for class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- MarkDuplicatesHelper - Interface in picard.sam.markduplicates
- MarkDuplicatesScoringStrategy - Enum Class in org.broadinstitute.hellbender.utils.read.markduplicates
-
This class helps us compute and compare duplicate scores, which are used for selecting the non-duplicate during duplicate marking (see MarkDuplicatesGATK).
- MarkDuplicatesSpark - Class in org.broadinstitute.hellbender.tools.spark.transforms.markduplicates
-
MarkDuplicates on Spark
- MarkDuplicatesSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- markDuplicatesSparkArgumentCollection - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.BwaAndMarkDuplicatesPipelineSpark
- markDuplicatesSparkArgumentCollection - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- markDuplicatesSparkArgumentCollection - Variable in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- MarkDuplicatesSparkArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
An argument collection for use with tools that mark optical duplicates.
- MarkDuplicatesSparkArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- MarkDuplicatesSparkRecord - Class in org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
-
A common interface for the data types that represent reads for mark duplicates spark.
- MarkDuplicatesSparkRecord.Type - Enum Class in org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
- MarkDuplicatesSparkUtils - Class in org.broadinstitute.hellbender.tools.spark.transforms.markduplicates
-
Utility classes and functions for Mark Duplicates.
- MarkDuplicatesSparkUtils() - Constructor for class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils
- MarkDuplicatesSparkUtils.IndexPair<T> - Class in org.broadinstitute.hellbender.tools.spark.transforms.markduplicates
-
Wrapper object used for storing an object and some type of index information.
- MarkDuplicatesSparkUtils.TransientFieldPhysicalLocationComparator - Class in org.broadinstitute.hellbender.tools.spark.transforms.markduplicates
-
Comparator for TransientFieldPhysicalLocation objects by their attributes and strandedness.
- MarkDuplicatesWithMateCigar - Class in picard.sam.markduplicates
-
An even better duplication marking algorithm that handles all cases including clipped and gapped alignments.
- MarkDuplicatesWithMateCigar() - Constructor for class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
- MarkDuplicatesWithMateCigarIterator - Class in picard.sam.markduplicates
-
This will iterate through a coordinate sorted SAM file (iterator) and either mark or remove duplicates as appropriate.
- MarkDuplicatesWithMateCigarIterator(SAMFileHeader, CloseableIterator<SAMRecord>, OpticalDuplicateFinder, DuplicateScoringStrategy.ScoringStrategy, int, boolean, boolean, int, int, List<File>) - Constructor for class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
-
Initializes the mark duplicates iterator.
- MarkedOpticalDuplicateReadFilter - Class in org.broadinstitute.hellbender.tools.spark.pathseq
- MarkedOpticalDuplicateReadFilter() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.MarkedOpticalDuplicateReadFilter
- MarkIlluminaAdapters - Class in picard.illumina
-
Command line program to mark the location of adapter sequences.
- MarkIlluminaAdapters() - Constructor for class picard.illumina.MarkIlluminaAdapters
- MarkQueue - Class in picard.sam.markduplicates.util
-
This is the mark queue.
- MarkQueue(DuplicateScoringStrategy.ScoringStrategy) - Constructor for class picard.sam.markduplicates.util.MarkQueue
- markTreesAsVisited(List<JunctionTreeLinkedDeBruijnGraph.ThreadingTree>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JTBestHaplotype
- mask - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
-
Any variant which overlaps entries from the provided mask file will be filtered.
- mask(int, int) - Method in class org.broadinstitute.hellbender.tools.dragstr.STRDecimationTable
- mask(SVKmerShort) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
- MASK_EXTENSION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- MASK_NAME_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- MASKED_ANY_BASE - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorConstants
-
A character representing any base as used in VCF files and IUPAC base standards.
- MASKED_ANY_BASE_STRING - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorConstants
-
A
Stringrepresenting any base as used in VCF files and IUPAC base standards. - maskExtension - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- MASKING_QUALITY - Static variable in class picard.illumina.parser.MultiTileBclParser
- maskName - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
-
When using the --mask argument, the mask-name will be annotated in the variant record.
- MATCH - Enum constant in enum class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner.State
- MATCH_BARCODES_INLINE - Variable in class picard.illumina.IlluminaBasecallsToFastq
- MATCH_BARCODES_INLINE - Variable in class picard.illumina.IlluminaBasecallsToSam
- matchAllelesOnly(VariantContext, VariantContext) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Attempt to match allele ref/alt pairs, even if the allele pairs in the given variant contexts are equivalent, but not exact.
- MATCHED_NORMAL_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination
- MATCHED_NORMAL_SEGMENT_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEvents
- MATCHED_NORMAL_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination
- matches(int, String) - Method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Checks a column names matches given one.
- matches(GATKRead) - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator
-
given a read and the query type, check if it matches our regions
- matchesAll(int, String...) - Method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Checks an array of column matches the column names starting from a given index.
- matchesExactly(String...) - Method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Checks whether columns contain all the names in an array and no other and in the very same order.
- MATCHING_DICTIONARY_TAGS - Variable in class picard.sam.MergeBamAlignment
- MatchingBasesAndQualsReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.MatchingBasesAndQualsReadFilter
- matchMatrix - Variable in class org.broadinstitute.hellbender.utils.pairhmm.FlowBasedPairHMM
- matchMatrix - Variable in class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM
- MatchMDElement(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.MatchMDElement
- matchOnKeyOrDefault(Set<Map.Entry<String, String>>, String, String) - Method in class org.broadinstitute.hellbender.tools.funcotator.filtrationRules.FuncotationFilter
-
Given a set of extracted funcotations of a variant, return a Stream of values that belong to the key.
- matchPattern - Variable in class picard.illumina.parser.ParameterizedFileUtil
-
A pattern that will match files of this type for this lane
- MatchResults - Class in picard.fingerprint
-
Represents the results of a fingerprint comparison between one dataset and a specific fingerprint file.
- matchToDeletion - Static variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Position in the transition probability array for the Match-to-Deletion transition.
- matchToInsertion - Static variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Position in the transition probability array for the Match-to-Insertion transition.
- matchToMatch - Static variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Position in the transition probability array for the Match-to-Match transition.
- matchToMatchProb(byte, byte) - Static method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Returns the probability that neither of two event takes place.
- matchToMatchProb(int, int) - Static method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Returns the probability that neither of two events, insertion and deletion, takes place.
- matchToMatchProbLog10(byte, byte) - Static method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Returns the log10 probability that neither of two events, insertion and deletion, takes place.
- matchToMatchProbLog10(int, int) - Static method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Returns the log-probability that neither of two events takes place.
- MATE_ALIGNMENT_LENGTH_UNCERTAINTY - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.DiscordantReadPairEvidence
- MATE_CONTIG_TAG_NAME - Static variable in class org.broadinstitute.hellbender.tools.AddOriginalAlignmentTags
- MATE_DIFFERENT_STRAND - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- MATE_DISTANT - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- MATE_ON_SAME_CONTIG_OR_NO_MAPPED_MATE - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- MATE_TOO_DISTANT_LENGTH - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- MATE_UNMAPPED_AND_UNMAPPED_READ_FILTER - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- MateDifferentStrandReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.MateDifferentStrandReadFilter
- MateDistantReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only paired reads that are not near each other in a coordinate-sorted source of reads.
- MateDistantReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.MateDistantReadFilter
- MateDistantReadFilter(int) - Constructor for class org.broadinstitute.hellbender.engine.filters.MateDistantReadFilter
- mateIsReverseStrand() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- mateIsReverseStrand() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- mateIsUnmapped() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
- mateIsUnmapped() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- mateIsUnplaced() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Does the reads mate have a position assigned to it for sorting purposes..
- mateIsUnplaced() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- MateOnSameContigOrNoMappedMateReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.MateOnSameContigOrNoMappedMateReadFilter
- MATERNAL_ID - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.PedReader.Field
- maternalRefPath - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- mateTooDistantLength - Variable in class org.broadinstitute.hellbender.engine.filters.MateDistantReadFilter
- MateUnmappedAndUnmappedReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.MateUnmappedAndUnmappedReadFilter
- MathUtil - Class in picard.util
-
General math utilities
- MathUtil.LogMath - Class in picard.util
-
A collection of common math operations that work with log values.
- MathUtils - Class in org.broadinstitute.hellbender.utils
-
MathUtils is a static class (no instantiation allowed!) with some useful math methods.
- MathUtils.IntToDoubleArrayFunction - Interface in org.broadinstitute.hellbender.utils
- MathUtils.RunningAverage - Class in org.broadinstitute.hellbender.utils
-
A utility class that computes on the fly average and standard deviation for a stream of numbers.
- MATRIX_OUTPUT - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- MATRIX_OUTPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
- matrixCsvFile - Variable in class org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeBasedVariantRecallerArgumentCollection
-
This argument specifies a CSV to be filled with likelihood matrix data
- MatrixSummaryUtils - Class in org.broadinstitute.hellbender.utils
-
Static class for implementing some matrix summary stats that are not in Apache, Spark, etc
- max() - Method in class org.broadinstitute.hellbender.utils.dragstr.DoubleSequence
-
Returns the maximum value of the sequence
- max() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Find the greatest interval in the tree.
- max(double[]) - Static method in class picard.util.MathUtil
-
Returns the largest value stored in the array.
- max(long[]) - Static method in class picard.util.MathUtil
-
Returns the largest value stored in the array.
- max(DoubleUnaryOperator, double, double, double, double, double, int) - Static method in class org.broadinstitute.hellbender.utils.OptimizationUtils
- max(Function<Double, Double>, double, double, double) - Static method in class org.broadinstitute.hellbender.utils.OptimizationUtils
- max(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
Returns the maximum GenomeLoc of this and other
- max(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Find the latest interval in the tree less than or equal to the specified interval.
- MAX_ADAPTER_MISMATCHES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- MAX_ADVI_ITER_FIRST_EPOCH - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- MAX_ADVI_ITER_FIRST_EPOCH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- MAX_ADVI_ITER_SUBSEQUENT_EPOCHS - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- MAX_ADVI_ITER_SUBSEQUENT_EPOCHS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- MAX_ALIGN_LENGTH - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH - Static variable in class picard.cmdline.CommandLineProgram
-
CommandLineProgramProperties oneLineSummary attribute must be shorted than this in order to maintain reasonable help output formatting.
- MAX_ALLOWED_LOW_HETS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MTLowHeteroplasmyFilterTool
- MAX_ALT_ALLELE_COUNT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- MAX_ALT_FRACTION_IN_NORMAL - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- MAX_ALT_HITS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection
- MAX_ALTERNATE_ALLELES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- MAX_ALTS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection
- MAX_APPARENT_BASES_PER_WINDOW - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
- MAX_ASSEMBLY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- max_attempts - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator
-
The statistical model being built by this tool may fail due to simple statistical sampling issues.
- MAX_BIAS_FACTORS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
- MAX_BND_LEN_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate
- MAX_CALLING_ITERS - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- MAX_CALLING_ITERS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- MAX_CATASTROPHIC_ERRORS_FOR_READ_CAP - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
- MAX_CHANGEPOINTS_PER_CHROMOSOME - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationSegmenter
- MAX_CLASS - Static variable in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- MAX_CLASS_READ_GROUP_TAG - Static variable in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- MAX_CLIQUE - Enum constant in enum class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine.CLUSTERING_TYPE
- MAX_COMBINED_DISTANCE - Static variable in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
- MAX_COPY_NUMBER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCallingArgumentCollection
- MAX_DEPTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsArgumentCollection
- MAX_DEPTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel
- MAX_DEPTH_PER_SAMPLE_NAME - Static variable in class org.broadinstitute.hellbender.engine.LocusWalker
- MAX_DIFF_RATE - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- MAX_DISCARD_FRACTION - Variable in class picard.sam.RevertSam
- MAX_DISTANCE_TO_FILTERED_CALL_ON_SAME_HAPLOTYPE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- MAX_DUST_SCORE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- MAX_EDIT_DISTANCE_TO_JOIN - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
- MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK - Variable in class picard.fingerprint.CrosscheckFingerprints
- MAX_EFFECTIVE_DEPTH_ADJUSTMENT_FOR_FRD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- MAX_EM_ITERATIONS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel
- MAX_ERROR_RATE - Static variable in class picard.util.ClippingUtility
-
The default value used for the maximum error rate when matching read bases to clippable sequence.
- MAX_ERROR_RATE_PE - Variable in class picard.illumina.MarkIlluminaAdapters
- MAX_ERROR_RATE_SE - Variable in class picard.illumina.MarkIlluminaAdapters
- MAX_ERRORS_FOR_READ_CAP - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
- MAX_EVENTS_IN_REGION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
-
Hard filter thresholds
- MAX_FILE_HANDLES_FOR_READ_ENDS_MAP - Variable in class picard.sam.markduplicates.MarkDuplicates
- MAX_FILTER_SIZE - Static variable in class org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile
- MAX_FRACTION_OF_BACKGROUND_TO_SPLIT_OFF - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel
- MAX_FRAGMENT_LENGTH_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- MAX_FS - Variable in class picard.vcf.filter.FilterVcf
- MAX_GATK_USABLE_Q_SCORE - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
-
Quals above this value should be capped down to this value (because they are too high) in the base quality score recalibrator
- MAX_GENOTYPE_COUNT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- MAX_GERMLINE_PROBABILITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals
- MAX_GROUP_RATIO - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- MAX_INDEL_LENGTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
- MAX_INSERT_SIZE - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The maximum measure insert size by alignment.
- MAX_INSERT_SIZE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
- MAX_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
-
The maximum measure insert size by alignment.
- MAX_INSERTIONS_OR_DELETIONS - Variable in class picard.sam.MergeBamAlignment
- MAX_INTERVAL_SIZE_ARGNAME - Static variable in class org.broadinstitute.hellbender.tools.sv.CondenseDepthEvidence
- MAX_KMER_FREQ - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBadGenomicKmersSpark
- MAX_LEADING_BASES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
- MAX_LOCI - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- MAX_MASKED_BASES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- MAX_MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- MAX_MERGE_DISTANCE - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsByAnnotation
- MAX_MISMATCH_RATE - Variable in class picard.analysis.CollectRrbsMetrics
- MAX_MISMATCHES - Variable in class picard.illumina.ExtractBarcodesProgram
- MAX_MNP_DISTANCE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- MAX_MNP_DISTANCE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- MAX_N_INDEL_INFORMATIVE_READS - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
- MAX_N_RATIO_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- MAX_NO_CALLS - Variable in class picard.illumina.ExtractBarcodesProgram
- MAX_NORMAL_QUAL_SUM - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- MAX_NUM_HAPLOTYPES_IN_POPULATION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- MAX_NUM_INTERVALS_TO_IMPORT_IN_PARALLEL - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- MAX_NUMBER_OF_VALUES_PER_HDF5_MATRIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils
- MAX_NUMT_COPIES_IN_AUTOSOME_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NuMTFilterTool
- MAX_OPEN_TEMP_FILES - Variable in class picard.sam.ValidateSamFile
- MAX_OPTICAL_DUPLICATE_SET_SIZE - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- MAX_OUTPUT - Variable in class picard.sam.ValidateSamFile
- MAX_PE_ERROR_RATE - Static variable in class picard.util.ClippingUtility
-
The default value used for the maximum error rate when matching paired end read bases to clippable sequence.
- MAX_PERIOD_ARGUMENT_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- MAX_POPULATION_AF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- MAX_POPULATION_AF_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- MAX_POS - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
- MAX_PROB_BELOW_ONE - Static variable in class picard.util.MathUtil
-
The double value closest to 1 while still being less than 1.
- MAX_Q - Variable in class picard.sam.FastqToSam
- MAX_QUAL - Static variable in class org.broadinstitute.hellbender.utils.QualityUtils
-
Maximum sense quality value.
- MAX_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The maximum read length.
- MAX_READ_LENGTH - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- MAX_READ_LENGTH_ARG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- MAX_READS_IN_RAM_PER_TILE - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
Deprecated.
- MAX_READS_IN_RAM_PER_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
- MAX_REASONABLE_Q_SCORE - Static variable in class org.broadinstitute.hellbender.utils.QualityUtils
-
bams containing quals above this value are extremely suspicious and we should warn the user
- MAX_RECALIBRATED_Q_SCORE - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- MAX_RECORDS_IN_RAM - Variable in class org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram
- MAX_RECORDS_IN_RAM - Static variable in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
- MAX_RECORDS_IN_RAM - Variable in class picard.cmdline.CommandLineProgram
- MAX_RECORDS_IN_RAM - Static variable in class picard.sam.AbstractAlignmentMerger
- MAX_RECORDS_TO_EXAMINE - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- MAX_REPEAT_LENGTH - Static variable in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
- MAX_REPEATS_ARGUMENT_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- MAX_SAM_QUAL_SCORE - Static variable in class org.broadinstitute.hellbender.utils.QualityUtils
-
Maximum quality score that can be encoded in a SAM/BAM file
- MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP - Variable in class picard.sam.markduplicates.MarkDuplicates
-
If more than this many sequences in SAM file, don't spill to disk because there will not be enough file handles.
- MAX_SITE_AF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- MAX_SITE_AF_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- MAX_SIZE_FOR_HISTOGRAM - Static variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelLengthHistogram
- MAX_SPLICES_TO_KEEP - Static variable in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager
- MAX_START_MIN_END - Enum constant in enum class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser.BreakpointSummaryStrategy
-
A permissive strategy to summarize a cluster by it largest extent
- MAX_STARTS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- MAX_STD_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAF
- MAX_STR_UNIT_LENGTH - Static variable in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
- MAX_SUSPICIOUS_READS_PER_ALIGNMENT_START_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- MAX_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
-
The maximum coverage of reads that mapped to target regions of an experiment.
- MAX_TO_MERGE - Variable in class picard.util.ScatterIntervalsByNs
- MAX_TRAINING_EPOCHS - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- MAX_TRAINING_EPOCHS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- MAX_UNPRUNED_VARIANTS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- MAX_UNSIGNED_SHORT - Static variable in class picard.arrays.illumina.InfiniumDataFile
- MAX_VALIDATION_NORMAL_COUNT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- MAX_VARIANTS_PER_SHARD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- maxAdapterMismatches - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- maxAlleleLength() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleAndContext
- maxAltCountForMutect3 - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
Downsample alt reads for Mutect3 data
- maxAlternateAlleles - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
-
If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES), then only this many alleles will be used.
- maxAlternateHits - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection
-
The maximum number of alternate alignments for each read, i.e.
- maxAmbiguousBaseFraction - Variable in class org.broadinstitute.hellbender.engine.filters.AmbiguousBaseReadFilter
- maxAmbiguousBases - Variable in class org.broadinstitute.hellbender.engine.filters.AmbiguousBaseReadFilter
- maxAmbiguousBases - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
-
This is the threshold for filtering reads based on the number of 'N' values present in the sequence.
- maxAssemblyRegionSize - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- maxCallableImpreciseVariantDeletionSize - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- maxClass - Variable in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils.ReadGroupInfo
- maxColumn() - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Element
- maxCombinedDistance - Variable in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
- maxDepth - Variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsArgumentCollection
- maxDepthPerSample - Variable in class org.broadinstitute.hellbender.engine.LocusWalker
- maxDepthPerSample - Variable in class org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark
- maxDiploidAltAllelesThatCanBeGenotyped - Variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection
-
Maximum number of alternate alleles that will report likelihoods after being combined on reading from GenomicsDB (including
) Must be at least one greater than the maximum number of alternate alleles for genotyping. - maxDistanceToFilteredCallOnSameHaplotype - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- maxDUSTScore - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- maxEffectiveDepthAdjustment - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- maxElementIndex(double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- maxElementIndex(double[], int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- maxElementIndex(double[], int, int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- maxElementIndex(int[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- maxEnd() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Return the interval having the largest ending value.
- maxEventsInRegion - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- maxExtensionIntoRegionPadding - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
-
The maximum extent into the full active region extension that we're willing to go in genotyping our events NOTE: this is only applicable to the legacy assembly region trimming currently
- maxFalsePositiveRate - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- maxFASTQSize - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- maxFragmentLength - Variable in class org.broadinstitute.hellbender.engine.filters.FragmentLengthReadFilter
- maxGenotypeCount - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
-
If there are more than this number of genotypes at a locus presented to the genotyper, then only this many genotypes will be used.
- maxGermlineProbability - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals
- maxGQ - Variable in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- maxHaplotypeLength - Variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- maxHmer - Variable in class org.broadinstitute.hellbender.engine.filters.flow.FlowBasedTPAttributeValidReadFilter
- maximalInterestingDistance - Variable in class picard.util.BarcodeEditDistanceQuery
-
maximal edit distance between reads and barcodes to be considered
- maximum() - Method in class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistribution
- MAXIMUM_CHUNK_SIZE - Static variable in class org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormals
- MAXIMUM_CYCLE_VALUE - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
-
The cycle covariate will generate an error if it encounters a cycle greater than this value.
- MAXIMUM_DYNAMIC_QUAL_THRESHOLD_ENTRY_BASEQ - Static variable in interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
- MAXIMUM_END_CLIPPED_BASES - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- MAXIMUM_GC_CONTENT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
- MAXIMUM_INSERT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- MAXIMUM_INSERT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
- MAXIMUM_MAPPABILITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
- MAXIMUM_MAPPING_QUALITY_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- MAXIMUM_NUMBER_OF_SEGMENTS_PER_CHROMOSOME_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- MAXIMUM_NUMBER_OF_SMOOTHING_ITERATIONS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- MAXIMUM_NUMBER_OF_UNLABELED_VARIANTS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations
- MAXIMUM_REFERENCE_SEQUENCE_BUFFER_SIZE - Static variable in class org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFile
- MAXIMUM_SEGMENTAL_DUPLICATION_CONTENT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
- MAXIMUM_STRONG_REF_GENOTYPE_PER_PLOIDY - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculators
-
Maximum possible number of genotypes that this calculator can handle.
- MAXIMUM_ZEROS_IN_INTERVAL_PERCENTAGE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormals
- MAXIMUM_ZEROS_IN_SAMPLE_PERCENTAGE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormals
- maximumAlleleIndex() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Returns the largest allele index present in the genotype.
- maximumKeyValue() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ContextCovariate
- maximumKeyValue() - Method in interface org.broadinstitute.hellbender.utils.recalibration.covariates.Covariate
-
Returns the maximum value possible for any key representing this covariate
- maximumKeyValue() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.CycleCovariate
- maximumKeyValue() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.QualityScoreCovariate
- maximumKeyValue() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadGroupCovariate
- maximumLengthInBasePairs() - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParams
- maximumLikelihoodOverAllAlleles(int, int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
- maximumPeriod() - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParams
-
Return the maximum period this parameter collection has specified values for.
- maximumRepeats() - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParams
-
Return the maximum repeat length this parameter collection has specified values for.
- maxIndelSize - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
-
Maximum indel size to realign.
- maxLeadingBases - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
-
Distance in reference to look back before allele
- maxMADTolerance - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetricsArgumentCollection
- maxMappingQualityScore - Variable in class org.broadinstitute.hellbender.engine.filters.MappingQualityReadFilter
- maxMedianFragmentLengthDifference - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- maxMnpDistance - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
-
Two or more phased substitutions separated by this distance or less are merged into MNPs.
- maxNumHaplotypesInPopulation - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
The assembly graph can be quite complex, and could imply a very large number of possible haplotypes.
- maxNumSegmentsPerChromosome - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- maxNumSmoothingIterations - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- maxNuMTAutosomalCopies - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NuMTFilterTool
- maxOutputReads - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- maxPeriod - Variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- maxPopulationAlleleFrequency - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
In tumor-only mode, we discard variants with population allele frequencies greater than this threshold.
- maxProbPropagationDistance - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- maxProbPropagationDistance - Variable in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
- maxReadLength - Variable in class org.broadinstitute.hellbender.engine.filters.ReadLengthReadFilter
- maxReadLength - Variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- maxReadQuality - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- maxReadsPerAlignmentStart - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
-
Other parameters
- maxReasonableFragmentLength - Variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
-
Maximum fragment length to be considered a reasonable pair alignment
- maxRefCountForMutect3 - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
Downsample ref reads for Mutect3 data
- maxRepeatLength - Variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- maxScore - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
threshold of score delta to for emitting (will be emitted if lower)
- maxSize() - Method in class org.broadinstitute.hellbender.utils.DigammaCache
- maxSize() - Method in class org.broadinstitute.hellbender.utils.IntToDoubleFunctionCache
- maxSize() - Method in class org.broadinstitute.hellbender.utils.Log10Cache
- maxSize() - Method in class org.broadinstitute.hellbender.utils.Log10FactorialCache
- maxSuspiciousReadsPerAlignmentStart - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
Maximum number of suspicious reads (mediocre mapping quality or too many substitutions) allowed in a downsampling stride.
- maxTrackedFragmentLength - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- maxUnprunedVariants - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
The maximum number of variants in graph the adaptive pruner will allow
- maxValidationNormalCount - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- maybeAdvance() - Method in class picard.illumina.parser.PerTileParser
- maybeDemultiplex(ClusterData, Map<String, BarcodeMetric>, BarcodeMetric, ReadStructure) - Method in class picard.illumina.BasecallsConverter
-
If we are demultiplexing and a barcodeExtractor is defined then this method will perform on-the-fly demuxing.
- MC3_ALT_COUNT_KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3
- MC3_REF_COUNT_KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3
- MD5_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
- MDElement(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.MDElement
- mean() - Method in class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistribution
- mean() - Method in class org.broadinstitute.hellbender.utils.MathUtils.RunningAverage
- mean(double...) - Method in class picard.util.MathUtil.LogMath
-
Computes the mean of the provided log values.
- mean(double[]) - Static method in class picard.util.MathUtil
- mean(double[], int, int) - Static method in class picard.util.MathUtil
-
Calculated the mean of an array of doubles.
- mean(int, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- MEAN_ALIGNED_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The mean aligned read length of the set of reads examined.
- MEAN_AMPLICON_COVERAGE - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The mean read coverage of all amplicon regions in the experiment.
- MEAN_BAIT_COVERAGE - Variable in class picard.analysis.directed.HsMetrics
-
The mean coverage of all baits in the experiment.
- MEAN_BASE_QUALITY - Variable in class picard.analysis.GcBiasDetailMetrics
-
The mean quality (determined via the error rate) of all bases of all reads that are assigned to windows of this GC.
- MEAN_BIAS - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionParameter
- MEAN_BIAS_STANDARD_DEVIATION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineContigPloidyModelArgumentCollection
- MEAN_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The mean number of clusters per tile.
- MEAN_COVERAGE - Variable in class picard.analysis.WgsMetrics
-
The mean coverage in bases of the genome territory, after all filters are applied.
- MEAN_CPG_COVERAGE - Variable in class picard.analysis.RrbsSummaryMetrics
-
Mean coverage of CpG sites
- MEAN_INSERT_SIZE - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The mean insert size of the "core" of the distribution.
- MEAN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
-
The mean insert size of the "core" of the distribution.
- MEAN_PCT_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The mean percentage of pf clusters per tile.
- MEAN_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The mean number of pf clusters per tile.
- MEAN_PROBE_COVERAGE - Variable in class picard.analysis.directed.TargetMetrics
-
The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.
- MEAN_R - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- MEAN_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The mean read length of the set of reads examined.
- MEAN_START_MEAN_END - Enum constant in enum class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser.BreakpointSummaryStrategy
-
Summarize a cluster using the mean value for each end, even if that value was not represented in any sample
- MEAN_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
-
The mean coverage of targets.
- MEAN_THETA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- MEAN_UMI_LENGTH - Variable in class picard.sam.markduplicates.UmiMetrics
-
Number of bases in each UMI
- MEAN_X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- MEAN_Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- MeanQualityByCycle - Class in picard.analysis
-
Program to generate a data table and chart of mean quality by cycle from a BAM file.
- MeanQualityByCycle - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- MeanQualityByCycle() - Constructor for class picard.analysis.MeanQualityByCycle
- MeanQualityByCycleSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines.metrics
-
Program to generate a data table and chart of mean quality by cycle from a BAM file.
- MeanQualityByCycleSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MeanQualityByCycleSpark
- meanR - Variable in class picard.arrays.illumina.InfiniumEGTFile
- meanTheta - Variable in class picard.arrays.illumina.InfiniumEGTFile
- meanWeights() - Method in class org.broadinstitute.hellbender.utils.Dirichlet
- median() - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.CDF
- median() - Method in class org.broadinstitute.hellbender.utils.Histogram
- median(double[]) - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU
-
Finds or calculates the median value of a sorted array of double.
- median(double...) - Static method in class picard.util.MathUtil
-
Calculate the median of an array of doubles.
- median(int[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- median(int[], Percentile.EstimationType) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- median(Collection<T>) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Compute the median of a list of numbers If values.length is odd, this will be the middle value when the elements are sorted If values.length is even then it will be the mean of the two values closest to the middle.
- MEDIAN_3PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
-
The median 3 prime bias of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter, where 3 prime bias is calculated per transcript as: mean coverage of the 3 prime-most number of bases, divided by the mean coverage of the whole transcript.
- MEDIAN_5PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
-
The median 5 prime bias of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter.
- MEDIAN_5PRIME_TO_3PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
-
The ratio of coverage at the 5 prime end to the 3 prime end based on the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter.
- MEDIAN_ABSOLUTE_DEVIATION - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The median absolute deviation of the distribution.
- MEDIAN_ABSOLUTE_DEVIATION - Variable in class picard.analysis.InsertSizeMetrics
-
The median absolute deviation of the distribution.
- MEDIAN_AUTOSOMAL_COVERAGE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NuMTFilterTool
- MEDIAN_BASE_QUALITY_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- MEDIAN_BASE_QUALITY_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- MEDIAN_COVERAGE - Variable in class picard.analysis.WgsMetrics
-
The median coverage in bases of the genome territory, after all filters are applied.
- MEDIAN_CPG_COVERAGE - Variable in class picard.analysis.RrbsSummaryMetrics
-
Median coverage of CpG sites
- MEDIAN_CV_COVERAGE - Variable in class picard.analysis.RnaSeqMetrics
-
The median coefficient of variation (CV) or stdev/mean for coverage values of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter.
- MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- MEDIAN_FRAGMENT_LENGTH_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- MEDIAN_INSERT_SIZE - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.
- MEDIAN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
-
The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.
- MEDIAN_MAPPING_QUALITY_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- MEDIAN_MAPPING_QUALITY_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- MEDIAN_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The median read length of the set of reads examined.
- MEDIAN_READ_POSITON_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- MEDIAN_START_MEDIAN_END - Enum constant in enum class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser.BreakpointSummaryStrategy
-
Use the (first) middle value to summarize cluster starts and ends, such that the start and end were seen in the data
- MEDIAN_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
-
The median coverage of targets.
- medianAutosomalCoverage - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NuMTFilterTool
- meetsMinMergableSequenceForEitherPrefixOrSuffix(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SharedVertexSequenceSplitter
-
Does either the common suffix or prefix have at least minCommonSequence bases in it?
- meetsMinMergableSequenceForPrefix(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SharedVertexSequenceSplitter
-
Does the common prefix have at least minCommonSequence bases in it?
- meetsMinMergableSequenceForSuffix(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SharedVertexSequenceSplitter
-
Does the common suffix have at least minCommonSequence bases in it?
- MemoryBasedReadEndsForMarkDuplicatesMap - Class in picard.sam.markduplicates.util
-
Map from String to ReadEnds object.
- MemoryBasedReadEndsForMarkDuplicatesMap() - Constructor for class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
- MendelianViolation - Class in org.broadinstitute.hellbender.utils.samples
-
Class for the identification and tracking of mendelian violation.
- MendelianViolation(double) - Constructor for class org.broadinstitute.hellbender.utils.samples.MendelianViolation
- MendelianViolation(double, boolean, boolean) - Constructor for class org.broadinstitute.hellbender.utils.samples.MendelianViolation
- MendelianViolationEvaluator - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
-
Mendelian violation detection and counting
- MendelianViolationEvaluator(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- MendelianViolationMetrics - Class in picard.vcf.MendelianViolations
-
Describes the type and number of mendelian violations found within a Trio.
- MendelianViolationMetrics() - Constructor for class picard.vcf.MendelianViolations.MendelianViolationMetrics
- mendelianViolationQualThreshold - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- MendelianViolationsByFamily - Class in picard.vcf.MendelianViolations
-
Created by farjoun on 6/25/16.
- MendelianViolationsByFamily() - Constructor for class picard.vcf.MendelianViolations.MendelianViolationsByFamily
- merge(Collection<? extends MergeableMetricBase>) - Method in class picard.analysis.MergeableMetricBase
-
for a collection of MergeableMetricBase, merge them all into "this" one.
- merge(Collection<CallingMetricAccumulator.Result>) - Static method in class picard.vcf.CallingMetricAccumulator.Result
- merge(Collection<RESULT>) - Method in interface picard.vcf.processor.VariantProcessor.ResultMerger
- merge(List<VariantContext>) - Static method in class picard.arrays.CombineGenotypingArrayVcfs
-
Merges multiple VariantContexts all for the same locus into a single hybrid.
- merge(List<VariantContext>, Locatable, Byte, boolean, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
-
Merges VariantContexts from gVCFs into a single hybrid.
- merge(SortedSet<T>) - Static method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
Merges a list of *sorted* *contiguous* locs into 1
- merge(FlagStat.FlagStatus) - Method in class org.broadinstitute.hellbender.tools.FlagStat.FlagStatus
- merge(DepthOfCoverageStats) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
- merge(SeqGraph, SeqVertex) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SharedSequenceMerger
-
Attempt to merge the incoming vertices of v
- merge(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
Returns a new GenomeLoc that represents the entire span of this and that.
- merge(MathUtils.RunningAverage) - Method in class org.broadinstitute.hellbender.utils.MathUtils.RunningAverage
- merge(QualQuantizer.QualInterval) - Method in class org.broadinstitute.hellbender.utils.recalibration.QualQuantizer.QualInterval
-
Create a interval representing the merge of this interval and toMerge Errors and observations are combined Subintervals updated in order of left to right (determined by qStart) Level is 1 + highest level of this and toMerge Order must be updated elsewhere
- merge(MergeableMetricBase) - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
- merge(MergeableMetricBase) - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- merge(MergeableMetricBase) - Method in class picard.analysis.MergeableMetricBase
-
Merge another metric into this one
- merge(MergeableMetricBase) - Method in class picard.analysis.WgsMetrics
-
Merges the various PCT_EXC_* metrics.
- merge(Fingerprint) - Method in class picard.fingerprint.Fingerprint
-
Merges the likelihoods from the supplied Fingerprint into the likelihoods for this fingerprint.
- merge(FingerprintIdDetails) - Method in class picard.fingerprint.FingerprintIdDetails
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilities
-
Merges in the likelihood information from the supplied haplotype probabilities object.
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
Merges information from another haplotype probabilities object for the same haplotype into this object.
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.CappedHaplotypeProbabilities
-
Merges information from another haplotype probabilities object for the same haplotype into this object.
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- merge(BarcodeMetric) - Method in class picard.illumina.BarcodeMetric
-
Adds the non-calculated
- merge(CollectHiSeqXPfFailMetrics.PFFailSummaryMetric) - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
Adds the non-calculated fields from the other metric to this one.
- merge(T, T) - Static method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
Merges 2 *contiguous* locs into 1
- MERGE_CONTIGS_INTO_NUM_PARTITIONS - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- MERGE_FILTER_IN_ALL - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- MERGE_FILTER_PREFIX - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- MERGE_INPUT_INTERVALS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- MERGE_INTERSECTION - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- MERGE_NEARBY_TARGETS - Variable in class picard.util.BaitDesigner
- MERGE_REF_IN_ALL - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- MERGE_SEQUENCE_DICTIONARIES - Variable in class picard.sam.MergeSamFiles
- MergeableMetricBase - Class in picard.analysis
-
An extension of MetricBase that knows how to merge-by-adding fields that are appropriately annotated (
MergeByAdding). - MergeableMetricBase() - Constructor for class picard.analysis.MergeableMetricBase
- MergeableMetricBase.MergeByAdding - Annotation Interface in picard.analysis
-
Metrics whose values can be merged by adding.
- MergeableMetricBase.MergeByAssertEquals - Annotation Interface in picard.analysis
-
Metrics whose values should be equal when merging.
- MergeableMetricBase.MergingIsManual - Annotation Interface in picard.analysis
-
Metrics that are merged manually in the
MergeableMetricBase.merge(MergeableMetricBase)()}. - MergeableMetricBase.NoMergingIsDerived - Annotation Interface in picard.analysis
-
Metrics that are not merged, but are subsequently derived from other metrics, for example by
MergeableMetricBase.calculateDerivedFields(). - MergeableMetricBase.NoMergingKeepsValue - Annotation Interface in picard.analysis
-
Metrics that are not merged.
- mergeAlignment(File) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
-
/** Merges the alignment data with the non-aligned records from the source BAM file.
- mergeAlignment(File) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.SamAlignmentMerger
-
Merges the alignment from the map file with the non-aligned records from the source BAM file.
- mergeAlignment(File) - Method in class picard.sam.AbstractAlignmentMerger
-
Merges the alignment data with the non-aligned records from the source BAM file.
- mergeAlignment(File) - Method in class picard.sam.SamAlignmentMerger
-
Merges the alignment from the map file with the non-aligned records from the source BAM file.
- mergeAndConvertTranches(List<VQSLODTranche>, VariantRecalibratorArgumentCollection.Mode) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VQSLODTranche
- mergeAndConvertTranches(TreeMap<Double, List<VQSLODTranche>>, List<Double>, VariantRecalibratorArgumentCollection.Mode) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VQSLODTranche
- MergeAnnotatedRegions - Class in org.broadinstitute.hellbender.tools.copynumber.utils
- MergeAnnotatedRegions() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegions
- MergeAnnotatedRegionsByAnnotation - Class in org.broadinstitute.hellbender.tools.copynumber.utils
- MergeAnnotatedRegionsByAnnotation() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsByAnnotation
- MergeBamAlignment - Class in picard.sam
-
Summary
- MergeBamAlignment() - Constructor for class picard.sam.MergeBamAlignment
- MERGED_VCF_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark
- mergeDesignMatrices(List<AltSiteRecord>, List<AltSiteRecord>) - Static method in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel
-
Contract: this method must be called after grouping the design matrices by context.
- mergedSampleName(String, String, boolean) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- mergeEvals - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
-
If true, VariantEval will treat -eval 1 -eval 2 as separate tracks from the same underlying variant set, and evaluate the union of the results.
- mergeFingerprintsBy(Map<FingerprintIdDetails, Fingerprint>, Function<FingerprintIdDetails, String>) - Static method in class picard.fingerprint.Fingerprint
- mergeIfCan(MergeableMetricBase) - Method in class picard.analysis.MergeableMetricBase
-
Merges another MergableMetricBase if possible
- mergeIntervalLocations(List<GenomeLoc>, IntervalMergingRule) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
merge a list of genome locs that may be overlapping, returning the list of unique genomic locations
- mergeLinearChainVertex(LinkedList<SeqVertex>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqGraph
- mergeListsBySetOperator(List<GenomeLoc>, List<GenomeLoc>, IntervalSetRule) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
merge two interval lists, using an interval set rule
- MergeMutect2CallsWithMC3 - Class in org.broadinstitute.hellbender.tools.walkers.validation
- MergeMutect2CallsWithMC3() - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3
- MergeMutectStats - Class in org.broadinstitute.hellbender.tools.walkers.mutect
-
Merge the stats output by scatters of a single Mutect2 job.
- MergeMutectStats() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.MergeMutectStats
- MergePedIntoVcf - Class in picard.arrays
-
Class to take genotype calls from a ped file output from zCall and merge them into a vcf from autocall.
- MergePedIntoVcf() - Constructor for class picard.arrays.MergePedIntoVcf
- mergeRegions(List<AnnotatedInterval>, SAMSequenceDictionary, String, Consumer<Locatable>) - Static method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalUtils
-
Merge AnnotatedIntervals by whether the regions overlap.
- mergeRegionsByAnnotation(List<AnnotatedInterval>, SAMSequenceDictionary, List<String>, Consumer<Locatable>, String, int) - Static method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalUtils
-
Merge AnnotatedIntervals by whether the given annotation values match (all annotations must match).
- MergeSamFiles - Class in picard.sam
-
This tool is used for combining SAM and/or BAM files from different runs or read groups into a single file, similar to the \"merge\" function of Samtools (http://www.htslib.org/doc/samtools.html).
- MergeSamFiles() - Constructor for class picard.sam.MergeSamFiles
- MergeVcfs - Class in picard.vcf
-
Combines multiple variant files into a single variant file.
- MergeVcfs() - Constructor for class picard.vcf.MergeVcfs
- mergeWithContiguous(Locatable) - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
-
Returns a new SimpleInterval that represents the entire span of this and that.
- mergeWithNewVCs(List<VariantContext>, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
-
Method which calls endPreviousStates at the appropriate places on the given a new startingStates object and an OverallState object corresponding to the currently accumulated reads.
- MergingIterator(SAMSequenceDictionary, FeatureManager, List<SimpleInterval>) - Constructor for class org.broadinstitute.hellbender.engine.MultiFeatureWalker.MergingIterator
- messageDigest - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- metadata - Variable in class org.broadinstitute.hellbender.tools.spark.PileupSpark
-
This enables annotating the pileup to show overlaps with metadata from a Feature file(s).
- metadata - Variable in class org.broadinstitute.hellbender.tools.walkers.qc.Pileup
-
This enables annotating the pileup to show overlaps with metadata from a Feature file(s).
- Metadata - Interface in org.broadinstitute.hellbender.tools.copynumber.formats.metadata
-
Interface for marking objects that contain metadata that can be represented as a
SAMFileHeader. - METADATA_TAG - Static variable in class org.broadinstitute.hellbender.utils.tsv.TableWriter
- Metadata.Type - Enum Class in org.broadinstitute.hellbender.tools.copynumber.formats.metadata
- metadataFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- MetadataUtils - Class in org.broadinstitute.hellbender.tools.copynumber.formats.metadata
- MetagenomicsProgramGroup - Class in org.broadinstitute.hellbender.cmdline.programgroups
-
Tools that perform metagenomic analysis, e.g.
- MetagenomicsProgramGroup() - Constructor for class org.broadinstitute.hellbender.cmdline.programgroups.MetagenomicsProgramGroup
- METHIONINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- METHYLATION_REFERENCE_CONTEXT_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- MethylationProgramGroup - Class in org.broadinstitute.hellbender.cmdline.programgroups
-
Tools that performs methylation calling and methylation-based coverage for bisulfite BAMs
- MethylationProgramGroup() - Constructor for class org.broadinstitute.hellbender.cmdline.programgroups.MethylationProgramGroup
- MethylationTypeCaller - Class in org.broadinstitute.hellbender.tools.walkers
-
Identifies methylated bases from bisulfite sequencing data.
- MethylationTypeCaller() - Constructor for class org.broadinstitute.hellbender.tools.walkers.MethylationTypeCaller
- METRIC - Variable in class picard.analysis.CompareMetrics.MetricComparisonDifferences
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectGcBiasMetrics
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectInsertSizeMetrics
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectMultipleMetrics
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectRnaSeqMetrics
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectRrbsMetrics
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.directed.CollectTargetedMetrics
- METRIC_ACCUMULATION_LEVEL_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- METRIC_ACCUMULATION_LEVEL_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- METRIC_ALLOWABLE_RELATIVE_CHANGE - Variable in class picard.analysis.CompareMetrics
- METRIC_TYPE - Variable in class org.broadinstitute.hellbender.metrics.analysis.AlleleFrequencyQCMetric
- METRIC_VALUE - Variable in class org.broadinstitute.hellbender.metrics.analysis.AlleleFrequencyQCMetric
- metricAccumulationLevel - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetricsArgumentCollection
- MetricAccumulationLevel - Enum Class in org.broadinstitute.hellbender.metrics
-
For use with Picard metrics programs that may output metrics for multiple levels of aggregation with an analysis.
- MetricAccumulationLevel - Enum Class in picard.analysis
-
For use with Picard metrics programs that may output metrics for multiple levels of aggregation with an analysis.
- MetricAccumulationLevelArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
- MetricAccumulationLevelArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.MetricAccumulationLevelArgumentCollection
- MetricComparisonDifferences() - Constructor for class picard.analysis.CompareMetrics.MetricComparisonDifferences
- metricOutput - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.AlleleFrequencyQC
- metrics - Variable in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
- METRICS - Variable in class picard.illumina.MarkIlluminaAdapters
- METRICS_FILE - Variable in class picard.illumina.ExtractBarcodesProgram
- METRICS_FILE - Variable in class picard.sam.DownsampleSam
- METRICS_FILE - Variable in class picard.sam.markduplicates.CollectDuplicateMetrics
- METRICS_FILE - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- METRICS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- METRICS_FILE_PREFIX - Variable in class picard.analysis.CollectRrbsMetrics
- METRICS_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- METRICS_FILE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- METRICS_NOT_REQUIRED - Variable in class picard.analysis.CompareMetrics
- METRICS_TO_IGNORE - Variable in class picard.analysis.CompareMetrics
- MetricsArgumentCollection - Class in org.broadinstitute.hellbender.metrics
-
Base class for defining a set of metrics collector arguments.
- MetricsArgumentCollection() - Constructor for class org.broadinstitute.hellbender.metrics.MetricsArgumentCollection
- MetricsCollection - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
-
Created by knoblett on 9/15/15.
- MetricsCollection(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MetricsCollection
- MetricsCollectorSpark<T extends MetricsArgumentCollection> - Interface in org.broadinstitute.hellbender.tools.spark.pipelines.metrics
-
Each metrics collector has to be able to run from 4 different contexts: - a standalone walker tool - the
org.broadinstitute.hellbender.metrics.analysis.CollectMultipleMetricswalker tool - a standalone Spark tool - theCollectMultipleMetricsSparktool In order to allow a single collector implementation to be shared across all of these contexts (standalone and CollectMultiple, Spark and non-Spark), collectors should be factored into the following classes, where X in the class names represents the specific type of metrics being collected: XMetrics extendsMetricBase: defines the aggregate metrics that we're trying to collect XMetricsArgumentCollection: defines parameters for XMetrics, extendsMetricsArgumentCollectionXMetricsCollector: processes a single read, and has a reduce/combiner For multi level collectors, XMetricsCollector is composed of several classes: XMetricsCollector extendsMultiLevelReducibleCollector< XMetrics, HISTOGRAM_KEY, XMetricsCollectorArgs, XMetricsPerUnitCollector> XMetricsPerUnitCollector: per level collector, implementsPerUnitMetricCollector<XMetrics, HISTOGRAM_KEY, XMetricsCollectorArgs> (requires a combiner) XMetricsCollectorArgs per-record argument (type argument forMultiLevelReducibleCollector) XMetricsCollectorSpark: adapter/bridge between RDD and the (read-based) XMetricsCollector, implementsMetricsCollectorSparkCollectXMetrics extends org.broadinstitute.hellbender.metrics.analysis.SinglePassSamProgramCollectXMetricsSpark extendsMetricsCollectorSparkToolThe following schematic shows the general relationships of these collector component classes in the context of various tools, with the arrows indicating a "delegates to" relationship via composition or inheritance: CollectXMetrics CollectMultipleMetrics \ / \ / v v _______________________________________ | XMetricsCollector =========|=========> MultiLevelReducibleCollector | | | | | V | | | XMetrics | V | XMetricsCollectorArgumentCollection | PerUnitXMetricCollector --------------------------------------- ^ | | XMetricsCollectorSpark ^ ^ / \ / \ CollectXMetricsSpark CollectMultipleMetricsSpark The general lifecycle of a Spark collector (XMetricsCollectorSpark in the diagram above) looks like this: CollectorType collector = new CollectorType () CollectorArgType args = // get metric-specific input arguments // NOTE: getDefaultReadFilters is called before the collector's initialize // method is called, so the read filters cannot access argument values ReadFilter filter == collector.getDefaultReadFilters(); // pass the input arguments to the collector for initialization collector.initialize(args, defaultMetricsHeaders); collector.collectMetrics( getReads().filter(filter), samFileHeader ); collector.saveMetrics(getReadSourceName()); - MetricsCollectorSparkTool<T extends MetricsArgumentCollection> - Class in org.broadinstitute.hellbender.tools.spark.pipelines.metrics
-
Base class for standalone Spark metrics collector tools.
- MetricsCollectorSparkTool() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSparkTool
- metricsFile - Variable in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- MetricsReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads that: Fail platform/vendor quality checks (0x200) Are unmapped (0x4) Represent secondary/supplementary alignments (0x100 or 0x800)
- MetricsReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.MetricsReadFilter
- MetricsReadFilter(boolean, boolean) - Constructor for class org.broadinstitute.hellbender.engine.filters.MetricsReadFilter
- MetricsUtils - Class in org.broadinstitute.hellbender.metrics
-
Utility methods for dealing with
MetricsFileand related classes. - MetricToAllowableRelativeChange - Variable in class picard.analysis.CompareMetrics
- MICROBE_BWA_IMAGE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection
- MICROBE_MIN_SEED_LENGTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection
- MICROBE_REF_DICT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection
- microbeDictionary - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection
- microbial - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
-
Microbial mode excludes the filters
ClusteredEventsFilter,MultiallelicFilter,FilteredHaplotypeFilter,FragmentLengthFilter, andGermlineFilter - MICROBIAL_MODE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- midpoint() - Method in class org.broadinstitute.hellbender.utils.SVInterval
- MILLISECONDS_PER_MINUTE - Static variable in class org.broadinstitute.hellbender.engine.ProgressMeter
-
Number of milliseconds in a minute
- MILLISECONDS_PER_SECOND - Static variable in class org.broadinstitute.hellbender.engine.ProgressMeter
-
Number of milliseconds in a second
- min() - Method in class org.broadinstitute.hellbender.utils.dragstr.DoubleSequence
-
Returns the minimum value of the sequence.
- min() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Find the least interval in the tree.
- min(byte[]) - Static method in class picard.util.MathUtil
-
Returns the smallest value stored in the array.
- min(double[]) - Static method in class picard.util.MathUtil
-
Returns the smallest value stored in the array.
- min(int[]) - Static method in class picard.util.MathUtil
-
Returns the smallest value stored in the array.
- min(short[]) - Static method in class picard.util.MathUtil
-
Returns the smallest value stored in the array.
- min(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Find the earliest interval in the tree greater than or equal to the specified interval.
- MIN_AB - Variable in class picard.vcf.filter.FilterVcf
- MIN_ACCEPTABLE_LOD_SCORE - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorEngine
- MIN_ADAPTER_LENGTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- MIN_AF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- MIN_ASSEMBLY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- MIN_BASE_Q - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- MIN_BASE_QUAL - Static variable in enum class org.broadinstitute.hellbender.utils.read.markduplicates.MarkDuplicatesScoringStrategy
- MIN_BASE_QUALITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- MIN_BASE_QUALITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsArgumentCollection
- MIN_BASE_QUALITY_SCORE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- MIN_BASE_QUALITY_SCORE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- MIN_CLIPPED_READ_LENGTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- MIN_CONTIG_SIZE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- MIN_COUNT - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
- MIN_COUNT - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils
- MIN_DANGLING_BRANCH_LENGTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- MIN_DEPTH_ARGUMENT_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- MIN_DEPTH_ARGUMENT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- MIN_DEPTH_EVIDENCE_MAPQ_ARGUMENT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- MIN_DP - Variable in class picard.vcf.filter.FilterVcf
- MIN_DP - Variable in class picard.vcf.GenotypeConcordance
- MIN_DP - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- MIN_DP_FORMAT_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- MIN_FRACTION_OF_MATCHING_BASES - Static variable in class org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer
- MIN_FRAGMENT_LENGTH_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- MIN_GAPFILL_COUNT_DEFAULT - Static variable in class org.broadinstitute.hellbender.tools.LocalAssembler
- MIN_GQ - Variable in class picard.vcf.filter.FilterVcf
- MIN_GQ - Variable in class picard.vcf.GenotypeConcordance
- MIN_GQ - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- MIN_GROUP_COUNT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- MIN_HET_FRACTION - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- MIN_HET_PROBABILITY - Static variable in class org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAF
- MIN_HISTOGRAM_WIDTH - Variable in class picard.analysis.CollectInsertSizeMetrics
- MIN_IDENTICAL_BASES - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- MIN_INDEL_SPACING_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.RemoveNearbyIndels
- MIN_INSERT_SIZE - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The minimum measured insert size.
- MIN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
-
The minimum measured insert size.
- MIN_INTERVAL_SIZE_ARGNAME - Static variable in class org.broadinstitute.hellbender.tools.sv.CondenseDepthEvidence
- MIN_LIFTOVER_PCT - Variable in class picard.util.LiftOverIntervalList
- MIN_LOCI_COUNT_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- MIN_MAPPING_Q - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- MIN_MAPPING_QUALITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- MIN_MAPPING_QUALITY_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- MIN_MATCH_BASES - Static variable in class picard.util.ClippingUtility
-
The default value used for the minimum number of contiguous bases to match against.
- MIN_MATCH_BASES_PE - Variable in class picard.illumina.MarkIlluminaAdapters
- MIN_MATCH_BASES_SE - Variable in class picard.illumina.MarkIlluminaAdapters
- MIN_MATCH_PE_BASES - Static variable in class picard.util.ClippingUtility
-
The default value used for the minimum number of contiguous bases to match against in a paired end read
- MIN_MEAN_QUALITY - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- MIN_MEDIAN_BASE_QUALITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- MIN_MEDIAN_MAPPING_QUALITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- MIN_MEDIAN_MQ_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsArgumentCollection
- MIN_MEDIAN_READ_POSITION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- MIN_MISMATCH_DELTA - Variable in class picard.illumina.ExtractBarcodesProgram
- MIN_NON_VIRUS_CONTIG_LENGTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
- MIN_NON_VIRUS_CONTIG_LENGTH_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
- MIN_NUM_BASES_FOR_SEGMENT_FUNCOTATION - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- MIN_NUMBER_OF_EVENTS_TO_COMBINE_INTO_BLOCK_SUBSTITUTION - Static variable in class org.broadinstitute.hellbender.utils.haplotype.EventMap
- MIN_OBSERVATIONS_FOR_KMER_TO_BE_SOLID_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- MIN_PALINDROME_SIZE - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- MIN_PHRED_SCALED_QUAL - Static variable in class org.broadinstitute.hellbender.utils.QualityUtils
- MIN_POLYMERASE_SLIPPAGE_LENGTH - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- MIN_POS - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
At least one NextSeq run produced a small negative value for y coordinate (-5), so allow small negative values and see what happens.
- MIN_POWER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- MIN_PRUNING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- MIN_PVALUE - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
- MIN_Q - Variable in class picard.sam.FastqToSam
- MIN_QD - Variable in class picard.vcf.filter.FilterVcf
- MIN_QUALITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- MIN_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The minimum read length.
- MIN_READ_LENGTH_ARG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- MIN_READ_LENGTH_TO_REPORT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- MIN_READ_SPAN_AFTER_DEOVERLAP - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInterpreter
- MIN_READS_ON_EACH_STRAND_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- MIN_REPORTABLE_ERROR_PROBABILITY - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- MIN_REQUIRED_READS_NAME - Static variable in class org.broadinstitute.hellbender.engine.DuplicateSetWalker
- MIN_REQUIRED_READS_PER_STRAND_NAME - Static variable in class org.broadinstitute.hellbender.engine.DuplicateSetWalker
- MIN_SAMPLE_COUNT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals
- MIN_SAMPLE_NUM_OVERLAP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- MIN_SAMPLES - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_InbreedingCoeff
- MIN_SCORE_IDENTITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- MIN_SCORE_IDENTITY_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- MIN_SITE_AF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- MIN_SITE_AF_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- MIN_SITE_DEPTH_BASEQ_ARGUMENT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- MIN_SITE_DEPTH_MAPQ_ARGUMENT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- MIN_START_MAX_END - Enum constant in enum class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser.BreakpointSummaryStrategy
-
A conservative strategy to summarize a cluster by its smallest extent
- MIN_SV_SIZE_DEFAULT - Static variable in class org.broadinstitute.hellbender.tools.LocalAssembler
- MIN_TAIL_QUALITY - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- MIN_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
-
The minimum coverage of reads that mapped to target regions of an experiment.
- MIN_THIN_OBS_DEFAULT - Static variable in class org.broadinstitute.hellbender.tools.LocalAssembler
- MIN_TOTAL_DEPTH_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAF
- MIN_TRAINING_EPOCHS - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- MIN_TRAINING_EPOCHS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- MIN_TRIMMED_LENGTH - Variable in class picard.illumina.IlluminaBasecallsToFastq
- MIN_UNCLIPPED_BASES - Variable in class picard.sam.MergeBamAlignment
- MIN_USABLE_Q_SCORE - Static variable in class org.broadinstitute.hellbender.utils.QualityUtils
-
The lowest quality score for a base that is considered reasonable for statistical analysis.
- MIN_USABLE_Q_SCORE_DEFAULT - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedHMMEngine
- minAdapterLength - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
-
Adapter trimming will require a match of at least this length to a known adapter.
- minAf - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- minAF - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- minAlignerScoreDifferencePerBase - Variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
-
Minimum difference between best and second-best alignment for a read to be considered well-mapped
- minAlignLength - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- MinAlleleFractionFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- MinAlleleFractionFilter(double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MinAlleleFractionFilter
- minAssemblyRegionSize - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
-
Parameters that control active regions
- minBaseQuality - Variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsArgumentCollection
- minBaseQuality - Variable in class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter
-
If this argument is enabled, bases with quality scores lower than this threshold will not be counted.
- minBaseQualityScore - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
-
Bases with a quality below this threshold will not be used for annotation.
- minBaseQualityScore - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
-
Bases with a quality below this threshold will not be used for calling.
- minBaseQualityToUseInAssembly - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
- minBaseQualityToUseInAssembly - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- minBasesForValidSegment - Variable in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
Minimum number of bases for a segment to be considered valid.
- minBqCutoff - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- minCoherentEvidenceWeightPerCoverage - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- minColumn() - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Element
- minDanglingBranchLength - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
When constructing the assembly graph we are often left with "dangling" branches.
- minDepth - Variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- minDepthEvidenceMapQ - Variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- minDepthOfNonFilteredBases - Variable in class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter
-
If this argument is enabled, loci with total depth lower than this threshold after all filters have been applied will be skipped.
- minDistance(SVCallRecord, SVCallRecord) - Static method in class org.broadinstitute.hellbender.tools.sv.concordance.ClosestSVFinder
-
Distance between closest breakends, or
Integer.MAX_VALUEif one record is null. - minDistance(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
Return the minimum distance between any pair of bases in this and that GenomeLocs:
- minElementIndex(int[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- minEvidenceMapQ - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- minEvidenceMatchLength - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- minEvidenceWeightPerCoverage - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- minFragmentLength - Variable in class org.broadinstitute.hellbender.engine.filters.FragmentLengthReadFilter
- minGQ - Variable in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- minHaplotypeScore - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- minHaplotypeScoreDelta - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- MinibatchSliceSampler<DATA> - Class in org.broadinstitute.hellbender.utils.mcmc
-
Implements slice sampling of a continuous, univariate, unnormalized probability density function (PDF), which is assumed to be unimodal.
- MinibatchSliceSampler(RandomGenerator, List<DATA>, Function<Double, Double>, BiFunction<DATA, Double, Double>, double, double, double, int, double) - Constructor for class org.broadinstitute.hellbender.utils.mcmc.MinibatchSliceSampler
-
Creates a new sampler for a bounded univariate random variable, given a random number generator, a list of data, a continuous, univariate, unimodal, unnormalized log probability density function (assumed to be a posterior and specified by a prior and a likelihood), hard limits on the random variable, a step width, a minibatch size, and a minibatch approximation threshold.
- MinibatchSliceSampler(RandomGenerator, List<DATA>, Function<Double, Double>, BiFunction<DATA, Double, Double>, double, int, double) - Constructor for class org.broadinstitute.hellbender.utils.mcmc.MinibatchSliceSampler
-
Creates a new sampler for an unbounded univariate random variable, given a random number generator, a list of data, a continuous, univariate, unimodal, unnormalized log probability density function (assumed to be a posterior and specified by a prior and a likelihood), a step width, a minibatch size, and a minibatch approximation threshold.
- minIdentity - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
-
Controls the stringency of read filtering based on alignment to the host reference.
- minIdentity - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
-
This parameter controls the stringency of the microbe alignment.
- MINIMAL - Enum constant in enum class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter.Verbosity
-
Output logging messages at the start and end of the copy, but no progress during.
- MinimalGenotypingEngine - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
-
A stripped-down version of the former UnifiedGenotyper's genotyping strategy implementation, used only by the HaplotypeCaller for its isActive() determination.
- MinimalGenotypingEngine(StandardCallerArgumentCollection, SampleList) - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine
-
Creates a new genotyping engine given the configuration parameters and the targeted set of samples
- MinimalGenotypingEngine(StandardCallerArgumentCollection, SampleList, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine
-
Creates a new genotyping engine given the configuration parameters and the targeted set of samples
- MinimalGenotypingEngine(StandardCallerArgumentCollection, SampleList, boolean, DragstrParams) - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine
-
Creates a new genotyping engine given the configuration parameters and the targeted set of samples
- MinimalVariant - Class in org.broadinstitute.hellbender.utils.variant
-
MinimalVariant is a minimal implementation of the
GATKVariantinterface. - MinimalVariant(SimpleInterval, boolean, boolean) - Constructor for class org.broadinstitute.hellbender.utils.variant.MinimalVariant
- minimum() - Method in class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistribution
- MINIMUM_ALLELE_FRACTION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- MINIMUM_ALLELE_FRACTION_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- MINIMUM_BAITS_PER_TARGET - Variable in class picard.util.BaitDesigner
- MINIMUM_BARCODE_BQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- MINIMUM_BASE_QUALITY - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- MINIMUM_BASE_QUALITY - Variable in class picard.analysis.CollectWgsMetrics
- MINIMUM_BASE_QUALITY - Variable in class picard.analysis.directed.CollectTargetedMetrics
- MINIMUM_BASE_QUALITY - Variable in class picard.illumina.ExtractBarcodesProgram
- MINIMUM_BASE_QUALITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCounts
- MINIMUM_BQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- MINIMUM_DISTANCE - Variable in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
- MINIMUM_DOWN_SAMPLE_SIZE - Static variable in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- MINIMUM_GC_CONTENT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
- MINIMUM_GENOME_FRACTION - Variable in class picard.analysis.CollectGcBiasMetrics
- MINIMUM_GQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- MINIMUM_INSERT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- MINIMUM_INSERT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
- MINIMUM_INTERVAL_MEDIAN_PERCENTILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormals
- MINIMUM_LENGTH - Variable in class picard.analysis.CollectRnaSeqMetrics
- MINIMUM_LINE_FIELD_COUNT - Static variable in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- MINIMUM_LOD_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- MINIMUM_MAPPABILITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectJumpingLibraryMetrics
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectOxoGMetrics
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectWgsMetrics
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.directed.CollectTargetedMetrics
- MINIMUM_MAPPING_QUALITY_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- MINIMUM_MAPPING_QUALITY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- MINIMUM_MQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- MINIMUM_NUM_READS_FOR_SIGNAL_COUNT - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.PowerCalculationUtils
- MINIMUM_PCT - Variable in class picard.analysis.CollectInsertSizeMetrics
- MINIMUM_QUALITY - Variable in class picard.illumina.ExtractBarcodesProgram
- MINIMUM_QUALITY_SCORE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- MINIMUM_QUALITY_SCORE - Variable in class picard.analysis.CollectOxoGMetrics
- MINIMUM_READ_LENGTH - Variable in class picard.analysis.CollectRrbsMetrics
- MINIMUM_READ_LENGTH_AFTER_TRIMMING - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- MINIMUM_REFERENCE_SEQUENCE_BUFFER_SIZE - Static variable in class org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFile
- MINIMUM_SEGMENTAL_DUPLICATION_CONTENT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
- MINIMUM_SHARD_SIZE - Static variable in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- MINIMUM_TOTAL_ALLELE_COUNT_CASE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticGenotypingArgumentCollection
- MINIMUM_TOTAL_ALLELE_COUNT_NORMAL_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticGenotypingArgumentCollection
- MINIMUM_UNSCRUPULOUS_HOM_REF_ALT_FRACTION_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel
- minimumAlleleIndex() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Returns the smallest allele index present in the genotype.
- minimumBaseQuality - Variable in class picard.util.BarcodeEditDistanceQuery
-
minimal base quality to condiser informative
- minimumPct - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetricsArgumentCollection
- minKmerLength(Collection<byte[]>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.GraphUtils
-
Get the minimum length of a collection of byte[]
- minKmersPerInterval - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- minMappingQuality - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- minMappingQuality - Variable in class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter
-
If this argument is enabled, reads with mapping quality values lower than this threshold will not be counted.
- minMappingQualityScore - Variable in class org.broadinstitute.hellbender.engine.filters.MappingQualityReadFilter
- minMapQ - Variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- minMatchingBasesToDanglingEndRecovery - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- minMedianBaseQuality - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- minMedianMappingQuality - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- minMedianMapQual - Variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsArgumentCollection
- minMedianReadPosition - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- minMismatchDifferencePerBase - Variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
-
Minimum ratio between the number of mismatches in the second best and best alignments
- minMQ - Variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- minMQ - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- minNonVirusContigLength - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
-
Sequences from non-virus organisms less than this length will be filtered out such that any reads aligning to them will be ignored.
- minNumBasesForValidSegment - Variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
- minObservationsForKmerToBeSolid - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- MINOR_ALLELE_FRACTION_PRIOR_ALPHA_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- MINOR_ALLELE_FRACTIONS - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionParameter
- minorAlleleFractionPriorAlpha - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- MinorAlleleFractionRecord - Class in org.broadinstitute.hellbender.tools.walkers.contamination
-
Created by David Benjamin on 2/13/17.
- MinorAlleleFractionRecord(SimpleInterval, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.contamination.MinorAlleleFractionRecord
- MinorAlleleFractionRecord.MinorAlleleFractionTableReader - Class in org.broadinstitute.hellbender.tools.walkers.contamination
- MinorAlleleFractionTableReader(Path) - Constructor for class org.broadinstitute.hellbender.tools.walkers.contamination.MinorAlleleFractionRecord.MinorAlleleFractionTableReader
- minOverlapper(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Find the earliest interval in the tree that overlaps the specified interval.
- minPhaseQuality - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- minPower - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- minPruneFactor - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
Paths with fewer supporting kmers than the specified threshold will be pruned from the graph.
- minQ - Variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- minReadLength - Variable in class org.broadinstitute.hellbender.engine.filters.ReadLengthReadFilter
- minReadLength - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
-
Reads are trimmed based on base call quality and low-complexity content.
- minReadsOnEachStrand - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- minSampleOverlap - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.CNVLinkage
- minScore - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
minimal threshold of score delta to for emitting (will be emitted if higher)
- minSeedLength - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
-
Controls the sensitivity of BWA alignment to the host reference.
- minSeedLength - Variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
-
BWA-mem minimum seed length
- minSlippageLength - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- minSVSize - Variable in class org.broadinstitute.hellbender.tools.LocalAssembler
- minTotalAlleleCountCase - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticGenotypingArgumentCollection
- minTotalAlleleCountNormal - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticGenotypingArgumentCollection
- MINUS - Enum constant in enum class picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
- minUsableIndelScoreToUse - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- MINUTE_IN_MS - Static variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- minVisitNum - Variable in class org.broadinstitute.hellbender.tools.LocalAssembler.WalkData
- MIRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- MIRNA_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- MISALIGNED - Enum constant in enum class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
- MISC_RNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- MISC_RNA_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- MisencodedBaseQualityReadTransformer - Class in org.broadinstitute.hellbender.transformers
-
Checks for and errors out (or fixes if requested) when it detects reads with base qualities that are not encoded with phred-scaled quality scores.
- MisencodedBaseQualityReadTransformer() - Constructor for class org.broadinstitute.hellbender.transformers.MisencodedBaseQualityReadTransformer
- MisencodedQualityScoresRead(GATKRead, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MisencodedQualityScoresRead
- MismatchCount() - Constructor for class org.broadinstitute.hellbender.utils.read.AlignmentUtils.MismatchCount
- mismatches - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
Number of mismatches,
AlignmentInterval.NO_NMif unknown or unspecified. - MISMATCHES_CONTEXT_SIZE - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
-
The context covariate will use a context of this size to calculate its covariate value for base mismatches.
- MISMATCHES_DEFAULT_QUALITY - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
-
A default base qualities to use as a prior (reported quality) in the mismatch covariate model.
- mismatchesInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies according to the overall mismatches (from NM) that the read has against the reference, NOT including the current base.
- MismatchesInReadStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.MismatchesInReadStratifier
- MismatchMDElement() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.MismatchMDElement
- mismatchQualities - Variable in class org.broadinstitute.hellbender.utils.read.AlignmentUtils.MismatchCount
- missense - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.FunctionalClass.FunctionalType
- MISSENSE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
The point mutation alters the protein structure by one amino acid.
- MISSENSE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectFunctionalClass
- MISSING - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- MISSING - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- MISSING_ALLELE_B_PROBESEQ - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Manifest contained no allele B probe sequence
- MISSING_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
-
These codes allow for constants in the truth state enum and the call state enum to be compared.
- MISSING_DATA - Static variable in class org.broadinstitute.hellbender.tools.sv.DepthEvidence
- MISSING_ENTRY_DISPLAY_STRING - Static variable in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
- MISSING_LEFT - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records which are found in right file but not found in left file
- MISSING_REFERENCE_FOR_CRAM - Static variable in exception org.broadinstitute.hellbender.exceptions.UserException
- MISSING_RIGHT - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records which are found in left file but not found in right file
- MISSING_SITES_HOM_REF - Variable in class picard.vcf.GenotypeConcordance
- MISSING_VAL_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- MISSING_VALUE - Static variable in class org.broadinstitute.hellbender.tools.sv.BafEvidence
- MissingContigInSequenceDictionary(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MissingContigInSequenceDictionary
- MissingContigInSequenceDictionary(String, SAMSequenceDictionary) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MissingContigInSequenceDictionary
- MissingIndex(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MissingIndex
- MissingIndex(String, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MissingIndex
- MissingReadField(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.GATKException.MissingReadField
- MissingReadField(String, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.GATKException.MissingReadField
- MissingReadField(String, GATKRead) - Constructor for exception org.broadinstitute.hellbender.exceptions.GATKException.MissingReadField
- MissingReference(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MissingReference
- MissingReference(String, boolean) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MissingReference
- MissingReferenceDictFile(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MissingReferenceDictFile
- MissingReferenceDictFile(Path, Path) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MissingReferenceDictFile
- MissingReferenceFaiFile(Path, Path) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MissingReferenceFaiFile
- MissingReferenceGziFile(Path, Path) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.MissingReferenceGziFile
- mitochondria - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
-
Mitochondria mode excludes the filters
ClusteredEventsFilter,MultiallelicFilter,PolymeraseSlippageFilter,FilteredHaplotypeFilter,FragmentLengthFilter, andGermlineFilter - mitochondria - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
Mitochondria mode changes default values for --tumor-lod-to-emit and --initial-tumor-lod to 0 to increase sensitivity.
- MITOCHONDRIA_MODE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- MITOCHONDRIAL_CONTIG_NAMES - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorConstants
- MIXED_BREAKEND_WINDOW_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- MIXED_INTERVAL_OVERLAP_FRACTION_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- MIXED_SAMPLE_OVERLAP_FRACTION_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- mixedBreakendWindow - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
-
Maximum allowed distance between endpoints (in bp) to cluster depth-only/PESR variant pairs.
- mixedOverlapFraction - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
-
Minimum interval reciprocal overlap fraction to cluster depth-only/PESR variant pairs.
- mixedParams - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- mixedSampleOverlapFraction - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
-
Minimum carrier sample reciprocal overlap fraction to cluster depth-only/PESR variant pairs.
- MIXING_FRACTIONS_TABLE_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithExpectedAlleleFraction
- MixingFraction - Class in org.broadinstitute.hellbender.tools.walkers.validation
-
Simple class for storing a sample and its mixing fraction within a pooled bam.
- MixingFraction(String, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.MixingFraction
- MLE_ALLELE_COUNT_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- MLE_ALLELE_FREQUENCY_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- mLogLikelihoodArray - Variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- MMapBackedIteratorFactory - Class in picard.illumina.parser.readers
-
MMapBackedIteratorFactory a file reader that takes a header size and a binary file, maps the file to a read-only byte buffer and provides methods to retrieve the header as it's own bytebuffer and create iterators of different data types over the values of file (starting after the end of the header).
- MMapBackedIteratorFactory() - Constructor for class picard.illumina.parser.readers.MMapBackedIteratorFactory
- MNP - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantType
- MODE - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.GatherTranches
-
Use either SNP for recalibrating only SNPs (emitting indels untouched in the output VCF) or INDEL for indels (emitting SNPs untouched in the output VCF).
- MODE - Variable in class picard.sam.markduplicates.CheckDuplicateMarking
- MODE - Variable in class picard.sam.ValidateSamFile
- MODE_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
-
The MODE insert size of all paired end reads where both ends mapped to the same chromosome.
- MODE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
- MODE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
- ModeArgumentUtils - Class in org.broadinstitute.hellbender.cmdline
-
This class is a static helper for implementing 'mode arguments' by tools.
- ModeArgumentUtils() - Constructor for class org.broadinstitute.hellbender.cmdline.ModeArgumentUtils
- MODEL_BACKEND_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- MODEL_BACKEND_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
- MODEL_CALL_INTERVALS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- MODEL_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument
- MODEL_PATH_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy
- MODEL_PATH_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller
- MODEL_PREFIX_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- MODEL_SHARD_PATH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- ModeledSegment - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
- ModeledSegment(SimpleInterval, int, int, ModeledSegment.SimplePosteriorSummary, ModeledSegment.SimplePosteriorSummary) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment
- ModeledSegment.SimplePosteriorSummary - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
- ModeledSegmentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
- ModeledSegmentCollection(File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.ModeledSegmentCollection
- ModeledSegmentCollection(SampleLocatableMetadata, List<ModeledSegment>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.ModeledSegmentCollection
- ModelSegments - Class in org.broadinstitute.hellbender.tools.copynumber
-
Models segmented copy ratios from denoised copy ratios and segmented minor-allele fractions from allelic counts.
- ModelSegments() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.ModelSegments
- ModelSegments.RunMode - Enum Class in org.broadinstitute.hellbender.tools.copynumber
- MODERATE - Enum constant in enum class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter.Verbosity
-
Output basic progress information during the copy.
- modulesToUse - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
-
See the -list argument to view available modules.
- MOLECULAR_BARCODE_NAME - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The barcode name for which the metrics were calculated.
- MOLECULAR_BARCODE_SEQUENCE_1 - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The barcode sequence for which the metrics were calculated.
- MOLECULAR_IDENTIFIER_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
- MOLECULAR_INDEX_BASE_QUALITY_TAG - Variable in class picard.illumina.IlluminaBasecallsToSam
- MOLECULAR_INDEX_TAG - Variable in class picard.illumina.IlluminaBasecallsToSam
- molecularBarcode - Variable in class picard.illumina.parser.ReadStructure
- MolecularIndex - Static variable in enum class picard.illumina.parser.ReadType
- moleculeID - Variable in class org.broadinstitute.hellbender.tools.walkers.consensus.ReadsWithSameUMI
- MoleculeID - Class in org.broadinstitute.hellbender.tools.walkers.consensus
-
A container class for the molecule ID, which consists of an integer ID and a binary strand.
- MoleculeID(int, String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.consensus.MoleculeID
- MoleculeID(GATKRead) - Constructor for class org.broadinstitute.hellbender.tools.walkers.consensus.MoleculeID
- molten() - Element in annotation interface org.broadinstitute.hellbender.tools.walkers.varianteval.util.Analysis
- Molten - Annotation Interface in org.broadinstitute.hellbender.tools.walkers.varianteval.util
-
Molten for @Analysis modules.
- MORE_THAN_ONE - Enum constant in enum class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert.NumPrimaryAlignmentState
- MOST_SPECIFIC_SUBTYPE - Enum constant in enum class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser.AltAlleleSummaryStrategy
-
Use the most specific subtype that doesn't conflict with any of the other alleles.
- MostDistantPrimaryAlignmentSelectionStrategy - Class in org.broadinstitute.hellbender.utils.read.mergealignment
-
For a paired-end aligner that aligns each end independently, select the pair of alignments that result in the largest insert size.
- MostDistantPrimaryAlignmentSelectionStrategy - Class in picard.sam
-
For a paired-end aligner that aligns each end independently, select the pair of alignments that result in the largest insert size.
- MostDistantPrimaryAlignmentSelectionStrategy() - Constructor for class org.broadinstitute.hellbender.utils.read.mergealignment.MostDistantPrimaryAlignmentSelectionStrategy
- MostDistantPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.MostDistantPrimaryAlignmentSelectionStrategy
- mostRepeatedPeriod(int) - Method in class org.broadinstitute.hellbender.utils.pairhmm.DragstrReadSTRAnalyzer
-
Returns the period length with the larger repeat length in a particular positions.
- MOTHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The ID of the mother within the trio.
- MOTIF_SIZE - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- MOVE_TO_TAG - Enum constant in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- moveBuilderStart(VariantContextBuilder, int, CachingIndexedFastaSequenceFile) - Static method in class org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFBlockCombiner
-
Modifies ref block builder to change start position and update ref allele accordingly in VC and genotypes
- mpileup - Variable in class org.broadinstitute.hellbender.tools.walkers.qc.CheckPileup
-
This is the existing mpileup against which we'll compare GATK's internal pileup at each genome position in the desired interval.
- MRNA_END_NF - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
the mRNA end could not be confirmed.
- MRNA_START_NF - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
the mRNA start could not be confirmed.
- MS_TO_SEC - Static variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- MSV_EXON_OVERLAP - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- MT_RRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- MT_TRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- MT_TRNA_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- MTAC - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- MTFAC - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls
- MTLowHeteroplasmyFilterTool - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- MTLowHeteroplasmyFilterTool() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MTLowHeteroplasmyFilterTool
- MULTIALLELIC_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- MultiallelicFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- MultiallelicFilter(int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MultiallelicFilter
- MultiallelicSummary - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
- MultiallelicSummary(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- MultiallelicSummary.Type - Enum Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
- MultiDeBruijnVertex - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
-
A DeBruijnVertex that supports multiple copies of the same kmer
- MultiDeBruijnVertex(byte[]) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex
-
Create a new MultiDeBruijnVertex with kmer sequence
- MultiDeBruijnVertex(byte[], boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex
-
Create a new MultiDeBruijnVertex with kmer sequence
- MultidimensionalModeller - Class in org.broadinstitute.hellbender.tools.copynumber.models
-
Represents a segmented model for copy ratio and allele fraction.
- MultidimensionalModeller(SimpleIntervalCollection, CopyRatioCollection, AllelicCountCollection, AlleleFractionPrior, int, int, int, int) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.models.MultidimensionalModeller
-
Constructs a copy-ratio and allele-fraction modeller, specifying number of total samples and number of burn-in samples for Markov-Chain Monte Carlo model fitting.
- MultiFeatureWalker<F extends htsjdk.tribble.Feature> - Class in org.broadinstitute.hellbender.engine
-
A MultiFeatureWalker is a tool that presents one
Featureat a time in sorted order from multiple sources of Features. - MultiFeatureWalker() - Constructor for class org.broadinstitute.hellbender.engine.MultiFeatureWalker
- MultiFeatureWalker.DictSource - Class in org.broadinstitute.hellbender.engine
- MultiFeatureWalker.MergingIterator<F extends htsjdk.tribble.Feature> - Class in org.broadinstitute.hellbender.engine
- MultiFeatureWalker.PQContext<F extends htsjdk.tribble.Feature> - Class in org.broadinstitute.hellbender.engine
- MultiFeatureWalker.PQEntry<F extends htsjdk.tribble.Feature> - Class in org.broadinstitute.hellbender.engine
- MultiHitAlignedReadIterator - Class in org.broadinstitute.hellbender.utils.read.mergealignment
-
Iterate over queryname-sorted SAM, and return each group of reads with the same queryname.
- MultiIntervalLocalReadShard - Class in org.broadinstitute.hellbender.engine
-
A class to represent shards of read data spanning multiple intervals.
- MultiIntervalLocalReadShard(List<SimpleInterval>, int, ReadsDataSource) - Constructor for class org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard
-
Create a new MultiIntervalLocalReadShard spanning the given intervals, with each interval expanded on both sides by the specified number of padding bases.
- MultiIntervalLocalReadShard(List<SimpleInterval>, ReadsDataSource) - Constructor for class org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard
-
Create a new MultiIntervalLocalReadShard spanning the given intervals, with no padding around intervals.
- MultiIntervalShard<T> - Interface in org.broadinstitute.hellbender.engine
-
An interface to represent shards of arbitrary data spanning multiple intervals.
- MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,
HISTOGRAM_KEY extends Comparable<HISTOGRAM_KEY>, ARGTYPE> - Class in org.broadinstitute.hellbender.metrics -
MultiLevelCollector handles accumulating Metrics at different MetricAccumulationLevels(ALL_READS, SAMPLE, LIBRARY, READ_GROUP).
- MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,
Histogram_KEY extends Comparable, ARGTYPE> - Class in picard.metrics -
MultiLevelCollector handles accumulating Metrics at different MetricAccumulationLevels(ALL_READS, SAMPLE, LIBRARY, READ_GROUP).
- MultiLevelCollector() - Constructor for class org.broadinstitute.hellbender.metrics.MultiLevelCollector
- MultiLevelCollector() - Constructor for class picard.metrics.MultiLevelCollector
- MultilevelMetrics - Class in picard.metrics
- MultilevelMetrics() - Constructor for class picard.metrics.MultilevelMetrics
- MultiLevelMetrics - Class in org.broadinstitute.hellbender.metrics
- MultiLevelMetrics() - Constructor for class org.broadinstitute.hellbender.metrics.MultiLevelMetrics
- MultiLevelReducibleCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,
HISTOGRAM_KEY extends Comparable<HISTOGRAM_KEY>, ARGTYPE, UNIT_COLLECTOR extends PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE>> - Class in org.broadinstitute.hellbender.metrics -
Abstract base class for reducible multi-level metrics collectors.
- MultiLevelReducibleCollector() - Constructor for class org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector
- MULTIPLE_SAMPLE - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.ModelSegments.RunMode
- multipleAtWhichToBreakBands - Variable in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
-
To reduce file sizes our gVCFs group similar reference positions into bands.
- MultiplePassReadWalker - Class in org.broadinstitute.hellbender.engine
-
A MultiplePassReadWalker traverses input reads multiple times.
- MultiplePassReadWalker() - Constructor for class org.broadinstitute.hellbender.engine.MultiplePassReadWalker
- MultiplePassReadWalker.GATKReadConsumer - Interface in org.broadinstitute.hellbender.engine
-
Implemented by MultiplePassReadWalker-derived tools.
- MultiplePassVariantWalker - Class in org.broadinstitute.hellbender.engine
-
A VariantWalker that makes multiple passes through the variants.
- MultiplePassVariantWalker() - Constructor for class org.broadinstitute.hellbender.engine.MultiplePassVariantWalker
- MULTIPLEX_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToFastq
- multiply(double[], double[]) - Static method in class picard.util.MathUtil
-
Calculates the product of two arrays of the same length.
- MultiSampleEdge - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
-
Edge class for connecting nodes in the graph that tracks some per-sample information.
- MultiSampleEdge(boolean, int, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MultiSampleEdge
-
Create a new MultiSampleEdge with weight multiplicity and, if isRef == true, indicates a path through the reference
- MultisampleMultidimensionalKernelSegmenter - Class in org.broadinstitute.hellbender.tools.copynumber.segmentation
-
Segments copy-ratio data and/or alternate-allele-fraction data from one or more samples using kernel segmentation.
- MultisampleMultidimensionalKernelSegmenter(List<CopyRatioCollection>, List<AllelicCountCollection>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.segmentation.MultisampleMultidimensionalKernelSegmenter
- MultiSegmentsCpxVariantExtractor() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor.MultiSegmentsCpxVariantExtractor
- MultiThreadedChunkBased(int, VariantIteratorProducer, VariantProcessor.AccumulatorGenerator<A, R>) - Constructor for class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
- multithreadingBy(int) - Method in class picard.vcf.processor.VariantProcessor.Builder
- MultiTileBcl - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- MultiTileBclFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- MultiTileBclFileFaker() - Constructor for class picard.illumina.parser.fakers.MultiTileBclFileFaker
- MultiTileBclFileUtil - Class in picard.illumina.parser
-
NextSeq-style bcl's have all tiles for a cycle in a single file.
- MultiTileBclParser - Class in picard.illumina.parser
-
Parse .bcl.bgzf files that contain multiple tiles in a single file.
- MultiTileBclParser(File, int, CycleIlluminaFileMap, OutputMapping, boolean, BclQualityEvaluationStrategy, TileIndex) - Constructor for class picard.illumina.parser.MultiTileBclParser
- MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
-
For file types for which there is one file per lane, with fixed record size, and all the tiles in it, so the s_
.bci file can be used to figure out where each tile starts and ends. - MultiTileFilter - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- MultiTileFilterParser - Class in picard.illumina.parser
-
Read filter file that contains multiple tiles in a single file.
- MultiTileFilterParser(TileIndex, List<Integer>, File) - Constructor for class picard.illumina.parser.MultiTileFilterParser
- MultiTileLocs - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- MultiTileLocsFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- MultiTileLocsFileFaker() - Constructor for class picard.illumina.parser.fakers.MultiTileLocsFileFaker
- MultiTileLocsParser - Class in picard.illumina.parser
-
Read locs file that contains multiple tiles in a single file.
- MultiTileLocsParser(TileIndex, List<Integer>, File, int) - Constructor for class picard.illumina.parser.MultiTileLocsParser
- MultiTileParser<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
-
Abstract class for files with fixed-length records for multiple tiles, e.g.
- MultiTileParser(TileIndex, List<Integer>, Set<IlluminaDataType>) - Constructor for class picard.illumina.parser.MultiTileParser
- MultiVariantDataSource - Class in org.broadinstitute.hellbender.engine
-
MultiVariantDataSource aggregates multiple FeatureDataSources of variants, and enables traversals and queries over those sources through a single interface.
- MultiVariantDataSource(List<FeatureInput<VariantContext>>, int) - Constructor for class org.broadinstitute.hellbender.engine.MultiVariantDataSource
-
Creates a MultiVariantDataSource backed by the provided FeatureInputs.
- MultiVariantDataSource(List<FeatureInput<VariantContext>>, int, int, int, Path, boolean) - Constructor for class org.broadinstitute.hellbender.engine.MultiVariantDataSource
-
Creates a MultiVariantDataSource backed by the provided FeatureInputs.
- multiVariantInputArgumentCollection - Variable in class org.broadinstitute.hellbender.engine.MultiVariantWalker
- MultiVariantInputArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
Class that defines the variant arguments used for a MultiVariantWalker.
- MultiVariantInputArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.MultiVariantInputArgumentCollection
- MultiVariantInputArgumentCollection.DefaultMultiVariantInputArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
- MultiVariantWalker - Class in org.broadinstitute.hellbender.engine
-
A MultiVariantWalker is a tool that processes one variant at a time, in position order, from multiple sources of variants, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features.
- MultiVariantWalker() - Constructor for class org.broadinstitute.hellbender.engine.MultiVariantWalker
- MultiVariantWalkerGroupedOnStart - Class in org.broadinstitute.hellbender.engine
-
A MultiVariantWalker that walks over multiple variant context sources in reference order and emits to client tools groups of all input variant contexts by their start position.
- MultiVariantWalkerGroupedOnStart() - Constructor for class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
- MUMMER_X86_64_LINUX_BINARIES_ZIPFILE - Static variable in class org.broadinstitute.hellbender.utils.alignment.MummerExecutor
- MUMMER_X86_64_MAC_BINARIES_ZIPFILE - Static variable in class org.broadinstitute.hellbender.utils.alignment.MummerExecutor
- MummerExecutor - Class in org.broadinstitute.hellbender.utils.alignment
-
Class for executing MUMmer alignment pipeline to detect SNPs and INDELs in mismatching sequences.
- MummerExecutor() - Constructor for class org.broadinstitute.hellbender.utils.alignment.MummerExecutor
-
Returns a MummerExecutor pointing to the unzipped MUMmer executables packaged in GATK
- MummerExecutor(File) - Constructor for class org.broadinstitute.hellbender.utils.alignment.MummerExecutor
-
Returns a MummerExecutor pointing to the provided directory
- MUS - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.Genus
-
Mice
- MUTECT_AS_FILTER_NAMES - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- MUTECT_FILTER_NAMES - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- MUTECT_STATS_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- Mutect2 - Class in org.broadinstitute.hellbender.tools.walkers.mutect
-
Call somatic short mutations via local assembly of haplotypes.
- Mutect2() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- Mutect2AlleleFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
-
Base class for filters that apply at the allele level.
- Mutect2AlleleFilter() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2AlleleFilter
- Mutect2Engine - Class in org.broadinstitute.hellbender.tools.walkers.mutect
-
Created by davidben on 9/15/16.
- Mutect2Engine(M2ArgumentCollection, AssemblyRegionArgumentCollection, boolean, boolean, SAMFileHeader, GATKPath, VariantAnnotatorEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
-
Create and initialize a new HaplotypeCallerEngine given a collection of HaplotypeCaller arguments, a reads header, and a reference file
- Mutect2Filter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
-
Base class for all Mutect2Filters
- Mutect2Filter() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2Filter
- Mutect2FilteringEngine - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- Mutect2FilteringEngine(M2FiltersArgumentCollection, VCFHeader, File) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- Mutect2VariantFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- Mutect2VariantFilter() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2VariantFilter
- MUTECT3_ALT_DOWNSAMPLE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- MUTECT3_DATASET_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- MUTECT3_REF_DOWNSAMPLE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- MUTECT3_TRAINING_MODE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- MUTECT3_TRAINING_NON_ARTIFACT_RATIO - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- MUTECT3_TRAINING_TRUTH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- mutect3Dataset - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
Destination for Mutect3 data collection
- Mutect3DatasetEngine - Class in org.broadinstitute.hellbender.tools.walkers.mutect
- Mutect3DatasetEngine(File, boolean, int, int, int, Set<String>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect3DatasetEngine
- mutect3NonArtifactRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
Number of non-artifact data per artifact datum in Mutect3 training
- mutect3TrainingDataMode - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
If true, collect Mutect3 data for learning; otherwise collect data for generating calls with a pre-trained model
- mutect3TrainingTruth - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
VCF of known calls for a sample used for generating a Mutect3 training dataset.
- MutectDownsampler - Class in org.broadinstitute.hellbender.utils.downsampling
- MutectDownsampler(int, int, int) - Constructor for class org.broadinstitute.hellbender.utils.downsampling.MutectDownsampler
- MutectReadThreadingAssemblerArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
- MutectReadThreadingAssemblerArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.MutectReadThreadingAssemblerArgumentCollection
- MutectStats - Class in org.broadinstitute.hellbender.tools.walkers.mutect
- MutectStats(String, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.MutectStats
- mvRefHet_Var - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- mvRefRef_Het - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- mvRefRef_Var - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- mvRefVar_Ref - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- mvRefVar_Var - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- mvVarHet_Ref - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- mvVarVar_Het - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- mvVarVar_Ref - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
N
- n - Variable in class picard.arrays.illumina.InfiniumEGTFile
- N - Enum constant in enum class org.broadinstitute.hellbender.utils.BaseUtils.Base
- N - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- N - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- n_coding_indels_frameshifting - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- n_coding_indels_in_frame - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- N_COUNT_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- N_CYCLES - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- n_deletions - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- n_indels - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- n_indels_matching_gold_standard - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- n_insertions - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- n_large_deletions - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- n_large_insertions - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- n_multiallelic_indel_sites - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- n_novel_indels - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- N_RATIO_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- n_singleton_indels - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- n_singleton_SNPs - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- n_SNPs - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- NA - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantType
- NA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.TranscriptSupportLevel
-
the transcript was not analyzed
- NA - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
- NA - Static variable in class picard.vcf.GenotypeConcordanceScheme
-
These are convenience variables for defining a scheme.
- nAdapterClippedBases - Variable in class org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- NAGNAG_SPLICE_SITE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
in-frame type of variation where, at the acceptor site, some variants splice after the first AG and others after the
- NaiveHeterozygousPileupGenotypingUtils - Class in org.broadinstitute.hellbender.tools.copynumber.utils.genotyping
-
Naive methods for binomial genotyping of heterozygous sites from pileup allele counts.
- NaiveHeterozygousPileupGenotypingUtils.NaiveHeterozygousPileupGenotypingResult - Class in org.broadinstitute.hellbender.tools.copynumber.utils.genotyping
- nAlternateAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of doubletons where the two reads matched the alternate.
- nAlternateAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of tripletons where the two reads matched the alternate.
- nAlternateReads - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of alternate alleles in the reads.
- name - Variable in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord
- name - Variable in class picard.annotation.Gene.Transcript
- name() - Element in annotation interface org.broadinstitute.hellbender.tools.walkers.varianteval.util.Analysis
- NAME - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.TableNameHeaderFields
- NAME - Variable in class picard.util.FifoBuffer
- NAME_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- nameAt(int) - Method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Returns the name of a column by its index.
- names() - Method in class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Returns the column names ordered by column index.
- nameSuffix() - Method in enum class org.broadinstitute.hellbender.tools.spark.sv.evidence.TemplateFragmentOrdinal
- NANOS_TO_MILLIS - Static variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- NANOS_TO_SECONDS - Static variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- NativeUtils - Class in org.broadinstitute.hellbender.utils
-
Utilities to provide architecture-dependent native functions
- NATURAL_LOG_INFORMATIVE_THRESHOLD - Static variable in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
- NATURAL_LOG_MATH - Static variable in class picard.util.MathUtil
- NaturalLogUtils - Class in org.broadinstitute.hellbender.utils
- nBadBarcodes - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of sets where the UMIs had poor quality bases and were not used for any comparisons.
- nCalledLoci - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nCalledNotFiltered - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.GenotypeFilterSummary
- NCBI_35 - Static variable in class picard.arrays.illumina.IlluminaManifest
- NCBI_36 - Static variable in class picard.arrays.illumina.IlluminaManifest
- NCBI_37 - Static variable in class picard.arrays.illumina.IlluminaManifest
- nClippedBases - Variable in class org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- nClippedReads - Variable in class org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- nComp - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- nComplex - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nConcordant - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap
- NCRNA_HOST - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
the locus is a host for small non-coding RNAs.
- nDeletedBases - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
-
Total number of deleted bases
- nDeletions - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nDeletions - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
-
Total number of deletions
- nDifferentAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of doubletons where the two reads had different bases in the locus.
- nDifferentAlleleSites - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- nDifferentAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of tripletons where at least one of the reads didn't match either allele of the het site.
- NDNCigarReadTransformer - Class in org.broadinstitute.hellbender.transformers
-
A read transformer that refactors NDN cigar elements to one N element.
- NDNCigarReadTransformer() - Constructor for class org.broadinstitute.hellbender.transformers.NDNCigarReadTransformer
- nDuplicateSets - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of duplicate sets examined.
- NEAR_AMPLICON_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a baited region.
- NEAR_BAIT_BASES - Variable in class picard.analysis.directed.HsMetrics
-
The number of PF_BASES_ALIGNED that are mapped to within a fixed interval containing a baited region, but not within the baited section per se.
- NEAR_DISTANCE - Variable in class picard.analysis.directed.CollectTargetedMetrics
- NEAR_PROBE_BASES - Variable in class picard.analysis.directed.TargetMetrics
-
The number of PF aligned bases that mapped to within a fixed interval of a probed region, but not on a probed region.
- NEAR_PROBE_DISTANCE_DEFAULT - Static variable in class picard.analysis.directed.TargetMetricsCollector
-
Default distance for a read to be considered "selected".
- NearbyKmerErrorCorrector - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Utility class that error-corrects reads.
- NearbyKmerErrorCorrector(int, byte, int, boolean, byte[]) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NearbyKmerErrorCorrector
-
Simple constructor with sensible defaults
- NearbyKmerErrorCorrector(int, int, int, byte, int, boolean, byte, boolean, byte[]) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NearbyKmerErrorCorrector
-
Create a new kmer corrector
- NearbyKmerErrorCorrector.CorrectionSet - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Wrapper utility class that holds, for each position in read, a list of bytes representing candidate corrections.
- NEAREST_TSS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- needsCollapsing(byte[], int, Logger) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LongHomopolymerHaplotypeCollapsingEngine
-
Determine if given bases (normally a reference region) will require collapsing support for haplotypes created over it.
- needsReferenceSequence() - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
- needsRefflatFile() - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
- needsRemapping() - Method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.AlleleMapper
- negate() - Method in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter
-
Specialization of negate so that the resulting object is still a CountingReadFilter
- negate() - Method in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter
-
Specialization of negate so that the resulting object is still a CountingVariantFilter
- negate() - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilter
-
Specialization of negate so that the resulting object is still a ReadFilter
- negate() - Method in interface org.broadinstitute.hellbender.engine.filters.VariantFilter
- NEGATIVE - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.Strand
- NEGATIVE - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
- NEGATIVE_LABEL_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- NEGATIVE_TAG - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
- neighboringVerticesOf(V) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Get the set of vertices connected to v by incoming or outgoing edges
- NESTED_454_RNA_SEQ_SUPPORTED - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
annotated based on RNA-seq data.
- NestedIntegerArray<T extends Serializable> - Class in org.broadinstitute.hellbender.utils.collections
- NestedIntegerArray(int...) - Constructor for class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray
- NestedIntegerArray.Leaf<T> - Class in org.broadinstitute.hellbender.utils.collections
- NEUTRAL - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledCopyRatioSegment.Call
- NEUTRAL_SEGMENT_COPY_RATIO_LOWER_BOUND_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegments
- NEUTRAL_SEGMENT_COPY_RATIO_UPPER_BOUND_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegments
- nEvalVariants - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap
- NEW - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapTargetStatus
-
Gene or transcript was not in target annotations.
- NEW_SAMPLE_NAME - Variable in class picard.vcf.RenameSampleInVcf
- NEW_SW_PARAMETERS - Static variable in class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAlignmentConstants
-
NEW_SW_PARAMETERSis the default forCigarUtils.calculateCigar(byte[], byte[], org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner, org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters, org.broadinstitute.gatk.nativebindings.smithwaterman.SWOverhangStrategy)for haplotype-to-reference alignment. - newCounter() - Method in class picard.analysis.CounterManager
-
Creates a new Counter object and adds it to the list of managed Counters.
- newEmptyFragment(GATKRead, SAMFileHeader, Map<String, Byte>, MarkDuplicatesSparkArgumentCollection) - Static method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord
- newFragment(GATKRead, SAMFileHeader, int, MarkDuplicatesScoringStrategy, Map<String, Byte>, MarkDuplicatesSparkArgumentCollection) - Static method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord
- newInstance(byte) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.StandardPairHMMInputScoreImputator
- newInstance(byte, byte, byte) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NonSymmetricalPairHMMInputScoreImputator
- newInstance(SAMSequenceDictionary, STRDecimationTable, boolean, int, int) - Static method in class org.broadinstitute.hellbender.utils.dragstr.STRTableFileBuilder
-
Creates a new builder.
- newList(List<A>) - Static method in interface org.broadinstitute.hellbender.utils.genotyper.AlleleList
- newPair(GATKRead, GATKRead, SAMFileHeader, int, MarkDuplicatesScoringStrategy, Map<String, Byte>) - Static method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord
- newSimpleReport(String, GATKReportTable.Sorting, String...) - Static method in class org.broadinstitute.hellbender.utils.report.GATKReport
-
The constructor for a simplified GATK Report.
- newSimpleReportWithDescription(String, String, GATKReportTable.Sorting, String...) - Static method in class org.broadinstitute.hellbender.utils.report.GATKReport
- nExactlyDouble - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of sets of size exactly 2 found.
- nExactlyTriple - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of sets of size exactly 3 found.
- next - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- next - Variable in class org.broadinstitute.hellbender.utils.SVIntervalTree.OverlapIterator
- next() - Method in class org.broadinstitute.hellbender.engine.ActivityProfileStateIterator
- next() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionFromActivityProfileStateIterator
- next() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionIterator
- next() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker.MergingIterator
- next() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointDensityFilter
- next() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.PairedStrandedIntervalTreeIterator
- next() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.PairedStrandedIntervalTreeOverlapperIterator
- next() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- next() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils.IteratorFilter
- next() - Method in class org.broadinstitute.hellbender.tools.spark.utils.FlatMapGluer
- next() - Method in interface org.broadinstitute.hellbender.tools.spark.utils.LongIterator
- next() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Calculates the next genotype in likelihood indexing order.
- next() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence.BAFSiteIterator
- next() - Method in class org.broadinstitute.hellbender.utils.BaseUtils.HmerIterator
- next() - Method in class org.broadinstitute.hellbender.utils.bigquery.StorageAPIAvroReader
- next() - Method in class org.broadinstitute.hellbender.utils.BinaryTableReader
- next() - Method in class org.broadinstitute.hellbender.utils.iterators.AllLocusIterator
- next() - Method in class org.broadinstitute.hellbender.utils.iterators.ByteArrayIterator
- next() - Method in class org.broadinstitute.hellbender.utils.iterators.CloseAtEndIterator
- next() - Method in class org.broadinstitute.hellbender.utils.iterators.IntervalLocusIterator
- next() - Method in class org.broadinstitute.hellbender.utils.iterators.IntervalOverlappingIterator
- next() - Method in class org.broadinstitute.hellbender.utils.iterators.PushToPullIterator
- next() - Method in class org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator
- next() - Method in class org.broadinstitute.hellbender.utils.iterators.ReadFilteringIterator
- next() - Method in class org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator
- next() - Method in class org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator
- next() - Method in class org.broadinstitute.hellbender.utils.iterators.SAMRecordToReadIterator
- next() - Method in class org.broadinstitute.hellbender.utils.iterators.ShardedIntervalIterator
- next() - Method in class org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator
- next() - Method in class org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState
-
Get the next AlignmentContext available from the reads.
- next() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- next() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.MultiHitAlignedReadIterator
- next() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree.FwdIterator
- next() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree.OverlapIterator
- next() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree.RevIterator
- next() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree.ValuesIterator
- next() - Method in class org.broadinstitute.hellbender.utils.text.XReadLines
-
Returns the next line (optionally minus whitespace)
- next() - Method in class picard.illumina.parser.MultiTileBclParser
- next() - Method in class picard.illumina.parser.MultiTileParser
- next() - Method in class picard.illumina.parser.PerTileParser
- next() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
Return the next set of coordinates in a given file.
- next() - Method in class picard.illumina.parser.readers.BarcodeFileReader
- next() - Method in class picard.illumina.parser.readers.BclReader
- next() - Method in class picard.illumina.parser.readers.CbclReader
- next() - Method in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader
- next() - Method in class picard.illumina.parser.readers.FilterFileReader
- next() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
- next() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- next() - Method in class picard.util.AsyncIterator
- next() - Method in interface picard.util.AtomicIterator
-
Produces the next element from the iterator, if there is one; otherwise, produces
Optional.EMPTY - next() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- next() - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
- next() - Method in class picard.vcf.ByIntervalListVariantContextIterator
- next() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
-
Provides the next record from the underlying iterator after applying filter strings generated by the set of filters in use by the iterator.
- next() - Method in class picard.vcf.PairedVariantSubContextIterator
- next() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
- NEXT_BASE_QUALITY_THRESHOLD - Variable in class picard.analysis.CollectRrbsMetrics
- nextAlignmentMayBeInsertion(AlignmentInterval, AlignmentInterval, Integer, Integer, boolean) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.ContigChimericAlignmentIterativeInterpreter
-
To implement the idea that for two consecutive alignment regions of a contig, the one with higher reference coordinate might be a novel insertion.
- NEXTERA_V1 - Enum constant in enum class org.broadinstitute.hellbender.utils.illumina.IlluminaAdapterPair
- NEXTERA_V1 - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- NEXTERA_V2 - Enum constant in enum class org.broadinstitute.hellbender.utils.illumina.IlluminaAdapterPair
- NEXTERA_V2 - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- nextKmer - Variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- nextKmer(SVKmer, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVDUSTFilteredKmerizer
- nextKmer(SVKmer, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- nextReadBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies bases into the following (uppercase) base as it was read from the sequencer (i.e.
- nextSequence() - Method in class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
-
Retrieves the next whole sequence from the file.
- nFamCalled - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- nGoodBarcodes - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
the number of sets where the UMIs had good quality bases and were used for any comparisons.
- NGSPlatform - Enum Class in org.broadinstitute.hellbender.utils
-
A canonical, master list of the standard NGS platforms.
- nHets - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- NHOM - Variable in class picard.arrays.BafRegressMetrics
-
The number of homozygous genotypes used to fit the model
- nHomDerived - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nHomRef - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nHomVar - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nIndelLoci - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MetricsCollection
- nIndels - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MetricsCollection
- nIndels - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- nIndels - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- nIndelSites - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- nIndelsPerSample - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- nInsertedBases - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
-
Total number of inserted bases
- nInsertions - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nInsertions - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
-
Total number of inserts
- NIO_MAX_REOPENS - Variable in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- NIO_MAX_REOPENS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- NIO_MAX_REOPENS_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- NIO_PROJECT_FOR_REQUESTER_PAYS - Variable in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- NIO_PROJECT_FOR_REQUESTER_PAYS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- NioFileCopierWithProgressMeter - Class in org.broadinstitute.hellbender.utils.nio
-
Class to copy a file using
java.nio. - NioFileCopierWithProgressMeter(Path, Path, boolean, NioFileCopierWithProgressMeter.Verbosity) - Constructor for class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
-
NioFileCopierWithProgressMeteruses a factory pattern. - NioFileCopierWithProgressMeter.ChecksumCalculator - Interface in org.broadinstitute.hellbender.utils.nio
-
An interface that defines a method to use to calculate a checksum on an
InputStream. - NioFileCopierWithProgressMeter.Verbosity - Enum Class in org.broadinstitute.hellbender.utils.nio
-
An enum to allow for verbosity of logging progress of an
NioFileCopierWithProgressMeter. - NioFileCopierWithProgressMeterResults - Class in org.broadinstitute.hellbender.utils.nio
-
An object to hold the results of a copy operation performed by
NioFileCopierWithProgressMeterResults. - nLociViolations - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- nLowQual - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- nMatchingUMIsInDiffBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of UMIs that are match within Bi-sets that come from different alleles.
- nMatchingUMIsInSameBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of UMIs that are match within Bi-sets that come from the same alleles.
- NMD_EXCEPTION - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
the transcript looks like it is subject to NMD but publications, experiments or conservation support the translation of
- NMD_LIKELY_IF_EXTENDED - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
codon if the transcript were longer but cannot currently be annotated as NMD as does not fulfil all criteria - most
- nMismatchingAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of tripletons where the two reads had different bases in the locus.
- nMismatchingAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of tripletons where at least one of the reads didn't match either allele of the het site.
- nMismatchingBases - Variable in class picard.sam.SamErrorMetric.SimpleErrorCalculator
- nMismatchingUMIsInContraOrientedBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of bi-sets with mismatching UMIs and opposite orientation.
- nMismatchingUMIsInCoOrientedBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of bi-sets with mismatching UMIs and same orientation.
- nMismatchingUMIsInDiffBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of UMIs that are different within Bi-sets that come from different alleles.
- nMismatchingUMIsInSameBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of UMIs that are different within Bi-sets that come from the same alleles.
- nMissing - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.PrintMissingComp
- nMixed - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nMNPs - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nMultiIndels - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- nMultiSNPs - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- NN - Enum constant in enum class picard.arrays.illumina.IlluminaGenotype
- nNoCall - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- nNoCallOrFiltered - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.GenotypeFilterSummary
- nNoCalls - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nNovelSites() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap
- NO_APPLICABLE_END - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- NO_APPLICABLE_LEN - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- NO_AS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
Indicates that no AS (alignment score) annotation is present.
- NO_BASE - Static variable in interface org.broadinstitute.hellbender.utils.IntervalPileup
- NO_BASE_COMPARISON - Enum constant in enum class org.broadinstitute.hellbender.tools.reference.CompareReferences.BaseComparisonMode
- NO_BQ - Static variable in interface org.broadinstitute.hellbender.utils.IntervalPileup
- NO_CALL - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- NO_CALL - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- NO_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
- NO_CALL_ALLELES - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Deprecated.you should use
GATKVariantContextUtils.noCallAlleles(int)instead. It indicates the presence of a hardcoded diploid assumption which is bad. - NO_CALL_BASE - Static variable in class picard.illumina.parser.readers.BaseBclReader
- NO_CALL_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- NO_CALL_GTS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- NO_CALLS - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- NO_COMMON_CONTIGS - Enum constant in enum class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.SequenceDictionaryCompatibility
- NO_DECIMATION_STR - Static variable in class org.broadinstitute.hellbender.tools.dragstr.STRDecimationTable
-
String that represents the special DT with no decimation ...
- NO_DOWNSAMPLING - Static variable in class org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState
-
Indicates that we shouldn't do any downsampling
- NO_EXON_NUMBER - Static variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- NO_FAMILY_ID - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.PedReader.MissingPedField
-
The PED records do not have the first (FAMILY_ID) argument.
- NO_FEATURE_ORDER - Static variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- NO_FILTER - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.SingleSequenceReferenceAligner
- NO_GOOD_MAPPING_TO_NON_CANONICAL_CHROMOSOME - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
-
See
AlignedContig.getBetterNonCanonicalMapping(Set, List, int). - NO_HAPLOTYPES - Enum constant in enum class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter.WriterType
-
With this option, haplotypes will not be included in the output bam.
- NO_JOINT_VALUE - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.FamilyLikelihoods
- NO_LENGTH - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVContext
-
Indicates that the variant does not have a length or this could not be determined, e.g.
- NO_LIBRARIES_SPECIFIED_IN_HEADER - Static variable in class picard.sam.SplitSamByLibrary
- NO_LINE_NUMBER - Static variable in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Constant to indicate that a data-line has no line number assigned.
- NO_MAPPING_QUALITY - Static variable in class org.broadinstitute.hellbender.utils.read.ReadConstants
-
Value used to represent the absence of a mapping quality in a read
- NO_MATCH - Static variable in class picard.util.ClippingUtility
-
The value returned by methods returning int when no match is found.
- NO_NM - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
Indicates that no NM (number of mismatches) annotation is present.
- NO_NORMAL - Static variable in class org.broadinstitute.hellbender.tools.funcotator.metadata.SamplePairExtractor
- NO_OPTICAL_MARKER - Static variable in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- NO_PARENTS - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.PedReader.MissingPedField
-
The PED records do not have either the paternal or maternal IDs, so the corresponding IDs are set to null.
- NO_PHENO - Static variable in class picard.pedigree.PedFile
- NO_PHENOTYPE - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.PedReader.MissingPedField
-
The PED records do not have the PHENOTYPE field, so the phenotype of each sample will be set to UNKNOWN.
- NO_SEQ_MAP - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapStatus
-
The source sequence is not in the assembly alignments.
- NO_SEX - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.PedReader.MissingPedField
-
The PED records do not have the GENDER field, so the sex of each sample will be set to UNKNOWN.
- NO_SINGLE_TRANSCRIPT_SUPPORT - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.TranscriptSupportLevel
-
no single transcript supports the model structure
- NO_SWITCH - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.StrandSwitch
- NO_TRANSCRIPT_AVAILABLE_KEY - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
- NO_VALUE - Static variable in interface picard.sam.util.PhysicalLocation
- NO_VALUE_STR - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
Represents the lack of a value for a field in a string representation.
- NOCALL_CHROM_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- noCallAlleles(int) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Returns a
NO_CALLallele list provided the ploidy. - noExtraAttributes - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- noFeatureButFilterAt(GATKRead, ReferenceContext, int) - Method in interface org.broadinstitute.hellbender.tools.walkers.featuremapping.FeatureMapper
- noFeatureButFilterAt(GATKRead, ReferenceContext, int) - Method in class org.broadinstitute.hellbender.tools.walkers.featuremapping.SNVMapper
- noMatchMetric - Variable in class picard.illumina.ExtractBarcodesProgram
- NON_ATG_START - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
the CDS has a non-ATG start and its validity is supported by publication or conservation.
- NON_CANONICAL_CONSERVED - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
the transcript has a non-canonical splice site conserved in other species.
- NON_CANONICAL_GENOME_SEQUENCE_ERROR - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
the transcript has a non-canonical splice site explained by a genomic sequencing error.
- NON_CANONICAL_HUMAN_ORDER - Enum constant in enum class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.SequenceDictionaryCompatibility
- NON_CANONICAL_OTHER - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
the transcript has a non-canonical splice site explained by other reasons.
- NON_CANONICAL_POLYMORPHISM - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
the transcript has a non-canonical splice site explained by a SNP.
- NON_CANONICAL_TEC - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
the transcript has a non-canonical splice site that needs experimental confirmation.
- NON_CANONICAL_U12 - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
the transcript has a non-canonical splice site explained by a U12 intron (i.e.
- NON_CHIMERIC_ORIGINAL_ALIGNMENT_READ_FILTER - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- NON_CODING - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- NON_CODING_BED_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate
- NON_CPG_BASES - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of times a non-CpG cytosine was encountered
- NON_CPG_CONVERTED_BASES - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of times a non-CpG cytosine was converted (C->T for +, G->A for -)
- NON_REF_ALLELE_DESCRIPTION - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
- NON_REF_GENOTYPE_CONCORDANCE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The non-ref genotype concordance, ie for all var states only.
- NON_REF_GENOTYPE_CONCORDANCE_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- NON_REF_SYMBOLIC_ALLELE_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- NON_SOMATIC - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorType
- NON_STOP_DECAY - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- NON_SUBMITTED_EVIDENCE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
a splice variant for which supporting evidence has not been submitted to databases, i.e.
- NON_SYNONYMOUS_CODING - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- NON_SYNONYMOUS_START - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- NON_SYNONYMOUS_STOP - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- NON_ZERO_REFERENCE_LENGTH_ALIGNMENT - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- NON_ZERO_REGIONS - Enum constant in enum class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
- nonCanonicalChromosomeNamesFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantReInterpreterSpark
- NonChecksumLocalFileSystem - Class in org.broadinstitute.hellbender.engine.spark
-
An extension of Hadoop's
LocalFileSystemthat doesn't write (or verify) .crc files. - NonChecksumLocalFileSystem() - Constructor for class org.broadinstitute.hellbender.engine.spark.NonChecksumLocalFileSystem
- NonChimericOriginalAlignmentReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.NonChimericOriginalAlignmentReadFilter
- NONCODING_BREAKPOINT - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- NONCODING_SPAN - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- nonCoOcurringColumns() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.OccurrenceMatrix
-
find pairs of columns which do not both have a true value at any row
- NONE - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier.AlnModType
- NONE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection.FlowMode
- NONE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.PCRErrorModel
-
no specialized PCR error model will be applied; if base insertion/deletion qualities are present they will be used
- NONE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection.OffRampTypeEnum
- NONE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection.OnRampTypeEnum
- NONE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceMode
-
Regular calling without emitting reference confidence calls.
- NONE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection.FlowMode
- NONE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectFunctionalClass
- NONE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- NONE - Enum constant in enum class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState.Type
- NONE - Enum constant in enum class org.broadinstitute.hellbender.utils.downsampling.DownsampleType
- NONE - Enum constant in enum class org.broadinstitute.hellbender.utils.GenomeLocParser.ValidationLevel
-
Don't do any real checking at all
- NONE - Enum constant in enum class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert.NumPrimaryAlignmentState
- NONE - Enum constant in enum class picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
- NONE - Enum constant in enum class picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
- NONE - Static variable in class org.broadinstitute.hellbender.tools.dragstr.STRDecimationTable
-
The no-decimating table.
- NONE - Static variable in class org.broadinstitute.hellbender.utils.downsampling.DownsamplingMethod
-
Expresses no downsampling applied at all.
- nonEmpty(String) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Checks that a
Stringis notnulland that it is not empty. - nonEmpty(String, String) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Checks that a
Stringis notnulland that it is not empty. - nonEmpty(T) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Checks that a
Collectionis notnulland that it is not empty. - nonEmpty(T, String) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Checks that a
Collectionis notnulland that it is not empty. - NONJUMP_DUPLICATE_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of inward-facing pais that are duplicates
- NONJUMP_DUPLICATE_PCT - Variable in class picard.analysis.JumpingLibraryMetrics
-
The fraction of inward-facing pairs that are marked as duplicates
- NONJUMP_LIBRARY_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
-
The estimated library size for inward-facing pairs
- NONJUMP_MEAN_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
-
The mean insert size for inward-facing pairs
- NONJUMP_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of inward-facing pairs in the SAM file
- NONJUMP_STDEV_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
-
The standard deviation on the insert size for inward-facing pairs
- NonLocatableDoubleCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
A collection representing a real valued vector generated by
GermlineCNVCaller - NonLocatableDoubleCollection(File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.NonLocatableDoubleCollection
- NonNFastaSize - Class in picard.reference
-
A tool to count the number of non-N bases in a fasta file
- NonNFastaSize() - Constructor for class picard.reference.NonNFastaSize
- nonNull(T) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Checks that an Object
objectis not null and returns the same object or throws anIllegalArgumentException - nonNull(T, String) - Static method in class org.broadinstitute.hellbender.utils.Utils
- nonNull(T, Supplier<String>) - Static method in class org.broadinstitute.hellbender.utils.Utils
- NONOVERLAP - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapTargetStatus
-
Gene or transcript exists in target, however source mapping is to a different location.
- NonPF - Enum constant in enum class picard.sam.ViewSam.PfStatus
- nonRandomDownsamplingMode() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionWalker
- nonRandomDownsamplingMode() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCaller
- NONREF_FILL_VALUE - Static variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- nonRefDepth - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceResult
- nonsense - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.FunctionalClass.FunctionalType
- NONSENSE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
A premature stop codon is created by the variant.
- NONSENSE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectFunctionalClass
- NONSENSE_MEDIATED_DECAY - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- nonSkips - Variable in class picard.illumina.parser.ReadStructure
- NONSTOP - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Variant removes stop codon.
- nonStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
A constant stratifier which places all the reads into a single stratum.
- NonSymmetricalPairHMMInputScoreImputator - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
A version of the classic
StandardPairHMMInputScoreImputatorthat allows for decoupled insertion and deletion penalties for the model. - nonUniqueKmers - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
-
A set of non-unique kmers that cannot be used as merge points in the graph
- nonVariantLeftFlankRegion() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer.Result
-
Returns the trimmed out left non-variant region.
- nonVariantRightFlankRegion() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer.Result
-
Returns the trimmed out right non-variant region.
- NONZERO_FRAGMENT_LENGTH_READ_FILTER - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- NonZeroFragmentLengthReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.NonZeroFragmentLengthReadFilter
- NonZeroReferenceLengthAlignmentReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.NonZeroReferenceLengthAlignmentReadFilter
- noOutput - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- noQuantization() - Method in class org.broadinstitute.hellbender.utils.recalibration.QuantizationInfo
- NORMAL - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments.AlignmentSignatureBasicType
- NORMAL - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistributionShape
-
The insert size distribution follow a normal distribution truncated at 0.
- NORMAL_ALLELIC_COUNTS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- NORMAL_ALLELIC_COUNTS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument
- NORMAL_ALLELIC_COUNTS_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- NORMAL_ARTIFACT_LOG_10_ODDS_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- NORMAL_BAM_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- NORMAL_BAM_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- NORMAL_HET_ALLELIC_COUNTS_FILE_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.ModelSegments
- NORMAL_LOG_10_ODDS_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- NORMAL_LOG_10_ODDS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- NORMAL_P_VALUE_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- NORMAL_SAMPLE_KEY_IN_VCF_HEADER - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- NORMAL_SAMPLE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- NORMAL_SAMPLE_NAME_LIST - Static variable in class org.broadinstitute.hellbender.tools.funcotator.metadata.SamplePairExtractor
- NORMAL_SAMPLE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- NormalArtifactFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- NormalArtifactFilter(double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NormalArtifactFilter
- NormalArtifactRecord - Class in org.broadinstitute.hellbender.tools.walkers.mutect
- NormalArtifactRecord(int, int, int, int, double, String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.NormalArtifactRecord
- NormalArtifactRecord.NormalArtifactWriter - Class in org.broadinstitute.hellbender.tools.walkers.mutect
- NormalArtifactWriter(Path) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.NormalArtifactRecord.NormalArtifactWriter
- normalDistribution(double, double, double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Calculate f(x) = Normal(x | mu = mean, sigma = sd)
- normalDistributionLog10(double, double, double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Calculate f(x) = log10 ( Normal(x | mu = mean, sigma = sd) )
- normalizationVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
- normalizeAlleles(VariantContext, String, VariantContext, String, Boolean) - Static method in class picard.vcf.GenotypeConcordance
-
Gets the alleles for the truth and call genotypes.
- normalizeAlleles(List<byte[]>, List<IndexRange>, int, boolean) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Example usage: reference = GAAT, read = GAAAT (insertion of one A) and we initially consider the insertion of the A to occur before the T.
- NORMALIZED_COVERAGE - Variable in class picard.analysis.GcBiasDetailMetrics
-
The ratio of "coverage" in this GC bin vs.
- normalizeData(boolean, List<Integer>) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
-
Normalize annotations to mean 0 and standard deviation 1.
- normalizedXIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- normalizedYIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- NormalizeFasta - Class in picard.reference
-
Little program to "normalize" a fasta file to ensure that all line of sequence are the same length, and are a reasonable length!
- NormalizeFasta() - Constructor for class picard.reference.NormalizeFasta
- normalizeFromLog10ToLinearSpace(double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
normalizes the log-probability array in-place.
- normalizeFromLogToLinearSpace(double[]) - Static method in class org.broadinstitute.hellbender.utils.NaturalLogUtils
-
normalizes the log-probability array in-place.
- normalizeHistogram(Histogram<Integer>) - Static method in class picard.analysis.TheoreticalSensitivity
- normalizeLikelihoods(double, boolean) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Adjusts likelihoods so that for each unit of evidence, the best allele likelihood is 0 and caps the minimum likelihood of any allele for each unit of evidence based on the maximum alternative allele likelihood.
- normalizeLog(double[]) - Static method in class org.broadinstitute.hellbender.utils.NaturalLogUtils
-
normalizes the log-probability array in-place.
- normalizeLog(double[], boolean, boolean) - Static method in class org.broadinstitute.hellbender.utils.NaturalLogUtils
-
See #normalizeFromLog but with the additional option to use an approximation that keeps the calculation always in log-space
- normalizeLog10(double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
normalizes the log-probability array in-place.
- normalizeLog10(double[], boolean, boolean) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
See #normalizeFromLog but with the additional option to use an approximation that keeps the calculation always in log-space
- normalizeLog10DeleteMePlease(double[], boolean) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- normalizePLs(int[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- normalizeSumToOne(double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
normalizes the real-space probability array.
- normalLog10Odds - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
This is a measure of the minimum evidence to support that a variant observed in the tumor is not also present in the normal.
- normalPileupPValueThreshold - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- normalSamples - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactData
- normalSamples - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- NORMX - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- NORMY - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- noStandardModules - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- noStandardStratifications - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- NoSuitableCodecs(Path) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.NoSuitableCodecs
- NOT_ALIGNED_ERROR - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
- NOT_BEST_IN_GENOME_EVIDENCE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
a transcript is supported by evidence from same species paralogous loci.
- NOT_CLINSIG_FILTER - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsConstants
-
FILTER value applied by
FilterFuncotationsto all variants which have no clinically-significant Funcotations. - NOT_CLINSIG_FILTER_DESCRIPTION - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsConstants
-
Description for "NOT_CLINSIG" to include in VCF headers.
- NOT_DUPLICATE - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- NOT_EQUAL - Enum constant in enum class org.broadinstitute.hellbender.engine.filters.ReadTagValueFilter.Operator
- NOT_NORMALIZED_BY_KINGDOM_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- NOT_NORMALIZED_BY_KINGDOM_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- NOT_ORGANISM_SUPPORTED - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
evidence from other species was used to build model.
- NOT_PROPERLY_PAIRED - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- NOT_SECONDARY_ALIGNMENT - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- NOT_SUPPLEMENTARY_ALIGNMENT - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- NOT_SV_OR_SYMBOLIC - Static variable in class org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary
- NOTAGS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.HtsgetReader
- NotDuplicateReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.NotDuplicateReadFilter
- notJunk(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter
- notNormalizedByKingdom - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
-
Comparmentalizes the normalized abundance scores by kingdom.
- NotOpticalDuplicateReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filters out reads marked as duplicates.
- NotOpticalDuplicateReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.NotOpticalDuplicateReadFilter
- NotProperlyPairedReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.NotProperlyPairedReadFilter
- NotReported - Enum constant in enum class picard.pedigree.Sex
- NotSecondaryAlignmentReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.NotSecondaryAlignmentReadFilter
- NotSupplementaryAlignmentReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.NotSupplementaryAlignmentReadFilter
- NotSymbolicOrSVVariantFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary.NotSymbolicOrSVVariantFilter
- NoValidationCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection.NoValidationCollection
- noVariation(AssemblyRegion) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer
-
Creates a result indicating that no variation was found.
- NOVEL - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.GeneTranscriptStatus
- NOVEL_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing indels called that were not found in dbSNP
- NOVEL_INS_DEL_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The Insertion/Deletion ratio of the indel calls made at non-dbSNP sites
- NOVEL_SNPS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The number of high confidence SNPS called that were not found in dbSNP
- NOVEL_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing bi-allelic SNPS called that were not found in dbSNP
- NOVEL_TITV - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The Transition/Transversion ratio of the passing bi-allelic SNP calls made at non-dbSNP sites
- NovelAdjacencyAndAltHaplotype - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
This class represents a pair of inferred genomic locations on the reference whose novel adjacency is generated due to an SV event (in other words, a simple rearrangement between two genomic locations) that is suggested by the input
SimpleChimera, and complications as enclosed inBreakpointComplicationsin pinning down the locations to exact base pair resolution. - NovelAdjacencyAndAltHaplotype(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- NovelAdjacencyAndAltHaplotype(SimpleChimera, byte[], SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- NovelAdjacencyAndAltHaplotype(SimpleInterval, SimpleInterval, StrandSwitch, BreakpointComplications, TypeInferredFromSimpleChimera, byte[]) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- NovelAdjacencyAndAltHaplotype.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- novelSites - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap
- Novelty - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies by whether a site in in the list of known RODs (e.g., dbsnp by default)
- Novelty(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Novelty
- NP - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVSegmentVariantComposer
-
Number of points in the segment
- nProcessedLoci - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nProcessedLoci - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- nProcessedLoci - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- nQClippedBases - Variable in class org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- nRangeClippedBases - Variable in class org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- nRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- NRatioFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- NRatioFilter(double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NRatioFilter
- nReadsInBigSets - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of reads in duplicate of sizes greater than 3.
- nRecordsInMemory - Variable in class picard.annotation.SortGff
- nReferenceAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of doubletons where the two reads matched the reference.
- nReferenceAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of tripletons where the two reads matched the reference.
- nReferenceReads - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of reference alleles in the reads.
- nRefLoci - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nSamples - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- nSeqClippedBases - Variable in class org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- nSingletons - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratify by the number of Ns found in the read.
- NsInReadStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.NsInReadStratifier
- nSites - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The count of sites used.
- nSkipped - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- nSNPloci - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MetricsCollection
- nSNPs - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nSNPs - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MetricsCollection
- nSNPs - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- nSNPs - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- nSNPsPerSample - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- nSVs - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- nSVsPerSample - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- nSymbolic - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nthPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext, int) - Method in class org.broadinstitute.hellbender.engine.MultiplePassVariantWalker
-
nth pass through the variants.
- nthPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext, int) - Method in class org.broadinstitute.hellbender.engine.TwoPassVariantWalker
- nthPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext, int) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls
- nthPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext, int) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations
- nthPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext, int) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- nThreeAllelesSites - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The count of sites in which a third allele was found.
- nTi - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- nTi - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator
- nTiDerived - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator
- nTiInComp - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator
- nTotalBases - Variable in class org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- nTotalReads - Variable in class org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- nTotalReads - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The total number of reads over the het sites.
- nTv - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- nTv - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator
- nTvDerived - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator
- nTvInComp - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator
- Nucleotide - Enum Class in org.broadinstitute.hellbender.utils
-
Represents the nucleotide alphabet with support for IUPAC ambiguity codes.
- Nucleotide.Counter - Class in org.broadinstitute.hellbender.utils
-
Helper class to count the number of occurrences of each nucleotide code in a sequence.
- Null - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportDataType
-
The null type should not be used.
- NULL_NODE - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- NULL_SEQUENCE_STRING - Static variable in class org.broadinstitute.hellbender.utils.read.ReadConstants
-
Value used for String representation of a non-existent sequence
- nullStrands() - Method in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- NUM_ADAPTERS_TO_KEEP - Variable in class picard.illumina.MarkIlluminaAdapters
- NUM_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The total number of assays (SNP and indels) in the VCF
- NUM_AUTOCALL_CALLS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The number of passing autocall calls
- NUM_BASES_WITH_OVERLAPPING_READS - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
-
The number of bases for which an overlapping base from the mate read was found
- NUM_CALLS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The number of passing calls
- NUM_CHANNELS - Static variable in enum class picard.illumina.parser.IntensityChannel
- NUM_DELETED_BASES - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
-
The number of deleted bases.
- NUM_DELETIONS - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
-
The number of deletions.
- NUM_DIPLOID_DENOVO - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of diploid sites at which a potential de-novo mutation was observed (i.e.
- NUM_DISAGREES_WITH_REF_AND_MATE - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
-
The number of bases that disagree with both the reference and their mate (which agree with each other)
- NUM_DISAGREES_WITH_REFERENCE_ONLY - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
-
The number of bases that disagree with the reference, but agree with their mate
- NUM_FILTERED_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The total number of filtered assays in the VCF
- NUM_GC_BINS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
- NUM_HAPLOID_DENOVO - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of sites at which the offspring is haploid, the parent is homozygous reference and the offspring is non-reference.
- NUM_HAPLOID_OTHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of sites at which the offspring is haploid and exhibits a reference allele that is not present in the parent.
- NUM_HAPLOTYPES_TO_INJECT_FORCE_CALLING_ALLELES_INTO - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- NUM_HET - Variable in class picard.fingerprint.FingerprintMetrics
-
Number of heterozygous calls
- NUM_HOM_ALLELE1 - Variable in class picard.fingerprint.FingerprintMetrics
-
Number of major allele homozygous calls
- NUM_HOM_ALLELE2 - Variable in class picard.fingerprint.FingerprintMetrics
-
Number of minor allele homozygous calls
- NUM_HOM_ANY - Variable in class picard.fingerprint.FingerprintMetrics
-
Number of homozygous calls of either allele (might not be the sum of
FingerprintMetrics.NUM_HOM_ALLELE1andFingerprintMetrics.NUM_HOM_ALLELE1due to rounding - NUM_HOM_HET_HOM - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of sites at which one parent is homozygous, the other is heterozygous and the offspring is the alternative homozygote.
- NUM_HOMREF_HOMVAR_HOM - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of sites at which the one parent is homozygous reference, the other homozygous variant and the offspring is homozygous.
- NUM_HOMVAR_HOMVAR_HET - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of sites at which both parents are homozygous for a non-reference allele and the offspring is heterozygous.
- NUM_IN_DB_SNP - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The number of high confidence SNPs found in dbSNP
- NUM_IN_DB_SNP - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing bi-allelic SNPs found in dbSNP
- NUM_IN_DB_SNP_COMPLEX_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing complex indels found in dbSNP
- NUM_IN_DB_SNP_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing indels found in dbSNP
- NUM_IN_DB_SNP_MULTIALLELIC - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing multi-allelic SNPs found in dbSNP
- NUM_INDELS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The number of indel calls
- NUM_INSERTED_BASES - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
-
The number of inserted bases.
- NUM_INSERTIONS - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
-
The number of insertions.
- NUM_KMERS - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterConstants
- NUM_MARKERS_FILE - Variable in class picard.arrays.VcfToAdpc
- NUM_MATCHING_BASES_IN_DANGLING_END_TO_RECOVER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- NUM_N - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
The number of Ns found in this read
- NUM_NO_CALLS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The number of no-calls
- NUM_NON_FILTERED_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The total number of NON-filtered assays in the VCF
- NUM_OF_STRANDS - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
- NUM_OTHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of otherwise unclassified events.
- NUM_PROCESSORS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
- NUM_PROCESSORS - Variable in class picard.illumina.ExtractIlluminaBarcodes
- NUM_PROCESSORS - Variable in class picard.illumina.IlluminaBasecallsToFastq
- NUM_PROCESSORS - Variable in class picard.illumina.IlluminaBasecallsToSam
- NUM_PROCESSORS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- NUM_PRUNING_SAMPLES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- NUM_Q_GT_TWO - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
The number of Quality scores greater than 2 found in this read
- NUM_R1_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
The number of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand.
- NUM_R2_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand.
- NUM_REDUCERS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- NUM_REF_SAMPLES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- NUM_REF_SAMPLES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
- NUM_SAMPLES_CR_APPROX_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
- NUM_SEQUENCES - Variable in class picard.sam.CreateSequenceDictionary
- NUM_SINGLETONS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
For summary metrics, the number of variants that appear in only one sample.
- NUM_SINGLETONS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
For summary metrics, the number of variants that appear in only one sample.
- NUM_SNPS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The number of bi-allelic SNP calls
- NUM_STATES - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterConstants
- NUM_THERMAL_ADVI_ITERS - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- NUM_THERMAL_ADVI_ITERS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- NUM_THREADS - Variable in class picard.fingerprint.CrosscheckFingerprints
- NUM_THREADS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.HtsgetReader
- NUM_THREE_WAYS_DISAGREEMENT - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
-
The number of bases that disagree with both the reference and their mate (which also disagree)
- NUM_UNCERTAIN_FLOWS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- NUM_UNEXPLAINED_READS - Variable in class picard.analysis.RnaSeqMetrics
-
The fraction of reads for which the transcription strand model could not be inferred.
- NUM_VARIANT_SITES - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of biallelic, SNP sites at which all relevant samples exceeded the minimum genotype quality and depth and at least one of the samples was variant.
- NUM_ZEROED_OUT_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The total number of zeroed-out (filtered out by Illumina in chip design) assays in the VCF
- numAltAllelesThreshold - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- NUMBER_ERRORS_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- NUMBER_ERRORS_DECIMAL_PLACES - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- NUMBER_OBSERVATIONS_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- NUMBER_OF_BURN_IN_SAMPLES_ALLELE_FRACTION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- NUMBER_OF_BURN_IN_SAMPLES_COPY_RATIO_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- NUMBER_OF_CHANGEPOINTS_PENALTY_FACTOR_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- NUMBER_OF_CHUNKS_SUB_PATH - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils
- NUMBER_OF_COLUMNS_SUB_PATH - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils
- NUMBER_OF_DISCOVERED_ALLELES_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- NUMBER_OF_EIGENSAMPLES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument
- NUMBER_OF_GENOTYPE_COUNTS - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet
- NUMBER_OF_POSSIBLE_PROBS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- NUMBER_OF_ROWS_SUB_PATH - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils
- NUMBER_OF_SAMPLES_ALLELE_FRACTION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- NUMBER_OF_SAMPLES_COPY_RATIO_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- NUMBER_OF_SAMPLING - Variable in class picard.fingerprint.CalculateFingerprintMetrics
- NUMBER_OF_SMOOTHING_ITERATIONS_PER_FIT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- numberOfAlignments() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.ReadPair
- numberOfAlleles() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingData
- numberOfAlleles() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingLikelihoods
- numberOfAlleles() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix
- numberOfAlleles() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Returns number of alleles in the collection.
- numberOfAlleles() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.ActualPermutation
- numberOfAlleles() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.NonPermutation
- numberOfAlleles() - Method in interface org.broadinstitute.hellbender.utils.genotyper.AlleleList
-
Returns the number of alleles in this AlleleList.
- numberOfAlleles() - Method in class org.broadinstitute.hellbender.utils.genotyper.IndexedAlleleList
- numberOfAlleles() - Method in interface org.broadinstitute.hellbender.utils.genotyper.LikelihoodMatrix
-
Number of allele in the matrix.
- numberOfGenomes - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
- numberOfMostRepeats(int) - Method in class org.broadinstitute.hellbender.utils.pairhmm.DragstrReadSTRAnalyzer
-
Returns the number of repeat units for the period with largest count.
- numberOfPasses() - Method in class org.broadinstitute.hellbender.engine.MultiplePassVariantWalker
- numberOfPasses() - Method in class org.broadinstitute.hellbender.engine.TwoPassVariantWalker
- numberOfPasses() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls
- numberOfPasses() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
- numberOfPasses() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- numberOfRecords() - Method in class org.broadinstitute.hellbender.utils.BinaryTableWriter
- numberOfRepeats(int, int) - Method in class org.broadinstitute.hellbender.utils.pairhmm.DragstrReadSTRAnalyzer
-
Returns the maximum number of repeats for any repeat unit of a particular period size at that position.
- numberOfSamples() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingData
- numberOfSamples() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingLikelihoods
- numberOfSamples() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.HeterogeneousPloidyModel
- numberOfSamples() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.HomogeneousPloidyModel
- numberOfSamples() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Number of samples included in the likelihood collection.
- numberOfSamples() - Method in class org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList
- numberOfSamples() - Method in interface org.broadinstitute.hellbender.utils.genotyper.SampleList
-
Returns number of elements in the list.
- numberOfSpecialCovariates() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList
-
Returns 2.
- numBurnInAlleleFraction - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- numBurnInCopyRatio - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- numChangepointsPenaltyFactor - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- numCigarElements() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
The number of cigar elements in this read.
- numCigarElements() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
-
This implementation saves time by not making an unmodifiable view of the list of elements but returns the length of the list directly (or 0 if there's no cigar).
- numClusters - Variable in class picard.illumina.parser.readers.FilterFileReader
-
The number of cluster's pf values stored in this file
- numCodes - Variable in class picard.arrays.illumina.InfiniumEGTFile
- numDigits - Variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- numDimensions - Variable in class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray
- numeratorFormat - Static variable in class org.broadinstitute.hellbender.tools.SplitCRAM
- numHaplotypesToIterate - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- numHits() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
-
Note that a single alignment for each end of a read pair is counted as a single hit.
- numMates - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenAlignmentHit
- numMismatches - Variable in class org.broadinstitute.hellbender.utils.read.AlignmentUtils.MismatchCount
- numOutputReads() - Method in class picard.illumina.parser.OutputMapping
- numPartitions() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.ComplexityPartitioner
- numProcessors(int) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures how many processors this converter will use.
- numPruningSamples - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
If fewer samples than the specified number pass the minPruning threshold for a given path, that path will be eliminated from the graph.
- NUMREADS - Variable in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetrics
- NUMREADS - Variable in class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetrics
- numReducers - Variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- numRefIfMissing - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
-
When a variant is not seen in any panel, this argument controls whether to infer (and with what effective strength) that only reference alleles were observed at that site.
- numRefIfMissing - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
-
When a variant is not seen in a panel, this argument controls whether to infer (and with what effective strength) that only reference alleles were observed at that site.
- numRegularContigs - Variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
-
Number of regular i.e.
- numSamplesAlleleFraction - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- numSamplesCopyRatio - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- numSamplesFromArgument - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- numSmoothingIterationsPerFit - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- numTables() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
- NuMTFilterTool - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- NuMTFilterTool() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NuMTFilterTool
- numWindowLeadingBases() - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
-
Get the number of extra bases of context before the start of our interval, as configured by a call to
ReferenceContext.setWindow(int, int)or at construction time. - numWindowTrailingBases() - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
-
Get the number of extra bases of context after the end of our interval, as configured by a call to
ReferenceContext.setWindow(int, int)or at construction time. - nVarFamCalled - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- nVariantLoci - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- nVariants - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- nVariantsAtComp - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap
- nViolations - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
O
- O - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier.AlnModType.ModTypeString
- OA_SEPARATOR - Static variable in class org.broadinstitute.hellbender.tools.AddOriginalAlignmentTags
- OA_TAG_NAME - Static variable in class org.broadinstitute.hellbender.tools.AddOriginalAlignmentTags
- OBS_A - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The number of observations of the first, or A, allele of the SNP in the sequencing data.
- OBS_B - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The number of observations of the second, or B, allele of the SNP in the sequencing data.
- obsAllele1 - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- obsAllele2 - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- obsAlleleOther - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- observationCount() - Method in class org.broadinstitute.hellbender.utils.MathUtils.RunningAverage
- observe() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.TransitPairCount
- observe(int) - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepth
- observe(LocalAssembler.KmerAdjacency, LocalAssembler.KmerAdjacency) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- observe(LocalAssembler.KmerAdjacency, LocalAssembler.KmerAdjacency, int) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- observe(LocalAssembler.KmerAdjacency, LocalAssembler.KmerAdjacency, int) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- observe(LocalAssembler.KmerAdjacency, LocalAssembler.KmerAdjacency, int) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- OBSERVED_BASE_ERRORS - Variable in class picard.sam.markduplicates.UmiMetrics
-
Number of errors inferred by comparing the observed and inferred UMIs
- OBSERVED_GENOTYPE - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The most likely genotype given the observed evidence at the SNP locus in the sequencing data.
- OBSERVED_SAMPLE_ALIAS - Variable in class picard.fingerprint.CheckFingerprint
- OBSERVED_UMI_ENTROPY - Variable in class picard.sam.markduplicates.UmiMetrics
-
Entropy (in base 4) of the observed UMI sequences, indicating the effective number of bases in the UMIs.
- OBSERVED_UNIQUE_UMIS - Variable in class picard.sam.markduplicates.UmiMetrics
-
Number of different UMI sequences observed
- OccurrenceMatrix<R,
C> - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller -
Class to work with exclusive pairs of elements, example - pairs of alleles that do not occur in the haplotypes
- OccurrenceMatrix(Map<R, Collection<C>>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.OccurrenceMatrix
- of(boolean) - Static method in enum class org.broadinstitute.hellbender.utils.Trilean
- of(byte[], int, int, int) - Static method in class org.broadinstitute.hellbender.utils.dragstr.DragstrReferenceAnalyzer
- of(int, int, double[][], double[][], double[][]) - Static method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParams
- of(int, int, double[][], double[][], double[][], String) - Static method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParams
- of(SAMRecord) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
- of(SAMRecord) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
- of(SAMRecord) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
- of(SAMRecord) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
- of(SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.reference.AbsoluteCoordinates
- of(Locatable, ReadsDataSource, ReferenceDataSource) - Static method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- of(Allele, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.InverseAllele
- of(VariantContext) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVContext
-
Returns an instance given a plain
VariantContextinstance. - of(Path) - Static method in interface org.broadinstitute.hellbender.engine.ReferenceDataSource
-
Initialize this data source using a fasta file.
- of(Path, boolean) - Static method in interface org.broadinstitute.hellbender.engine.ReferenceDataSource
-
Initialize this data source using a fasta file.
- of(List<GATKRead>, ReferenceBases) - Static method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- of(K, V) - Static method in class org.broadinstitute.hellbender.utils.KV
- of(DragstrParams) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.DragstrPairHMMInputScoreImputator
-
Constructs an inputator given the DragstrParameter collection.
- of(GATKRead, int) - Static method in class org.broadinstitute.hellbender.utils.pairhmm.DragstrReadSTRAnalyzer
-
Creates an analyzer for a read.
- of(ReferenceBases, SAMSequenceDictionary) - Static method in interface org.broadinstitute.hellbender.engine.ReferenceDataSource
-
Initialize this data source using ReferenceBases and corresponding sequence dictionary.
- of(T, Consumer<T>) - Static method in class org.broadinstitute.hellbender.utils.AutoCloseableReference
-
Creates a new reference given the subject object an the close action.
- OFF - Enum constant in enum class org.broadinstitute.hellbender.utils.baq.BAQ.CalculationMode
- OFF_AMPLICON_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of PF_BASES_ALIGNED that mapped neither on or near an amplicon.
- OFF_BAIT_BASES - Variable in class picard.analysis.directed.HsMetrics
-
The number of PF_BASES_ALIGNED that are mapped away from any baited region.
- OFF_PROBE_BASES - Variable in class picard.analysis.directed.TargetMetrics
-
The number of PF aligned bases that mapped to neither on or near a probe.
- OFF_RAMP_FILE - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection
- OFF_RAMP_TYPE - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection
-
The following definition related to an haplotype caller feature under development (experimental), colloquially called 'ramps'.
- OffRamp - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase.Type
- OffRampBase - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
- OffRampBase(String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OffRampBase
- offRampFile - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection
- offRampType - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection
-
The following parameters related to an haplotype caller feature under development (experimental), colloquially called 'ramps'.
- offset() - Method in class org.broadinstitute.hellbender.utils.BinaryTableWriter
- offset(int, int, int) - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusUtils.BinaryTableIndex
- OFFSPRING - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The ID of the offspring within the trio.
- OFFSPRING_SEX - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The sex of the offspring.
- OjAlgoSingularValueDecomposer - Class in org.broadinstitute.hellbender.utils.svd
-
SVD using the ojAlgo library.
- OjAlgoSingularValueDecomposer() - Constructor for class org.broadinstitute.hellbender.utils.svd.OjAlgoSingularValueDecomposer
- OLD_SAMPLE_NAME - Variable in class picard.vcf.RenameSampleInVcf
- OMIT_ALLELES_IN_HDF5_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
- OMIT_MEMBERS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- OMP - Enum constant in enum class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM.Implementation
-
OpenMP multi-threaded AVX-accelerated version of PairHMM
- ON_AMPLICON_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of PF_BASES_ALIGNED that mapped to an amplified region of the genome.
- ON_AMPLICON_VS_SELECTED - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The fraction of bases mapping to regions on or near amplicons, which mapped directly to but not near amplicons, ON_AMPLICON_BASES/(NEAR_AMPLICON_BASES + ON_AMPLICON_BASES)
- ON_BAIT_BASES - Variable in class picard.analysis.directed.HsMetrics
-
The number of PF_BASES_ALIGNED that are mapped to the baited regions of the genome.
- ON_BAIT_VS_SELECTED - Variable in class picard.analysis.directed.HsMetrics
-
The fraction of bases on or near baits that are covered by baits, ON_BAIT_BASES/(ON_BAIT_BASES + NEAR_BAIT_BASES).
- ON_PROBE_BASES - Variable in class picard.analysis.directed.TargetMetrics
-
The number of PF aligned probed bases that mapped to a baited region of the genome.
- ON_PROBE_VS_SELECTED - Variable in class picard.analysis.directed.TargetMetrics
-
The fraction of on+near probe bases that are on as opposed to near, ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES).
- ON_RAMP_FILE - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection
- ON_RAMP_TYPE - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection
- ON_TARGET_BASES - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of PF aligned bases that mapped to a targeted region of the genome.
- ON_TARGET_FROM_PAIR_BASES - Variable in class picard.analysis.directed.TargetMetricsBase
-
The number of PF aligned bases that are mapped in pair to a targeted region of the genome.
- onBoundary(SVInterval) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.PartitionCrossingChecker
- ONE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.GenomicPhase
- ONE - Enum constant in enum class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert.NumPrimaryAlignmentState
- ONE_MISMATCH_MATCHES - Variable in class picard.illumina.BarcodeMetric
-
The number of all reads matching this barcode that matched with 1 error or no-call.
- oneBasePaddedContextStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into the one base context of the base, which includes one read-base on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencer
- OneBPIndel - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies the eval RODs into sites where the indel is 1 bp in length and those where the event is 2+.
- OneBPIndel(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.OneBPIndel
- oneShotAnnotationLogger - Variable in class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
- oneShotHeaderLineLogger - Variable in class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
- oneShotLogger - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
- OneShotLogger - Class in org.broadinstitute.hellbender.utils.logging
-
A logger wrapper class which only outputs the first warning provided to it
- OneShotLogger(Class<?>) - Constructor for class org.broadinstitute.hellbender.utils.logging.OneShotLogger
- OneShotLogger(Logger) - Constructor for class org.broadinstitute.hellbender.utils.logging.OneShotLogger
- onIntervalEnd(Locatable) - Method in class org.broadinstitute.hellbender.engine.LocusWalkerByInterval
-
Perform any closing operations needed once the provided getIntervalObjectsToQueryOver() interval has been passed by the tool NOTE: This will only ever be called on an interval that has been covered by
LocusWalkerByInterval.onIntervalStart(Locatable) - onIntervalEnd(Locatable) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage
-
When this method is called, we expect at some point in the past onIntervalStart() was called on the same Locatable object and that we have been continuously tracking and adding per-base information for each base in the pileup that overlaps those objects.
- onIntervalStart(Locatable) - Method in class org.broadinstitute.hellbender.engine.LocusWalkerByInterval
-
Perform any initialization needed the first time a provided interval is seen.
- onIntervalStart(Locatable) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage
-
Ensure that we are tracking the newly provided interval with per-locus data
- onLeadingBoundary(SVInterval) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.PartitionCrossingChecker
- ONLY_OUTPUT_CALLS_STARTING_IN_INTERVALS_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- onlyInsOrDel - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- onlyProducedIGRs() - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine
-
Returns whether this
FuncotatorEnginehas only produced annotations on variants that have been labeled by theGencodeFuncotationFactoryasGencodeFuncotation.VariantClassification.IGR. - ONP - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantType
- OnRamp - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase.Type
- OnRampBase - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
- OnRampBase(String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OnRampBase
- OnRampBase.CSVReader - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
- onRampFile - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection
- onRampType - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection
- onSameContig(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- onShutdown() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
-
Perform cleanup after doWork() is finished.
- onShutdown() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- onShutdown() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionWalker
-
Shutdown data sources.
- onShutdown() - Method in class org.broadinstitute.hellbender.engine.FeatureWalker
-
Close the reads and reference data sources.
- onShutdown() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Close all data sources on shutdown.
- onShutdown() - Method in class org.broadinstitute.hellbender.engine.IntervalWalker
-
Close data sources.
- onShutdown() - Method in class org.broadinstitute.hellbender.engine.LocusWalker
-
Marked final so that tool authors don't override it.
- onShutdown() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalker
-
Close all data sources.
- onShutdown() - Method in class org.broadinstitute.hellbender.engine.ReadWalker
-
Shutdown data sources.
- onShutdown() - Method in class org.broadinstitute.hellbender.engine.ReferenceWalker
-
Shutdown data sources.
- onShutdown() - Method in class org.broadinstitute.hellbender.engine.VariantLocusWalker
-
Close all data sources.
- onShutdown() - Method in class org.broadinstitute.hellbender.engine.VariantWalker
-
Close all data sources.
- onShutdown() - Method in class org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFile
- onShutdown() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- onShutdown() - Method in class org.broadinstitute.hellbender.tools.HtsgetReader
- onShutdown() - Method in class org.broadinstitute.hellbender.tools.PrintBGZFBlockInformation
- onStartup() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
-
Perform initialization/setup after command-line argument parsing but before doWork() is invoked.
- onStartup() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- onStartup() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionWalker
-
Initialize data sources for traversal.
- onStartup() - Method in class org.broadinstitute.hellbender.engine.FeatureWalker
-
Set the intervals for traversal in the driving features.
- onStartup() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Initialize our data sources, make sure that all tool requirements for input data have been satisfied and start the progress meter.
- onStartup() - Method in class org.broadinstitute.hellbender.engine.IntervalWalker
-
Initialize data sources.
- onStartup() - Method in class org.broadinstitute.hellbender.engine.LocusWalker
-
Marked final so that tool authors don't override it.
- onStartup() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker
-
Operations performed just prior to the start of traversal.
- onStartup() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalker
-
Marked final so that tool authors don't override it.
- onStartup() - Method in class org.broadinstitute.hellbender.engine.ReadWalker
-
Initialize data sources for traversal.
- onStartup() - Method in class org.broadinstitute.hellbender.engine.ReferenceWalker
-
Initialize data sources for traversal.
- onStartup() - Method in class org.broadinstitute.hellbender.engine.VariantLocusWalker
-
Marked final so that tool authors don't override it.
- onStartup() - Method in class org.broadinstitute.hellbender.engine.VariantWalker
-
Marked final so that tool authors don't override it.
- onStartup() - Method in class org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy
- onStartup() - Method in class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller
- onStartup() - Method in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- onStartup() - Method in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- onStartup() - Method in class org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFile
- onStartup() - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader
- onStartup() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
-
Before traversal starts, create the feature readers for all the input GVCFs, create the merged header and initialize the interval
- onStartup() - Method in class org.broadinstitute.hellbender.tools.HtsgetReader
- onStartup() - Method in class org.broadinstitute.hellbender.tools.PrintBGZFBlockInformation
- onStartup() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.SortSamSpark
- onStartup() - Method in class org.broadinstitute.hellbender.tools.SplitCRAM
- onStartup() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.GatherPileupSummaries
- onStartup() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNVariantTrain
- onStartup() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNVariantWriteTensors
- onTrailingBoundary(SVInterval) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.PartitionCrossingChecker
- onTraversalStart() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Operations performed just prior to the start of traversal.
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.AddOriginalAlignmentTags
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.AnalyzeSaturationMutagenesis
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.CalculateAverageCombinedAnnotations
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.ClipReads
-
The initialize function.
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervals
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCounts
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
-
Performs various validations on input arguments.
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervals
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalker
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleFeatureWalker
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalker
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleLocusWalker
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.examples.ExamplePartialReadWalker
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.examples.ExamplePostTraversalPythonExecutor
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReference
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariants
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleStreamingPythonExecutor
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalker
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.FixMisencodedBaseQualityReads
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotateSegments
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.funcotator.Funcotator
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
-
Before traversal, fix configuration parameters and initialize GenomicsDB.
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.GetSampleName
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.LeftAlignIndels
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.PrintDistantMates
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.PrintReads
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.reference.CheckReferenceCompatibility
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.reference.CompareReferences
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.SplitReads
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.StructuralVariantDiscoverer
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.sv.CondenseDepthEvidence
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.sv.PrintReadCounts
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.sv.PrintSVEvidence
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAF
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
-
Prepare the output file and the list of available features.
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator
-
Parse the -cov arguments and create a list of covariates to be used here Based on the covariates' estimates for initial capacity allocate the data hashmap
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSet
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyper
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCaller
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.MethylationTypeCaller
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MTLowHeteroplasmyFilterTool
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NuMTFilterTool
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactData
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.CheckPileup
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.Pileup
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.PostProcessReadsForRSEM
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.TransferReadTags
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.ReadAnonymizer
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2Counts
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.RevertBaseQualityScores
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVConcordance
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.UnmarkDuplicates
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithBamDepth
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithExpectedAlleleFraction
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.CalculateMixingFractions
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.CountFalsePositives
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.RemoveNearbyIndels
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.AlleleFrequencyQC
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
-
Set up the VCF writer, the sample expressions and regexs, filters inputs, and the JEXL matcher
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionary
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTable
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSR
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.FilterVariantTranches
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
- onTraversalStart() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal).
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.AnalyzeSaturationMutagenesis
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.ClipReads
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervals
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCounts
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervals
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.CountBases
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.CountReads
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.examples.ExamplePostTraversalPythonExecutor
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalker
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleStreamingPythonExecutor
-
On traversal success, write the remaining batch.
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.FlagStat
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotateSegments
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.funcotator.Funcotator
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.StructuralVariantDiscoverer
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.sv.CondenseDepthEvidence
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.sv.PrintReadCounts
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.sv.PrintSVEvidence
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAF
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSet
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.CountVariants
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage
-
When we finish traversal we should have the following held in state: 1.
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactData
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.PairWalker
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.CheckPileup
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.PostProcessReadsForRSEM
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.TransferReadTags
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2Counts
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVConcordance
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.CalculateMixingFractions
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.CountFalsePositives
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.RemoveNearbyIndels
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.AlleleFrequencyQC
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
-
Print out message of how many variants were realigned
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
-
write out all remaining pending variants
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- onTraversalSuccess() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator
- open - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
-
Is this iterator currently open or closed? Closed iterators can be reused.
- open(GATKPath) - Static method in class org.broadinstitute.hellbender.utils.dragstr.STRTableFile
-
Instantiates an STR table given the location of the file it is stored in.
- openAckFIFOForRead() - Method in class org.broadinstitute.hellbender.utils.runtime.StreamingProcessController
-
Open a stream on the ack FIFO for reading.
- openFile(String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Open a file for reading regardless of whether it's on GCS, HDFS or local disk.
- openInputs(boolean) - Method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
Since this may read its inputs more than once this method does all the opening and checking of the inputs.
- OPT_BUILD_DIR - Static variable in class org.broadinstitute.hellbender.utils.help.GATKWDLDoclet
- OPTICAL_DUPLICATE_MARKER - Static variable in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- OPTICAL_DUPLICATE_PIXEL_DISTANCE - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.OpticalDuplicatesArgumentCollection
- OPTICAL_DUPLICATE_PIXEL_DISTANCE - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- OPTICAL_DUPLICATE_PIXEL_DISTANCE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.OpticalDuplicatesArgumentCollection
- OPTICAL_DUPLICATE_TOTAL_ATTRIBUTE_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils
- opticalDuplicateFinder - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- OpticalDuplicateFinder - Class in picard.sam.markduplicates.util
-
Contains methods for finding optical/co-localized/sequencing duplicates.
- OpticalDuplicateFinder() - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
-
Uses the default duplicate distance
OpticalDuplicateFinder.DEFAULT_OPTICAL_DUPLICATE_DISTANCE(100) and the default read name regexReadNameParser.DEFAULT_READ_NAME_REGEX. - OpticalDuplicateFinder(String, int, long, Log) - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
- OpticalDuplicateFinder(String, int, Log) - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
- opticalDuplicateIndexes - Variable in class picard.sam.markduplicates.MarkDuplicates
- opticalDuplicatePixelDistance - Variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
- opticalDuplicatesArgumentCollection - Variable in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- OpticalDuplicatesArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
An argument collection for use with tools that mark optical duplicates.
- OpticalDuplicatesArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.OpticalDuplicatesArgumentCollection
- OpticalOnly - Enum constant in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
- OPTIMAL_F_SCORE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ThresholdCalculator.Strategy
- OPTIMAL_GVCF_INDEX_BIN_SIZE - Static variable in class org.broadinstitute.hellbender.tools.IndexFeatureFile
- OptimizationUtils - Class in org.broadinstitute.hellbender.utils
-
Created by davidben on 4/27/16.
- optimumHashSize(int) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Calculates the optimum initial size for a hash table given the maximum number of elements it will need to hold.
- OptionalFeatureInputArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
An argument collection for use with tools that accept zero or more input files containing Feature records (eg., BED files, hapmap files, etc.).
- OptionalFeatureInputArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalFeatureInputArgumentCollection
- OptionalField(String, T) - Constructor for class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.OptionalField
- optionalFields - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
-
Optional GENCODE GTF Fields.
- OptionalIntervalArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
An interval argument class that allows -L to be specified but does not require it.
- OptionalIntervalArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalIntervalArgumentCollection
- OptionalReadInputArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
An argument collection for use with tools that accept zero or more input files containing reads (eg., BAM/SAM/CRAM files).
- OptionalReadInputArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalReadInputArgumentCollection
- OptionalReferenceArgumentCollection - Class in picard.cmdline.argumentcollections
-
Picard default argument collection for an optional reference.
- OptionalReferenceArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection
- OptionalReferenceInputArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
An argument collection for use with tools that optionally accept a reference file as input.
- OptionalReferenceInputArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalReferenceInputArgumentCollection
- OptionalTextOutputArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
An ArgumentCollection with an optional output argument, and utility methods for printing String output to it To use this class add an @ArgumentCollection variable to your tool like so:
- OptionalTextOutputArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalTextOutputArgumentCollection
- OptionalVariantInputArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
An argument collection for use with tools that accept zero or more input files containing VariantContext records (eg., VCF files).
- OptionalVariantInputArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalVariantInputArgumentCollection
- or(CountingReadFilter) - Method in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter
-
Specialization of
Predicate.or(Predicate)so that CountingReadFilter ored with other CountingReadFilter produce a CountingReadFilter - or(CountingVariantFilter) - Method in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter
-
Specialization of
Predicate.or(Predicate)so that CountingVariantFilter ored with other CountingVariantFilter produce a CountingVariantFilter - or(ReadFilter) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilter
-
Specialization of
Predicate.or(Predicate)so that ReadFilters or'ed with other ReadFilters produce a ReadFilter - or(VariantFilter) - Method in interface org.broadinstitute.hellbender.engine.filters.VariantFilter
- orderAndValidateAnnotations(GATKReportTable, List<String>) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator
-
Order and validate annotations according to the annotations in the serialized model Annotations on the command line must be the same as those in the model report or this will throw an exception.
- org.broadinstitute.hellbender - package org.broadinstitute.hellbender
- org.broadinstitute.hellbender.cmdline - package org.broadinstitute.hellbender.cmdline
- org.broadinstitute.hellbender.cmdline.argumentcollections - package org.broadinstitute.hellbender.cmdline.argumentcollections
- org.broadinstitute.hellbender.cmdline.GATKPlugin - package org.broadinstitute.hellbender.cmdline.GATKPlugin
- org.broadinstitute.hellbender.cmdline.programgroups - package org.broadinstitute.hellbender.cmdline.programgroups
- org.broadinstitute.hellbender.engine - package org.broadinstitute.hellbender.engine
- org.broadinstitute.hellbender.engine.filters - package org.broadinstitute.hellbender.engine.filters
- org.broadinstitute.hellbender.engine.filters.flow - package org.broadinstitute.hellbender.engine.filters.flow
- org.broadinstitute.hellbender.engine.spark - package org.broadinstitute.hellbender.engine.spark
- org.broadinstitute.hellbender.engine.spark.datasources - package org.broadinstitute.hellbender.engine.spark.datasources
- org.broadinstitute.hellbender.exceptions - package org.broadinstitute.hellbender.exceptions
- org.broadinstitute.hellbender.metrics - package org.broadinstitute.hellbender.metrics
- org.broadinstitute.hellbender.metrics.analysis - package org.broadinstitute.hellbender.metrics.analysis
- org.broadinstitute.hellbender.testutils - package org.broadinstitute.hellbender.testutils
- org.broadinstitute.hellbender.tools - package org.broadinstitute.hellbender.tools
- org.broadinstitute.hellbender.tools.copynumber - package org.broadinstitute.hellbender.tools.copynumber
- org.broadinstitute.hellbender.tools.copynumber.arguments - package org.broadinstitute.hellbender.tools.copynumber.arguments
- org.broadinstitute.hellbender.tools.copynumber.caller - package org.broadinstitute.hellbender.tools.copynumber.caller
- org.broadinstitute.hellbender.tools.copynumber.datacollection - package org.broadinstitute.hellbender.tools.copynumber.datacollection
- org.broadinstitute.hellbender.tools.copynumber.denoising - package org.broadinstitute.hellbender.tools.copynumber.denoising
- org.broadinstitute.hellbender.tools.copynumber.formats - package org.broadinstitute.hellbender.tools.copynumber.formats
- org.broadinstitute.hellbender.tools.copynumber.formats.collections - package org.broadinstitute.hellbender.tools.copynumber.formats.collections
- org.broadinstitute.hellbender.tools.copynumber.formats.metadata - package org.broadinstitute.hellbender.tools.copynumber.formats.metadata
- org.broadinstitute.hellbender.tools.copynumber.formats.records - package org.broadinstitute.hellbender.tools.copynumber.formats.records
- org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation - package org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation
- org.broadinstitute.hellbender.tools.copynumber.gcnv - package org.broadinstitute.hellbender.tools.copynumber.gcnv
- org.broadinstitute.hellbender.tools.copynumber.models - package org.broadinstitute.hellbender.tools.copynumber.models
- org.broadinstitute.hellbender.tools.copynumber.plotting - package org.broadinstitute.hellbender.tools.copynumber.plotting
- org.broadinstitute.hellbender.tools.copynumber.segmentation - package org.broadinstitute.hellbender.tools.copynumber.segmentation
- org.broadinstitute.hellbender.tools.copynumber.utils - package org.broadinstitute.hellbender.tools.copynumber.utils
- org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval - package org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
- org.broadinstitute.hellbender.tools.copynumber.utils.genotyping - package org.broadinstitute.hellbender.tools.copynumber.utils.genotyping
- org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging - package org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging
- org.broadinstitute.hellbender.tools.copynumber.utils.optimization - package org.broadinstitute.hellbender.tools.copynumber.utils.optimization
- org.broadinstitute.hellbender.tools.copynumber.utils.segmentation - package org.broadinstitute.hellbender.tools.copynumber.utils.segmentation
- org.broadinstitute.hellbender.tools.dragstr - package org.broadinstitute.hellbender.tools.dragstr
- org.broadinstitute.hellbender.tools.examples - package org.broadinstitute.hellbender.tools.examples
- org.broadinstitute.hellbender.tools.examples.metrics.multi - package org.broadinstitute.hellbender.tools.examples.metrics.multi
- org.broadinstitute.hellbender.tools.examples.metrics.single - package org.broadinstitute.hellbender.tools.examples.metrics.single
- org.broadinstitute.hellbender.tools.funcotator - package org.broadinstitute.hellbender.tools.funcotator
- org.broadinstitute.hellbender.tools.funcotator.compositeoutput - package org.broadinstitute.hellbender.tools.funcotator.compositeoutput
- org.broadinstitute.hellbender.tools.funcotator.dataSources - package org.broadinstitute.hellbender.tools.funcotator.dataSources
- org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic - package org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic
- org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode - package org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode
- org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment - package org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment
- org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf - package org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf
- org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv - package org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv
- org.broadinstitute.hellbender.tools.funcotator.filtrationRules - package org.broadinstitute.hellbender.tools.funcotator.filtrationRules
- org.broadinstitute.hellbender.tools.funcotator.genelistoutput - package org.broadinstitute.hellbender.tools.funcotator.genelistoutput
- org.broadinstitute.hellbender.tools.funcotator.mafOutput - package org.broadinstitute.hellbender.tools.funcotator.mafOutput
- org.broadinstitute.hellbender.tools.funcotator.metadata - package org.broadinstitute.hellbender.tools.funcotator.metadata
- org.broadinstitute.hellbender.tools.funcotator.simpletsvoutput - package org.broadinstitute.hellbender.tools.funcotator.simpletsvoutput
- org.broadinstitute.hellbender.tools.funcotator.vcfOutput - package org.broadinstitute.hellbender.tools.funcotator.vcfOutput
- org.broadinstitute.hellbender.tools.genomicsdb - package org.broadinstitute.hellbender.tools.genomicsdb
- org.broadinstitute.hellbender.tools.htsgetreader - package org.broadinstitute.hellbender.tools.htsgetreader
- org.broadinstitute.hellbender.tools.readersplitters - package org.broadinstitute.hellbender.tools.readersplitters
- org.broadinstitute.hellbender.tools.reference - package org.broadinstitute.hellbender.tools.reference
- org.broadinstitute.hellbender.tools.spark - package org.broadinstitute.hellbender.tools.spark
- org.broadinstitute.hellbender.tools.spark.bwa - package org.broadinstitute.hellbender.tools.spark.bwa
- org.broadinstitute.hellbender.tools.spark.pathseq - package org.broadinstitute.hellbender.tools.spark.pathseq
- org.broadinstitute.hellbender.tools.spark.pathseq.loggers - package org.broadinstitute.hellbender.tools.spark.pathseq.loggers
- org.broadinstitute.hellbender.tools.spark.pipelines - package org.broadinstitute.hellbender.tools.spark.pipelines
- org.broadinstitute.hellbender.tools.spark.pipelines.metrics - package org.broadinstitute.hellbender.tools.spark.pipelines.metrics
- org.broadinstitute.hellbender.tools.spark.sv - package org.broadinstitute.hellbender.tools.spark.sv
- org.broadinstitute.hellbender.tools.spark.sv.discovery - package org.broadinstitute.hellbender.tools.spark.sv.discovery
- org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment - package org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference - package org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- org.broadinstitute.hellbender.tools.spark.sv.evidence - package org.broadinstitute.hellbender.tools.spark.sv.evidence
- org.broadinstitute.hellbender.tools.spark.sv.utils - package org.broadinstitute.hellbender.tools.spark.sv.utils
- org.broadinstitute.hellbender.tools.spark.transforms - package org.broadinstitute.hellbender.tools.spark.transforms
- org.broadinstitute.hellbender.tools.spark.transforms.markduplicates - package org.broadinstitute.hellbender.tools.spark.transforms.markduplicates
- org.broadinstitute.hellbender.tools.spark.utils - package org.broadinstitute.hellbender.tools.spark.utils
- org.broadinstitute.hellbender.tools.spark.validation - package org.broadinstitute.hellbender.tools.spark.validation
- org.broadinstitute.hellbender.tools.sv - package org.broadinstitute.hellbender.tools.sv
- org.broadinstitute.hellbender.tools.sv.cluster - package org.broadinstitute.hellbender.tools.sv.cluster
- org.broadinstitute.hellbender.tools.sv.concordance - package org.broadinstitute.hellbender.tools.sv.concordance
- org.broadinstitute.hellbender.tools.validation - package org.broadinstitute.hellbender.tools.validation
- org.broadinstitute.hellbender.tools.walkers - package org.broadinstitute.hellbender.tools.walkers
- org.broadinstitute.hellbender.tools.walkers.annotator - package org.broadinstitute.hellbender.tools.walkers.annotator
- org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific - package org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
- org.broadinstitute.hellbender.tools.walkers.annotator.flow - package org.broadinstitute.hellbender.tools.walkers.annotator.flow
- org.broadinstitute.hellbender.tools.walkers.bqsr - package org.broadinstitute.hellbender.tools.walkers.bqsr
- org.broadinstitute.hellbender.tools.walkers.consensus - package org.broadinstitute.hellbender.tools.walkers.consensus
- org.broadinstitute.hellbender.tools.walkers.contamination - package org.broadinstitute.hellbender.tools.walkers.contamination
- org.broadinstitute.hellbender.tools.walkers.coverage - package org.broadinstitute.hellbender.tools.walkers.coverage
- org.broadinstitute.hellbender.tools.walkers.fasta - package org.broadinstitute.hellbender.tools.walkers.fasta
- org.broadinstitute.hellbender.tools.walkers.featuremapping - package org.broadinstitute.hellbender.tools.walkers.featuremapping
- org.broadinstitute.hellbender.tools.walkers.filters - package org.broadinstitute.hellbender.tools.walkers.filters
- org.broadinstitute.hellbender.tools.walkers.genotyper - package org.broadinstitute.hellbender.tools.walkers.genotyper
- org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc - package org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
- org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper - package org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper
- org.broadinstitute.hellbender.tools.walkers.groundtruth - package org.broadinstitute.hellbender.tools.walkers.groundtruth
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller - package org.broadinstitute.hellbender.tools.walkers.haplotypecaller
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs - package org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps - package org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading - package org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
- org.broadinstitute.hellbender.tools.walkers.mutect - package org.broadinstitute.hellbender.tools.walkers.mutect
- org.broadinstitute.hellbender.tools.walkers.mutect.clustering - package org.broadinstitute.hellbender.tools.walkers.mutect.clustering
- org.broadinstitute.hellbender.tools.walkers.mutect.filtering - package org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- org.broadinstitute.hellbender.tools.walkers.qc - package org.broadinstitute.hellbender.tools.walkers.qc
- org.broadinstitute.hellbender.tools.walkers.readorientation - package org.broadinstitute.hellbender.tools.walkers.readorientation
- org.broadinstitute.hellbender.tools.walkers.realignmentfilter - package org.broadinstitute.hellbender.tools.walkers.realignmentfilter
- org.broadinstitute.hellbender.tools.walkers.rnaseq - package org.broadinstitute.hellbender.tools.walkers.rnaseq
- org.broadinstitute.hellbender.tools.walkers.sv - package org.broadinstitute.hellbender.tools.walkers.sv
- org.broadinstitute.hellbender.tools.walkers.validation - package org.broadinstitute.hellbender.tools.walkers.validation
- org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup - package org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
- org.broadinstitute.hellbender.tools.walkers.varianteval - package org.broadinstitute.hellbender.tools.walkers.varianteval
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators - package org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications - package org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager - package org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager
- org.broadinstitute.hellbender.tools.walkers.varianteval.util - package org.broadinstitute.hellbender.tools.walkers.varianteval.util
- org.broadinstitute.hellbender.tools.walkers.variantrecalling - package org.broadinstitute.hellbender.tools.walkers.variantrecalling
- org.broadinstitute.hellbender.tools.walkers.variantutils - package org.broadinstitute.hellbender.tools.walkers.variantutils
- org.broadinstitute.hellbender.tools.walkers.vqsr - package org.broadinstitute.hellbender.tools.walkers.vqsr
- org.broadinstitute.hellbender.tools.walkers.vqsr.scalable - package org.broadinstitute.hellbender.tools.walkers.vqsr.scalable
- org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data - package org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data
- org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling - package org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling
- org.broadinstitute.hellbender.transformers - package org.broadinstitute.hellbender.transformers
- org.broadinstitute.hellbender.utils - package org.broadinstitute.hellbender.utils
- org.broadinstitute.hellbender.utils.activityprofile - package org.broadinstitute.hellbender.utils.activityprofile
- org.broadinstitute.hellbender.utils.alignment - package org.broadinstitute.hellbender.utils.alignment
- org.broadinstitute.hellbender.utils.baq - package org.broadinstitute.hellbender.utils.baq
- org.broadinstitute.hellbender.utils.bigquery - package org.broadinstitute.hellbender.utils.bigquery
- org.broadinstitute.hellbender.utils.bwa - package org.broadinstitute.hellbender.utils.bwa
- org.broadinstitute.hellbender.utils.clipping - package org.broadinstitute.hellbender.utils.clipping
- org.broadinstitute.hellbender.utils.clustering - package org.broadinstitute.hellbender.utils.clustering
- org.broadinstitute.hellbender.utils.codecs - package org.broadinstitute.hellbender.utils.codecs
- org.broadinstitute.hellbender.utils.codecs.copynumber - package org.broadinstitute.hellbender.utils.codecs.copynumber
- org.broadinstitute.hellbender.utils.codecs.gtf - package org.broadinstitute.hellbender.utils.codecs.gtf
- org.broadinstitute.hellbender.utils.codecs.refseq - package org.broadinstitute.hellbender.utils.codecs.refseq
- org.broadinstitute.hellbender.utils.codecs.sampileup - package org.broadinstitute.hellbender.utils.codecs.sampileup
- org.broadinstitute.hellbender.utils.codecs.table - package org.broadinstitute.hellbender.utils.codecs.table
- org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable - package org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable
- org.broadinstitute.hellbender.utils.collections - package org.broadinstitute.hellbender.utils.collections
- org.broadinstitute.hellbender.utils.config - package org.broadinstitute.hellbender.utils.config
- org.broadinstitute.hellbender.utils.downsampling - package org.broadinstitute.hellbender.utils.downsampling
- org.broadinstitute.hellbender.utils.dragstr - package org.broadinstitute.hellbender.utils.dragstr
- org.broadinstitute.hellbender.utils.fasta - package org.broadinstitute.hellbender.utils.fasta
- org.broadinstitute.hellbender.utils.fragments - package org.broadinstitute.hellbender.utils.fragments
- org.broadinstitute.hellbender.utils.functional - package org.broadinstitute.hellbender.utils.functional
- org.broadinstitute.hellbender.utils.gcs - package org.broadinstitute.hellbender.utils.gcs
- org.broadinstitute.hellbender.utils.genotyper - package org.broadinstitute.hellbender.utils.genotyper
- org.broadinstitute.hellbender.utils.haplotype - package org.broadinstitute.hellbender.utils.haplotype
- org.broadinstitute.hellbender.utils.help - package org.broadinstitute.hellbender.utils.help
- org.broadinstitute.hellbender.utils.illumina - package org.broadinstitute.hellbender.utils.illumina
- org.broadinstitute.hellbender.utils.io - package org.broadinstitute.hellbender.utils.io
- org.broadinstitute.hellbender.utils.iterators - package org.broadinstitute.hellbender.utils.iterators
- org.broadinstitute.hellbender.utils.locusiterator - package org.broadinstitute.hellbender.utils.locusiterator
- org.broadinstitute.hellbender.utils.logging - package org.broadinstitute.hellbender.utils.logging
- org.broadinstitute.hellbender.utils.mcmc - package org.broadinstitute.hellbender.utils.mcmc
- org.broadinstitute.hellbender.utils.nio - package org.broadinstitute.hellbender.utils.nio
- org.broadinstitute.hellbender.utils.pairhmm - package org.broadinstitute.hellbender.utils.pairhmm
- org.broadinstitute.hellbender.utils.param - package org.broadinstitute.hellbender.utils.param
- org.broadinstitute.hellbender.utils.pileup - package org.broadinstitute.hellbender.utils.pileup
- org.broadinstitute.hellbender.utils.python - package org.broadinstitute.hellbender.utils.python
- org.broadinstitute.hellbender.utils.R - package org.broadinstitute.hellbender.utils.R
- org.broadinstitute.hellbender.utils.read - package org.broadinstitute.hellbender.utils.read
- org.broadinstitute.hellbender.utils.read.markduplicates - package org.broadinstitute.hellbender.utils.read.markduplicates
- org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords - package org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
- org.broadinstitute.hellbender.utils.read.mergealignment - package org.broadinstitute.hellbender.utils.read.mergealignment
- org.broadinstitute.hellbender.utils.recalibration - package org.broadinstitute.hellbender.utils.recalibration
- org.broadinstitute.hellbender.utils.recalibration.covariates - package org.broadinstitute.hellbender.utils.recalibration.covariates
- org.broadinstitute.hellbender.utils.reference - package org.broadinstitute.hellbender.utils.reference
- org.broadinstitute.hellbender.utils.report - package org.broadinstitute.hellbender.utils.report
- org.broadinstitute.hellbender.utils.runtime - package org.broadinstitute.hellbender.utils.runtime
- org.broadinstitute.hellbender.utils.samples - package org.broadinstitute.hellbender.utils.samples
- org.broadinstitute.hellbender.utils.smithwaterman - package org.broadinstitute.hellbender.utils.smithwaterman
- org.broadinstitute.hellbender.utils.spark - package org.broadinstitute.hellbender.utils.spark
- org.broadinstitute.hellbender.utils.svd - package org.broadinstitute.hellbender.utils.svd
- org.broadinstitute.hellbender.utils.text - package org.broadinstitute.hellbender.utils.text
- org.broadinstitute.hellbender.utils.tsv - package org.broadinstitute.hellbender.utils.tsv
-
Utility classes to read and write tab separated value (tsv) files.
- org.broadinstitute.hellbender.utils.variant - package org.broadinstitute.hellbender.utils.variant
- org.broadinstitute.hellbender.utils.variant.writers - package org.broadinstitute.hellbender.utils.variant.writers
- orientation - Variable in class picard.sam.markduplicates.util.ReadEnds
- OrientationBiasReadCounts - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Count of read pairs in the F1R2 and F2R1 configurations supporting the reference and alternate alleles
- OrientationBiasReadCounts() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.OrientationBiasReadCounts
- orientationForOpticalDuplicates - Variable in class picard.sam.markduplicates.util.ReadEnds
-
For optical duplicate detection the orientation matters regard to 1st or 2nd end of a mate
- ORIGINAL - Enum constant in enum class org.broadinstitute.hellbender.utils.pairhmm.PairHMM.Implementation
- ORIGINAL_AC_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- ORIGINAL_AF_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- ORIGINAL_ALLELES - Static variable in class picard.vcf.LiftoverVcf
-
Attribute used to store the list of original alleles (including REF), in the original order prior to liftover.
- ORIGINAL_AN_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- ORIGINAL_BASE_QUALITIES_TAG - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- ORIGINAL_CONTIG - Static variable in class picard.vcf.LiftoverVcf
-
Attribute used to store the name of the source contig/chromosome prior to liftover.
- ORIGINAL_CONTIG_MISMATCH_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- ORIGINAL_DEFAULT - Static variable in class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAlignmentConstants
-
ORIGINAL_DEFAULTis only used in test code. - ORIGINAL_DP_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- ORIGINAL_SOFTCLIP_END_TAG - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
- ORIGINAL_SOFTCLIP_START_TAG - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
- ORIGINAL_START - Static variable in class picard.vcf.LiftoverVcf
-
Attribute used to store the position of the variant on the source contig prior to liftover.
- ORIGINAL_VCF - Variable in class picard.arrays.MergePedIntoVcf
- OriginalAlignment - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Original Alignment annotation counts the number of alt reads where the original alignment contig doesn't match the current alignment contig
- OriginalAlignment() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.OriginalAlignment
- originalRegion - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer.Result
-
Holds the input active region.
- ORPHAN - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
protein-coding locus with no paralogues or orthologs.
- OTHER - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.Affection
-
An "other" trait: value of the trait is stored elsewhere and is an arbitrary string
- OTHER - Enum constant in enum class org.broadinstitute.hellbender.utils.SequencerFlowClass
- OTHER_TRANSCRIPT_DELIMITER - Static variable in class org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer
-
The delimiter for the `Other Transcript` field within the Funcotation annotation in the VCF.
- OTHER_TRANSCRIPTS_INFO_SEP - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
- OtherProgramGroup - Class in picard.cmdline.programgroups
-
Miscellaneous tools, e.g.
- OtherProgramGroup() - Constructor for class picard.cmdline.programgroups.OtherProgramGroup
- out - Variable in class org.broadinstitute.hellbender.tools.CountBases
- out - Variable in class org.broadinstitute.hellbender.tools.CountReads
- out - Variable in class org.broadinstitute.hellbender.tools.FlagStat
- out - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.CountBasesSpark
- out - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark
- out - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.CountVariantsSpark
- out - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.FlagStatSpark
- out - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectBaseDistributionByCycleSpark
- out - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MeanQualityByCycleSpark
- out - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityScoreDistributionSpark
- out - Variable in class org.broadinstitute.hellbender.tools.walkers.CountVariants
- out - Variable in class org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference
- out - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- out - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
- out - Variable in class picard.sam.FixMateInformation
- out - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- out - Variable in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- OUT_OF_ORDER - Enum constant in enum class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.SequenceDictionaryCompatibility
- OUT_PREFIX - Variable in class picard.sam.SplitSamByNumberOfReads
- outFile - Variable in class org.broadinstitute.hellbender.tools.walkers.qc.CheckPileup
- outFile - Variable in class org.broadinstitute.hellbender.tools.walkers.qc.Pileup
- outFile - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval
- outFile - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
-
Output file to which to write left aligned variants
- outFile - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionary
- outgoingEdgeOf(V) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Get the outgoing edge of v.
- outgoingVerticesOf(V) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Get the set of vertices connected by outgoing edges of V NOTE: We return a LinkedHashSet here in order to preserve the determinism in the output order of VertexSet(), which is deterministic in output due to the underlying sets all being LinkedHashSets.
- OUTLIER_INDICATORS - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioParameter
- OUTLIER_NEUTRAL_SEGMENT_COPY_RATIO_Z_SCORE_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegments
- OUTLIER_PROBABILITY - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionParameter
- OUTLIER_PROBABILITY - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioParameter
- output - Variable in class org.broadinstitute.hellbender.metrics.MetricsArgumentCollection
- output - Variable in class org.broadinstitute.hellbender.tools.AddOriginalAlignmentTags
- output - Variable in class org.broadinstitute.hellbender.tools.GatherVcfsCloud
- output - Variable in class org.broadinstitute.hellbender.tools.HaplotypeCallerSpark
- output - Variable in class org.broadinstitute.hellbender.tools.PrintDistantMates
- output - Variable in class org.broadinstitute.hellbender.tools.PrintReads
- output - Variable in class org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndex
- output - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark
- output - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.BwaAndMarkDuplicatesPipelineSpark
- output - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark
- output - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.PrintVariantsSpark
- output - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- output - Variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- output - Variable in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- output - Variable in class org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark
- output - Variable in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker
- output - Variable in class org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta
- output - Variable in class org.broadinstitute.hellbender.tools.walkers.ReadAnonymizer
- output - Variable in class picard.analysis.SinglePassSamProgram
- OUTPUT - Variable in class org.broadinstitute.hellbender.tools.FixMisencodedBaseQualityReads
- OUTPUT - Variable in class org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR
- OUTPUT - Variable in class org.broadinstitute.hellbender.tools.walkers.RevertBaseQualityScores
- OUTPUT - Variable in class org.broadinstitute.hellbender.tools.walkers.UnmarkDuplicates
- OUTPUT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
- OUTPUT - Variable in class picard.analysis.CollectMultipleMetrics
- OUTPUT - Variable in class picard.analysis.CollectOxoGMetrics
- OUTPUT - Variable in class picard.analysis.CollectWgsMetrics
- OUTPUT - Variable in class picard.analysis.CompareMetrics
- OUTPUT - Variable in class picard.analysis.directed.CollectTargetedMetrics
- OUTPUT - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- OUTPUT - Variable in class picard.analysis.SinglePassSamProgram
- OUTPUT - Variable in class picard.annotation.SortGff
- OUTPUT - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
- OUTPUT - Variable in class picard.arrays.CombineGenotypingArrayVcfs
- OUTPUT - Variable in class picard.arrays.CreateBafRegressMetricsFile
- OUTPUT - Variable in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
- OUTPUT - Variable in class picard.arrays.GtcToVcf
- OUTPUT - Variable in class picard.arrays.illumina.BpmToNormalizationManifestCsv
- OUTPUT - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- OUTPUT - Variable in class picard.arrays.MergePedIntoVcf
- OUTPUT - Variable in class picard.arrays.VcfToAdpc
- OUTPUT - Variable in class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
- OUTPUT - Variable in class picard.fingerprint.CalculateFingerprintMetrics
- OUTPUT - Variable in class picard.fingerprint.CheckFingerprint
- OUTPUT - Variable in class picard.fingerprint.ClusterCrosscheckMetrics
- OUTPUT - Variable in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
- OUTPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
- OUTPUT - Variable in class picard.fingerprint.ExtractFingerprint
- OUTPUT - Variable in class picard.fingerprint.IdentifyContaminant
- OUTPUT - Variable in class picard.fingerprint.LiftOverHaplotypeMap
- OUTPUT - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
- OUTPUT - Variable in class picard.illumina.IlluminaBasecallsToSam
- OUTPUT - Variable in class picard.illumina.MarkIlluminaAdapters
- OUTPUT - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- OUTPUT - Variable in class picard.reference.ExtractSequences
- OUTPUT - Variable in class picard.reference.NonNFastaSize
- OUTPUT - Variable in class picard.reference.NormalizeFasta
- OUTPUT - Variable in class picard.sam.AddCommentsToBam
- OUTPUT - Variable in class picard.sam.AddOATag
- OUTPUT - Variable in class picard.sam.AddOrReplaceReadGroups
- OUTPUT - Variable in class picard.sam.BuildBamIndex
- OUTPUT - Variable in class picard.sam.CalculateReadGroupChecksum
- OUTPUT - Variable in class picard.sam.CleanSam
- OUTPUT - Variable in class picard.sam.CompareSAMs
- OUTPUT - Variable in class picard.sam.CreateSequenceDictionary
- OUTPUT - Variable in class picard.sam.DownsampleSam
- OUTPUT - Variable in class picard.sam.FastqToSam
- OUTPUT - Variable in class picard.sam.FilterSamReads
- OUTPUT - Variable in class picard.sam.FixMateInformation
- OUTPUT - Variable in class picard.sam.GatherBamFiles
- OUTPUT - Variable in class picard.sam.markduplicates.CheckDuplicateMarking
- OUTPUT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- OUTPUT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- OUTPUT - Variable in class picard.sam.MergeBamAlignment
- OUTPUT - Variable in class picard.sam.MergeSamFiles
- OUTPUT - Variable in class picard.sam.PositionBasedDownsampleSam
- OUTPUT - Variable in class picard.sam.ReorderSam
- OUTPUT - Variable in class picard.sam.ReplaceSamHeader
- OUTPUT - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- OUTPUT - Variable in class picard.sam.RevertSam
- OUTPUT - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- OUTPUT - Variable in class picard.sam.SamFormatConverter
- OUTPUT - Variable in class picard.sam.SetNmMdAndUqTags
- OUTPUT - Variable in class picard.sam.SortSam
- OUTPUT - Variable in class picard.sam.SplitSamByLibrary
- OUTPUT - Variable in class picard.sam.SplitSamByNumberOfReads
- OUTPUT - Variable in class picard.sam.ValidateSamFile
- OUTPUT - Variable in class picard.util.AccumulateQualityYieldMetrics
- OUTPUT - Variable in class picard.util.BedToIntervalList
- OUTPUT - Variable in class picard.util.IntervalListToBed
- OUTPUT - Variable in class picard.util.IntervalListTools
- OUTPUT - Variable in class picard.util.LiftOverIntervalList
- OUTPUT - Variable in class picard.util.ScatterIntervalsByNs
- OUTPUT - Variable in class picard.vcf.AccumulateVariantCallingMetrics
- OUTPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
- OUTPUT - Variable in class picard.vcf.filter.FilterVcf
- OUTPUT - Variable in class picard.vcf.FixVcfHeader
- OUTPUT - Variable in class picard.vcf.GatherVcfs
- OUTPUT - Variable in class picard.vcf.GenotypeConcordance
- OUTPUT - Variable in class picard.vcf.LiftoverVcf
- OUTPUT - Variable in class picard.vcf.MakeSitesOnlyVcf
- OUTPUT - Variable in class picard.vcf.MakeVcfSampleNameMap
- OUTPUT - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- OUTPUT - Variable in class picard.vcf.MergeVcfs
- OUTPUT - Variable in class picard.vcf.RenameSampleInVcf
- OUTPUT - Variable in class picard.vcf.SortVcf
- OUTPUT - Variable in class picard.vcf.UpdateVcfSequenceDictionary
- OUTPUT - Variable in class picard.vcf.VcfFormatConverter
- OUTPUT - Variable in class picard.vcf.VcfToIntervalList
- OUTPUT_AGILENT_FILES - Variable in class picard.util.BaitDesigner
- OUTPUT_ALL_ROWS - Variable in class picard.vcf.GenotypeConcordance
- OUTPUT_BASE - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- OUTPUT_BLOCK_LOWER_BOUNDS - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- OUTPUT_BY_READGROUP - Variable in class picard.sam.RevertSam
- OUTPUT_BY_READGROUP_FILE_FORMAT - Variable in class picard.sam.RevertSam
- OUTPUT_BY_READGROUP_FILE_FORMAT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- OUTPUT_BY_READGROUP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- OUTPUT_DENOISED_COPY_RATIOS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- OUTPUT_DIR - Variable in class picard.illumina.ExtractIlluminaBarcodes
- OUTPUT_DIR - Variable in class picard.sam.SamToFastq
- OUTPUT_DIRECTORY - Variable in class org.broadinstitute.hellbender.tools.SplitReads
- OUTPUT_DIRECTORY - Variable in class picard.illumina.CollectIlluminaLaneMetrics
- OUTPUT_DIRECTORY - Variable in class picard.util.BaitDesigner
- OUTPUT_ERRORS_ONLY - Variable in class picard.fingerprint.CrosscheckFingerprints
- OUTPUT_FILE_PREFIX - Variable in class picard.fastq.BamToBfq
- OUTPUT_FILES_ARGNAME - Static variable in class org.broadinstitute.hellbender.tools.sv.PrintReadCounts
- OUTPUT_FORMAT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- OUTPUT_HDFS_DIRECTORY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.ParallelCopyGCSDirectoryIntoHDFSSpark
- OUTPUT_INDEX_COMPANION - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- OUTPUT_INTERVALS_VCF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- OUTPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- OUTPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBam
- OUTPUT_MAP - Variable in class picard.sam.RevertSam
- OUTPUT_MAP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- OUTPUT_MAP_OUTPUT_FILE_FIELD_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- OUTPUT_MAP_READ_GROUP_FIELD_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- OUTPUT_PER_RG - Variable in class picard.sam.SamToFastq
- OUTPUT_PREFIX - Variable in class picard.illumina.CollectIlluminaLaneMetrics
- OUTPUT_PREFIX - Variable in class picard.illumina.IlluminaBasecallsToFastq
- OUTPUT_PREFIX_ARGNAME - Static variable in class org.broadinstitute.hellbender.tools.sv.PrintReadCounts
- OUTPUT_PREFIX_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument
- OUTPUT_SEGMENTS_VCF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- OUTPUT_SHARD_DIR_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- OUTPUT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- OUTPUT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBam
- OUTPUT_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- OUTPUT_STATISTICS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- OUTPUT_STATISTICS_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- OUTPUT_TABLE - Variable in class picard.analysis.CompareMetrics
- OUTPUT_TYPE - Variable in class picard.util.ScatterIntervalsByNs
- OUTPUT_VALUE - Variable in class picard.util.IntervalListTools
- OUTPUT_VCF - Variable in class picard.vcf.GenotypeConcordance
- OUTPUT_VCF_CALL_SAMPLE_NAME - Static variable in class picard.vcf.GenotypeConcordance
- OUTPUT_VCF_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
- OUTPUT_VCF_TRUTH_SAMPLE_NAME - Static variable in class picard.vcf.GenotypeConcordance
- output2 - Variable in class org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark
- OutputArgumentCollection - Interface in picard.cmdline.argumentcollections
-
Base interface for an output argument collection.
- outputBam - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- outputBam - Variable in class org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSet
- outputBaseName - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark
- outputByReadGroup - Variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- outputByReadgroupFileFormat - Variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- OutputCapture(CAPTURE_POLICY, ProcessControllerBase.ProcessStream, String, int) - Constructor for class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase.OutputCapture
-
Reads in the output of a stream on a background thread to keep the output pipe from backing up and freezing the called process.
- OutputCluster(List<SVCallRecord>) - Constructor for class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine.OutputCluster
- outputCsvPath - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- outputDetailMetricsFile(VariantContext.Type, MetricsFile<GenotypeConcordanceDetailMetrics, ?>, GenotypeConcordanceCounts, String, String, boolean, boolean) - Static method in class picard.vcf.GenotypeConcordance
-
Outputs the detailed statistics tables for SNP and Indel match categories.
- outputDir - Variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- outputFile - Variable in class org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerSpark
- outputFile - Variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
- outputFile - Variable in class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations
- outputFile - Variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader
- outputFile - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
- outputFile - Variable in class org.broadinstitute.hellbender.tools.spark.PileupSpark
- outputFile - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
- outputFile - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- outputFile - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- outputFilename - Variable in class org.broadinstitute.hellbender.tools.validation.CompareBaseQualities
- outputFlowLength - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- outputFormat - Variable in class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter
-
Available options are csv, table, rtable.
- outputFormatType - Variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
- outputInsertLength - Variable in class org.broadinstitute.hellbender.tools.spark.PileupSpark
-
Adds the length of the insert each base comes from to the output pileup.
- outputInsertLength - Variable in class org.broadinstitute.hellbender.tools.walkers.qc.Pileup
-
Adds the length of the insert each base comes from to the output pileup.
- outputMap - Variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- OutputMapping - Class in picard.illumina.parser
-
In multiple locations we need to know what cycles are output, as of now we output all non-skip cycles, but rather than sprinkle this knowledge throughout the parser code, instead OutputMapping provides all the data a client might want about the cycles to be output including what ReadType they are.
- OutputMapping(ReadStructure) - Constructor for class picard.illumina.parser.OutputMapping
-
Create an OutputMapping from a readStructure, currently the outputSubstructure just references the readStructure.nonSkips Substructure
- outputMetrics() - Method in class picard.illumina.ExtractBarcodesProgram
- outputMode - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection
- OutputMode - Enum Class in org.broadinstitute.hellbender.tools.walkers.genotyper
-
Describes the mode of output for the caller.
- outputPaired - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSpark
- outputPaired - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSpark
- outputPath - Variable in class org.broadinstitute.hellbender.tools.IndexFeatureFile
- outputPath - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
- outputPath - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark
- outputPath - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreSpark
-
Records have a "YP" tag that lists the NCBI taxonomy IDs of any mapped organisms.
- outputRecalibrationReport(PrintStream, RecalibrationArgumentCollection, QuantizationInfo, RecalibrationTables, StandardCovariateList) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
-
Outputs the GATK report to RAC.RECAL_TABLE.
- outputRenderer - Variable in class org.broadinstitute.hellbender.tools.funcotator.Funcotator
- OutputRenderer - Class in org.broadinstitute.hellbender.tools.funcotator
-
An abstract class to allow for writing output for the Funcotator.
- OutputRenderer(String) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.OutputRenderer
-
Initialize an OutputRenderer
- outputReport - Variable in class org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReports
- outputReport - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.GatherTranches
- outputSampleNameFile - Variable in class org.broadinstitute.hellbender.tools.GetSampleName
- outputSingletonValueAsHistogram(Double) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
- outputSink - Variable in class org.broadinstitute.hellbender.tools.sv.AbstractEvidenceSortMerger
- outputSitesOnlyVCFs - Variable in class org.broadinstitute.hellbender.engine.GATKTool
- OutputStreamSettings - Class in org.broadinstitute.hellbender.utils.runtime
-
Settings that define text to capture from a process stream.
- OutputStreamSettings() - Constructor for class org.broadinstitute.hellbender.utils.runtime.OutputStreamSettings
- outputUnpaired - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSpark
- outputUnpaired - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSpark
- outputVcf - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3
- outputVCF - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper
- outputVCF - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
-
A raw, unfiltered, highly sensitive callset in VCF format.
- outputVCF - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- outputWriter - Variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVVariantComposer
- outputZip - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OffRampBase
- outSam - Variable in class org.broadinstitute.hellbender.tools.walkers.qc.PostProcessReadsForRSEM
- outSamFile - Variable in class org.broadinstitute.hellbender.tools.walkers.qc.TransferReadTags
- OverclippedReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads where the number of bases without soft-clips (M, I, X, and = CIGAR operators) is lower than a threshold.
- OverclippedReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.OverclippedReadFilter
- OverhangFixingManager - Class in org.broadinstitute.hellbender.tools.walkers.rnaseq
-
The class manages reads and splices and tries to apply overhang clipping when appropriate.
- OverhangFixingManager(SAMFileHeader, GATKReadWriter, GenomeLocParser, ReferenceSequenceFile, int, int, int, boolean, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager
- OverhangFixingManager.Splice - Class in org.broadinstitute.hellbender.tools.walkers.rnaseq
- OverhangFixingManager.SplitRead - Class in org.broadinstitute.hellbender.tools.walkers.rnaseq
- overhangingBasesMismatch(byte[], int, int, byte[], int, int) - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager
-
Are there too many mismatches to the reference among the overhanging bases?
- OVERLAP - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapTargetStatus
-
Gene or transcript overlaps previous version of annotation on target genome.
- overlapFraction(SVIntervalTree<?>) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
fraction of the intervals in this tree that overlap with intervals in some other tree
- OverlapIterator(SVInterval) - Constructor for class org.broadinstitute.hellbender.utils.SVIntervalTree.OverlapIterator
- overlapLen(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVInterval
- overlapOnContig(AlignmentInterval, AlignmentInterval) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- overlapOnRefSpan(AlignmentInterval, AlignmentInterval) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
Computes overlap between reference span of the two input alignment intervals.
- overlappers(PairedStrandedIntervals) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree
- overlappers(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Return an iterator over all intervals overlapping the specified interval.
- overlapping - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator
- OVERLAPPING_LOCUS - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
exon(s) of the locus overlap exon(s) of a readthrough transcript or a transcript belonging to another locus.
- OVERLAPPING_ONLY - Enum constant in enum class org.broadinstitute.hellbender.utils.IntervalMergingRule
- OVERLAPPING_UORF - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
a low confidence upstream ATG existing in other coding variant would lead to NMD in this trancript, that uses the high
- OverlappingErrorMetric - Class in picard.sam.SamErrorMetric
-
An error metric for the errors invovling bases in the overlapping region of a read-pair.
- OverlappingErrorMetric() - Constructor for class picard.sam.SamErrorMetric.OverlappingErrorMetric
- OverlappingErrorMetric(String, long, long, long, long, long) - Constructor for class picard.sam.SamErrorMetric.OverlappingErrorMetric
- OverlappingIntegerCopyNumberSegmentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
- OverlappingIntegerCopyNumberSegmentCollection(File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.OverlappingIntegerCopyNumberSegmentCollection
- OverlappingReadsErrorCalculator - Class in picard.sam.SamErrorMetric
-
A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.
- OverlappingReadsErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
- overlaps(Locatable) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
-
Checks if
otheroverlaps with thisGencodeGtfFeature. - overlaps(Locatable) - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
-
Determines whether this interval overlaps the provided locatable.
- overlaps(Locatable, Locatable) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Check whether two locatables overlap.
- overlaps(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
Determine if the given loc overlaps any loc in the sorted set
- overlaps(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVInterval
-
This definition is appropriate for half-open intervals.
- OVERLAPS - Enum constant in enum class picard.util.IntervalListTools.Action
- overlapsP(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- overlapsWithMargin(Locatable, int) - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
-
Determines whether this interval comes within "margin" of overlapping the provided locatable.
- OVERRIDE_FRAGMENT_SOFTCLIP_CHECK_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- overrideSoftclipFragmentCheck - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- OVERWRITE_ARG_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader
- OVERWRITE_EXISTING_DEFAULT - Static variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- OVERWRITE_QUALS - Enum constant in enum class org.broadinstitute.hellbender.utils.baq.BAQ.QualityMode
- OVERWRITE_WORKSPACE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- overwriteExisting - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- OXIDATION_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The oxo error rate, calculated as max(ALT_OXO_BASES - ALT_NONOXO_BASES, 1) / TOTAL_BASES
- OXIDATION_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
-10 * log10(OXIDATION_ERROR_RATE)
- OXOG_METRICS_EXT - Static variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- OXOG_OUT - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
P
- P_95_GREEN - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- P_95_RED - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- P_ACTIVE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCallingArgumentCollection
- P_ALT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCallingArgumentCollection
- P_VALUE_FOR_NOISE - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.PowerCalculationUtils
- P95_GREEN - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The 95th Intensity Percentile for the green color channel for this sample
- P95_RED - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The 95th Intensity Percentile for the red color channel for this sample
- PACBIO - Enum constant in enum class org.broadinstitute.hellbender.utils.NGSPlatform
- PACKED_STRING_REP_SEPARATOR - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- padded - Variable in class org.broadinstitute.hellbender.engine.ShardBoundary
- paddedHaplotypeLength - Variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- paddedMaxHaplotypeLength - Variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- paddedMaxReadLength - Variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- paddedReadLength - Variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- paddedShardBoundary() - Method in class org.broadinstitute.hellbender.engine.ReadlessAssemblyRegion
- paddedShardBoundary() - Method in class org.broadinstitute.hellbender.engine.ShardBoundary
- paddedSpan - Variable in class org.broadinstitute.hellbender.engine.ShardBoundary
- paddedSpan - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer.Result
-
The trimmed variant region span including the extension.
- PADDING - Variable in class picard.util.BaitDesigner
- PADDING - Variable in class picard.util.IntervalListTools
- PADDING_IN_BP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEvents
- PADDING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervals
- paddingFraction - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.CNVLinkage
- Pair - Class in org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
-
Class representing a pair of reads together with accompanying optical duplicate marking information.
- Pair<X extends Comparable<X>,
Y extends Comparable<Y>> - Class in picard.sam.util -
Simple Pair class.
- Pair(GATKRead, GATKRead, SAMFileHeader, int, MarkDuplicatesScoringStrategy, Map<String, Byte>) - Constructor for class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair
- Pair(X, Y) - Constructor for class picard.sam.util.Pair
- PAIR - Enum constant in enum class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord.Type
- PAIR - Enum constant in enum class picard.analysis.AlignmentSummaryMetrics.Category
- PAIR_HMM_GAP_CONTINUATION_PENALTY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- PAIR_HMM_IMPLEMENTATION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- PAIR_ORIENTATION - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The pair orientation of the reads in this data category.
- PAIR_ORIENTATION - Variable in class picard.analysis.InsertSizeMetrics
-
The pair orientation of the reads in this data category.
- Pair.Serializer - Class in org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
-
Serializers for each subclass of PairedEnds which rely on implementations of serializations within each class itself
- PAIRED - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- PAIRED_END - Enum constant in enum class org.broadinstitute.hellbender.utils.illumina.IlluminaAdapterPair
- PAIRED_END - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
-
The following sequences can be found in https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf and are protected by the following copyright notice: Oligonucleotide sequences (c) 2016 Illumina, Inc.
- PAIRED_END_FILE_ARGUMENT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- PAIRED_END_FILE_ARGUMENT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- PAIRED_FIRST - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.evidence.TemplateFragmentOrdinal
-
For the first and only first fragment in a paired sequenced template.
- PAIRED_INPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSpark
- PAIRED_INPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreSpark
- PAIRED_INTERIOR - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.evidence.TemplateFragmentOrdinal
-
For inner fragments in a paired sequenced template.
- PAIRED_OUTPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSpark
- PAIRED_OUTPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSpark
- PAIRED_RUN - Variable in class picard.fastq.BamToBfq
- PAIRED_RUN - Variable in class picard.illumina.MarkIlluminaAdapters
- PAIRED_RUN - Variable in class picard.sam.MergeBamAlignment
-
Deprecated.
- PAIRED_SECOND - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.evidence.TemplateFragmentOrdinal
-
For the second/last and only second/last fragment in a paired sequenced template.
- PAIRED_UNKNOWN - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.evidence.TemplateFragmentOrdinal
-
For fragment in paired sequenced templates with unknown ordinal.
- PairedEnds - Class in org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
-
Struct-like class to store information about the paired reads for mark duplicates.
- pairedInput - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreSpark
- PairedReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.PairedReadFilter
- PairedStrandedIntervals - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- PairedStrandedIntervals(StrandedInterval, StrandedInterval) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervals
- PairedStrandedIntervalTree<V> - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- PairedStrandedIntervalTree() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree
- PairedStrandedIntervalTree(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree
- PairedStrandedIntervalTree.PairedStrandedIntervalTreeIterator - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- PairedStrandedIntervalTree.PairedStrandedIntervalTreeOverlapperIterator - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- PairedStrandedIntervalTree.Serializer<T> - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- PairedStrandedIntervalTreeOverlapperIterator(PairedStrandedIntervalTree<V>, PairedStrandedIntervals) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.PairedStrandedIntervalTreeOverlapperIterator
- PairedVariantSubContextIterator - Class in picard.vcf
-
An iterator that takes a pair of iterators over VariantContexts and iterates over them in tandem.
- PairedVariantSubContextIterator(Iterator<VariantContext>, String, Iterator<VariantContext>, String, SAMSequenceDictionary) - Constructor for class picard.vcf.PairedVariantSubContextIterator
- PairedVariantSubContextIterator.VcfTuple - Class in picard.vcf
-
Little class to hold a pair of VariantContexts that are in sync with one another.
- pairHMM - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
-
The PairHMM implementation to use for genotype likelihood calculations.
- PairHMM - Class in org.broadinstitute.hellbender.utils.pairhmm
-
Class for performing the pair HMM for global alignment.
- PairHMM - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine.Implementation
-
Classic full pair-hmm all haplotypes vs all reads.
- PairHMM() - Constructor for class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- PairHMM.Implementation - Enum Class in org.broadinstitute.hellbender.utils.pairhmm
- pairHMMComputeTime - Static variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- PairHMMInputScoreImputation - Interface in org.broadinstitute.hellbender.utils.pairhmm
- PairHMMInputScoreImputator - Interface in org.broadinstitute.hellbender.utils.pairhmm
-
Common interface for pair-hmm score calculators.
- PairHMMLikelihoodCalculationEngine - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
- PairHMMLikelihoodCalculationEngine(byte, DragstrParams, PairHMMNativeArguments, PairHMM.Implementation, double, PairHMMLikelihoodCalculationEngine.PCRErrorModel) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine
-
Create a new PairHMMLikelihoodCalculationEngine using provided parameters and hmm to do its calculations
- PairHMMLikelihoodCalculationEngine(byte, DragstrParams, PairHMMNativeArguments, PairHMM.Implementation, GATKPath, double, PairHMMLikelihoodCalculationEngine.PCRErrorModel, byte, boolean, double, double, boolean, boolean, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine
-
Create a new PairHMMLikelihoodCalculationEngine using provided parameters and hmm to do its calculations
- PairHMMLikelihoodCalculationEngine.PCRErrorModel - Enum Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
- PairHMMModel - Class in org.broadinstitute.hellbender.utils.pairhmm
-
Helper class that implement calculations required to implement the PairHMM Finite State Automation (FSA) model.
- pairHMMNativeArgs - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- PairHMMNativeArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Arguments for native PairHMM implementations
- PairHMMNativeArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMNativeArgumentCollection
- pairHmmResultsFile - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
-
Argument for generating a file of all of the inputs and outputs for the pair hmm
- pairSort - Variable in class picard.sam.markduplicates.MarkDuplicates
- PairStratifier(ReadBaseStratification.RecordAndOffsetStratifier<T>, ReadBaseStratification.RecordAndOffsetStratifier<R>) - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.PairStratifier
- PairStratifierFactory(ReadBaseStratification.RecordAndOffsetStratifier<T>, ReadBaseStratification.RecordAndOffsetStratifier<S>, String) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
-
A factory for generating "pair" stratifier instances from two stratifiers and a string
- PairWalker - Class in org.broadinstitute.hellbender.tools.walkers
- PairWalker() - Constructor for class org.broadinstitute.hellbender.tools.walkers.PairWalker
- PalindromeArtifactClipReadTransformer - Class in org.broadinstitute.hellbender.transformers
-
Trims (hard clips) soft-clipped bases due to the following artifact: When a sequence and its reverse complement occur near opposite ends of a fragment DNA damage (especially in the case of FFPE samples and ancient DNA) can disrupt base-pairing causing a single-strand loop of the sequence and its reverse complement, after which end repair copies the true 5' end of the fragment onto the 3' end of the fragment.
- PalindromeArtifactClipReadTransformer(ReferenceDataSource, int) - Constructor for class org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer
- PANEL_OF_NORMALS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- PANEL_OF_NORMALS_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- PanelMetricsBase - Class in picard.analysis.directed
-
A base class for Metrics for targeted panels.
- PanelMetricsBase() - Constructor for class picard.analysis.directed.PanelMetricsBase
- PanelOfNormalsFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- PanelOfNormalsFilter() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.PanelOfNormalsFilter
- PAR - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
annotation in the pseudo-autosomal region, which is duplicated between chromosomes X and Y.
- PARALLEL_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- ParallelCopyGCSDirectoryIntoHDFSSpark - Class in org.broadinstitute.hellbender.tools.spark
-
Parallel copy a file or directory from Google Cloud Storage into the HDFS file system used by Spark
- ParallelCopyGCSDirectoryIntoHDFSSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.ParallelCopyGCSDirectoryIntoHDFSSpark
- Parameter<T extends Enum<T> & ParameterEnum,
U> - Class in org.broadinstitute.hellbender.utils.mcmc -
Represents a parameter value with a named
ParameterEnumkey. - Parameter(T, U) - Constructor for class org.broadinstitute.hellbender.utils.mcmc.Parameter
-
Constructs a
Parametergiven aParameterEnumkey name and value. - PARAMETER_DOC - Static variable in class picard.illumina.parser.ReadStructure
- PARAMETER_NAME - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
- ParameterDecileCollection<T extends Enum<T> & ParameterEnum> - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
- ParameterDecileCollection(File, Class<T>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.ParameterDecileCollection
- ParameterDecileCollection(SampleMetadata, Map<T, DecileCollection>, Class<T>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.ParameterDecileCollection
- ParameterEnum - Interface in org.broadinstitute.hellbender.utils.mcmc
-
Interface for tagging an enum that represents the name of every
Parametercomprising aParameterizedState. - ParameterizedFileUtil - Class in picard.illumina.parser
- ParameterizedFileUtil(boolean, String, File, FileFaker, int) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
- ParameterizedFileUtil(boolean, String, File, FileFaker, int, boolean) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
- ParameterizedFileUtil(String, String, File, FileFaker, int) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
- ParameterizedModel<V1 extends Enum<V1> & ParameterEnum,
S1 extends ParameterizedState<V1>, T1 extends DataCollection> - Class in org.broadinstitute.hellbender.utils.mcmc -
Represents a parameterized model.
- ParameterizedModel.GibbsBuilder<V2 extends Enum<V2> & ParameterEnum,
S2 extends ParameterizedState<V2>, T2 extends DataCollection> - Class in org.broadinstitute.hellbender.utils.mcmc -
Builder for constructing a ParameterizedModel to be Gibbs sampled using
GibbsSampler. - ParameterizedModel.UpdateMethod - Enum Class in org.broadinstitute.hellbender.utils.mcmc
- ParameterizedState<T extends Enum<T> & ParameterEnum> - Class in org.broadinstitute.hellbender.utils.mcmc
-
Represents a mapped collection of
Parameterobjects, i.e., named, ordered, enumerated keys associated with values of mixed type via a key -> key, value map. - ParameterizedState(List<Parameter<T, ?>>) - Constructor for class org.broadinstitute.hellbender.utils.mcmc.ParameterizedState
-
Constructs a
ParameterizedStatewith parameters enumerated byParameterEnumfrom a List ofParameterobjects with values of mixed type, checking that all parameters are present without duplicates. - ParameterizedState(ParameterizedState<T>) - Constructor for class org.broadinstitute.hellbender.utils.mcmc.ParameterizedState
-
Copy constructor.
- ParameterSampler<U,
V extends Enum<V> & ParameterEnum, S extends ParameterizedState<V>, T extends DataCollection> - Interface in org.broadinstitute.hellbender.utils.mcmc -
Interface for generating random samples of a
Parametervalue, given anParameterizedStateand aDataCollection. - ParameterTableColumn - Enum Class in org.broadinstitute.hellbender.utils.mcmc
- ParamUtils - Class in org.broadinstitute.hellbender.utils.param
-
This class should eventually be merged into Utils, which is in hellbender, and then this class should be deleted.
- parse(File, EnumSet<PedReader.MissingPedField>, SampleDB) - Method in class org.broadinstitute.hellbender.utils.samples.PedReader
- parse(Reader, EnumSet<PedReader.MissingPedField>, SampleDB) - Method in class org.broadinstitute.hellbender.utils.samples.PedReader
- parse(String, EnumSet<PedReader.MissingPedField>, SampleDB) - Method in class org.broadinstitute.hellbender.utils.samples.PedReader
- parse(GATKPath) - Static method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParamUtils
- parseArgs(String[]) - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
-
Parse arguments and initialize any values annotated with
Argument - parseArgs(String[]) - Method in class picard.cmdline.CommandLineProgram
- parseArgsForConfigSetup(String[]) - Method in class org.broadinstitute.hellbender.Main
-
Reads from the given command-line arguments, pulls out configuration options, and initializes the configuration for this instance of Main.
- parseBasesAndQuals(String, String, byte) - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupCodec
- parseCatalog(BufferedReader, Map<String, Tuple2<String, Long>>, Map<Integer, PSPathogenReferenceTaxonProperties>, boolean, Set<String>) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBuildReferenceTaxonomyUtils
-
Builds maps of reference contig accessions to their taxonomic ids and vice versa.
- parseClusterRecordsFromTileMetrics(Collection<File>, Map<Integer, File>, ReadStructure) - Static method in class picard.illumina.parser.TileMetricsUtil
- parseCommaDelimitedArgList(String) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSUtils
- parseCPXIntervalString(String) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Parse one interval string from CPX_INTERVALS INFO field into an SVSegment representing the SV type and interval of one of the components of the complex event
- parseDirective(String) - Static method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
-
Parses a "Directive" of the form "ERROR,STRATIFIER,STRATIFIER...etc." into a
BaseErrorAggregationconsisting of the appropriateBaseCalculatorand theCollectionStratifierconstructed from the various individual stratifiers. - parseFilterLowerLimit(String) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSR
- parseGenomeLoc(String) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
parse a genome interval, from a location string Performs interval-style validation: contig is valid; start and stop less than the end; start <= stop, and start/stop are on the contig
- parseInputFile(File, ReadStructure) - Static method in class picard.illumina.ExtractBarcodesProgram
-
Parses any one of the following types of files: ExtractIlluminaBarcodes BARCODE_FILE IlluminaBasecallsToFastq MULTIPLEX_PARAMS IlluminaBasecallsToSam LIBRARY_PARAMS This will validate to file format as well as populate a Map of barcodes to metrics.
- parseIntervalArguments(GenomeLocParser, String) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
- parseIntervalArguments(GenomeLocParser, List<String>) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Turns a set of strings describing intervals into a parsed set of intervals.
- parseMask(String, int) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSUtils
-
Parses command-line option for specifying kmer spacing masks
- parseMDString(String) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec
- parseMissingFieldTags(Object, List<String>) - Static method in class org.broadinstitute.hellbender.utils.samples.PedReader
-
Parses a list of tags from the command line, assuming it comes from the GATK Engine tags, and returns the corresponding EnumSet.
- parseNameForReport() - Method in interface org.broadinstitute.hellbender.utils.recalibration.covariates.Covariate
-
Returns the names of the covariate, which is the simple class name without the "Covariate" part;
- parseNamesFile(BufferedReader, Map<Integer, PSPathogenReferenceTaxonProperties>) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBuildReferenceTaxonomyUtils
-
Parses scientific name of each taxon and puts it in taxIdToProperties
- parseNodesFile(BufferedReader, Map<Integer, PSPathogenReferenceTaxonProperties>) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBuildReferenceTaxonomyUtils
-
Gets the rank and parent of each taxon.
- parseOneContig(AlignedContig, SAMSequenceDictionary, boolean, int, int, boolean) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.ContigChimericAlignmentIterativeInterpreter
-
Parse all alignment records for a single locally-assembled contig and generate chimeric alignments if available.
- parsePlatformForRead(GATKRead, SAMFileHeader, RecalibrationArgumentCollection) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
-
Section of code shared between the two recalibration walkers which uses the command line arguments to adjust attributes of the read such as quals or platform string
- parsePosteriorsIntoPhredSpace(Genotype) - Static method in class org.broadinstitute.hellbender.tools.walkers.variantutils.PosteriorProbabilitiesUtils
- parsePosteriorsIntoProbSpace(Genotype) - Static method in class org.broadinstitute.hellbender.tools.walkers.variantutils.PosteriorProbabilitiesUtils
- parseQualList(VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth
- parseRawDataString(ReducibleAnnotationData<Double>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality
- parseRawDataString(ReducibleAnnotationData<List<Integer>>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
- parseRawDataString(ReducibleAnnotationData<Histogram>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
- parseReadsAndOptionallySplitGappedAlignments(Iterable<SAMRecord>, int, boolean) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
-
Iterates through the input
noSecondaryAlignments, which are assumed to contain no secondary alignment (i.e. - parseReferenceRecords(List<SAMSequenceRecord>, Map<Integer, PSPathogenReferenceTaxonProperties>) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBuildReferenceTaxonomyUtils
-
Build set of accessions contained in the reference.
- parseTileMetrics(File, ReadStructure, ValidationStringency) - Static method in class picard.illumina.parser.TileMetricsUtil
-
Returns an unmodifiable collection of tile data read from the provided file.
- parseTrainingSets(FeatureContext, VariantContext, VariantDatum, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- PARTIAL - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapStatus
-
Gene or transcript partially mapped to the target genome.
- PARTIAL_EXON_DUP - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- PartialReadWalker - Class in org.broadinstitute.hellbender.engine
-
A specialized read walker that may be gracefully stopped before the input stream ends A tool derived from this class should implement
PartialReadWalker.shouldExitEarly(GATKRead)to indicate when to stop. - PartialReadWalker() - Constructor for class org.broadinstitute.hellbender.engine.PartialReadWalker
- PartitionBounds(int, int, int, int, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionBounds
- PartitionCrossingChecker - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
It allows you to ask whether a given interval is near the beginning or end of the partition.
- PartitionCrossingChecker() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.PartitionCrossingChecker
-
A constructor that will always report onBoundary to be false.
- PartitionCrossingChecker(int, ReadMetadata, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.PartitionCrossingChecker
-
A constructor from the metadata with a specified boundary width.
- partitionIndex - Variable in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord
- partitionPrecision - Variable in class org.broadinstitute.hellbender.utils.variant.writers.SomaticGVCFBlockCombiner
- PartitionStatistics(Iterator<GATKRead>, SVReadFilter, int, Map<String, String>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionStatistics
- PASS - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
The record in the manifest passes validation and will be used in VCF generation
- PASS_FILTER - Static variable in class picard.vcf.filter.FilterApplyingVariantIterator
-
The "PASS"ing filter String.
- PASSES_FILTERS - Static variable in class org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary
- PASSES_VENDOR_QUALITY_CHECK - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- passesCallThreshold(double) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
- passesEmitThreshold(double, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
- PassesFiltersVariantFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary.PassesFiltersVariantFilter
- passesMinimumThreshold(int[], int) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest
-
Does this strand data array pass the minimum threshold for inclusion?
- passesMinimumThreshold(ReducibleAnnotationData<List<Integer>>, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils
-
Does this strand data array pass the minimum threshold for inclusion?
- passesRSEMFilter(GATKRead, GATKRead) - Method in class org.broadinstitute.hellbender.tools.walkers.qc.PostProcessReadsForRSEM
-
For the list of conditions required by RSEM, see: https://github.com/deweylab/RSEM/blob/master/samValidator.cpp
- passesThreshold(Allele, double) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculationResult
-
Are we confident that an allele is present
- PassesVendorQualityCheckReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.PassesVendorQualityCheckReadFilter
- Passthrough - Class in org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
-
Dummy class used for preserving reads that need to be marked as non-duplicate despite not wanting to perform any processing on the reads.
- PASSTHROUGH - Enum constant in enum class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord.Type
- PassThroughDownsampler - Class in org.broadinstitute.hellbender.utils.downsampling
-
Pass-Through Downsampler: Implementation of the ReadsDownsampler interface that does no downsampling whatsoever, and instead simply "passes-through" all the reads it's given.
- PassThroughDownsampler() - Constructor for class org.broadinstitute.hellbender.utils.downsampling.PassThroughDownsampler
- PATERNAL_ID - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.PedReader.Field
- paternalRefPath - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- Path<V extends BaseVertex,
E extends BaseEdge> - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs -
A path thought a BaseGraph class to keep track of paths
- Path(byte[], LocalAssembler.PathBuilder) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.Path
- Path(E, Path<V, E>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
-
Prepend a path with an edge.
- Path(List<E>, V, BaseGraph<V, E>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
-
Constructor that does not check arguments' validity i.e.
- Path(Path<V, E>, E) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
-
Create a new Path extending p with edge
- Path(Path<V, E>, List<E>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
-
Create a new Path extending p with edge
- Path(V, BaseGraph<V, E>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
-
Create a new Path containing no edges and starting at initialVertex
- PathBuilder(LocalAssembler.KmerSet<LocalAssembler.KmerAdjacency>) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.PathBuilder
- PathLineIterator - Class in org.broadinstitute.hellbender.utils.nio
-
Iterate through the lines of a Path.
- PathLineIterator(Path) - Constructor for class org.broadinstitute.hellbender.utils.nio.PathLineIterator
-
Returns an iterator so you can iterate over the lines in the text file like so: for (String line: new PathLineIterator(path)) { // do something with the line } It's also closeable so you can close it when done, or use it in a try-with-resources to close it automatically.
- PathPartContig(LocalAssembler.Contig, int) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartContig
- PathPartContig(LocalAssembler.Contig, int, int) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartContig
- PathPartGap(LocalAssembler.KmerAdjacency) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartGap
- PathProvider - Enum Class in picard.nio
-
A class whose purpose is to initialize the various plugins that provide Path support.
- PATHS - Static variable in class org.broadinstitute.hellbender.utils.runtime.RuntimeUtils
- PathSeqBuildKmers - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Produce a set of k-mers from the given host reference.
- PathSeqBuildKmers() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
- PathSeqBuildReferenceTaxonomy - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Build an annotated taxonomy datafile for a given microbe reference.
- PathSeqBuildReferenceTaxonomy() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
- PathSeqBwaSpark - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Align reads to a microbe reference using BWA-MEM and Spark.
- PathSeqBwaSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSpark
- PathSeqFilterSpark - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Filters low complexity, low quality, duplicate, and host reads.
- PathSeqFilterSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSpark
- pathseqGetRecommendedNumReducers(String, int, int) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSUtils
-
Same as GATKSparkTool's getRecommendedNumReducers(), but can specify input BAM path (for when --input is not used)
- PathSeqPipelineSpark - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Combined tool that performs all PathSeq steps: read filtering, microbe reference alignment and abundance scoring
- PathSeqPipelineSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark
- PathSeqScoreSpark - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Classify reads and estimate abundances of each taxon in the reference.
- PathSeqScoreSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreSpark
- PATTERN - Static variable in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.Strand
- PCR_INDEL_MODEL_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- PCR_INDEL_QUAL_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- PCR_SLIPPAGE_RATE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- PCR_SNV_QUAL_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- pcrErrorModel - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
-
When calculating the likelihood of variants, we can try to correct for PCR errors that cause indel artifacts.
- pcrIndelQual - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- pcrSnvQual - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- PCT_100X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 100X sequence coverage in post-filtering bases.
- PCT_10X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 10X sequence coverage in post-filtering bases.
- PCT_15X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 15X sequence coverage in post-filtering bases.
- PCT_1X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 1X sequence coverage in post-filtering bases.
- PCT_20X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 20X sequence coverage in post-filtering bases.
- PCT_25X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 25X sequence coverage in post-filtering bases.
- PCT_30X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 30X sequence coverage in post-filtering bases.
- PCT_40X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 40X sequence coverage in post-filtering bases.
- PCT_50X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 50X sequence coverage in post-filtering bases.
- PCT_5X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.
- PCT_60X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 60X sequence coverage in post-filtering bases.
- PCT_70X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 70X sequence coverage in post-filtering bases.
- PCT_80X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 80X sequence coverage in post-filtering bases.
- PCT_90X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 90X sequence coverage in post-filtering bases.
- PCT_A - Variable in class org.broadinstitute.hellbender.metrics.analysis.BaseDistributionByCycleMetrics
- PCT_A - Variable in class picard.analysis.BaseDistributionByCycleMetrics
- PCT_ADAPTER - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The fraction of PF reads that are unaligned or aligned with MQ0 and match to a known adapter sequence right from the start of the read (indication of adapter-dimer pairs).
- PCT_AMPLIFIED_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES + NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED.
- PCT_C - Variable in class org.broadinstitute.hellbender.metrics.analysis.BaseDistributionByCycleMetrics
- PCT_C - Variable in class picard.analysis.BaseDistributionByCycleMetrics
- PCT_CHIMERAS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The fraction of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes.
- PCT_CHIMERAS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of chimeric pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
- PCT_CODING_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Fraction of PF_ALIGNED_BASES that mapped to protein coding regions of genes, CODING_BASES/PF_ALIGNED_BASES
- PCT_CONVERTED - Variable in class picard.analysis.RrbsCpgDetailMetrics
-
CpG CONVERTED_BASES / CpG TOTAL_BASES (fraction)
- PCT_CORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
Fraction of reads corresponding to mRNA transcripts which map to the correct strand of a reference genome = CORRECT_STRAND_READS/(CORRECT_STRAND_READS + INCORRECT_STRAND_READS).
- PCT_CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
-
CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction)
- PCT_DBSNP - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The fraction of high confidence SNPs in dbSNP
- PCT_DBSNP - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The fraction of passing bi-allelic SNPs in dbSNP
- PCT_DBSNP_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The fraction of passing indels in dbSNP
- PCT_EXC_ADAPTER - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of aligned bases in reads that have MQ=0 and whose 5' end consists of adapter sequence.
- PCT_EXC_ADAPTER - Variable in class picard.analysis.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were in reads with mapping quality 0 and the looked like adapter reads.
- PCT_EXC_BASEQ - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of aligned bases that were filtered out because they were of low base quality.
- PCT_EXC_BASEQ - Variable in class picard.analysis.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were of low base quality (lower than MIN_BASE_QUALITY).
- PCT_EXC_CAPPED - Variable in class picard.analysis.WgsMetrics
-
The fraction of aligned bases that were filtered out because they would have raised coverage above COVERAGE_CAP.
- PCT_EXC_DUPE - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
- PCT_EXC_DUPE - Variable in class picard.analysis.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
- PCT_EXC_MAPQ - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
- PCT_EXC_MAPQ - Variable in class picard.analysis.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (lower than MIN_MAPPING_QUALITY).
- PCT_EXC_OFF_TARGET - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of aligned bases that were filtered out because they did not align over a target base.
- PCT_EXC_OVERLAP - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
- PCT_EXC_OVERLAP - Variable in class picard.analysis.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
- PCT_EXC_TOTAL - Variable in class picard.analysis.WgsMetrics
-
The total fraction of aligned bases excluded due to all filters.
- PCT_EXC_UNPAIRED - Variable in class picard.analysis.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair.
- PCT_G - Variable in class org.broadinstitute.hellbender.metrics.analysis.BaseDistributionByCycleMetrics
- PCT_G - Variable in class picard.analysis.BaseDistributionByCycleMetrics
- PCT_GQ0_VARIANTS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
-
The percentage of variants in a particular sample that have a GQ score of 0.
- PCT_HARDCLIP - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The fraction of PF bases that are (on primary, aligned reads and) hard-clipped, as a fraction of the PF_ALIGNED_BASES (even though these are not aligned!)
- PCT_INTERGENIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Fraction of PF_ALIGNED_BASES that mapped to intergenic regions of genomic DNA, INTERGENIC_BASES/PF_ALIGNED_BASES
- PCT_INTRONIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Fraction of PF_ALIGNED_BASES that correspond to gene introns, INTRONIC_BASES/PF_ALIGNED_BASES
- PCT_JUMPS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of outward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
- PCT_MATCHES - Variable in class picard.illumina.BarcodeMetric
-
The fraction of all reads in the lane that matched to this barcode.
- PCT_MIX - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
-
The percent mixture (contamination) of the sample for ID
- PCT_MRNA_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Sum of bases mapped to regions corresponding to UTRs and coding regions of mRNA transcripts, PCT_UTR_BASES + PCT_CODING_BASES
- PCT_N - Variable in class org.broadinstitute.hellbender.metrics.analysis.BaseDistributionByCycleMetrics
- PCT_N - Variable in class picard.analysis.BaseDistributionByCycleMetrics
- PCT_NON_CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
-
NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction)
- PCT_NONJUMPS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of inward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
- PCT_OFF_AMPLICON - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon, OFF_AMPLICON_BASES/PF_BASES_ALIGNED
- PCT_OFF_BAIT - Variable in class picard.analysis.directed.HsMetrics
-
The fraction of PF_BASES_ALIGNED that are mapped away from any baited region, OFF_BAIT_BASES/PF_BASES_ALIGNED.
- PCT_OFF_PROBE - Variable in class picard.analysis.directed.TargetMetrics
-
The fraction of aligned PF bases that mapped neither on or near a probe, OFF_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
- PCT_PF_FAIL_EMPTY - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The fraction of non-PF reads in this tile that are deemed empty (as fraction of all non-PF reads).
- PCT_PF_FAIL_MISALIGNED - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The fraction of non-PF reads in this tile that are deemed "misaligned" (as fraction of all non-PF reads).
- PCT_PF_FAIL_POLYCLONAL - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The fraction of non-PF reads in this tile that are deemed multiclonal (as fraction of all non-PF reads).
- PCT_PF_FAIL_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The fraction of PF_READS
- PCT_PF_FAIL_UNKNOWN - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The fraction of non-PF reads in this tile that have not been classified (as fraction of all non-PF reads).
- PCT_PF_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The fraction of reads that are PF (PF_READS / TOTAL_READS)
- PCT_PF_READS - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of reads passing filter, PF_READS/TOTAL_READS.
- PCT_PF_READS_ALIGNED - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The percentage of PF reads that aligned to the reference sequence.
- PCT_PF_READS_IMPROPER_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The fraction of (primary) reads that are *not* "properly" aligned in pairs (as per SAM flag 0x2).
- PCT_PF_UQ_READS - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of unique reads passing filter, PF_UNIQUE_READS/TOTAL_READS.
- PCT_PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of unique reads passing filter that align to the reference, PF_UQ_READS_ALIGNED/PF_UNIQUE_READS.
- PCT_R1_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
The fraction of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand.
- PCT_R2_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand.
- PCT_READS_ALIGNED_IN_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The fraction of aligned reads whose mate pair was also aligned to the reference.
- PCT_RIBOSOMAL_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Fraction of PF_ALIGNED_BASES that mapped to regions encoding ribosomal RNA, RIBOSOMAL_BASES/PF_ALIGNED_BASES
- PCT_SELECTED_BASES - Variable in class picard.analysis.directed.HsMetrics
-
The fraction of PF_BASES_ALIGNED located on or near a baited region (ON_BAIT_BASES + NEAR_BAIT_BASES)/PF_BASES_ALIGNED.
- PCT_SELECTED_BASES - Variable in class picard.analysis.directed.TargetMetrics
-
The fraction of bases that map on or near a probe (ON_PROBE_BASES + NEAR_PROBE_BASES)/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
- PCT_SOFTCLIP - Variable in class picard.analysis.AlignmentSummaryMetrics
-
the fraction of PF bases that are on (primary) aligned reads and are soft-clipped, as a fraction of the PF_ALIGNED_BASES (even though these are not aligned!)
- PCT_T - Variable in class org.broadinstitute.hellbender.metrics.analysis.BaseDistributionByCycleMetrics
- PCT_T - Variable in class picard.analysis.BaseDistributionByCycleMetrics
- PCT_TARGET_BASES_100000X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 100000X or greater coverage.
- PCT_TARGET_BASES_10000X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 10000X or greater coverage.
- PCT_TARGET_BASES_1000X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 1000X or greater coverage.
- PCT_TARGET_BASES_100X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 100X or greater coverage.
- PCT_TARGET_BASES_10X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 10X or greater coverage.
- PCT_TARGET_BASES_1X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 1X or greater coverage.
- PCT_TARGET_BASES_20X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 20X or greater coverage.
- PCT_TARGET_BASES_25000X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 25000X or greater coverage.
- PCT_TARGET_BASES_2500X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 2500X or greater coverage.
- PCT_TARGET_BASES_250X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 250X or greater coverage.
- PCT_TARGET_BASES_2X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 2X or greater coverage.
- PCT_TARGET_BASES_30X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 30X or greater coverage.
- PCT_TARGET_BASES_40X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 40X or greater coverage.
- PCT_TARGET_BASES_50000X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 50000X or greater coverage.
- PCT_TARGET_BASES_5000X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 5000X or greater coverage.
- PCT_TARGET_BASES_500X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 500X or greater coverage.
- PCT_TARGET_BASES_50X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 50X or greater coverage.
- PCT_UMI_WITH_N - Variable in class picard.sam.markduplicates.UmiMetrics
-
The percentage of reads that contain an UMI that contains at least one N
- PCT_USABLE_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
The fraction of bases mapping to mRNA divided by the total number of PF bases, (CODING_BASES + UTR_BASES)/PF_BASES.
- PCT_USABLE_BASES_ON_BAIT - Variable in class picard.analysis.directed.HsMetrics
-
The number of aligned, de-duped, on-bait bases out of the PF bases available.
- PCT_USABLE_BASES_ON_TARGET - Variable in class picard.analysis.directed.HsMetrics
-
The number of aligned, de-duped, on-target bases out of all of the PF bases available.
- PCT_UTR_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Fraction of PF_ALIGNED_BASES that mapped to untranslated regions (UTR) of genes, UTR_BASES/PF_ALIGNED_BASES
- PDF_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
- pdfFile - Variable in class org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates
-
Output report file name.
- PED_FILE - Variable in class picard.arrays.MergePedIntoVcf
- PedFile - Class in picard.pedigree
-
Represents a .ped file of family information as documented here: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml Stores the information in memory as a map of individualId -> Pedigree information for that individual
- PedFile(boolean) - Constructor for class picard.pedigree.PedFile
- PedFile.PedTrio - Class in picard.pedigree
- PEDIGREE_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- PEDIGREE_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- PedigreeAnnotation - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
A common interface for handling annotations that require pedigree file information either in the form of explicitly selected founderIDs or in the form of an imported pedigreeFile.
- PedigreeAnnotation(Set<String>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation
- PedigreeAnnotation(GATKPath) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation
- pedigreeFile - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- pedigreeValidationType - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- PedigreeValidationType - Enum Class in org.broadinstitute.hellbender.utils.samples
- PedReader - Class in org.broadinstitute.hellbender.utils.samples
-
Reads PED file-formatted tabular text files See http://www.broadinstitute.org/mpg/tagger/faq.html See http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped The "ped" file format refers to the widely-used format for linkage pedigree data.
- PedReader() - Constructor for class org.broadinstitute.hellbender.utils.samples.PedReader
- PedReader.Field - Enum Class in org.broadinstitute.hellbender.utils.samples
- PedReader.MissingPedField - Enum Class in org.broadinstitute.hellbender.utils.samples
-
An enum that specifies which, if any, of the standard PED fields are missing from the input records.
- PedTrio(String, String, String, String, Sex, Number) - Constructor for class picard.pedigree.PedFile.PedTrio
-
Constructs a TRIO that cannot be modified after the fact.
- peek() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
-
peek at the next sam record
- peek() - Method in class picard.sam.markduplicates.util.MarkQueue
-
Returns the first element in this queue
- peekFinalized() - Method in class org.broadinstitute.hellbender.utils.downsampling.Downsampler
-
Peek at the first finalized item stored in this downsampler (or null if there are no finalized items)
- peekFinalized() - Method in class org.broadinstitute.hellbender.utils.downsampling.FractionalDownsampler
- peekFinalized() - Method in class org.broadinstitute.hellbender.utils.downsampling.LevelingDownsampler
- peekFinalized() - Method in class org.broadinstitute.hellbender.utils.downsampling.MutectDownsampler
- peekFinalized() - Method in class org.broadinstitute.hellbender.utils.downsampling.PassThroughDownsampler
- peekFinalized() - Method in class org.broadinstitute.hellbender.utils.downsampling.PositionalDownsampler
- peekFinalized() - Method in class org.broadinstitute.hellbender.utils.downsampling.ReservoirDownsampler
- peekPending() - Method in class org.broadinstitute.hellbender.utils.downsampling.Downsampler
-
Peek at the first pending item stored in this downsampler (or null if there are no pending items)
- peekPending() - Method in class org.broadinstitute.hellbender.utils.downsampling.FractionalDownsampler
- peekPending() - Method in class org.broadinstitute.hellbender.utils.downsampling.LevelingDownsampler
- peekPending() - Method in class org.broadinstitute.hellbender.utils.downsampling.MutectDownsampler
- peekPending() - Method in class org.broadinstitute.hellbender.utils.downsampling.PassThroughDownsampler
- peekPending() - Method in class org.broadinstitute.hellbender.utils.downsampling.PositionalDownsampler
- peekPending() - Method in class org.broadinstitute.hellbender.utils.downsampling.ReservoirDownsampler
- peFile - Variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- pending - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Sequences added for read threading before we've actually built the graph
- PER_BASE_COVERAGE - Variable in class picard.analysis.directed.CollectTargetedMetrics
- PER_TARGET_COVERAGE - Variable in class picard.analysis.directed.CollectTargetedMetrics
- PER_TILE_PATTERN_STRING - Static variable in class picard.illumina.parser.ParameterizedFileUtil
- PerAlleleAnnotation - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Apply an annotation based on aggregation data from all reads supporting each allele.
- PerAlleleAnnotation() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.PerAlleleAnnotation
- PerAlleleCollection<X extends Number> - Class in org.broadinstitute.hellbender.tools.walkers.mutect
-
A container for allele to value mapping.
- PerAlleleCollection(PerAlleleCollection.Type) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection
- PerAlleleCollection.Type - Enum Class in org.broadinstitute.hellbender.tools.walkers.mutect
- PERCENT_DUPLICATION - Variable in class picard.sam.DuplicationMetrics
-
The fraction of mapped sequence that is marked as duplicate.
- percent_of_sites_with_more_than_2_alleles - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- percentageOrNull(Long, Long) - Static method in class picard.util.MathUtil
-
Obtains percentage of two Longs
- PERFECT_MATCHES - Variable in class picard.illumina.BarcodeMetric
-
The number of all reads matching this barcode that matched with 0 errors or no-calls.
- performSequenceDictionaryValidation() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection.NoValidationCollection
- performSequenceDictionaryValidation() - Method in interface org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection
-
Should sequence dictionary validation be performed
- performSequenceDictionaryValidation() - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection.StandardValidationCollection
- period(int) - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrReferenceAnalyzer
-
Returns the STR period at a given position.ß
- permutation(AlleleList<A>) - Method in interface org.broadinstitute.hellbender.utils.genotyper.AlleleList
-
Returns a permutation between two allele lists.
- Permutation<E> - Interface in org.broadinstitute.hellbender.utils.collections
-
Represent a permutation of an ordered set or list of elements.
- permutationTest(double[], double[], double) - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU
-
Creates histogram of test statistics from a permutation test.
- permute(double[], RandomDataGenerator) - Static method in class picard.util.MathUtil
-
permute the input array randomly (using a RandomDataGenerator)
- PersistenceOptimizer - Class in org.broadinstitute.hellbender.tools.copynumber.utils.optimization
-
Given 1-dimensional data, finds all local minima sorted by decreasing topological persistence.
- PersistenceOptimizer(double[]) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.utils.optimization.PersistenceOptimizer
-
Identifies the local minima of
databased on topological persistence upon construction. - PerTileBarcodeExtractor(int, File, IlluminaDataProviderFactory, BarcodeExtractor) - Constructor for class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
-
Constructor
- PerTileFileUtil - Class in picard.illumina.parser
- PerTileFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTileFileUtil
- PerTileFileUtil(String, File, FileFaker, int, boolean) - Constructor for class picard.illumina.parser.PerTileFileUtil
- PerTileOrPerRunFileUtil - Class in picard.illumina.parser
- PerTileOrPerRunFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTileOrPerRunFileUtil
- PerTileParser<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
-
Abstract base class for Parsers that open a single tile file at a time and iterate through them.
- PerTileParser(IlluminaFileMap) - Constructor for class picard.illumina.parser.PerTileParser
- PerTileParser(IlluminaFileMap, int) - Constructor for class picard.illumina.parser.PerTileParser
- PerTilePerCycleFileUtil - Class in picard.illumina.parser
- PerTilePerCycleFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTilePerCycleFileUtil
- PerUnitExampleMultiMetricsCollector - Class in org.broadinstitute.hellbender.tools.examples.metrics.multi
-
A Collector for individual ExampleMultiMetrics for a given SAMPLE or SAMPLE/LIBRARY or SAMPLE/LIBRARY/READ_GROUP (depending on aggregation levels)
- PerUnitExampleMultiMetricsCollector(String, String, String) - Constructor for class org.broadinstitute.hellbender.tools.examples.metrics.multi.PerUnitExampleMultiMetricsCollector
- PerUnitGcBiasMetricsCollector(String, String, String) - Constructor for class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
- PerUnitInsertSizeMetricsCollector - Class in org.broadinstitute.hellbender.metrics
-
A Collector for individual InsertSizeMetrics for a given SAMPLE or SAMPLE/LIBRARY or SAMPLE/LIBRARY/READ_GROUP (depending on aggregation levels)
- PerUnitInsertSizeMetricsCollector(String, String, String) - Constructor for class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
- PerUnitInsertSizeMetricsCollector(String, String, String, double, double, Integer) - Constructor for class org.broadinstitute.hellbender.metrics.PerUnitInsertSizeMetricsCollector
- PerUnitMetricCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,
HKEY extends Comparable<HKEY>, ARGTYPE> - Interface in org.broadinstitute.hellbender.metrics -
PerRecordCollector - An interface for classes that collect data in order to generate one or more metrics.
- PerUnitMetricCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,
HKEY extends Comparable, ARGTYPE> - Interface in picard.metrics -
PerRecordCollector - An interface for classes that collect data in order to generate one or more metrics.
- PerUnitRnaSeqMetricsCollector(String, String, String, Long) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
- PerUnitRnaSeqMetricsCollector(RnaSeqMetrics, String, String, String, Long) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
-
Derived classes that need to capture some additional metrics can use this ctor to supply a metrics instance that is a subclass of RnaSeqMetrics.
- PerUnitTargetMetricCollector(String, Set<Interval>, String, String, String, long, long, long, Map<Interval, Double>, int, int, boolean, boolean) - Constructor for class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Constructor that parses the squashed reference to genome reference file and stores the information in a map for later use.
- PESR_BREAKEND_WINDOW_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- PESR_INTERVAL_OVERLAP_FRACTION_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- PESR_SAMPLE_OVERLAP_FRACTION_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- pesrBreakendWindow - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
-
Maximum allowed distance between endpoints (in bp) to cluster PESR/PESR variant pairs.
- pesrOverlapFraction - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
-
Minimum interval reciprocal overlap fraction to cluster PESR/PESR variant pairs.
- pesrSampleOverlapFraction - Variable in class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
-
Minimum carrier sample reciprocal overlap fraction to cluster PESR/PESR variant pairs.
- PF - Enum constant in enum class picard.illumina.parser.IlluminaDataType
- PF - Enum constant in enum class picard.sam.ViewSam.PfStatus
- PF_ALIGNED_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence.
- PF_ALIGNED_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
The total number of aligned PF bases.
- PF_BASES - Variable in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
-
The total number of bases in all PF reads
- PF_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The total number of bases in all PF reads
- PF_BASES - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of bases in the PF_READS of a SAM or BAM file
- PF_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
The total number of PF bases including non-aligned reads.
- PF_BASES - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of passing-filter bases assigned to the index.
- PF_BASES_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of PF_BASES that are aligned with mapping score > 0 to the reference genome.
- PF_CLUSTERS - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of PF clusters assigned to the index.
- PF_FAIL_EMPTY - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The number of non-PF reads in this tile that are deemed empty.
- PF_FAIL_MISALIGNED - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The number of non-PF reads in this tile that are deemed "misaligned".
- PF_FAIL_POLYCLONAL - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The number of non-PF reads in this tile that are deemed multiclonal.
- PF_FAIL_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The number of non-PF reads in this tile.
- PF_FAIL_UNKNOWN - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The number of non-PF reads in this tile that have not been classified.
- PF_HQ_ALIGNED_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of bases aligned to the reference sequence in reads that were mapped at high quality.
- PF_HQ_ALIGNED_Q20_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The subset of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher.
- PF_HQ_ALIGNED_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of PF reads that were aligned to the reference sequence with a mapping quality of Q20 or higher signifying that the aligner estimates a 1/100 (or smaller) chance that the alignment is wrong.
- PF_HQ_ERROR_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The fraction of bases that mismatch the reference in PF HQ aligned reads.
- PF_HQ_MEDIAN_MISMATCHES - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The median number of mismatches versus the reference sequence in reads that were aligned to the reference at high quality (i.e.
- PF_INDEL_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of insertion and deletion events per 100 aligned bases.
- PF_MISMATCH_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The rate of bases mismatching the reference for all bases aligned to the reference sequence.
- PF_NOISE_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of PF reads that are marked as noise reads.
- PF_NORMALIZED_MATCHES - Variable in class picard.illumina.BarcodeMetric
-
The "normalized" matches to each barcode.
- PF_ONE_MISMATCH_MATCHES - Variable in class picard.illumina.BarcodeMetric
-
The number of PF reads matching this barcode that matched with 1 error or no-call.
- PF_PCT_MATCHES - Variable in class picard.illumina.BarcodeMetric
-
The fraction of PF reads in the lane that matched to this barcode.
- PF_PERFECT_MATCHES - Variable in class picard.illumina.BarcodeMetric
-
The number of PF reads matching this barcode that matched with 0 errors or no-calls.
- PF_Q20_BASES - Variable in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
-
The number of bases in PF reads that achieve quality score 20 or higher
- PF_Q20_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The number of bases in PF reads that achieve quality score 20 or higher
- PF_Q20_EQUIVALENT_YIELD - Variable in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
-
The sum of quality scores of all bases divided by 20
- PF_Q20_EQUIVALENT_YIELD - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The sum of quality scores of all bases in PF reads divided by 20
- PF_Q30_BASES - Variable in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
-
The number of bases in PF reads that achieve quality score 30 or higher
- PF_Q30_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The number of bases in PF reads that achieve quality score 30 or higher
- PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT - Variable in class picard.illumina.BarcodeMetric
-
The rate of PF reads matching this barcode to PF reads matching the most prevalent barcode.
- PF_READS - Variable in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
-
The number of reads that are PF - pass filter
- PF_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of PF reads where PF is defined as passing Illumina's filter.
- PF_READS - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The number of reads that are PF - pass filter
- PF_READS - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of passing filter reads (PF).
- PF_READS - Variable in class picard.illumina.BarcodeMetric
-
The number of PF reads matching this barcode (always less than or equal to READS).
- PF_READS - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of passing-filter reads assigned to the index.
- PF_READS_ALIGNED - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of PF reads that were aligned to the reference sequence.
- PF_READS_IMPROPER_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of (primary) aligned reads that are **not** "properly" aligned in pairs (as per SAM flag 0x2).
- PF_READS_ONLY - Variable in class picard.analysis.CollectBaseDistributionByCycle
- PF_READS_ONLY - Variable in class picard.analysis.MeanQualityByCycle
- PF_READS_ONLY - Variable in class picard.analysis.QualityScoreDistribution
- PF_READS_ONLY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- PF_SELECTED_PAIRS - Variable in class picard.analysis.directed.TargetMetricsBase
-
Tracks the number of read pairs that we see that are PF (used to calculate library size)
- PF_SELECTED_UNIQUE_PAIRS - Variable in class picard.analysis.directed.TargetMetricsBase
-
Tracks the number of unique PF_SELECTED_PAIRS we see (used to calc library size)
- PF_STATUS - Variable in class picard.sam.ViewSam
- PF_UNIQUE_READS - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of PF_READS that are not marked as duplicates.
- PF_UQ_BASES_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
- PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of PF_UNIQUE_READS that are aligned with mapping score > 0 to the reference genome.
- PFFailDetailedMetric() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
This ctor is necessary for when reading metrics from file
- PFFailDetailedMetric(Integer, int, int, int, int, CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
- PFFailSummaryMetric() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
This ctor is necessary for when reading metrics from file
- PFFailSummaryMetric(String) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
- pfReadsOnly - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectBaseDistributionByCycleSpark
- pfReadsOnly - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MeanQualityByCycleSpark
- pfReadsOnly - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityScoreDistributionSpark
- PG_PROGRAM_NAME - Static variable in class picard.sam.PositionBasedDownsampleSam
- pgIdsSeen - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
The program groups that have been seen during the course of examining the input records.
- pgTagArgumentCollection - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- pgTagArgumentCollection - Variable in class picard.sam.MergeBamAlignment
- PGTagArgumentCollection - Class in picard.sam.util
-
Argument Collection which holds parameters common to classes that want to add PG tags to reads in SAM/BAM files
- PGTagArgumentCollection() - Constructor for class picard.sam.util.PGTagArgumentCollection
- phaseCalls(List<VariantContext>, Set<Haplotype>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
-
Tries to phase the individual alleles based on pairwise comparisons to the other alleles based on all called haplotypes
- PHASED_HOM_VAR_STRING - Static variable in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- PHASESET_PREFIX - Static variable in class picard.fingerprint.HaplotypeMap
- PHASING_APPLIED - Variable in class picard.illumina.IlluminaPhasingMetrics
-
Median phasing value across all tiles in a lane, applied to the first and second template reads
- PHASING_BASE - Enum constant in enum class picard.illumina.parser.IlluminaMetricsCode
- phasingWeight - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
- PHENOTYPE - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.PedReader.Field
- PHENYLALANINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- PHRED_SCALED_GLOBAL_READ_MISMAPPING_RATE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
- PHRED_SCALED_MIN_P_VALUE - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet
- PHRED_SCALED_POSTERIORS_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- PHRED_TO_LOG_PROB_MULTIPLIER - Static variable in class org.broadinstitute.hellbender.utils.QualityUtils
-
conversion factor from phred scaled quality to log error probability and vice versa
- phredNoVariantPosteriorProbability(List<Allele>, GenotypesContext) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
- phredScaleCorrectRate(double) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Convert a probability of being right to a phred-scaled quality score of being wrong as a double This is a very generic method, that simply computes a phred-scaled double quality score given an error rate.
- phredScaledGlobalReadMismappingRate - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
-
The phredScaledGlobalReadMismappingRate reflects the average global mismapping rate of all reads, regardless of their mapping quality.
- phredScaledPosteriorAnnotationName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ContaminationFilter
- phredScaledPosteriorAnnotationName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteredHaplotypeFilter
- phredScaledPosteriorAnnotationName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.GermlineFilter
- phredScaledPosteriorAnnotationName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.HardAlleleFilter
- phredScaledPosteriorAnnotationName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.HardFilter
- phredScaledPosteriorAnnotationName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2Filter
- phredScaledPosteriorAnnotationName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NormalArtifactFilter
- phredScaledPosteriorAnnotationName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.PolymeraseSlippageFilter
- phredScaledPosteriorAnnotationName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadOrientationFilter
- phredScaledPosteriorAnnotationName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter
- phredScaledPosteriorAnnotationName() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.TumorEvidenceFilter
- phredScaleErrorRate(double) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Convert a probability of being wrong to a phred-scaled quality score as a double This is a very generic method, that simply computes a phred-scaled double quality score given an error rate.
- phredScaleLog10CorrectRate(double) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Convert a log10 probability of being right to a phred-scaled quality score of being wrong as a double This is a very generic method, that simply computes a phred-scaled double quality score given an error rate.
- phredScaleLog10ErrorRate(double) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Convert a log10 probability of being wrong to a phred-scaled quality score as a double This is a very generic method, that simply computes a phred-scaled double quality score given an error rate.
- phredSum(double[]) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Calculate the sum of phred scores.
- phredSum(double, double) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Calculate the sum of two phred scores.
- phredSum(double, double, double) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Calculate the sum of three phred scores.
- PhysicalLocation - Interface in picard.sam.util
-
Small interface that provides access to the physical location information about a cluster.
- PhysicalLocationForMateCigar - Class in picard.sam.markduplicates.util
-
Stores the minimal information needed for optical duplicate detection.
- PhysicalLocationForMateCigar(PhysicalLocation) - Constructor for class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
- PhysicalLocationForMateCigarSet - Class in picard.sam.markduplicates.util
-
This stores records that are comparable for detecting optical duplicates.
- PhysicalLocationForMateCigarSet() - Constructor for class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
- PhysicalLocationInt - Class in picard.sam.util
-
Small class that provides access to the physical location information about a cluster.
- PhysicalLocationInt() - Constructor for class picard.sam.util.PhysicalLocationInt
- PhysicalLocationShort - Class in picard.sam.util
-
Small class that provides access to the physical location information about a cluster.
- PhysicalLocationShort() - Constructor for class picard.sam.util.PhysicalLocationShort
- picard - package picard
- PICARD_INTERVAL_FILE_EXTENSION - Static variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- PICARD_INTERVAL_LIST_FILE_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.ModelSegments
- PICARD_TOOL_EXCEPTION - Static variable in class org.broadinstitute.hellbender.Main
-
Exit value used when a Picard tool returns a non-zero exit code (the actual value is displayed on the command line)
- picard.analysis - package picard.analysis
- picard.analysis.artifacts - package picard.analysis.artifacts
- picard.analysis.directed - package picard.analysis.directed
- picard.analysis.replicates - package picard.analysis.replicates
- picard.annotation - package picard.annotation
- picard.arrays - package picard.arrays
- picard.arrays.illumina - package picard.arrays.illumina
- picard.cmdline - package picard.cmdline
- picard.cmdline.argumentcollections - package picard.cmdline.argumentcollections
- picard.cmdline.programgroups - package picard.cmdline.programgroups
- picard.fastq - package picard.fastq
- picard.filter - package picard.filter
- picard.fingerprint - package picard.fingerprint
- picard.illumina - package picard.illumina
- picard.illumina.parser - package picard.illumina.parser
- picard.illumina.parser.fakers - package picard.illumina.parser.fakers
- picard.illumina.parser.readers - package picard.illumina.parser.readers
- picard.illumina.quality - package picard.illumina.quality
- picard.metrics - package picard.metrics
- picard.nio - package picard.nio
- picard.pedigree - package picard.pedigree
- picard.reference - package picard.reference
- picard.sam - package picard.sam
- picard.sam.markduplicates - package picard.sam.markduplicates
- picard.sam.markduplicates.util - package picard.sam.markduplicates.util
- picard.sam.SamErrorMetric - package picard.sam.SamErrorMetric
- picard.sam.util - package picard.sam.util
- picard.util - package picard.util
- picard.util.help - package picard.util.help
- picard.util.IntervalList - package picard.util.IntervalList
- picard.vcf - package picard.vcf
- picard.vcf.filter - package picard.vcf.filter
- picard.vcf.MendelianViolations - package picard.vcf.MendelianViolations
- picard.vcf.processor - package picard.vcf.processor
- picard.vcf.processor.util - package picard.vcf.processor.util
- PicardCommandLine - Class in picard.cmdline
-
This is the main class of Picard and is the way of executing individual command line programs.
- PicardCommandLine() - Constructor for class picard.cmdline.PicardCommandLine
- PicardCommandLineProgram - Class in org.broadinstitute.hellbender.cmdline
-
Base class for all Picard tools.
- PicardCommandLineProgram() - Constructor for class org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram
- PicardCommandLineProgramExecutor - Class in org.broadinstitute.hellbender.cmdline
-
Adapter shim for use within GATK to run Picard tools.
- PicardCommandLineProgramExecutor(CommandLineProgram) - Constructor for class org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor
- PicardException - Exception in picard
-
Basic Picard runtime exception that, for now, does nothing much
- PicardException(String) - Constructor for exception picard.PicardException
- PicardException(String, Throwable) - Constructor for exception picard.PicardException
- PicardHelpDoclet - Class in picard.util.help
-
Custom Barclay-based Javadoc Doclet used for generating Picard help/documentation.
- PicardHelpDoclet() - Constructor for class picard.util.help.PicardHelpDoclet
- PicardHelpDocWorkUnitHandler - Class in picard.util.help
-
The Picard Documentation work unit handler class that is the companion to PicardHelpDoclet.
- PicardHelpDocWorkUnitHandler(HelpDoclet) - Constructor for class picard.util.help.PicardHelpDocWorkUnitHandler
- PicardHtsPath - Class in picard.nio
- PicardHtsPath(HtsPath) - Constructor for class picard.nio.PicardHtsPath
-
Create a PicardHtsPath from an existing
HtsPathor subclass. - PicardHtsPath(File) - Constructor for class picard.nio.PicardHtsPath
-
Create a PicardHtsPath from a
Filereference. - PicardHtsPath(String) - Constructor for class picard.nio.PicardHtsPath
-
Create a PicardHtsPath from a raw input path string.
- PicardNonZeroExitException - Exception in org.broadinstitute.hellbender.exceptions
-
Exception used to propagate non-zero return values from Picard tools.
- PicardNonZeroExitException(int) - Constructor for exception org.broadinstitute.hellbender.exceptions.PicardNonZeroExitException
- pickAndFilterConfigurations(Set<String>, double) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
- pickBestConfigurations(Set<String>, double) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
-
Pick the best configurations based on a heuristic scoring scheme implemented in
AlignedContig.computeScoreOfConfiguration(List, Set, int). - pickPrimaryAlignment(HitsForInsert) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.BestEndMapqPrimaryAlignmentStrategy
-
Primary alignment was filtered out.
- pickPrimaryAlignment(HitsForInsert) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.BestMapqPrimaryAlignmentSelectionStrategy
-
Primary alignment was filtered out.
- pickPrimaryAlignment(HitsForInsert) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.EarliestFragmentPrimaryAlignmentSelectionStrategy
- pickPrimaryAlignment(HitsForInsert) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.MostDistantPrimaryAlignmentSelectionStrategy
- pickPrimaryAlignment(HitsForInsert) - Method in interface org.broadinstitute.hellbender.utils.read.mergealignment.PrimaryAlignmentSelectionStrategy
-
When this method returns, one alignment has been marked as primary according to the implementation's strategy.
- pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.BestEndMapqPrimaryAlignmentStrategy
-
Primary alignment was filtered out.
- pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.BestMapqPrimaryAlignmentSelectionStrategy
-
Primary alignment was filtered out.
- pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy
- pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.MostDistantPrimaryAlignmentSelectionStrategy
- pickPrimaryAlignment(HitsForInsert) - Method in interface picard.sam.PrimaryAlignmentSelectionStrategy
-
When this method returns, one alignment has been marked as primary according to the implementation's strategy.
- pickTranscripts(Map<Gene.Transcript, int[]>) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
-
Picks the set of transcripts on which the coverage metrics are to be calculated.
- piDUP_FR - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.ComplexVariantSubtype
- piDUP_RF - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.ComplexVariantSubtype
- Pileup - Class in org.broadinstitute.hellbender.tools.walkers.qc
-
Prints read alignments in
samtoolspileup format. - Pileup() - Constructor for class org.broadinstitute.hellbender.tools.walkers.qc.Pileup
- PILEUP_DETECTION_ABSOLUTE_ALT_DEPTH - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- PILEUP_DETECTION_ACETIVE_REGION_LOD_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- PILEUP_DETECTION_BAD_READ_RATIO_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- PILEUP_DETECTION_CHIMERIC_READ_BADNESS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- PILEUP_DETECTION_EDIT_DISTANCE_BADNESS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- PILEUP_DETECTION_ENABLE_INDELS - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- PILEUP_DETECTION_FILTER_COVERAGE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- PILEUP_DETECTION_INDEL_SNP_BLOCKING_RANGE - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- PILEUP_DETECTION_INDEL_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- PILEUP_DETECTION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- PILEUP_DETECTION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- PILEUP_DETECTION_PROPER_PAIR_READ_BADNESS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- PILEUP_DETECTION_SNP_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- PILEUP_DETECTION_TLEN_MEAN_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- PILEUP_DETECTION_TLEN_STD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- PILEUP_ERROR_CORRECTION_LOG_ODDS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- pileupAbsoluteDepth - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- PileupBasedAlleles - Class in org.broadinstitute.hellbender.utils.pileup
-
Helper class for handling pileup allele detection supplement for assembly.
- PileupBasedAlleles() - Constructor for class org.broadinstitute.hellbender.utils.pileup.PileupBasedAlleles
- pileupDetectionArgs - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- PileupDetectionArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Set of arguments for configuring the pileup detection code
- PileupDetectionArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- pileupDiff(ReadPileup, SAMPileupFeature) - Method in class org.broadinstitute.hellbender.tools.walkers.qc.CheckPileup
- PileupElement - Class in org.broadinstitute.hellbender.utils.pileup
-
Represents an individual base in a reads pileup.
- PileupElement(PileupElement) - Constructor for class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Create a new PileupElement that's a copy of toCopy
- PileupElement(GATKRead, int, CigarElement, int, int) - Constructor for class org.broadinstitute.hellbender.utils.pileup.PileupElement
-
Create a new pileup element
- pileupErrorCorrectionLogOdds - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
Enabling this argument may cause fundamental problems with the assembly graph itself.
- PileupReadErrorCorrector - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
- PileupReadErrorCorrector(double, SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupReadErrorCorrector
- PileupSpark - Class in org.broadinstitute.hellbender.tools.spark
-
Prints read alignments in
samtoolspileup format. - PileupSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.PileupSpark
- PileupSummary - Class in org.broadinstitute.hellbender.tools.walkers.contamination
-
Created by David Benjamin on 2/14/17.
- PileupSummary(VariantContext, ReadPileup) - Constructor for class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- PileupSummary(String, int, int, int, int, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- PileupSummary.PileupSummaryComparator - Class in org.broadinstitute.hellbender.tools.walkers.contamination
- PileupSummary.PileupSummaryTableWriter - Class in org.broadinstitute.hellbender.tools.walkers.contamination
- PileupSummaryComparator(SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary.PileupSummaryComparator
- PileupSummaryTableWriter(Path) - Constructor for class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary.PileupSummaryTableWriter
- PIPELINE_MAX_ALT_COUNT - Static variable in class org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyper
- PIPELINE_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The version of the pipeline used for this sample
- PIPELINE_VERSION - Variable in class picard.arrays.GtcToVcf
- PIPELINE_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- PL_FILTER_NAME_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- platform - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Partition
- PLATFORM - Variable in class picard.illumina.IlluminaBasecallsToSam
- PLATFORM - Variable in class picard.sam.FastqToSam
- PLATFORM_MODEL - Variable in class picard.sam.FastqToSam
- PLATFORM_UNIT - Variable in class picard.sam.FastqToSam
- PlatformReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads where the the Read Group platform attribute (RG:PL tag) contains the given string.
- PlatformReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.PlatformReadFilter
- PlatformReadFilter(SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.engine.filters.PlatformReadFilter
- PlatformUnitReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads where the the platform unit attribute (PU tag) contains the given string.
- PlatformUnitReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.PlatformUnitReadFilter
- PlatformUnitReadFilter(SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.engine.filters.PlatformUnitReadFilter
- PLFilterNames - Variable in class org.broadinstitute.hellbender.engine.filters.PlatformReadFilter
- ploidy - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- ploidy() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
- ploidy() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculator
-
Returns the ploidy for this genotype likelihood calculator.
- PLOIDY_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- PLOIDY_TABLE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- ploidyModel() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingData
-
Returns the ploidy model that corresponds to the data provided.
- PloidyModel - Interface in org.broadinstitute.hellbender.tools.walkers.genotyper
-
Information about the number of chromosome per sample at a given location.
- PloidyTable - Class in org.broadinstitute.hellbender.tools.sv.cluster
- PloidyTable(Path) - Constructor for class org.broadinstitute.hellbender.tools.sv.cluster.PloidyTable
- PloidyTable(Map<String, Map<String, Integer>>) - Constructor for class org.broadinstitute.hellbender.tools.sv.cluster.PloidyTable
- PlotDenoisedCopyRatios - Class in org.broadinstitute.hellbender.tools.copynumber.plotting
-
Creates plots of standardized and denoised copy ratios.
- PlotDenoisedCopyRatios() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.plotting.PlotDenoisedCopyRatios
- PlotModeledSegments - Class in org.broadinstitute.hellbender.tools.copynumber.plotting
-
Creates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates.
- PlotModeledSegments() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.plotting.PlotModeledSegments
- PLUS - Enum constant in enum class picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
- PNEXT - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestField
- pNormalizeLogProbability(double[]) - Static method in class picard.util.MathUtil
-
Takes a complete set of mutually exclusive logPosteriors and converts them to probabilities that sum to 1 with as much fidelity as possible.
- pNormalizeVector(double[]) - Static method in class picard.util.MathUtil
-
Takes a vector of numbers and converts it to a vector of probabilities that sum to 1 with as much fidelity as possible.
- POINTS_PER_SEGMENTATION_WINDOW - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationSegmenter
- poll(SamRecordTrackingBuffer, SAMFileHeader, OpticalDuplicateFinder, LibraryIdGenerator) - Method in class picard.sam.markduplicates.util.MarkQueue
-
The poll method will return the read end that is *not* the duplicate of all comparable read ends that have been seen.
- POLYCLONAL - Enum constant in enum class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
- POLYMERASE_SLIPPAGE - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- POLYMERASE_SLIPPAGE_QUAL_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- PolymeraseSlippageFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- PolymeraseSlippageFilter(int, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.PolymeraseSlippageFilter
- POLYMORPHIC_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- pon - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
-
A panel of normals can be a useful (optional) input to help filter out commonly seen sequencing noise that may appear as low allele-fraction somatic variants.
- PON_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- PON_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- PON_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- POOL_SIZE - Variable in class picard.util.BaitDesigner
- POOLED_BAM_DEPTH_ANNOTATION_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithBamDepth
- popReadyAssemblyRegions(int, int, int, boolean) - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
-
Get the next completed assembly regions from this profile, and remove all states supporting them from this profile Takes the current profile and finds all of the active / inactive from the start of the profile that are ready.
- popStat(float) - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.CDF
-
An observed value for which the specified fraction of the sample population has that value or less.
- populateGenotypesForMissingSamplesWithAlleles(SVCallRecord, Set<String>, boolean, PloidyTable, VCFHeader) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
-
Populates genotypes for samples not present in the given record.
- POPULATION_AF_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- popVariantBubbles - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- Pos - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- POS - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestField
- PosFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- PosFileFaker() - Constructor for class picard.illumina.parser.fakers.PosFileFaker
- PosFileReader - Class in picard.illumina.parser.readers
-
The pos file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
- PosFileReader(File) - Constructor for class picard.illumina.parser.readers.PosFileReader
- position - Variable in class org.broadinstitute.hellbender.utils.reference.AbsoluteCoordinates.Relative
- Position - Enum constant in enum class picard.illumina.parser.IlluminaDataType
- POSITION - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The position of the SNP on the chromosome.
- POSITION - Variable in class picard.analysis.RrbsCpgDetailMetrics
-
Position within the sequence of the CpG site
- PositionalDownsampler - Class in org.broadinstitute.hellbender.utils.downsampling
-
PositionalDownsampler: Downsample each stack of reads at each alignment start to a size <= a target coverage using a
ReservoirDownsampler. - PositionalDownsampler(int, SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.utils.downsampling.PositionalDownsampler
-
Construct a PositionalDownsampler
- PositionalDownsampler(int, SAMFileHeader, boolean) - Constructor for class org.broadinstitute.hellbender.utils.downsampling.PositionalDownsampler
- PositionBasedDownsampleSam - Class in picard.sam
-
Summary
- PositionBasedDownsampleSam() - Constructor for class picard.sam.PositionBasedDownsampleSam
- PositionInfo(float, float, int, int) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
- POSITIVE - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.Strand
- POSITIVE - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
- POSITIVE_LABEL_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- PosParser - Class in picard.illumina.parser
-
PosParser parses multiple files formatted as one of the three file formats that contain position information only (pos, locs, and clocs).
- PosParser(IlluminaFileMap, int, IlluminaFileUtil.SupportedIlluminaFormat) - Constructor for class picard.illumina.parser.PosParser
- PosParser(IlluminaFileMap, IlluminaFileUtil.SupportedIlluminaFormat) - Constructor for class picard.illumina.parser.PosParser
- POSSIBLE_FP_ADJACENT_TP_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- POSSIBLE_NUMT_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- PossibleDeNovo - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Existence of a de novo mutation in at least one of the given families
- PossibleDeNovo() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.PossibleDeNovo
- PossibleDeNovo(Set<Trio>, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.PossibleDeNovo
- PossibleDeNovo(GATKPath) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.PossibleDeNovo
- POST_ASSEMBLER_OFF - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection.OffRampTypeEnum
- POST_ASSEMBLER_ON - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection.OnRampTypeEnum
- POST_FILTER_ON - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection.OnRampTypeEnum
- postAssemblerOffRamp - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerEngine
- postAssemblerOnRamp - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerEngine
- PostAssemblerOnRamp - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
- PostAssemblerOnRamp(String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.PostAssemblerOnRamp
- postDiNucleotideStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies a base onto the reference base that it covers and the following base, possibly reverse complemented if the read has been reversed by the aligner.
- POSTERIOR_10 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
- POSTERIOR_20 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
- POSTERIOR_30 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
- POSTERIOR_40 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
- POSTERIOR_50 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
- POSTERIOR_60 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
- POSTERIOR_70 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
- POSTERIOR_80 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
- POSTERIOR_90 - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
- POSTERIOR_LOWER - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
- POSTERIOR_MODE - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
- POSTERIOR_UPPER - Enum constant in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
- PosteriorProbabilitiesOptions(double, double, boolean, boolean, boolean, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.variantutils.PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions
- PosteriorProbabilitiesUtils - Class in org.broadinstitute.hellbender.tools.walkers.variantutils
- PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions - Class in org.broadinstitute.hellbender.tools.walkers.variantutils
-
A class to wrangle all the various and sundry genotype posterior options, mostly from CalculateGenotypePosteriors
- posteriorProbabilityOfError(double, double) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- posteriorProbabilityOfError(VariantContext, double, int) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- posteriorProbabilityOfNormalArtifact(double) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- posteriors(double[], double[]) - Static method in class org.broadinstitute.hellbender.utils.NaturalLogUtils
- posteriorsKey - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- postFilterOnRamp - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerEngine
- PostFilterOnRamp - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
- PostFilterOnRamp(String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.PostFilterOnRamp
- postProcessForHaplotypeFinding(File, Locatable) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
- postProcessForHaplotypeFinding(File, Locatable) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
-
Generate the junction trees and prune them (optionally printing the graph stages as output)
- postProcessForHaplotypeFinding(File, Locatable) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
- PostprocessGermlineCNVCalls - Class in org.broadinstitute.hellbender.tools.copynumber
-
Postprocesses the output of
GermlineCNVCallerand generates VCF files as well as a concatenated denoised copy ratio file. - PostprocessGermlineCNVCalls() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- PostProcessReadsForRSEM - Class in org.broadinstitute.hellbender.tools.walkers.qc
-
Performs post-processing steps to get a bam aligned to a transcriptome ready for RSEM (https://github.com/deweylab/RSEM) Suppose the read name "Q1" aligns to multiple loci in the transcriptome.
- PostProcessReadsForRSEM() - Constructor for class org.broadinstitute.hellbender.tools.walkers.qc.PostProcessReadsForRSEM
- POWER_HEADER_LINE - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- POWER_INFO_FIELD_KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- PowerCalculationUtils - Class in org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
- Ppv(GenotypeConcordanceScheme, GenotypeConcordanceStates.CallState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the PPV defined by the scheme across the subset of call states.
- PPV - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- PQContext(Iterator<F>, SAMSequenceDictionary, Object) - Constructor for class org.broadinstitute.hellbender.engine.MultiFeatureWalker.PQContext
- PQEntry(MultiFeatureWalker.PQContext<F>, F) - Constructor for class org.broadinstitute.hellbender.engine.MultiFeatureWalker.PQEntry
- PRE_ADAPTER_DETAILS_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
- PRE_ADAPTER_IN - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- PRE_ADAPTER_SUMMARY_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
- PRE_ASSEMBLER_OFF - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection.OffRampTypeEnum
- PRE_FILTER_OFF - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection.OffRampTypeEnum
- PRE_INDEL_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- PRE_TANGENT_NORMALIZED_COUNTS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- PRE_TANGENT_NORMALIZED_COUNTS_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- PreAdapterDetailMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
- PreAdapterSummaryMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
- preAssemblerOffRamp - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerEngine
- predecessor(SVKmer.Base, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer
- predecessor(SVKmer.Base, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
-
Returns a new SVKmerLong that's like this one, but with its trailing base discarded and a new one added to the start.
- predecessor(SVKmer.Base, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
-
Returns a new SVKmerShort that's like this one, but with its trailing base discarded and a new one added to the start.
- PredicateFilterDecoratingClosableIterator<T> - Class in picard.vcf.processor.util
-
Performs on-the-fly filtering of the provided
VariantContextIteratorsuch that only variants that satisfy all predicates are emitted. - PredicateFilterDecoratingClosableIterator(CloseableIterator<T>, Collection<Predicate<T>>) - Constructor for class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
- PREDICTED_INSERT_SIZE - Variable in class picard.sam.FastqToSam
- preDiNucleotideStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies a base onto the reference base that it covers and the preceding base, possibly reverse complemented if the read has been reversed by the aligner.
- PREFER_PLS - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod
-
Use PLs unless they are unavailable, in which case use best match to original
- PREFILTER_QUAL_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
-
These are the parameters that control allele filtering / haplotype pruning behaviour.
- PREFILTER_SOR_THRESHOLD - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- preFilterOffRamp - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerEngine
- PreFilterOffRamp - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
- PreFilterOffRamp(String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.PreFilterOffRamp
- prefilterQualThreshold - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- prefilterSorThreshold - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- prefix - Variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- prependSequence - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- PREPHASING_APPLIED - Variable in class picard.illumina.IlluminaPhasingMetrics
-
Median pre-phasing value across all tiles in a lane, applied to the first and second template reads
- PREPHASING_BASE - Enum constant in enum class picard.illumina.parser.IlluminaMetricsCode
- prephasingWeight - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
- preprocess(double[][]) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.BGMMVariantAnnotationsScorer
- preprocess(SvDiscoveryInputMetaData, JavaRDD<GATKRead>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark
-
First parse the input alignments, then classify the assembly contigs based on their alignment signatures, and return the contigs that are classified together for downstream inference.
- preprocessAndStandardizeSample(double[], double[]) - Static method in class org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisingUtils
-
Preprocess (i.e., transform to fractional coverage and correct GC bias) and standardize read counts for samples when no panel of normals is available.
- preprocessAnnotationsWithBGMMAndWriteHDF5(List<String>, String, File, Logger) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.BGMMVariantAnnotationsScorer
- preprocessIntervalList(IntervalList) - Method in interface picard.util.IntervalList.IntervalListScatterer
-
A function that will be called on an IntervalList prior to splitting it into sub-lists, and is a point where implementations can chose to impose some conditions on the lists, for example, merging overlapping/abutting intervals, removing duplicates, etc.
- preprocessIntervalList(IntervalList) - Method in class picard.util.IntervalList.IntervalListScattererWithSubdivision
- PreprocessIntervals - Class in org.broadinstitute.hellbender.tools.copynumber
-
Prepares bins for coverage collection.
- PreprocessIntervals() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervals
- preprocessReads() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
- preprocessReads() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
- preprocessReads() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
-
Since we want to duplicate non-unique kmers in the graph code we must determine what those kmers are
- PRESERVE_QSCORES_LESS_THAN - Variable in class org.broadinstitute.hellbender.tools.ApplyBQSRArgumentCollection
-
This flag tells GATK not to modify quality scores less than this value.
- PRESERVE_QSCORES_LESS_THAN - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
-
This flag tells GATK not to modify quality scores less than this value.
- prettyPrint() - Method in enum class org.broadinstitute.hellbender.utils.recalibration.EventType
- prettyPrintSequenceRecords(SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
- previousHaplotypeBases - Variable in class org.broadinstitute.hellbender.utils.pairhmm.FlowBasedPairHMM
- previousHaplotypeBases - Variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- previousReadBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies bases into the previous (uppercase) base as it was read from the sequencer (i.e.
- PRIMARY_ALIGNMENT_STRATEGY - Variable in class picard.sam.MergeBamAlignment
- PRIMARY_LINE - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- PRIMARY_MAPPED_ONLY - Enum constant in enum class picard.sam.markduplicates.CheckDuplicateMarking.Mode
- PRIMARY_ONLY - Enum constant in enum class picard.sam.markduplicates.CheckDuplicateMarking.Mode
- PRIMARY_PROPER_PAIR_ONLY - Enum constant in enum class picard.sam.markduplicates.CheckDuplicateMarking.Mode
- PRIMARY_READS - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterMetrics
-
Number of input reads that are not secondary or supplementary alignments
- PrimaryAlignmentKey - Class in org.broadinstitute.hellbender.utils.read
-
It is useful to define a key such that the key will occur at most once among the primary alignments in a given file (assuming the file is valid).
- PrimaryAlignmentKey - Class in picard.sam.util
-
It is useful to define a key such that the key will occur at most once among the primary alignments in a given file (assuming the file is valid).
- PrimaryAlignmentKey(SAMRecord) - Constructor for class org.broadinstitute.hellbender.utils.read.PrimaryAlignmentKey
- PrimaryAlignmentKey(SAMRecord) - Constructor for class picard.sam.util.PrimaryAlignmentKey
- PrimaryAlignmentSelectionStrategy - Interface in org.broadinstitute.hellbender.utils.read.mergealignment
-
Given a set of alignments for a read or read pair, mark one alignment as primary, according to whatever strategy is appropriate.
- PrimaryAlignmentSelectionStrategy - Interface in picard.sam
-
Given a set of alignments for a read or read pair, mark one alignment as primary, according to whatever strategy is appropriate.
- PrimaryLineReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.PrimaryLineReadFilter
- primaryReads(JavaRDD<GATKRead>) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSUtils
- print(PrintStream) - Method in class org.broadinstitute.hellbender.utils.report.GATKReport
-
Print all tables contained within this container to a PrintStream
- print(PrintStream, GATKReportTable.Sorting) - Method in class org.broadinstitute.hellbender.utils.report.GATKReport
-
Print all tables contained within this container to a PrintStream
- print(PrintWriter) - Method in class org.broadinstitute.hellbender.tools.dragstr.STRDecimationTable
- print(Object) - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalTextOutputArgumentCollection
-
Prints value (value.toString()) to the output path, if output is not null Overwrites any pre-existing output file rather than appending.
- print(DragstrParams, GATKPath, Object...) - Static method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParamUtils
- PRINT_DELIM - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
- PRINT_SUMMARY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark
- PrintBGZFBlockInformation - Class in org.broadinstitute.hellbender.tools
-
A diagnostic tool that prints information about the compressed blocks in a BGZF format file, such as a .vcf.gz file or a .bam file.
- PrintBGZFBlockInformation() - Constructor for class org.broadinstitute.hellbender.tools.PrintBGZFBlockInformation
- printDebugHistograms() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
-
Print the generated graphs to the graphWriter
- printDecoratedExceptionMessage(PrintStream, Exception, String) - Static method in class org.broadinstitute.hellbender.Main
-
Prints the given message (may be null) to the provided stream, adding adornments and formatting.
- PrintDistantMates - Class in org.broadinstitute.hellbender.tools
- PrintDistantMates() - Constructor for class org.broadinstitute.hellbender.tools.PrintDistantMates
- printEfficiency(Level) - Method in class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
-
Print the efficiency (hits / queries) to logger with priority
- printGraph(File, int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Print out the graph in the dot language for visualization
- printGraph(PrintStream, boolean, int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
- printHeader() - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VQSLODTranche
- printIGVFormatHeader(PrintStream, String, String...) - Static method in class org.broadinstitute.hellbender.utils.IGVUtils
-
Prints a header for an IGV-format file.
- printIGVFormatRow(PrintStream, Locatable, String, double...) - Static method in class org.broadinstitute.hellbender.utils.IGVUtils
-
Prints a row in an IGV-format file.
- printLibraryVersions() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
-
Output versions of important dependencies to the logger.
- println(Object) - Method in class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalTextOutputArgumentCollection
-
Prints value (value.toString() + "\n") to the output path, if output is not null Overwrites any pre-existing output file rather than appending.
- println(String) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingDebugger
- PrintMissingComp - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
- PrintMissingComp(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.PrintMissingComp
- printOutResults(String) - Method in class org.broadinstitute.hellbender.tools.validation.CompareMatrix
- PrintReadCounts - Class in org.broadinstitute.hellbender.tools.sv
-
Prints (and optionally subsets) an rd (DepthEvidence) file or a counts file as one or more (for multi-sample DepthEvidence files) counts files for CNV determination.
- PrintReadCounts() - Constructor for class org.broadinstitute.hellbender.tools.sv.PrintReadCounts
- PrintReads - Class in org.broadinstitute.hellbender.tools
-
Write reads from SAM format file (SAM/BAM/CRAM) that pass criteria to a new file.
- PrintReads() - Constructor for class org.broadinstitute.hellbender.tools.PrintReads
- PrintReadsHeader - Class in org.broadinstitute.hellbender.tools
- PrintReadsHeader() - Constructor for class org.broadinstitute.hellbender.tools.PrintReadsHeader
- PrintReadsSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines
- PrintReadsSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark
- printSettings() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
-
Output a curated set of important settings to the logger.
- printSimplifiedGraph(File, int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
-
Print out the graph in the dot language for visualization for the graph after merging the graph into a seq graph.
- printStandard(boolean) - Method in class org.broadinstitute.hellbender.utils.runtime.OutputStreamSettings
- printStartupMessage(ZonedDateTime) - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
-
Prints a user-friendly message on startup with some information about who we are and the runtime environment.
- printSummary - Variable in class org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark
- PrintSVEvidence - Class in org.broadinstitute.hellbender.tools.sv
-
Merges locus-sorted files of evidence for structural variation into a single output file.
- PrintSVEvidence() - Constructor for class org.broadinstitute.hellbender.tools.sv.PrintSVEvidence
- printUnknown(Set<Class<?>>, String) - Static method in class picard.cmdline.PicardCommandLine
-
When a command does not match any known command, searches for similar commands, using the same method as GIT
- PrintVariantsSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines
-
Print out variants from a VCF file.
- PrintVariantsSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.PrintVariantsSpark
- printVersionInfo(PrintStream) - Method in class org.broadinstitute.hellbender.Main
-
Prints version information for the toolkit, including versions of important libraries.
- prior - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.AllelePseudoDepth
- prior - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrainingSet
- prior - Variable in class org.broadinstitute.hellbender.utils.pairhmm.FlowBasedPairHMM
- prior - Variable in class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM
- PRIOR_ERROR - Static variable in class picard.sam.SamErrorMetric.ErrorMetric
- PRIOR_Q - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- PRIORITIZE - Enum constant in enum class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.GenotypeMergeType
-
Take genotypes in priority order (see the priority argument).
- PRO_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that supports the presence of this artifact.
- PRO_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The number of REF_BASE:REF_BASE alignments having a read number and orientation that supports the presence of this artifact.
- PROB_EXPLICIT_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- PROB_SF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- probability(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistribution
- probability(int) - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BetaBinomialDistribution
- PROBABILITY - Variable in class picard.sam.DownsampleSam
- PROBABILITY - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- PROBABILITY_RATIO_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- probabilityOfSequencingError(Datum) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel
- probabilityQuantization - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- probabilityRatioThreshold - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- probabilityScalingFactor - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- PROBE_A - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- PROBE_B - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- PROBE_SEQUENCE_MISMATCH - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Probe sequence not found in reference.
- PROBE_SEQUENCE_STRAND_INVALID - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Deprecated.- but used in existing extended manifest files.
- PROBE_SET - Variable in class picard.analysis.directed.TargetMetrics
-
The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection run
- PROBE_TERRITORY - Variable in class picard.analysis.directed.TargetMetrics
-
The number of unique bases covered by the intervals of all probes in the probe set
- process - Variable in class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase
- process() - Method in class picard.vcf.processor.VariantProcessor
- process(ReadPileup, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2CountsCollector
- PROCESS_SINGLE_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
- processAlignments(JavaRDD<LocusWalkerContext>, JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark
-
Process the alignments and write output.
- processAlignments(JavaRDD<LocusWalkerContext>, JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSpark
- processAlignments(JavaRDD<LocusWalkerContext>, JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleLocusWalkerSpark
- processAlignments(JavaRDD<LocusWalkerContext>, JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.PileupSpark
- processAllCommandLinePrograms(List<String>, BiConsumer<Class<CommandLineProgram>, CommandLineProgramProperties>) - Static method in class picard.cmdline.PicardCommandLine
-
Process each
CommandLineProgram-derived class given a list of packages. - processAssemblyRegions(JavaRDD<AssemblyRegionWalkerContext>, JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark
-
Process the assembly regions and write output.
- processAssemblyRegions(JavaRDD<AssemblyRegionWalkerContext>, JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerSpark
- processAssemblyRegions(JavaRDD<AssemblyRegionWalkerContext>, JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.HaplotypeCallerSpark
- processCalls(byte[]) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathBuilder
- processCigarForInitialEvents(int) - Method in class org.broadinstitute.hellbender.utils.haplotype.EventMap
- processColumns(TableColumnCollection) - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Process the header line's column names.
- processCommentLine(String, long) - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Called with the content of the comment line every time one is found in the input.
- ProcessController - Class in org.broadinstitute.hellbender.utils.runtime
-
Facade to Runtime.exec() and java.lang.Process.
- ProcessController() - Constructor for class org.broadinstitute.hellbender.utils.runtime.ProcessController
- ProcessControllerAckResult - Class in org.broadinstitute.hellbender.utils.runtime
-
Command acknowledgements that are returned from a process managed by StreamingProcessController.
- ProcessControllerAckResult(boolean) - Constructor for class org.broadinstitute.hellbender.utils.runtime.ProcessControllerAckResult
-
Creates an ack result, for ACK or NCK.
- ProcessControllerAckResult(String) - Constructor for class org.broadinstitute.hellbender.utils.runtime.ProcessControllerAckResult
-
Creates an (negative NKM) ack result, with a message.
- ProcessControllerBase<CAPTURE_POLICY extends CapturedStreamOutput> - Class in org.broadinstitute.hellbender.utils.runtime
- ProcessControllerBase() - Constructor for class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase
- ProcessControllerBase.OutputCapture - Class in org.broadinstitute.hellbender.utils.runtime
- ProcessControllerBase.ProcessStream - Enum Class in org.broadinstitute.hellbender.utils.runtime
- processDeletionLocus(SamLocusIterator.RecordAndOffset, SamLocusIterator.LocusInfo) - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
-
Checks if the same record has been seen at the previous locus already, thereby determining whether or not a deletion has already been processed.
- PROCESSED_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- PROCESSED_TRANSCRIPT - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- processedMultiIndelRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- processedMultiSnpRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- processFile() - Method in interface picard.analysis.WgsMetricsProcessor
-
Method processes the input data and accumulates result data
- processFile() - Method in class picard.analysis.WgsMetricsProcessorImpl
-
Method gets the data from iterator for each locus and processes it with the help of collector.
- processIntervals(JavaRDD<IntervalWalkerContext>, JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.IntervalWalkerSpark
-
Process the intervals and write output.
- processIntervals(JavaRDD<IntervalWalkerContext>, JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalkerSpark
- processNamedArgument(Map<String, Object>, NamedArgumentDefinition, String) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLWorkUnitHandler
- processNamedArgument(DocWorkUnit, Map<String, List<Map<String, Object>>>, NamedArgumentDefinition) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLWorkUnitHandler
-
Add the named argument
argDefto the property map if applicable. - ProcessOutput - Class in org.broadinstitute.hellbender.utils.runtime
- ProcessOutput(int, StreamOutput, StreamOutput) - Constructor for class org.broadinstitute.hellbender.utils.runtime.ProcessOutput
-
The output of a process.
- processPositionalArguments(CommandLineArgumentParser, Map<String, List<Map<String, Object>>>) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLWorkUnitHandler
- processRead(GATKRead, ReferenceDataSource, Iterable<? extends Locatable>) - Method in class org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
-
For each read at this locus get the various covariate values and increment that location in the map based on whether or not the base matches the reference at this particular location
- processReads(JavaRDD<ReadWalkerContext>, JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.ReadWalkerSpark
-
Process the reads and write output.
- processReads(JavaRDD<ReadWalkerContext>, JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceSpark
- processReads(JavaRDD<ReadWalkerContext>, JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariantsSpark
- ProcessSettings - Class in org.broadinstitute.hellbender.utils.runtime
- ProcessSettings(String[]) - Constructor for class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- ProcessSettings(String[], boolean, File, Map<String, String>, InputStreamSettings, OutputStreamSettings, OutputStreamSettings) - Constructor for class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- processState(ActivityProfileState) - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
-
Process justAddedState, returning a collection of derived states that actually be added to the stateList The purpose of this function is to transform justAddedStates, if needed, into a series of atomic states that we actually want to track.
- processState(ActivityProfileState) - Method in class org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile
-
Band pass the probabilities in the ActivityProfile, producing a new profile that's band pass filtered
- processStream - Variable in class org.broadinstitute.hellbender.utils.runtime.CapturedStreamOutput
- processTilesAndWritePerSampleOutputs(Set<String>) - Method in class picard.illumina.BasecallsConverter
-
Abstract method for processing tiles of data and outputting records for each barcode.
- processTilesAndWritePerSampleOutputs(Set<String>) - Method in class picard.illumina.SortedBasecallsConverter
-
Set up tile processing and record writing threads for this converter.
- processTilesAndWritePerSampleOutputs(Set<String>) - Method in class picard.illumina.UnsortedBasecallsConverter
-
Set up tile processing and record writing threads for this converter.
- processTranscriptList(Set<String>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine
-
Processes the given
Setinto a list of transcript IDs. - processVariants(JavaRDD<VariantWalkerContext>, JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.VariantWalkerSpark
-
Process the variants and write output.
- processVariants(JavaRDD<VariantWalkerContext>, JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleVariantWalkerSpark
- processVariants(JavaRDD<VariantWalkerContext>, JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.PrintVariantsSpark
- processWorkUnitTemplate(Configuration, DocWorkUnit, List<Map<String, String>>, List<Map<String, String>>) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLDoclet
- produceAnnotatedVcFromAssemblyEvidence(SvType, SAMSequenceDictionary, SVIntervalTree<VariantContext>, String) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence
-
Produces a VC from a
NovelAdjacencyAndAltHaplotype(consensus among different assemblies if they all point to the same breakpoint). - produceAnnotatedVcFromEvidenceTargetLink(EvidenceTargetLink, SvType) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.AnnotatedVariantProducer
- produceLinkedAssemblyBasedVariants(SvType, SvType, SAMSequenceDictionary, SVIntervalTree<VariantContext>, String, String) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence
-
Given novel adjacency and inferred variant types that should be linked together, produce annotated, and linked VCF records.
- producePlot - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetricsArgumentCollection
- product(double...) - Method in class picard.util.MathUtil.LogMath
-
Computes the sum of the provided log values.
- PROGRAM - Variable in class picard.analysis.CollectMultipleMetrics
- PROGRAM_GROUP - Variable in class picard.sam.FastqToSam
- PROGRAM_GROUP_COMMAND_LINE - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- PROGRAM_GROUP_COMMAND_LINE - Variable in class picard.sam.MergeBamAlignment
- PROGRAM_GROUP_NAME - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- PROGRAM_GROUP_NAME - Variable in class picard.sam.MergeBamAlignment
- PROGRAM_GROUP_VERSION - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- PROGRAM_GROUP_VERSION - Variable in class picard.sam.MergeBamAlignment
- PROGRAM_RECORD_ID - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- PROGRAM_RECORD_ID - Variable in class picard.sam.MergeBamAlignment
- PROGRAM_RECORD_ID_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- PROGRAM_RECORD_ID_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- programName - Variable in class org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram
- PROGRESS_STEP_INTERVAL - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- PROGRESS_STEP_INTERVAL - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- progressBytesRead - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- ProgressLogger - Class in org.broadinstitute.hellbender.utils.runtime
-
Facilitate consistent logging output when progressing through a stream of SAM records.
- ProgressLogger(Logger) - Constructor for class org.broadinstitute.hellbender.utils.runtime.ProgressLogger
-
Construct a progress logger with the desired log, the verb "Processed" and a period of 1m records.
- ProgressLogger(Logger, int) - Constructor for class org.broadinstitute.hellbender.utils.runtime.ProgressLogger
-
Construct a progress logger with the desired log and frequency and the verb "Processed".
- ProgressLogger(Logger, int, String) - Constructor for class org.broadinstitute.hellbender.utils.runtime.ProgressLogger
-
Construct a progress logger.
- ProgressLogger(Logger, int, String, String) - Constructor for class org.broadinstitute.hellbender.utils.runtime.ProgressLogger
-
Construct a progress logger.
- progressMeter - Variable in class org.broadinstitute.hellbender.engine.GATKTool
-
Progress meter to print out traversal statistics.
- ProgressMeter - Class in org.broadinstitute.hellbender.engine
-
A basic progress meter to print out the number of records processed (and other metrics) during a traversal at a configurable time interval.
- ProgressMeter() - Constructor for class org.broadinstitute.hellbender.engine.ProgressMeter
-
Create a progress meter with the default update interval of
ProgressMeter.DEFAULT_SECONDS_BETWEEN_UPDATESseconds and the default time functionProgressMeter.DEFAULT_TIME_FUNCTION. - ProgressMeter(double) - Constructor for class org.broadinstitute.hellbender.engine.ProgressMeter
-
Create a progress meter with a custom update interval and the default time function
ProgressMeter.DEFAULT_TIME_FUNCTION - ProgressMeter(double, boolean) - Constructor for class org.broadinstitute.hellbender.engine.ProgressMeter
-
Create a progress meter with a custom update interval and the default time function
ProgressMeter.DEFAULT_TIME_FUNCTION, and allows the ProgressMeter to be set as disabled - progressPercentDisplayIncrement - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- ProgressReportingDelegatingCodec<A extends htsjdk.tribble.Feature,
B> - Class in org.broadinstitute.hellbender.utils.codecs -
This class is useful when we want to report progress when indexing.
- ProgressReportingDelegatingCodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec
- ProgressReportingDelegatingCodec(FeatureCodec<A, B>, double) - Constructor for class org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec
- PROLINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- promote(int[]) - Static method in class picard.util.MathUtil
-
"Promotes" an int[] into a double array with the same values (or as close as precision allows).
- PROMOTER - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- PROMOTER_WINDOW_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate
- PROPAGATION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- PROPER - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
- PROPERLY_PAIRED - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- ProperlyPairedReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.ProperlyPairedReadFilter
- PropertyUtils - Class in picard.util
-
Utility for loading properties files from resources.
- PropertyUtils() - Constructor for class picard.util.PropertyUtils
- proportionsAboveThresholds(List<ArrayList<Integer>>, List<Double>) - Static method in class picard.analysis.TheoreticalSensitivity
- PROTEIN_CODING - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- PROTEIN_CODING_GTF_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate
- ProteinChangeInfo - Class in org.broadinstitute.hellbender.tools.funcotator
-
Class representing the change in the protein sequence for a specific reference/alternate allele pair in a variant.
- PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN - Variable in class picard.illumina.MarkIlluminaAdapters
- pruneJunctionTrees(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
-
Traverse all of the junction trees in the graph and remove branches supported by < minimumEdgeWeight edges recursively.
- pruneLowWeightChains(BaseGraph<V, E>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.ChainPruner
- PRUNING_LOD_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- PRUNING_SEEDING_LOD_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- pruningLogOddsThreshold - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
Log-10 likelihood ratio threshold for adaptive pruning algorithm.
- pruningSeedingLogOddsThreshold - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
Log-10 likelihood ratio threshold for adaptive pruning algorithm.
- pSameAlleleWhenMismatchingUmi - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
When the UMIs mismatch, we expect about the same number of different alleles as the same (assuming that different UMI implies biological duplicate) thus, this value should be near 0.5
- pSameUmiInIndependentBiDup - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
When the alleles are different, we know that this is a biological duplication, thus we expect nearly all the UMIs to be different (allowing for equality due to chance).
- PSBuildReferenceTaxonomyUtils - Class in org.broadinstitute.hellbender.tools.spark.pathseq
- PSBuildReferenceTaxonomyUtils() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSBuildReferenceTaxonomyUtils
- PSBwaAligner - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Loads Bwa index and aligns reads.
- PSBwaAligner(PSBwaArgumentCollection, boolean) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaAligner
- PSBwaAlignerSpark - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Wrapper class for using the PathSeq Bwa aligner class in Spark.
- PSBwaAlignerSpark(JavaSparkContext, PSBwaArgumentCollection) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaAlignerSpark
- PSBwaArgumentCollection - Class in org.broadinstitute.hellbender.tools.spark.pathseq
- PSBwaArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection
- PSBwaFilter - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Aligns using BWA and filters out reads above the minimum coverage and identity.
- PSBwaFilter(String, int, int, int, boolean) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaFilter
- PSBwaUtils - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Utility functions for PathSeq Bwa tool
- PSBwaUtils() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaUtils
- PSEUDO_AUTOSOMAL_REGIONS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- PSEUDO_CONSENS - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
member of the pseudogene set predicted by YALE, UCSC and HAVANA.
- PSEUDO_DEPTH_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- PSEUDO_FRACTION_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapStatus
-
Pseudogene annotations (excluding polymorphic).
- PSFilter - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Performs PathSeq filtering steps and manages associated resources.
- PSFilter(JavaSparkContext, PSFilterArgumentCollection, SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilter
- PSFilterArgumentCollection - Class in org.broadinstitute.hellbender.tools.spark.pathseq
- PSFilterArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- PSFilterEmptyLogger - Class in org.broadinstitute.hellbender.tools.spark.pathseq.loggers
-
Dummy filter metrics class that does nothing
- PSFilterEmptyLogger() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterEmptyLogger
- PSFilterFileLogger - Class in org.broadinstitute.hellbender.tools.spark.pathseq.loggers
-
Logs filtering read counts to metrics file
- PSFilterFileLogger(MetricsFile<PSFilterMetrics, Long>, String) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterFileLogger
- PSFilterLogger - Interface in org.broadinstitute.hellbender.tools.spark.pathseq.loggers
-
Interface for filter metrics logging
- PSFilterMetrics - Class in org.broadinstitute.hellbender.tools.spark.pathseq.loggers
-
Metrics that are calculated during the PathSeq filter
- PSFilterMetrics() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterMetrics
- PSKmerBloomFilter - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Kmer Bloom Filter class that encapsulates the filter, kmer size, and kmer mask
- PSKmerBloomFilter(LongBloomFilter, int, SVKmerShort, long) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerBloomFilter
-
Note values in the Bloom filter should have been run through PSKmerCollection's canonicalizeAndMask()
- PSKmerBloomFilter.Serializer - Class in org.broadinstitute.hellbender.tools.spark.pathseq
- PSKmerCollection - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Classes that provide a way to test kmers for set membership and keep track of the kmer size and mask
- PSKmerCollection() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerCollection
- PSKmerSet - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Kmer Hopscotch set class that encapsulates the filter, kmer size, and kmer mask
- PSKmerSet(LargeLongHopscotchSet, int, SVKmerShort) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet
-
Note values in the input set should have been run through PSKmerCollection's canonicalizeAndMask()
- PSKmerSet.Serializer - Class in org.broadinstitute.hellbender.tools.spark.pathseq
- PSKmerUtils - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
PathSeq utilities for kmer libraries
- PSKmerUtils() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerUtils
- PSPairedUnpairedSplitterSpark - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Class for separating paired and unpaired reads in an RDD
- PSPairedUnpairedSplitterSpark(JavaRDD<GATKRead>, int, boolean) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSPairedUnpairedSplitterSpark
-
Gets RDDs of the paired and unpaired reads.
- PSPathogenAlignmentHit - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Stores taxonomic IDs that were hits of a read pair.
- PSPathogenAlignmentHit(Collection<Integer>, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenAlignmentHit
- PSPathogenReferenceTaxonProperties - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Helper class for ClassifyReads that stores the name, taxonomic class and parent, reference length, and reference contig names of a given taxon in the pathogen reference.
- PSPathogenReferenceTaxonProperties() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
- PSPathogenReferenceTaxonProperties(String) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
- PSPathogenTaxonScore - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Pathogen abundance scores assigned to a taxonomic node and reported by the PathSeqScoreSpark tool.
- PSPathogenTaxonScore() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- PSScoreArgumentCollection - Class in org.broadinstitute.hellbender.tools.spark.pathseq
- PSScoreArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- PSScoreFileLogger - Class in org.broadinstitute.hellbender.tools.spark.pathseq.loggers
-
Logs number of mapped and unmapped reads to metrics file
- PSScoreFileLogger(MetricsFile<PSScoreMetrics, Long>, String) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreFileLogger
- PSScoreLogger - Interface in org.broadinstitute.hellbender.tools.spark.pathseq.loggers
-
Interface for score metrics logging
- PSScoreMetrics - Class in org.broadinstitute.hellbender.tools.spark.pathseq.loggers
-
Metrics that are calculated during the PathSeq scoring
- PSScoreMetrics() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreMetrics
- PSScorer - Class in org.broadinstitute.hellbender.tools.spark.pathseq
- PSScorer(PSScoreArgumentCollection) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSScorer
- PSTaxonomyConstants - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Important NCBI taxonomy database constants
- PSTaxonomyConstants() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSTaxonomyConstants
- PSTaxonomyDatabase - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Helper class for holding taxonomy data used by ClassifyReads
- PSTaxonomyDatabase(PSTree, Map<String, Integer>) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSTaxonomyDatabase
- PSTaxonomyDatabase.Serializer - Class in org.broadinstitute.hellbender.tools.spark.pathseq
- PSTree - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Represents a taxonomic tree with nodes assigned a name and taxonomic rank (e.g.
- PSTree(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- PSTree(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- PSTree.Serializer - Class in org.broadinstitute.hellbender.tools.spark.pathseq
- PSTreeNode - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Node class for PSTree
- PSTreeNode() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- PSTreeNode.Serializer - Class in org.broadinstitute.hellbender.tools.spark.pathseq
- PSUtils - Class in org.broadinstitute.hellbender.tools.spark.pathseq
-
Common functions for PathSeq
- PSUtils() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSUtils
- PURINE - Static variable in enum class org.broadinstitute.hellbender.utils.Nucleotide
- PushPullTransformer<T> - Interface in org.broadinstitute.hellbender.utils.iterators
-
A class that receives a stream of elements and transforms or filters them in some way, such as by downsampling with a
Downsampler. - PushToPullIterator<T> - Class in org.broadinstitute.hellbender.utils.iterators
-
Iterator wrapper around our generic {@link PushPullTransformer)} interface.
- PushToPullIterator(Iterator<T>, PushPullTransformer<T>) - Constructor for class org.broadinstitute.hellbender.utils.iterators.PushToPullIterator
- put(int, int[][][]) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.CovariateKeyCache
-
Store the given array in the cache.
- put(int, Object) - Method in class org.broadinstitute.hellbender.utils.bigquery.QueryRecord
- put(int, String, ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
- put(int, String, ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
- put(int, String, ReadEndsForMarkDuplicates) - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
-
Store the element in the map with the given key.
- put(String, Object) - Method in class org.broadinstitute.hellbender.utils.bigquery.QueryRecord
- put(List<Object>, V) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- put(PairedStrandedIntervals, V) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree
- put(SVInterval, V) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Put a new interval into the tree (or update the value associated with an existing interval).
- put(T, int...) - Method in class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray
-
Insert a value at the position specified by the given keys.
- putAll(Map<? extends List<Object>, ? extends V>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- PUTATIVE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.GeneTranscriptStatus
- putAttribute(Allele, T) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData
- putReadsWithTheSameNameInTheSamePartition(SAMFileHeader, JavaRDD<GATKRead>, JavaSparkContext) - Static method in class org.broadinstitute.hellbender.utils.spark.SparkUtils
-
Ensure all reads with the same name appear in the same partition of a queryname sorted RDD.
- PVAL - Variable in class picard.arrays.BafRegressMetrics
-
The p-value of the estimate
- pValueForContingencyTable(int[][]) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.FisherStrand
- PYRIMIDINE - Static variable in enum class org.broadinstitute.hellbender.utils.Nucleotide
- PYTHON - Enum constant in enum class org.broadinstitute.hellbender.utils.python.PythonExecutorBase.PythonExecutableName
- PYTHON_EXTENSION - Static variable in class org.broadinstitute.hellbender.utils.python.PythonExecutorBase
- PYTHON_IFOREST - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsModelBackend
-
Use the script at org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/isolation-forest.py
- PYTHON_SCORER_PKL_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.PythonSklearnVariantAnnotationsScorer
- PYTHON_SCRIPT - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsModelBackend
-
Use a user-provided script.
- PYTHON_SCRIPT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- PYTHON_SCRIPT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
- PYTHON3 - Enum constant in enum class org.broadinstitute.hellbender.utils.python.PythonExecutorBase.PythonExecutableName
- pythonArg - Variable in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
- PythonExecutorBase - Class in org.broadinstitute.hellbender.utils.python
-
Base class for services for executing Python Scripts.
- PythonExecutorBase(boolean) - Constructor for class org.broadinstitute.hellbender.utils.python.PythonExecutorBase
- PythonExecutorBase(PythonExecutorBase.PythonExecutableName, boolean) - Constructor for class org.broadinstitute.hellbender.utils.python.PythonExecutorBase
- PythonExecutorBase.PythonExecutableName - Enum Class in org.broadinstitute.hellbender.utils.python
-
Enum of possible executables that can be launched by this executor.
- PythonScriptExecutor - Class in org.broadinstitute.hellbender.utils.python
-
Generic service for executing Python Scripts.
- PythonScriptExecutor(boolean) - Constructor for class org.broadinstitute.hellbender.utils.python.PythonScriptExecutor
- PythonScriptExecutor(PythonExecutorBase.PythonExecutableName, boolean) - Constructor for class org.broadinstitute.hellbender.utils.python.PythonScriptExecutor
- PythonScriptExecutorException - Exception in org.broadinstitute.hellbender.utils.python
-
Python script execution exception.
- PythonScriptExecutorException(String) - Constructor for exception org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException
- PythonSklearnVariantAnnotationsModel - Class in org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling
-
Given an HDF5 file containing annotations for a training set (in the format specified by
VariantAnnotationsModel.trainAndSerialize(java.io.File, java.lang.String)), a Python script containing modeling code, and a JSON file containing hyperparameters, thePythonSklearnVariantAnnotationsModel.trainAndSerialize(java.io.File, java.lang.String)method can be used to train a model. - PythonSklearnVariantAnnotationsModel(File, File) - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.PythonSklearnVariantAnnotationsModel
- PythonSklearnVariantAnnotationsScorer - Class in org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling
-
Given an HDF5 file containing annotations for a test set (in the format specified by
VariantAnnotationsScorer.score(java.io.File, java.io.File)), a Python script containing scoring code, and a file containing a pickled Python lambda function for scoring, thePythonSklearnVariantAnnotationsScorer.score(java.io.File, java.io.File)method can be used to generate scores. - PythonSklearnVariantAnnotationsScorer(File, File) - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.PythonSklearnVariantAnnotationsScorer
Q
- Q_SCORE - Variable in class picard.sam.SamErrorMetric.BaseErrorMetric
-
The (phred) rate of bases that disagree with the reference
- Q_TRIMMING_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- Q_TRIMMING_THRESHOLD_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- Q20_BASES - Variable in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
-
The number of bases in all reads that achieve quality score 20 or higher
- Q20_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The number of bases in all reads that achieve quality score 20 or higher
- Q20_EQUIVALENT_YIELD - Variable in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
-
The sum of quality scores of all bases divided by 20
- Q20_EQUIVALENT_YIELD - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The sum of quality scores of all bases divided by 20
- Q30_BASES - Variable in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
-
The number of bases in all reads that achieve quality score 30 or higher
- Q30_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The number of bases in all reads that achieve quality score 30 or higher
- QA - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVSegmentVariantComposer
-
Quality metric (all points called)
- QD_DISTANCE_FROM_MEAN - Static variable in class org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalker
- QdFilter - Class in picard.vcf.filter
-
Filters out sites that have a QD annotation applied to them and where the QD value is lower than a lower limit.
- QdFilter(double) - Constructor for class picard.vcf.filter.QdFilter
- QMIN_DEFAULT - Static variable in class org.broadinstitute.hellbender.tools.LocalAssembler
- QNAME - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestField
- QNameAndInterval - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
A template name and an intervalId.
- QNameAndInterval(String, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval
- QNameAndInterval.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- QNameFinder - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
Class to find the template names associated with reads in specified intervals.
- QNameFinder(ReadMetadata, List<SVInterval>, SVReadFilter, SVIntervalTree<SVInterval>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameFinder
- QNameIntervalFinder - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
Iterates over reads, kmerizing them, and checking the kmers against a set of KmerAndIntervals to figure out which intervals (if any) a read belongs in.
- QNameIntervalFinder(int, HopscotchUniqueMultiMapSpark<SVKmer, Integer, KmerAndInterval>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameIntervalFinder
- QNameKmerizer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
Class that acts as a mapper from a stream of reads to a stream of KmerAndIntervals.
- QNameKmerizer(HopscotchUniqueMultiMapSpark<String, Integer, QNameAndInterval>, Set<SVKmer>, int, int, SVReadFilter) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameKmerizer
- qNamesAssemblyFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- QNamesForKmersFinder - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
Class that acts as a mapper from a stream of reads to a stream of <kmer,qname> pairs for a set of interesting kmers.
- QNamesForKmersFinder(int, HopscotchUniqueMultiMapSpark<SVKmer, Integer, KmerAndInterval>, SVReadFilter) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNamesForKmersFinder
- qNamesMappedFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- QS - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVSegmentVariantComposer
-
Quality metric (some points called)
- QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
- QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
- QSE - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVSegmentVariantComposer
-
Quality metric (segment end)
- QSS - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVSegmentVariantComposer
-
Quality metric (segment start)
- QUAL - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestField
- QUAL_APPROX_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- QUAL_APPROX_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- QUAL_BY_DEPTH_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- qualAt(int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Element
- qualAt(int, int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- QualByDepth - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Variant confidence normalized by unfiltered depth of variant samples
- QualByDepth() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.QualByDepth
- qualifies(int, int, int) - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCase
-
Tests whether this site can be used for parameter estimation given the limits for relevant stats.
- qualifyingOnly(int, int, int) - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCases
-
Returns a new collection that contains only those cases are qualify for parameter estimation given the required constraints.
- QualInterval(int, int, long, long, int) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.QualQuantizer.QualInterval
- QualInterval(int, int, long, long, int, int) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.QualQuantizer.QualInterval
- QualInterval(int, int, long, long, int, int, Set<QualQuantizer.QualInterval>) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.QualQuantizer.QualInterval
- QualInterval(int, int, long, long, int, Set<QualQuantizer.QualInterval>) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.QualQuantizer.QualInterval
- qualities - Variable in class picard.illumina.parser.BclData
- qualities - Variable in class picard.util.BarcodeEditDistanceQuery
-
list of quality scores for reads
- QUALITY - Variable in class picard.sam.SamToFastq
- QUALITY_FORMAT - Variable in class picard.sam.FastqToSam
- QUALITY_SCORE_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- QUALITY_SCORE_REPORT_TABLE_TITLE - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- QUALITY_SCORE_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- QUALITY_TAG_GROUP - Variable in class picard.sam.SamToFastqWithTags
- QualityScoreCovariate - Class in org.broadinstitute.hellbender.utils.recalibration.covariates
-
The Reported Quality Score covariate.
- QualityScoreCovariate(RecalibrationArgumentCollection) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.covariates.QualityScoreCovariate
- QualityScoreDistribution - Class in picard.analysis
-
Charts quality score distribution within a BAM file.
- QualityScoreDistribution - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- QualityScoreDistribution() - Constructor for class picard.analysis.QualityScoreDistribution
- QualityScoreDistributionSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines.metrics
-
Charts quality score distribution within a BAM file.
- QualityScoreDistributionSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityScoreDistributionSpark
- QualityScores - Enum constant in enum class picard.illumina.parser.IlluminaDataType
- QualityUtils - Class in org.broadinstitute.hellbender.utils
-
QualityUtils is a static class with some utility methods for manipulating quality scores.
- QualityYieldMetrics - Class in org.broadinstitute.hellbender.metrics
-
A set of metrics used to describe the general quality of a BAM file
- QualityYieldMetrics() - Constructor for class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
- QualityYieldMetrics() - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
- QualityYieldMetrics(boolean) - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
- QualityYieldMetricsArgumentCollection - Class in org.broadinstitute.hellbender.metrics
-
MetricsArgumentCollection argument collection for QualityYield metrics.
- QualityYieldMetricsArgumentCollection() - Constructor for class org.broadinstitute.hellbender.metrics.QualityYieldMetricsArgumentCollection
- QualityYieldMetricsCollector(boolean, boolean, boolean) - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
- QualityYieldMetricsCollector(boolean, boolean, boolean, boolean) - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
- QualityYieldMetricsCollectorSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines.metrics
-
QualityYieldMetricsCollector for Spark.
- QualityYieldMetricsCollectorSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityYieldMetricsCollectorSpark
- QualityYieldMetricsFlow() - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- QualityYieldMetricsFlow(boolean) - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- QualityYieldMetricsFlow(boolean, HistogramGenerator) - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- qualPhredThresh - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- QualQuantizer - Class in org.broadinstitute.hellbender.utils.recalibration
-
A general algorithm for quantizing quality score distributions to use a specific number of levels Takes a histogram of quality scores and a desired number of levels and produces a map from original quality scores -> quantized quality scores.
- QualQuantizer(int) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.QualQuantizer
-
Protected creator for testng use only
- QualQuantizer(List<Long>, int, int) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.QualQuantizer
-
Creates a QualQuantizer for the histogram that has nLevels Note this is the only interface to the system.
- QualQuantizer.QualInterval - Class in org.broadinstitute.hellbender.utils.recalibration
-
Represents an contiguous interval of quality scores.
- quals() - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Insert
- qualToErrorProb(byte) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
v Convert a phred-scaled quality score to its probability of being wrong (Q30 => 0.001) This is the Phred-style conversion, *not* the Illumina-style conversion.
- qualToErrorProb(double) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Convert a phred-scaled quality score to its probability of being wrong (Q30 => 0.001) This is the Phred-style conversion, *not* the Illumina-style conversion.
- qualToErrorProbLog10(byte) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Convert a phred-scaled quality score to its log10 probability of being wrong (Q30 => log10(0.001)) This is the Phred-style conversion, *not* the Illumina-style conversion.
- qualToErrorProbLog10(double) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Convert a phred-scaled quality score to its log10 probability of being wrong (Q30 => log10(0.001)) This is the Phred-style conversion, *not* the Illumina-style conversion.
- qualToLogErrorProb(byte) - Static method in class org.broadinstitute.hellbender.utils.NaturalLogUtils
-
Convert a phred-scaled quality score to its log10 probability of being wrong (Q30 => log(0.001)) WARNING -- because this function takes a byte for maxQual, you must be careful in converting integers to byte.
- qualToLogErrorProb(double) - Static method in class org.broadinstitute.hellbender.utils.NaturalLogUtils
-
Convert a phred-scaled quality score to its log10 probability of being wrong (Q30 => log10(0.001)) This is the Phred-style conversion, *not* the Illumina-style conversion.
- qualToLogProb(byte) - Static method in class org.broadinstitute.hellbender.utils.NaturalLogUtils
- qualToProb(byte) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Convert a phred-scaled quality score to its probability of being true (Q30 => 0.999) This is the Phred-style conversion, *not* the Illumina-style conversion.
- qualToProb(double) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Convert a phred-scaled quality score to its probability of being true (Q30 => 0.999) This is the Phred-style conversion, *not* the Illumina-style conversion.
- qualToProbLog10(byte) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Convert a phred-scaled quality score to its log10 probability of being true (Q30 => log10(0.999)) This is the Phred-style conversion, *not* the Illumina-style conversion.
- qualToTransProbs(byte[], byte[], byte[]) - Static method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Returns a matrix with the transition probabilities for a number of bases.
- qualToTransProbs(byte, byte, byte) - Static method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Returns a transition probability array given the different quality scores affecting a read site.
- qualToTransProbs(double[][], byte[], byte[], byte[]) - Static method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Fills ax matrix with the transition probabilities for a number of bases.
- qualToTransProbs(double[], byte, byte, byte) - Static method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Fills a transition probability array given the different quality scores affecting a read site
- qualToTransProbsLog10(byte[], byte[], byte[]) - Static method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Returns a matrix with the log10 transition probabilities for a number of bases.
- qualToTransProbsLog10(byte, byte, byte) - Static method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Returns a transition log10 probability array given the different quality scores affecting a read site.
- qualToTransProbsLog10(double[][], byte[], byte[], byte[]) - Static method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Fills a matrix with the log10 transition probabilities for a number of bases.
- qualToTransProbsLog10(double[], byte, byte, byte) - Static method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Fills a transition log10-probability array given the different quality scores affecting a read site.
- QuantizationInfo - Class in org.broadinstitute.hellbender.utils.recalibration
-
Class that encapsulates the information necessary for quality score quantization for BQSR
- QuantizationInfo(List<Byte>, List<Long>) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.QuantizationInfo
- QuantizationInfo(RecalibrationTables, int) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.QuantizationInfo
- quantizationLevels - Variable in class org.broadinstitute.hellbender.tools.ApplyBQSRUniqueArgumentCollection
-
Turns on the base quantization module.
- QUANTIZED_COUNT_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- QUANTIZED_REPORT_TABLE_TITLE - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- QUANTIZED_VALUE_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- quantizeQualityScores(int) - Method in class org.broadinstitute.hellbender.utils.recalibration.QuantizationInfo
- QUANTIZING_LEVELS - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
-
BQSR generates a quantization table for quick quantization later by subsequent tools.
- query(String, int, int) - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- query(String, int, int, boolean) - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator
- query(SimpleInterval) - Method in class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Gets an iterator over all Features in this data source that overlap the provided interval.
- query(SimpleInterval) - Method in interface org.broadinstitute.hellbender.engine.GATKDataSource
- query(SimpleInterval) - Method in class org.broadinstitute.hellbender.engine.MultiVariantDataSource
-
Gets an iterator over all Variants in this data source that overlap the provided interval.
- query(SimpleInterval) - Method in class org.broadinstitute.hellbender.engine.ReadsPathDataSource
-
Query reads over a specific interval.
- query(SimpleInterval) - Method in interface org.broadinstitute.hellbender.engine.ReferenceDataSource
-
Query a specific interval on this reference, and get back an iterator over the bases spanning that interval.
- query(SimpleInterval) - Method in class org.broadinstitute.hellbender.engine.ReferenceMemorySource
-
Query a specific interval on this reference, and get back an iterator over the bases spanning that interval.
- queryAndPrefetch(Locatable) - Method in class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Returns a List of all Features in this data source that overlap the provided interval.
- queryAndPrefetch(String, long, long) - Method in interface org.broadinstitute.hellbender.engine.ReferenceDataSource
-
Query a specific interval on this reference, and get back all bases spanning that interval at once.
- queryAndPrefetch(String, long, long) - Method in class org.broadinstitute.hellbender.engine.ReferenceFileSource
-
Query a specific interval on this reference, and get back all bases spanning that interval at once.
- queryAndPrefetch(String, long, long) - Method in class org.broadinstitute.hellbender.engine.ReferenceMemorySource
-
Query a specific interval on this reference, and get back all bases spanning that interval at once.
- queryAndPrefetch(SimpleInterval) - Method in interface org.broadinstitute.hellbender.engine.ReferenceDataSource
-
Query a specific interval on this reference, and get back all bases spanning that interval at once.
- queryAndPrefetch(SimpleInterval) - Method in class org.broadinstitute.hellbender.engine.ReferenceMemorySource
-
Query a specific interval on this reference, and get back all bases spanning that interval at once.
- queryByMD5(String) - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
-
Given an MD5, returns its corresponding row
- queryBySequenceName(String) - Method in class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
-
Given a sequence name, returns the set of its corresponding rows or an empty set if no such rows found.
- queryContained(String, int, int) - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator
-
query containing - get reads contained by the specified interval
- queryFeaturesIncludingOverlapping(FeatureInput<T>, SimpleInterval) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.VariantEvalContext
- querynameSortReadsIfNecessary(JavaRDD<GATKRead>, int, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.spark.SparkUtils
-
Sort reads into queryname order if they are not already sorted
- queryOverlapping(String, int, int) - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator
-
query containing - get reads contained by the specified interval
- QueryRecord - Class in org.broadinstitute.hellbender.utils.bigquery
-
A BigQuery record for a row of results from a query.
- QueryRecord(FieldValueList) - Constructor for class org.broadinstitute.hellbender.utils.bigquery.QueryRecord
- QuerySortedReadPairIteratorUtil - Class in picard.util
-
A collection of helper utilities for iterating through reads that are in query-name sorted read order as pairs
- QuerySortedReadPairIteratorUtil() - Constructor for class picard.util.QuerySortedReadPairIteratorUtil
- QuerySortedReadPairIteratorUtil.ReadPair - Class in picard.util
- queryUnmapped() - Method in interface org.broadinstitute.hellbender.engine.ReadsDataSource
- queryUnmapped() - Method in class org.broadinstitute.hellbender.engine.ReadsPathDataSource
- QUIET - Variable in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- QUIET - Variable in class picard.cmdline.CommandLineProgram
- QUIET_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- QUINTILE_1 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
- QUINTILE_2 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
- QUINTILE_3 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
- QUINTILE_4 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
- QUINTILE_5 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
- QUOTE_CHARACTER - Static variable in class org.broadinstitute.hellbender.utils.tsv.TableUtils
-
Quote character .
- QUOTE_STRING - Static variable in class org.broadinstitute.hellbender.utils.tsv.TableUtils
-
Quote character as a string.
R
- R - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- R - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- R - Static variable in class picard.sam.markduplicates.util.ReadEnds
- R_LIBRARY_SUFFIX - Static variable in enum class org.broadinstitute.hellbender.utils.R.RScriptLibrary
- R1R2 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
- RampBase - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
- RampBase(String, RampBase.Type) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase
- RampBase.Type - Enum Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
- RampedHaplotypeCaller - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
This is a specialized HaplotypeCaller tool, designed to allow for breaking the monolithic haplotype caller process into smaller discrete steps.
- RampedHaplotypeCaller() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCaller
- RampedHaplotypeCallerArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
- RampedHaplotypeCallerArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection
- RampedHaplotypeCallerArgumentCollection.OffRampTypeEnum - Enum Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
- RampedHaplotypeCallerArgumentCollection.OnRampTypeEnum - Enum Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
- RampedHaplotypeCallerEngine - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
This is a specialized haplotype caller engine, designed to allow for breaking the monolithic haplotype caller process into smaller discrete steps.
- RampedHaplotypeCallerEngine(HaplotypeCallerArgumentCollection, AssemblyRegionArgumentCollection, boolean, boolean, SAMFileHeader, CachingIndexedFastaSequenceFile, VariantAnnotatorEngine, RampedHaplotypeCallerArgumentCollection) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerEngine
- RAMPS_DEBUG_POST_ASSEMBLER_ON_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection
- RAMPS_DEBUG_READS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection
- rampsDebugPostAssemblerOn - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection
- rampsDebugReads - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection
- RampUtils - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
- RampUtils() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampUtils
- RampUtils.GATKReadComparator - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
- RampUtils.HaplotypeComparator - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
- RANDOM - Enum constant in enum class org.broadinstitute.hellbender.utils.clustering.BayesianGaussianMixtureModeller.InitMethod
- RANDOM_SEED - Variable in class picard.sam.DownsampleSam
- RANDOM_SEED_TAG - Static variable in class picard.sam.DownsampleSam
- randomRemotePath(String, String, String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Picks a random name, by putting some random letters between "prefix" and "suffix".
- randomSelect(List<E>, Function<E, Double>, RandomGenerator) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- randomSublist(List<T>, int, Random) - Static method in class picard.util.MathUtil
-
A small utility function to choose n random elements (un-shuffled) from a list
- Range - Class in picard.illumina.parser
-
While structurally identical to CompositeIndex, this class is maintained as it makes code more readable when the two are used together (see QSeqParser)
- Range(int, int) - Constructor for class picard.illumina.parser.Range
- RankedData(MannWhitneyU.Rank[], ArrayList<Integer>) - Constructor for class org.broadinstitute.hellbender.utils.MannWhitneyU.RankedData
- RankSumTest - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Abstract root for all RankSum based annotations
- RankSumTest() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.RankSumTest
- rapidParseInt(String) - Static method in class picard.sam.util.ReadNameParser
-
Very specialized method to rapidly parse a sequence of digits from a String up until the first non-digit character.
- rate(long, long) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
- ratio(long, long) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
- ratio_of_1_and_2_to_3_bp_deletions - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- ratio_of_1_and_2_to_3_bp_insertions - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT - Variable in class picard.illumina.BarcodeMetric
-
The rate of all reads matching this barcode to all reads matching the most prevalent barcode.
- RAW_DELIM - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
- RAW_GENOTYPE_COUNT_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- RAW_MAP_QUAL_RANK_SUM_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- RAW_MAPPING_QUALITY_WITH_DEPTH_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- RAW_QUAL_APPROX_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- RAW_RMS_MAPPING_QUALITY_DEPRECATED - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- rawData - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData
- rawGenotypeLikelihoods(LikelihoodMatrix<EVIDENCE, A>) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculatorDRAGEN
-
See
GenotypeLikelihoodCalculator.getReadRawReadLikelihoodsByGenotypeIndex(org.broadinstitute.hellbender.utils.genotyper.LikelihoodMatrix<EVIDENCE, A>). - RawGtCount - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
INFO level annotation of the counts of genotypes with respect to the reference allele.
- RawGtCount() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.RawGtCount
- rawQuals - Variable in class org.broadinstitute.hellbender.utils.baq.BAQ.BAQCalculationResult
- rawValueAsString(int[][]) - Static method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
- RawWgsMetrics() - Constructor for class picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
- RawWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Constructor for class picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
- rawXIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- rawYIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- rc() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- rc() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- rc() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigListRC
- rc() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- rc() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- rc() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- rc() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- rc() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Path
- rc() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.PathPart
- rc() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartContig
- rc() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.PathPartGap
- rc() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- rCount - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- RE_REVERSE - Variable in class picard.sam.SamToFastq
- read - Variable in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.SplitRead
- read() - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Element
- read() - Method in class org.broadinstitute.hellbender.utils.runtime.CapturedStreamOutput
-
Drain the input stream to keep the process from backing up until it's empty.
- read() - Method in class org.broadinstitute.hellbender.utils.runtime.CapturedStreamOutputSnapshot
-
Drain the input stream to keep the process from backing up until it's empty.
- read(byte[], int, int) - Method in class picard.util.CircularByteBuffer
-
Read bytes from the buffer into the supplied array.
- read(char[], int, int) - Method in class org.broadinstitute.hellbender.utils.codecs.LineIteratorReader
-
Reads lines from the buffer, and if empty from the underlying line-iterator.
- read(Kryo, Input, Class<SAMRecord>) - Method in class org.broadinstitute.hellbender.engine.spark.SAMRecordSerializer
- read(Kryo, Input, Class<PSKmerBloomFilter>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerBloomFilter.Serializer
- read(Kryo, Input, Class<PSKmerSet>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet.Serializer
- read(Kryo, Input, Class<PSTaxonomyDatabase>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTaxonomyDatabase.Serializer
- read(Kryo, Input, Class<PSTree>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree.Serializer
- read(Kryo, Input, Class<PSTreeNode>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode.Serializer
- read(Kryo, Input, Class<AlignedAssembly>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedAssembly.Serializer
- read(Kryo, Input, Class<AlignedContig>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig.Serializer
- read(Kryo, Input, Class<AlignmentInterval>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval.Serializer
- read(Kryo, Input, Class<AssemblyContigWithFineTunedAlignments>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments.Serializer
- read(Kryo, Input, Class<BreakpointComplications.IntraChrStrandSwitchBreakpointComplications>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.IntraChrStrandSwitchBreakpointComplications.Serializer
- read(Kryo, Input, Class<BreakpointComplications.InvertedDuplicationBreakpointComplications>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.InvertedDuplicationBreakpointComplications.Serializer
- read(Kryo, Input, Class<BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications.Serializer
- read(Kryo, Input, Class<BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications.Serializer
- read(Kryo, Input, Class<BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications.Serializer
- read(Kryo, Input, Class<CpxVariantCanonicalRepresentation>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantCanonicalRepresentation.Serializer
- read(Kryo, Input, Class<CpxVariantInducingAssemblyContig>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInducingAssemblyContig.Serializer
- read(Kryo, Input, Class<NovelAdjacencyAndAltHaplotype>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype.Serializer
- read(Kryo, Input, Class<SimpleChimera>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera.Serializer
- read(Kryo, Input, Class<SimpleNovelAdjacencyAndChimericAlignmentEvidence>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence.Serializer
- read(Kryo, Input, Class<AlignedAssemblyOrExcuse>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse.Serializer
- read(Kryo, Input, Class<BreakpointEvidence.ExternalEvidence>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ExternalEvidence.Serializer
- read(Kryo, Input, Class<BreakpointEvidence.InterContigPair>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.InterContigPair.Serializer
- read(Kryo, Input, Class<BreakpointEvidence.LargeIndel>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.LargeIndel.Serializer
- read(Kryo, Input, Class<BreakpointEvidence.MateUnmapped>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.MateUnmapped.Serializer
- read(Kryo, Input, Class<BreakpointEvidence.OutiesPair>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.OutiesPair.Serializer
- read(Kryo, Input, Class<BreakpointEvidence.ReadEvidence>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence.Serializer
- read(Kryo, Input, Class<BreakpointEvidence.SameStrandPair>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SameStrandPair.Serializer
- read(Kryo, Input, Class<BreakpointEvidence.SplitRead>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SplitRead.Serializer
- read(Kryo, Input, Class<BreakpointEvidence.TemplateSizeAnomaly>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.TemplateSizeAnomaly.Serializer
- read(Kryo, Input, Class<BreakpointEvidence.WeirdTemplateSize>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.WeirdTemplateSize.Serializer
- read(Kryo, Input, Class<BreakpointEvidence>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.Serializer
- read(Kryo, Input, Class<EvidenceTargetLink>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink.Serializer
- read(Kryo, Input, Class<KmerAndInterval>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerAndInterval.Serializer
- read(Kryo, Input, Class<LibraryStatistics>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics.Serializer
- read(Kryo, Input, Class<QNameAndInterval>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval.Serializer
- read(Kryo, Input, Class<ReadMetadata.LibraryRawStatistics>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.LibraryRawStatistics.Serializer
- read(Kryo, Input, Class<ReadMetadata.PartitionBounds>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionBounds.Serializer
- read(Kryo, Input, Class<ReadMetadata.PartitionStatistics>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionStatistics.Serializer
- read(Kryo, Input, Class<ReadMetadata>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.Serializer
- read(Kryo, Input, Class<KmerAndCount>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.KmerAndCount.Serializer
- read(Kryo, Input, Class<PairedStrandedIntervalTree<T>>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.Serializer
- read(Kryo, Input, Class<Strand>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.Strand.Serializer
- read(Kryo, Input, Class<StrandedInterval>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval.Serializer
- read(Kryo, Input, Class<SVFastqUtils.FastqRead>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead.Serializer
- read(Kryo, Input, Class<SVKmerLong>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong.Serializer
- read(Kryo, Input, Class<SVKmerShort>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort.Serializer
- read(Kryo, Input, Class<HopscotchCollectionSpark<T>>) - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchCollectionSpark.Serializer
- read(Kryo, Input, Class<HopscotchMapSpark>) - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMapSpark.Serializer
- read(Kryo, Input, Class<HopscotchMultiMapSpark>) - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMultiMapSpark.Serializer
- read(Kryo, Input, Class<HopscotchSetSpark>) - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchSetSpark.Serializer
- read(Kryo, Input, Class<HopscotchUniqueMultiMapSpark>) - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchUniqueMultiMapSpark.Serializer
- read(Kryo, Input, Class<IntHistogram.CDF>) - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.CDF.Serializer
- read(Kryo, Input, Class<IntHistogram>) - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.Serializer
- read(Kryo, Input, Class<LargeLongHopscotchSet>) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet.Serializer
- read(Kryo, Input, Class<LongBloomFilter>) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter.Serializer
- read(Kryo, Input, Class<LongHopscotchSet>) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet.Serializer
- read(Kryo, Input, Class<Pair>) - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair.Serializer
- read(Kryo, Input, Class<SAMRecordToGATKReadAdapter>) - Method in class org.broadinstitute.hellbender.engine.spark.SAMRecordToGATKReadAdapterSerializer
- read(Kryo, Input, Class<SVInterval>) - Method in class org.broadinstitute.hellbender.utils.SVInterval.Serializer
- read(Kryo, Input, Class<SVIntervalTree<T>>) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree.Serializer
- read(File) - Static method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection
-
Read all counts from a file (HDF5 or TSV).
- read(HDF5File) - Static method in class org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals
-
Create an interface to an HDF5 file.
- read(GATKPath) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- READ_CHUNK_SIZE - Variable in class picard.fastq.BamToBfq
- READ_END - Variable in class org.broadinstitute.hellbender.metrics.analysis.BaseDistributionByCycleMetrics
- READ_END - Variable in class picard.analysis.BaseDistributionByCycleMetrics
- READ_FILTER_EXPRESSION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- READ_FILTER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- read_filter_packages() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- READ_FILTER_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- READ_FILTER_TAG - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- READ_FILTER_TAG_COMP - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- READ_FILTER_TAG_OP - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- READ_GROUP - Enum constant in enum class org.broadinstitute.hellbender.metrics.MetricAccumulationLevel
- READ_GROUP - Enum constant in enum class picard.analysis.MetricAccumulationLevel
- READ_GROUP - Variable in class org.broadinstitute.hellbender.metrics.MultiLevelMetrics
-
The read group to which these metrics apply.
- READ_GROUP - Variable in class org.broadinstitute.hellbender.tools.SplitReads
- READ_GROUP - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The sequencing read group from which sequence data was fingerprinted.
- READ_GROUP - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The read group from which sequence data was drawn for comparison.
- READ_GROUP - Variable in class picard.metrics.MultilevelMetrics
-
The read group to which these metrics apply.
- READ_GROUP_BLACK_LIST_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- READ_GROUP_HAS_FLOW_ORDER_READ_FILTER - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- READ_GROUP_ID - Static variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- READ_GROUP_ID - Variable in class picard.illumina.IlluminaBasecallsToSam
- READ_GROUP_ID_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- READ_GROUP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.SplitReads
- READ_GROUP_NAME - Variable in class picard.sam.FastqToSam
- READ_GROUP_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.SplitReads
- READ_INDEX_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- READ_INDEX_NOT_FOUND - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- READ_INDEX_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- READ_LENGTH - Variable in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
-
The average read length of all the reads (will be fixed for a lane)
- READ_LENGTH - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The average read length of all the reads
- READ_LENGTH - Variable in class picard.analysis.CollectWgsMetrics
- READ_LENGTH_AVG_Q_ABOVE_25 - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
-
The length of the longest interval on the reads where the average quality per-base is above (Q25)
- READ_LENGTH_AVG_Q_ABOVE_30 - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
-
The length of the longest interval on the reads where the average quality per-base is above (Q30)
- READ_LIST_FILE - Variable in class picard.sam.FilterSamReads
- READ_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- READ_NAME_FORMAT - Variable in class picard.illumina.IlluminaBasecallsToFastq
- READ_NAME_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- READ_NAME_PREFIX - Variable in class picard.fastq.BamToBfq
- READ_NAME_REGEX - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.OpticalDuplicatesArgumentCollection
- READ_NAME_REGEX - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- READ_NAME_REGEX - Variable in class picard.sam.PositionBasedDownsampleSam
- READ_NAME_REGEX_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.OpticalDuplicatesArgumentCollection
- READ_ONE_BARCODE_TAG - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- READ_ONE_BARCODE_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
- READ_ORIENTATION_ARTIFACT_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- READ_ORIENTATION_QUAL_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- READ_PAIR_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
-
The number of read pairs that were marked as duplicates.
- READ_PAIR_OPTICAL_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
-
The number of read pairs duplicates that were caused by optical duplication.
- READ_PAIR_SUPPORT - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- READ_PAIRS - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The total number of read pairs that were examined in the entire distribution.
- READ_PAIRS - Variable in class picard.analysis.InsertSizeMetrics
-
The total number of read pairs that were examined in the entire distribution.
- READ_PAIRS_EXAMINED - Variable in class picard.sam.DuplicationMetrics
-
The number of mapped read pairs examined.
- READ_POS_RANK_SUM_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- READ_POSITION_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- READ_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- READ_STARTS - Variable in class picard.analysis.GcBiasDetailMetrics
-
The number of reads whose start position is at the start of a window of this GC.
- READ_STRUCTURE - Variable in class picard.illumina.CheckIlluminaDirectory
- READ_STRUCTURE - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
- READ_STRUCTURE - Variable in class picard.illumina.CollectIlluminaLaneMetrics
- READ_STRUCTURE - Variable in class picard.illumina.ExtractBarcodesProgram
- read_tensor - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.TensorType
- READ_TWO_BARCODE_TAG - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- READ_TWO_BARCODE_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
- READ_VALIDATION_STRINGENCY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- READ_VALIDATION_STRINGENCY_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- read1 - Variable in class picard.util.QuerySortedReadPairIteratorUtil.ReadPair
- READ1_ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
- READ1_MAX_BASES_TO_WRITE - Variable in class picard.sam.SamToFastq
- READ1_TRIM - Variable in class picard.sam.MergeBamAlignment
- READ1_TRIM - Variable in class picard.sam.SamToFastq
- read1Coordinate - Variable in class picard.sam.markduplicates.util.ReadEnds
- read1IndexInFile - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- read1ReferenceIndex - Variable in class picard.sam.markduplicates.util.ReadEnds
- read2 - Variable in class picard.util.QuerySortedReadPairIteratorUtil.ReadPair
- READ2_ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
- READ2_MAX_BASES_TO_WRITE - Variable in class picard.sam.SamToFastq
- READ2_TRIM - Variable in class picard.sam.MergeBamAlignment
- READ2_TRIM - Variable in class picard.sam.SamToFastq
- read2Coordinate - Variable in class picard.sam.markduplicates.util.ReadEnds
- read2IndexInFile - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- read2ReferenceIndex - Variable in class picard.sam.markduplicates.util.ReadEnds
- readActualHeader(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.AnnotatedIntervalCodec
- readActualHeader(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.BafEvidenceCodec
- readActualHeader(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.copynumber.SimpleCountCodec
- readActualHeader(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.DepthEvidenceCodec
- readActualHeader(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceCodec
- readActualHeader(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- readActualHeader(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupCodec
- readActualHeader(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.SiteDepthCodec
- readActualHeader(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceCodec
- readActualHeader(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.table.TableCodec
- readActualHeader(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
-
Read until we get to the header of this xsv Dev note: We also determine the actual locatable columns here.
- readAll() - Method in class org.broadinstitute.hellbender.utils.BinaryTableReader
- readAltSiteRecords(Path) - Static method in class org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord
- readAltSiteRecords(Path, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord
-
Code for reading sample name and alt site records from a table
- readAndMateAreUnmapped(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Helper method for interrogating if a read and its mate (if it exists) are unmapped
- readAndSubset(File, Set<SimpleInterval>) - Static method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection
-
From a file (HDF5 or TSV), subset only the counts with intervals coinciding with intervals from a given list.
- readAnnotationNames(File) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- readAnnotations(File) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- ReadAnonymizer - Class in org.broadinstitute.hellbender.tools.walkers
-
Replace bases in reads with reference bases.
- ReadAnonymizer() - Constructor for class org.broadinstitute.hellbender.tools.walkers.ReadAnonymizer
- readArguments - Variable in class org.broadinstitute.hellbender.engine.GATKTool
- readArguments - Variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- readArtifactPriors(File) - Static method in class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPriorCollection
-
Contract: only read from the file created by
writeArtifactPriors - readAt(int, int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- ReadAttributeTypeMismatch(SAMRecord, String, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.GATKException.ReadAttributeTypeMismatch
- ReadAttributeTypeMismatch(SAMRecord, String, String, Object) - Constructor for exception org.broadinstitute.hellbender.exceptions.GATKException.ReadAttributeTypeMismatch
- ReadAttributeTypeMismatch(SAMRecord, String, String, Throwable) - Constructor for exception org.broadinstitute.hellbender.exceptions.GATKException.ReadAttributeTypeMismatch
- ReadAttributeTypeMismatch(String, String) - Constructor for exception org.broadinstitute.hellbender.exceptions.GATKException.ReadAttributeTypeMismatch
- ReadAttributeTypeMismatch(String, String, Throwable) - Constructor for exception org.broadinstitute.hellbender.exceptions.GATKException.ReadAttributeTypeMismatch
- readBases - Variable in class org.broadinstitute.hellbender.utils.baq.BAQ.BAQCalculationResult
- ReadBaseStratification - Class in picard.sam.SamErrorMetric
-
Classes, methods, and enums that deal with the stratification of read bases and reference information.
- ReadBaseStratification() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification
- ReadBaseStratification.BinnedReadCycleStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies into quintiles of read cycle.
- ReadBaseStratification.CigarOperatorsInReadStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies according to the number of matching cigar operators (from CIGAR string) that the read has.
- ReadBaseStratification.CollectionStratifier - Class in picard.sam.SamErrorMetric
-
A CollectionStratifier is a stratifier that uses a collection of stratifiers to inform the stratification.
- ReadBaseStratification.Consensus - Enum Class in picard.sam.SamErrorMetric
-
Types of consensus reads as determined by the number of duplicates used from first and second strands.
- ReadBaseStratification.ConsensusStratifier - Class in picard.sam.SamErrorMetric
-
Stratify by tags used during duplex and single index consensus calling.
- ReadBaseStratification.CycleBin - Enum Class in picard.sam.SamErrorMetric
-
An enum designed to hold a binned version of any probability-like number (between 0 and 1) in quintiles
- ReadBaseStratification.FlowCellTileStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies base into their read's tile which is parsed from the read-name.
- ReadBaseStratification.FlowCellXStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies base into their read's X coordinate which is parsed from the read-name.
- ReadBaseStratification.FlowCellYStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies base into their read's Y coordinate which is parsed from the read-name.
- ReadBaseStratification.GCContentStratifier - Class in picard.sam.SamErrorMetric
-
A stratifier that uses GC (of the read) to stratify.
- ReadBaseStratification.IndelLengthStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies according to the length of an insertion or deletion.
- ReadBaseStratification.IndelsInReadStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies according to the number of indel bases (from CIGAR string) that the read has.
- ReadBaseStratification.LongShortHomopolymer - Enum Class in picard.sam.SamErrorMetric
- ReadBaseStratification.LongShortHomopolymerStratifier - Class in picard.sam.SamErrorMetric
-
Stratify bases according to the type of Homopolymer that they belong to (repeating element, final reference base and whether the length is "long" or not).
- ReadBaseStratification.MismatchesInReadStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies according to the overall mismatches (from
SAMTag.NM) that the read has against the reference, NOT including the current base. - ReadBaseStratification.NsInReadStratifier - Class in picard.sam.SamErrorMetric
-
Stratify by the number of Ns found in the read.
- ReadBaseStratification.PairOrientation - Enum Class in picard.sam.SamErrorMetric
-
An enum for holding a reads read-pair's Orientation (i.e.
- ReadBaseStratification.PairStratifier<T extends Comparable<T>,
R extends Comparable<R>> - Class in picard.sam.SamErrorMetric -
A PairStratifier is a stratifier that uses two other stratifiers to inform the stratification.
- ReadBaseStratification.ProperPaired - Enum Class in picard.sam.SamErrorMetric
-
An enum to hold information about the "properness" of a read pair
- ReadBaseStratification.ReadDirection - Enum Class in picard.sam.SamErrorMetric
-
An enum for holding the direction for a read (positive strand or negative strand
- ReadBaseStratification.ReadOrdinality - Enum Class in picard.sam.SamErrorMetric
-
An enum to hold the ordinality of a read
- ReadBaseStratification.RecordAndOffsetStratifier<T extends Comparable<T>> - Interface in picard.sam.SamErrorMetric
-
The main interface for a stratifier.
- readBreakpointsFromTruthVCF(String, SAMSequenceDictionary, int) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVVCFReader
- readByte(InputStream) - Static method in class org.broadinstitute.hellbender.tools.DumpTabixIndex
- ReadCachingIterator - Class in org.broadinstitute.hellbender.utils.iterators
-
Trivial wrapper around a GATKRead iterator that saves all reads returned in a cache, which can be periodically returned and emptied by the client.
- ReadCachingIterator(Iterator<GATKRead>) - Constructor for class org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator
- readChunkedDoubleMatrix(HDF5File, String) - Static method in class org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils
-
Reads a large matrix stored as a set of chunks (submatrices) using the sub-paths and conventions used by
HDF5Utils.writeChunkedDoubleMatrix(org.broadinstitute.hdf5.HDF5File, java.lang.String, double[][], int). - ReadClassifier - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
Figures out what kind of BreakpointEvidence, if any, a read represents.
- ReadClassifier(ReadMetadata, GATKRead, int, SVReadFilter, SVIntervalTree<SVInterval>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadClassifier
- ReadClassifier(ReadData) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier
-
Heart of CLP.
- ReadClipper - Class in org.broadinstitute.hellbender.utils.clipping
-
A comprehensive clipping tool.
- ReadClipper(GATKRead) - Constructor for class org.broadinstitute.hellbender.utils.clipping.ReadClipper
-
Initializes a ReadClipper object.
- ReadClipper(GATKRead, int) - Constructor for class org.broadinstitute.hellbender.utils.clipping.ReadClipper
- ReadClipperWithData(GATKRead, List<ClipReads.SeqToClip>) - Constructor for class org.broadinstitute.hellbender.tools.ClipReads.ReadClipperWithData
- readColumnsFromHeader(File) - Static method in class org.broadinstitute.hellbender.tools.copynumber.formats.CopyNumberFormatsUtils
-
Extracts column names from a TSV file
- ReadConstants - Class in org.broadinstitute.hellbender.utils.read
-
Constants for use with the GATKRead interface
- ReadContextData - Class in org.broadinstitute.hellbender.engine
-
ReadContextData is additional data that's useful when processing reads.
- ReadContextData(ReferenceBases, Iterable<GATKVariant>) - Constructor for class org.broadinstitute.hellbender.engine.ReadContextData
- ReadContextData(ReferenceBases, List<GATKVariant>) - Constructor for class org.broadinstitute.hellbender.engine.ReadContextData
- readContigNames(InputStream, int, int) - Static method in class org.broadinstitute.hellbender.tools.DumpTabixIndex
- ReadCoordinateComparator - Class in org.broadinstitute.hellbender.utils.read
-
Comparator for sorting Reads by coordinate.
- ReadCoordinateComparator(SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.utils.read.ReadCoordinateComparator
- readCount - Variable in class picard.analysis.directed.TargetMetricsCollector.Coverage
- ReadCovariates - Class in org.broadinstitute.hellbender.utils.recalibration.covariates
-
The object temporarily held by a read that describes all of its covariates.
- ReadCovariates(int, int, CovariateKeyCache) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadCovariates
-
Use an LRU cache to keep cache of keys (int[][][]) arrays for each read length we've seen.
- ReadData - Class in picard.illumina.parser
-
Data for a single end of a paired-end read, a barcode read, or for the entire read if not paired end.
- ReadData() - Constructor for class picard.illumina.parser.ReadData
- ReadData(ReadType) - Constructor for class picard.illumina.parser.ReadData
- ReadDataManipulationProgramGroup - Class in picard.cmdline.programgroups
-
Tools that manipulate read data in SAM, BAM or CRAM format
- ReadDataManipulationProgramGroup() - Constructor for class picard.cmdline.programgroups.ReadDataManipulationProgramGroup
- ReadDescriptor - Class in picard.illumina.parser
-
Represents one set of cycles in an ReadStructure (e.g.
- ReadDescriptor(int, ReadType) - Constructor for class picard.illumina.parser.ReadDescriptor
- readDirectionStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies bases into their read's Direction (i.e.
- readDisqualificationThresholdConstant - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
-
Argument used to adjust the agressiveness of dynamic read disqualification
- readEndMarkedUncertain(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- readEndMarkedUnclipped(GATKRead, boolean) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- ReadEnds - Class in picard.sam.markduplicates.util
-
Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
- ReadEnds() - Constructor for class picard.sam.markduplicates.util.ReadEnds
- ReadEndsForMarkDuplicates - Class in picard.sam.markduplicates.util
-
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
- ReadEndsForMarkDuplicates() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- ReadEndsForMarkDuplicates(ReadEndsForMarkDuplicates) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- ReadEndsForMarkDuplicatesCodec - Class in picard.sam.markduplicates.util
-
Codec for ReadEnds that just outputs the primitive fields and reads them back.
- ReadEndsForMarkDuplicatesCodec() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- ReadEndsForMarkDuplicatesMap - Interface in picard.sam.markduplicates.util
-
Interface for storing and retrieving ReadEnds objects.
- ReadEndsForMarkDuplicatesWithBarcodes - Class in picard.sam.markduplicates.util
- ReadEndsForMarkDuplicatesWithBarcodes() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicates) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicatesWithBarcodes) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- ReadEndsForMarkDuplicatesWithBarcodesCodec - Class in picard.sam.markduplicates.util
-
Created by nhomer on 9/13/15.
- ReadEndsForMarkDuplicatesWithBarcodesCodec() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
- ReadEndsForMateCigar - Class in picard.sam.markduplicates.util
-
A class to store individual records for MarkDuplicatesWithMateCigar.
- ReadEndsForMateCigar(SAMFileHeader, SamRecordWithOrdinal, OpticalDuplicateFinder, short) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
Builds a read ends object that represents a single read.
- ReadEndsForMateCigar(ReadEndsForMateCigar, SamRecordWithOrdinal) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
Creates a shallow copy from the "other"
- reader(Reader, BiFunction<TableColumnCollection, Function<String, RuntimeException>, Function<DataLine, R>>) - Static method in class org.broadinstitute.hellbender.utils.tsv.TableUtils
-
Creates a new table reader given an record extractor factory based from the columns found in the input.
- reader(String, Reader, BiFunction<TableColumnCollection, Function<String, RuntimeException>, Function<DataLine, R>>) - Static method in class org.broadinstitute.hellbender.utils.tsv.TableUtils
-
Creates a new table reader given an record extractor factory based from the columns found in the input.
- reader(Path, BiFunction<TableColumnCollection, Function<String, RuntimeException>, Function<DataLine, R>>) - Static method in class org.broadinstitute.hellbender.utils.tsv.TableUtils
-
Creates a new table reader given an record extractor factory based from the columns found in the input.
- Reader(String, SeekableStream, FeatureCodec<T, BlockCompressedIntervalStream.Reader<T>>) - Constructor for class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- Reader(Path) - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceSummaryRecord.Reader
- Reader(FeatureInput<T>, FeatureCodec<T, BlockCompressedIntervalStream.Reader<T>>) - Constructor for class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- Reader(BlockCompressedIntervalStream.Reader<T>) - Constructor for class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- ReadErrorCorrector - Interface in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
- ReaderSplitter<T> - Class in org.broadinstitute.hellbender.tools.readersplitters
-
Splits a reader by some value.
- ReaderSplitter() - Constructor for class org.broadinstitute.hellbender.tools.readersplitters.ReaderSplitter
- ReadEvidence(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
-
a technical constructor for use in Kryo (de-)serialization.
- ReadEvidence(GATKRead, ReadMetadata, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
-
evidence offset and width is set to "the rest of the fragment" not covered by this read
- ReadEvidence(GATKRead, ReadMetadata, int, int, boolean, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
-
for use when the uncertainty in location has a fixed size
- readFastqFile(String) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils
- readFastqStream(BufferedReader, String) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils
- ReadFeatherEndForwardComparator() - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.DRAGENGenotypesModel.ReadFeatherEndForwardComparator
- ReadFeatherEndReverseComparator() - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.DRAGENGenotypesModel.ReadFeatherEndReverseComparator
- readFileIntoByteArray(File) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Reads the entirety of the given file into a byte array.
- readFileIntoByteArray(File, int) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Reads the entirety of the given file into a byte array using the requested read buffer size.
- readFilesNames - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredReadInputArgumentCollection
- ReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filters which operate on
GATKReadshould subclass this by overridingReadFilter.test(GATKRead)ReadFilter implements Predicate and Serializable. - ReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilter
- ReadFilter.ReadFilterAnd - Class in org.broadinstitute.hellbender.engine.filters
- ReadFilter.ReadFilterBinOp - Class in org.broadinstitute.hellbender.engine.filters
- ReadFilterAnd(ReadFilter, ReadFilter) - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilter.ReadFilterAnd
- ReadFilterArgumentDefinitions - Class in org.broadinstitute.hellbender.cmdline
- ReadFilterBinOp(ReadFilter, ReadFilter) - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilter.ReadFilterBinOp
- ReadFilteringIterator - Class in org.broadinstitute.hellbender.utils.iterators
-
An iterator that filters reads from an existing iterator of reads.
- ReadFilteringIterator(Iterator<GATKRead>, ReadFilter) - Constructor for class org.broadinstitute.hellbender.utils.iterators.ReadFilteringIterator
-
Create a ReadFilteringIterator given a pre-existing iterator of reads and a read filter.
- ReadFilterLibrary - Class in org.broadinstitute.hellbender.engine.filters
-
Standard ReadFilters
- ReadFilterLibrary.AllowAllReadsReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Do not filter out any read.
- ReadFilterLibrary.CigarContainsNoNOperator - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads containing skipped region from the reference (CIGAR strings with 'N' operator).
- ReadFilterLibrary.FirstOfPairReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads that are first of pair (0x1 and 0x40).
- ReadFilterLibrary.GoodCigarReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads containing good CIGAR strings.
- ReadFilterLibrary.HasReadGroupReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads without the SAM record RG (Read Group) tag.
- ReadFilterLibrary.MappedReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out unmapped reads.
- ReadFilterLibrary.MappingQualityAvailableReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads without available mapping quality (MAPQ=255).
- ReadFilterLibrary.MappingQualityNotZeroReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads with mapping quality equal to zero.
- ReadFilterLibrary.MatchingBasesAndQualsReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads where the bases and qualities do not match in length.
- ReadFilterLibrary.MateDifferentStrandReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
For paired reads (0x1), keep only reads that are mapped, have a mate that is mapped (read is not 0x8), and both the read and its mate are on different strands (when read is 0x20, it is not 0x10), as is the typical case.
- ReadFilterLibrary.MateOnSameContigOrNoMappedMateReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads that have a mate that maps to the same contig (RNEXT is "="), is single ended (not 0x1) or has an unmapped mate (0x8).
- ReadFilterLibrary.MateUnmappedAndUnmappedReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter reads whose mate is unmapped as well as unmapped reads.
- ReadFilterLibrary.NonChimericOriginalAlignmentReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
If original alignment and mate original alignment tags exist, filter reads that were originally chimeric (mates were on different contigs).
- ReadFilterLibrary.NonZeroFragmentLengthReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads with fragment length (insert size) different from zero.
- ReadFilterLibrary.NonZeroReferenceLengthAlignmentReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads that do not align to the reference.
- ReadFilterLibrary.NotDuplicateReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads marked as duplicate (0x400).
- ReadFilterLibrary.NotProperlyPairedReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only paired reads that are marked as not properly paired (0x1 and !0x2).
- ReadFilterLibrary.NotSecondaryAlignmentReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads representing secondary alignments (0x100).
- ReadFilterLibrary.NotSupplementaryAlignmentReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads representing supplementary alignments (0x800).
- ReadFilterLibrary.PairedReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out unpaired reads (not 0x1).
- ReadFilterLibrary.PassesVendorQualityCheckReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads failing platform/vendor quality checks (0x200).
- ReadFilterLibrary.PrimaryLineReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads representing primary alignments (those that satisfy both the NotSecondaryAlignment and NotSupplementaryAlignment filters, or in terms of SAM flag values, must have neither of the 0x100 or 0x800 flags set).
- ReadFilterLibrary.ProperlyPairedReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only paired reads that are properly paired (0x1 and 0x2).
- ReadFilterLibrary.ReadLengthEqualsCigarLengthReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads where the read and CIGAR do not match in length.
- ReadFilterLibrary.SecondOfPairReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only paired reads (0x1) that are second of pair (0x80).
- ReadFilterLibrary.SeqIsStoredReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads with sequenced bases.
- ReadFilterLibrary.ValidAlignmentEndReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads where the read end corresponds to a proper alignment -- that is, the read ends after the start (non-negative number of bases in the reference).
- ReadFilterLibrary.ValidAlignmentStartReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads with a valid alignment start (POS larger than 0) or is unmapped.
- ReadFilterSparkifier - Class in org.broadinstitute.hellbender.tools.spark.utils
- ReadFilterSparkifier(ReadFilter) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.ReadFilterSparkifier
- readFilterTagComp - Variable in class org.broadinstitute.hellbender.engine.filters.ReadTagValueFilter
- readFilterTagName - Variable in class org.broadinstitute.hellbender.engine.filters.ReadTagValueFilter
- readFilterTagOp - Variable in class org.broadinstitute.hellbender.engine.filters.ReadTagValueFilter
- readFromFile(File) - Static method in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationRecord
- readFromFile(File) - Static method in class org.broadinstitute.hellbender.tools.walkers.contamination.MinorAlleleFractionRecord
- readFromFile(File) - Static method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- readFromFile(File) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.MutectStats
- readFromFile(File) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.NormalArtifactRecord
- readFromFile(File) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
- readFromGCS(String) - Static method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection
-
Read all counts from a Google Cloud Storage URL.
- readFromPath(Path) - Static method in class org.broadinstitute.hellbender.tools.walkers.contamination.MinorAlleleFractionRecord
- readFromPath(Path) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
- readgroup - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Partition
- readGroup - Variable in class org.broadinstitute.hellbender.engine.filters.ReadGroupReadFilter
- readGroup - Variable in class picard.sam.markduplicates.util.ReadEnds
- READGROUP - Enum constant in enum class picard.fingerprint.CrosscheckMetric.DataType
- READGROUP_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- READGROUP_ID_REGEX - Static variable in class picard.sam.AddOrReplaceReadGroups
- READGROUP_REPORT_TABLE_TITLE - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- ReadGroupBlackListReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep records that don't match the specified filter string(s).
- ReadGroupBlackListReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadGroupBlackListReadFilter
- ReadGroupBlackListReadFilter(List<String>, SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadGroupBlackListReadFilter
-
Creates a filter using the list of blacklisted read groups.
- ReadGroupCovariate - Class in org.broadinstitute.hellbender.utils.recalibration.covariates
-
The Read Group covariate.
- ReadGroupCovariate(RecalibrationArgumentCollection, List<String>) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadGroupCovariate
- ReadGroupHasFlowOrderReadFilter - Class in org.broadinstitute.hellbender.engine.filters.flow
-
A read filter to test if the read's readGroup has a flow order associated with it
- ReadGroupHasFlowOrderReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.flow.ReadGroupHasFlowOrderReadFilter
- ReadGroupHasFlowOrderReadFilter(SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.engine.filters.flow.ReadGroupHasFlowOrderReadFilter
- ReadGroupIdSplitter - Class in org.broadinstitute.hellbender.tools.readersplitters
-
Splits readers read group id.
- ReadGroupIdSplitter() - Constructor for class org.broadinstitute.hellbender.tools.readersplitters.ReadGroupIdSplitter
- readGroupIndex - Variable in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- ReadGroupInfo(SAMReadGroupRecord) - Constructor for class org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils.ReadGroupInfo
- ReadGroupReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads from the specified read group.
- ReadGroupReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadGroupReadFilter
- ReadGroupSplitter<T> - Class in org.broadinstitute.hellbender.tools.readersplitters
-
Splits a reader based on a value from a read group.
- ReadGroupSplitter() - Constructor for class org.broadinstitute.hellbender.tools.readersplitters.ReadGroupSplitter
- readgroupStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies to the readgroup id of the read.
- readHasMappedMate(SAMRecord) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
- readHasMappedMate(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
- readHasNoAssignedPosition(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Checks whether the provided read has an assigned position.
- readHasReasonableMQ(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Used to be called isUsableRead()
- readHeader(int) - Method in class picard.illumina.parser.readers.CbclReader
-
Reads the Cbcl header and sets up the data streams.
- readHeader(B) - Method in class org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec
- readHeader(LineIterator) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec
- readHeader(BlockCompressedIntervalStream.Reader<F>) - Method in class org.broadinstitute.hellbender.utils.codecs.AbstractBCICodec
- readIndexInFile - Variable in class picard.sam.util.RepresentativeReadIndexer
- readIndices - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.ReadInputArgumentCollection
- readInfo(GATKRead) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampUtils
- ReadInputArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
An abstract argument collection for use with tools that accept input files containing reads (eg., BAM/SAM/CRAM files).
- ReadInputArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.ReadInputArgumentCollection
- readInt(InputStream) - Static method in class org.broadinstitute.hellbender.tools.DumpTabixIndex
- readIntervalAlignedToRefSpan(SimpleInterval) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
Given an alignment (represented by this AlignmentInterval) and a reference span (in this case
otherRefSpan), the overlap between the two reference spans, if any, has a corresponding span on the read to which the alignment belongs. - readIntervals(HDF5File, String) - Static method in class org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils
-
Reads a list of intervals from an HDF5 file using the sub-paths and conventions used by
HDF5Utils.writeIntervals(org.broadinstitute.hdf5.HDF5File, java.lang.String, java.util.List<T>). - readIntervalsFile(String, Map<String, Integer>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFileUtils
-
Read intervals from file.
- readKmerFilter(String) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerUtils
- readKmersFile(String, int) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFileUtils
-
Read a file of kmers.
- readLabel(File, String) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- readLaneTiles(File, ReadStructure, ValidationStringency, int) - Static method in class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
-
Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.
- READLENGTH_EQUALS_CIGARLENGTH - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- ReadLengthEqualsCigarLengthReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.ReadLengthEqualsCigarLengthReadFilter
- ReadLengthReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads whose length is ≥ min value and ≤ max value.
- ReadLengthReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadLengthReadFilter
- ReadLengthReadFilter(int, int) - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadLengthReadFilter
- readLengths - Variable in class picard.illumina.parser.ReadStructure
- ReadlessAssemblyRegion - Class in org.broadinstitute.hellbender.engine
-
A cut-down version of
AssemblyRegionthat doesn't store reads, used in the strict implementation ofFindAssemblyRegionsSpark. - ReadlessAssemblyRegion(AssemblyRegion) - Constructor for class org.broadinstitute.hellbender.engine.ReadlessAssemblyRegion
- ReadLikelihoodCalculationEngine - Interface in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Common interface for assembly-haplotype vs reads likelihood engines.
- ReadLikelihoodCalculationEngine.Implementation - Enum Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
- readLikelihoods() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingData
-
Returns read-likelihoods to use for genotyping.
- readLines() - Method in class org.broadinstitute.hellbender.utils.text.XReadLines
-
Reads all of the lines in the file, and returns them as a list of strings
- readLong(InputStream) - Static method in class org.broadinstitute.hellbender.tools.DumpTabixIndex
- readMetadata - Variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
- ReadMetadata - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
A bag of data about reads: contig name to id mapping, fragment length statistics by read group, mean length.
- ReadMetadata(Set<Integer>, SAMFileHeader, int, JavaRDD<GATKRead>, SVReadFilter, Logger) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- ReadMetadata.LibraryRawStatistics - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- ReadMetadata.LibraryRawStatistics.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- ReadMetadata.PartitionBounds - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
A class to track the genomic location of the start of the first and last mapped reads in a partition.
- ReadMetadata.PartitionBounds.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- ReadMetadata.PartitionStatistics - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- ReadMetadata.PartitionStatistics.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- ReadMetadata.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- readMetricsFile(File) - Static method in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel
- ReadMissingReadGroup(GATKRead) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.ReadMissingReadGroup
- readMixingFractions(File) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.MixingFraction
- readName - Variable in class org.broadinstitute.hellbender.engine.filters.ReadNameReadFilter
- ReadNameEncoder - Interface in picard.fastq
- ReadNameParser - Class in picard.sam.util
-
Provides access to the physical location information about a cluster.
- ReadNameParser() - Constructor for class picard.sam.util.ReadNameParser
-
Creates are read name parser using the default read name regex and optical duplicate distance.
- ReadNameParser(String) - Constructor for class picard.sam.util.ReadNameParser
-
Creates are read name parser using the given read name regex.
- ReadNameParser(String, Log) - Constructor for class picard.sam.util.ReadNameParser
-
Creates are read name parser using the given read name regex.
- ReadNameReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads with this read name.
- ReadNameReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadNameReadFilter
- readNameRegex - Variable in class picard.sam.util.ReadNameParser
- readNextLine() - Method in class picard.util.AbstractInputParser
- readNextLine() - Method in class picard.util.BasicInputParser
-
Workhorse method that reads the next line from the underlying reader
- readObject(ObjectInputStream) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.ContainsKmerReadFilterSpark
- readOneBarcode - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- readOrdinalityStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies bases into their read's Ordinality (i.e.
- ReadOrientation - Enum Class in org.broadinstitute.hellbender.tools.walkers.readorientation
-
Created by tsato on 3/28/18.
- ReadOrientationFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- ReadOrientationFilter(List<File>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadOrientationFilter
- readOrientationPriorTarGzs - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- readOrientationStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies bases into their read-pair's Orientation (i.e.
- readOverlappingSubsetFromGCS(String, List<SimpleInterval>) - Static method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection
-
From a Google Cloud Storage URL, subset only the counts with intervals overlapping with intervals from a given list.
- ReadPair - Class in org.broadinstitute.hellbender.tools.walkers.qc
-
Data structure that contains the set of reads sharing the same queryname, including the primary, secondary (i.e.
- ReadPair() - Constructor for class picard.util.QuerySortedReadPairIteratorUtil.ReadPair
- ReadPair(GATKRead) - Constructor for class org.broadinstitute.hellbender.tools.walkers.qc.ReadPair
- readPairednessStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies bases into their read's Proper-pairedness
- ReadPileup - Class in org.broadinstitute.hellbender.utils.pileup
-
Represents a pileup of reads at a given position.
- ReadPileup(Locatable) - Constructor for class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Create a new pileup without any aligned reads
- ReadPileup(Locatable, Iterable<GATKRead>) - Constructor for class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Get the pileup of reads covering a locus.
- ReadPileup(Locatable, List<PileupElement>) - Constructor for class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Create a new pileup at loc, using the reads and their corresponding offsets.
- ReadPileup(Locatable, List<GATKRead>, int) - Constructor for class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Create a new pileup with the given reads.
- ReadPileup(Locatable, List<GATKRead>, List<Integer>) - Constructor for class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Create a new pileup with the given reads.
- ReadPileup(Locatable, Map<String, ReadPileup>) - Constructor for class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Create a new pileup at loc, using an stratified pileup Note: the current implementation of ReadPileup does not efficiently retrieve the stratified pileup
- ReadPosition - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Median distance of variant starts from ends of reads supporting each alt allele.
- ReadPosition() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosition
- ReadPositionFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- ReadPositionFilter(double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadPositionFilter
- ReadPosRankSumTest - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Rank Sum Test for relative positioning of REF versus ALT alleles within reads
- ReadPosRankSumTest() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosRankSumTest
- ReadQueryNameComparator - Class in org.broadinstitute.hellbender.utils.read
-
compare
GATKReadby queryname duplicates the exact ordering ofSAMRecordQueryNameComparator - ReadQueryNameComparator() - Constructor for class org.broadinstitute.hellbender.utils.read.ReadQueryNameComparator
- ReadRecalibrationInfo - Class in org.broadinstitute.hellbender.utils.recalibration
- ReadRecalibrationInfo(GATKRead, ReadCovariates, boolean[], double[], double[], double[]) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.ReadRecalibrationInfo
- readRecord() - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Returns the next record form the source.
- readRecord(DataInput) - Method in class org.broadinstitute.hellbender.utils.BinaryTableReader
- readRecord(String) - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Reads the record from a string rather than from the input reader.
- reads() - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- READS - Variable in class picard.illumina.BarcodeMetric
-
The total number of reads matching the barcode.
- READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The total number of reads examined
- READS_AFTER_DEDUPLICATION - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterMetrics
-
The number of reads after deduplication
- READS_AFTER_HOST_FILTER - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterMetrics
-
The number of reads after host read filtering
- READS_AFTER_PREALIGNED_HOST_FILTER - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterMetrics
-
The number of reads after filtering prealigned reads
- READS_AFTER_QUALITY_AND_COMPLEXITY_FILTER - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterMetrics
-
The number of reads after low-quality and low-complexity filtering
- READS_ALIGNED - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of mapped reads processed
- READS_ALIGNED_IN_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of aligned reads whose mate pair was also aligned to the reference.
- READS_IGNORED_MISMATCHES - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of reads discarded for exceeding the mismatch threshold
- READS_IGNORED_SHORT - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of reads discarded due to being too short
- READS_PER_PARTITION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark
- READS_TO_ALIGN - Variable in class picard.fastq.BamToBfq
- READS_USED - Variable in class picard.analysis.GcBiasDetailMetrics
-
This option is used to mark including or excluding duplicates.
- READS_USED - Variable in class picard.analysis.GcBiasSummaryMetrics
-
This option is used to mark including or excluding duplicates.
- READS_WITH_NO_CPG - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of reads discarded for having no CpG sites
- readSampleName(SAMFileHeader) - Static method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.MetadataUtils
- readsAt(int, int) - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- ReadsContext - Class in org.broadinstitute.hellbender.engine
-
Wrapper around ReadsDataSource that presents reads overlapping a specific interval to a client, without improperly exposing the entire ReadsDataSource interface.
- ReadsContext() - Constructor for class org.broadinstitute.hellbender.engine.ReadsContext
-
Create an empty ReadsContext with no backing data source or interval.
- ReadsContext(GATKDataSource<GATKRead>, SimpleInterval) - Constructor for class org.broadinstitute.hellbender.engine.ReadsContext
-
Create a ReadsContext backed by the supplied source of reads.
- ReadsContext(GATKDataSource<GATKRead>, SimpleInterval, ReadFilter) - Constructor for class org.broadinstitute.hellbender.engine.ReadsContext
-
Create a ReadsContext backed by the supplied source of reads.
- ReadsContext(ReadsContext, SimpleInterval) - Constructor for class org.broadinstitute.hellbender.engine.ReadsContext
-
Create a ReadsContext using the data source from the provided ReadsContext, with the supplied interval.
- readScores(File) - Static method in interface org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsScorer
-
Reads a double array of scores from "/data/scores" in an HDF5 file.
- ReadsDataSource - Interface in org.broadinstitute.hellbender.engine
-
An interface for managing traversals over sources of reads.
- ReadsDownsampler - Class in org.broadinstitute.hellbender.utils.downsampling
-
An extension of the basic downsampler API with reads-specific operations
- ReadsDownsampler() - Constructor for class org.broadinstitute.hellbender.utils.downsampling.ReadsDownsampler
- ReadsDownsamplingIterator - Class in org.broadinstitute.hellbender.utils.downsampling
-
Iterator wrapper around our generic {@link ReadsDownsampler)} interface.
- ReadsDownsamplingIterator(Iterator<GATKRead>, ReadsDownsampler) - Constructor for class org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator
- ReadsForQNamesFinder - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
Find <intervalId,list
> pairs for interesting template names. - ReadsForQNamesFinder(HopscotchUniqueMultiMapSpark<String, Integer, QNameAndInterval>, int, boolean, Iterator<GATKRead>, SVReadFilter) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadsForQNamesFinder
- readShardPadding - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionReadShardArgumentCollection
- readShardSize - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionReadShardArgumentCollection
- readShardSize - Variable in class org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark
- readsHeader - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- readShort(InputStream) - Static method in class org.broadinstitute.hellbender.tools.DumpTabixIndex
- ReadsKey - Class in org.broadinstitute.hellbender.utils.read.markduplicates
-
Encodes a unique key for read, read pairs and fragments.
- ReadsKey() - Constructor for class org.broadinstitute.hellbender.utils.read.markduplicates.ReadsKey
- ReadsKey.KeyForFragment - Class in org.broadinstitute.hellbender.utils.read.markduplicates
-
Key class for representing relevant duplicate marking identifiers into a single long key for fragment data.
- ReadsKey.KeyForPair - Class in org.broadinstitute.hellbender.utils.read.markduplicates
-
Key class for representing relevant duplicate marking identifiers into a two long key values for pair data data.
- ReadsPathDataSource - Class in org.broadinstitute.hellbender.engine
-
Manages traversals and queries over sources of reads which are accessible via
Paths (for now, SAM/BAM/CRAM files only). - ReadsPathDataSource(Path) - Constructor for class org.broadinstitute.hellbender.engine.ReadsPathDataSource
-
Initialize this data source with a single SAM/BAM file and validation stringency SILENT.
- ReadsPathDataSource(Path, SamReaderFactory) - Constructor for class org.broadinstitute.hellbender.engine.ReadsPathDataSource
-
Initialize this data source with a single SAM/BAM file and a custom SamReaderFactory
- ReadsPathDataSource(List<Path>) - Constructor for class org.broadinstitute.hellbender.engine.ReadsPathDataSource
-
Initialize this data source with multiple SAM/BAM files and validation stringency SILENT.
- ReadsPathDataSource(List<Path>, SamReaderFactory) - Constructor for class org.broadinstitute.hellbender.engine.ReadsPathDataSource
-
Initialize this data source with multiple SAM/BAM files and a custom SamReaderFactory
- ReadsPathDataSource(List<Path>, List<Path>) - Constructor for class org.broadinstitute.hellbender.engine.ReadsPathDataSource
-
Initialize this data source with multiple SAM/BAM/CRAM files, and explicit indices for those files.
- ReadsPathDataSource(List<Path>, List<Path>, SamReaderFactory) - Constructor for class org.broadinstitute.hellbender.engine.ReadsPathDataSource
-
Initialize this data source with multiple SAM/BAM/CRAM files, explicit indices for those files, and a custom SamReaderFactory.
- ReadsPathDataSource(List<Path>, List<Path>, SamReaderFactory, int, int) - Constructor for class org.broadinstitute.hellbender.engine.ReadsPathDataSource
-
Initialize this data source with multiple SAM/BAM/CRAM files, explicit indices for those files, and a custom SamReaderFactory.
- ReadsPathDataSource(List<Path>, List<Path>, SamReaderFactory, Function<SeekableByteChannel, SeekableByteChannel>, Function<SeekableByteChannel, SeekableByteChannel>) - Constructor for class org.broadinstitute.hellbender.engine.ReadsPathDataSource
-
Initialize this data source with multiple SAM/BAM/CRAM files, explicit indices for those files, and a custom SamReaderFactory.
- readsPerPartition - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark
- readsPerPartitionEstimate - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
-
This parameter is for fine-tuning memory performance.
- readsPerPartitionOutput - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark
-
Because numReducers is based on the input size, it causes too many partitions to be produced when the output size is much smaller.
- ReadsPipelineSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines
-
ReadsPipelineSpark is our standard pipeline that takes unaligned or aligned reads and runs BWA (if specified), MarkDuplicates, BQSR, and HaplotypeCaller.
- ReadsPipelineSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- ReadsSparkSink - Class in org.broadinstitute.hellbender.engine.spark.datasources
-
ReadsSparkSink writes GATKReads to a file.
- ReadsSparkSink() - Constructor for class org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink
- ReadsSparkSource - Class in org.broadinstitute.hellbender.engine.spark.datasources
-
Loads the reads from disk either serially (using samReaderFactory) or in parallel using Hadoop-BAM.
- ReadsSparkSource(JavaSparkContext) - Constructor for class org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource
- ReadsSparkSource(JavaSparkContext, ValidationStringency) - Constructor for class org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource
- readsTaken() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
-
some instrumentation methods
- readStandalone(String) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.Serializer
-
Reads a read-metadata from a file or resource.
- ReadStrandFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads whose strand is either forward (not 0x10) or reverse (0x10), as specified.
- ReadStrandFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadStrandFilter
- ReadStrandFilter(boolean) - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadStrandFilter
- readStream() - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- readStreamIntoByteArray(InputStream, int) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Reads all data from the given stream into a byte array using the requested read buffer size.
- ReadStructure - Class in picard.illumina.parser
-
Describes the intended logical output structure of clusters of an Illumina run.
- ReadStructure(String) - Constructor for class picard.illumina.parser.ReadStructure
-
Converts readStructureString into a List
and calls the primary constructor using this List as it's argument. - ReadStructure(List<ReadDescriptor>) - Constructor for class picard.illumina.parser.ReadStructure
-
Copies collection into descriptors (making descriptors unmodifiable) and then calculates relevant statistics about descriptors.
- ReadStructure.Substructure - Class in picard.illumina.parser
-
Represents a subset of ReadDescriptors in the containing ReadStructure, they ARE NOT necessarily contiguous in the containing ReadStructure but they ARE in the order they appear in the containing ReadStructure
- readSubsequence - Variable in class picard.util.BarcodeEditDistanceQuery
-
list of barcode reads
- ReadsWithSameUMI - Class in org.broadinstitute.hellbender.tools.walkers.consensus
-
A container class for a set of reads that share the same unique molecular identifier (UMI) as judged by FGBio GroupReadsByUmi (http://fulcrumgenomics.github.io/fgbio/tools/latest/GroupReadsByUmi.html) Examples of molecule IDs (MI tag): "0/A" (The first molecule in the bam, A strand) "0/B" (The first molecule in the bam, B strand) "99/A" (100th molecule in the bam, A strand) For a given set of reads with the same molecule number, the strand with a larger number of reads is defined as the A strand.
- ReadsWithSameUMI(GATKRead) - Constructor for class org.broadinstitute.hellbender.tools.walkers.consensus.ReadsWithSameUMI
- ReadsWriteFormat - Enum Class in org.broadinstitute.hellbender.utils.read
-
Possible output formats when writing reads.
- readTags - Variable in class org.broadinstitute.hellbender.tools.walkers.qc.TransferReadTags
- ReadTagValueFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads that contain a tag with a value that agrees with parameters as specified.
- ReadTagValueFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadTagValueFilter
- ReadTagValueFilter(String, float, ReadTagValueFilter.Operator) - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadTagValueFilter
- ReadTagValueFilter.Operator - Enum Class in org.broadinstitute.hellbender.engine.filters
- readTaxonomyDatabase(String) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScorer
-
Reads taxonomy database that has been serialized to a file
- ReadThreadingAssembler - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
- ReadThreadingAssembler(int, List<Integer>, boolean, boolean, int, int, boolean, double, double, double, int, boolean, boolean, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- ReadThreadingAssemblerArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Set of arguments related to the
ReadThreadingAssembler - ReadThreadingAssemblerArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- ReadThreadingGraph - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
-
Note: not final but only intended to be subclassed for testing.
- ReadThreadingGraph(int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
-
Constructs an empty read-threading-grpah provided the kmerSize.
- ReadThreadingGraph(int, EdgeFactory<MultiDeBruijnVertex, MultiSampleEdge>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
-
Constructs a read-threading-graph for a string representation.
- READTHROUGH_TRANSCRIPT - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
a transcript that overlaps two or more independent loci but is considered to belong to a third, separate locus.
- readToAlignmentByteArray(Cigar, byte[]) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Generate an array of bases for just those that are aligned to the reference (i.e.
- readToFastqSeqId(GATKRead, boolean) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils
-
Convert a read's name into a FASTQ record sequence ID
- readTranches(GATKPath) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VQSLODTranche
-
Returns a list of tranches, sorted from most to least specific, read in from file f.
- ReadTransformer - Interface in org.broadinstitute.hellbender.transformers
-
Classes which perform transformations from GATKRead -> GATKRead should implement this interface by overriding
SerializableFunction<GATKRead,GATKRead>#apply(GATKRead) - ReadTransformerSparkifier - Class in org.broadinstitute.hellbender.tools.spark.utils
- ReadTransformerSparkifier(ReadTransformer) - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.ReadTransformerSparkifier
- ReadTransformingIterator - Class in org.broadinstitute.hellbender.utils.iterators
-
An iterator that transforms read (i.e.
- ReadTransformingIterator(Iterator<GATKRead>, ReadTransformer) - Constructor for class org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator
-
Create a ReadFilteringIterator given a pre-existing iterator of reads and a read filter.
- readTrimThresh - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
-
Controls the stingency of base call quality-based read trimming.
- readTwoBarcode - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- ReadType - Enum Class in picard.illumina.parser
-
A read type describes a stretch of cycles in an ReadStructure (e.g.
- ReadUtils - Class in org.broadinstitute.hellbender.utils.read
-
A miscellaneous collection of utilities for working with reads, headers, etc.
- readValidationStringency - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.ReadInputArgumentCollection
- readValidationStringency - Variable in class org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndex
- readValuesFromFile(File) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Reads a double array from the given filename.
- ReadWalker - Class in org.broadinstitute.hellbender.engine
-
A ReadWalker is a tool that processes a single read at a time from one or multiple sources of reads, with optional contextual information from a reference and/or sets of variants/Features.
- ReadWalker() - Constructor for class org.broadinstitute.hellbender.engine.ReadWalker
- ReadWalkerContext - Class in org.broadinstitute.hellbender.engine.spark
- ReadWalkerContext(GATKRead, ReferenceContext, FeatureContext) - Constructor for class org.broadinstitute.hellbender.engine.spark.ReadWalkerContext
- ReadWalkerSpark - Class in org.broadinstitute.hellbender.engine.spark
-
A Spark version of
ReadWalker. - ReadWalkerSpark() - Constructor for class org.broadinstitute.hellbender.engine.spark.ReadWalkerSpark
- realign(byte[]) - Method in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentEngine
- realignmentArgumentCollection - Variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- RealignmentArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.realignmentfilter
- RealignmentArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
- RealignmentEngine - Class in org.broadinstitute.hellbender.tools.walkers.realignmentfilter
- RealignmentEngine(RealignmentArgumentCollection) - Constructor for class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentEngine
- realignReadsToTheirBestHaplotype(AlleleLikelihoods<GATKRead, Haplotype>, Haplotype, Locatable, SmithWatermanAligner, SWParameters) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
-
Returns a map with the original read as a key and the realigned read as the value.
- reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingAdapterFilter
- reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingDuplicateFilter
- reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingFilter
-
Return true if we are to filter this record out, false otherwise.
- reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingMapQFilter
- reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingPairedFilter
- REANNOTATE_VCF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- reannotateVCF - Variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorVariantArgumentCollection
- ReblockGVCF - Class in org.broadinstitute.hellbender.tools.walkers.variantutils
-
Condense homRef blocks in a single-sample GVCF
- ReblockGVCF() - Constructor for class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- ReblockGVCF.AlleleLengthComparator - Class in org.broadinstitute.hellbender.tools.walkers.variantutils
- ReblockingGVCFBlockCombiner - Class in org.broadinstitute.hellbender.utils.variant.writers
-
Combines variants into GVCF blocks.
- ReblockingGVCFWriter - Class in org.broadinstitute.hellbender.utils.variant.writers
- ReblockingGVCFWriter(VariantContextWriter, List<? extends Number>, boolean, CachingIndexedFastaSequenceFile, ReblockingOptions) - Constructor for class org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFWriter
- ReblockingOptions - Class in org.broadinstitute.hellbender.utils.variant.writers
- ReblockingOptions() - Constructor for class org.broadinstitute.hellbender.utils.variant.writers.ReblockingOptions
- ReblockingOptions(boolean, boolean, double) - Constructor for class org.broadinstitute.hellbender.utils.variant.writers.ReblockingOptions
- RECAL_FILE - Static variable in class org.broadinstitute.hellbender.utils.report.GATKReport
- RECALCULATE - Enum constant in enum class org.broadinstitute.hellbender.utils.baq.BAQ.CalculationMode
- RECALCULATE_IF_MISSING - Enum constant in enum class org.broadinstitute.hellbender.tools.reference.CompareReferences.MD5CalculationMode
- RecalDatum - Class in org.broadinstitute.hellbender.utils.recalibration
-
An individual piece of recalibration data.
- RecalDatum(long, double, byte) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
-
Create a new RecalDatum with given observation and mismatch counts, and an reported quality
- RecalDatum(RecalDatum) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
-
Copy copy into this recal datum, overwriting all of this objects data
- RecalibrationArgumentCollection - Class in org.broadinstitute.hellbender.utils.recalibration
-
A collection of the arguments that are used for BQSR.
- RecalibrationArgumentCollection() - Constructor for class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
- RecalibrationReport - Class in org.broadinstitute.hellbender.utils.recalibration
-
This class has all the static functionality for reading a recalibration report file into memory.
- RecalibrationReport(File) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport
- RecalibrationReport(InputStream) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport
- RecalibrationReport(GATKReport) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport
- RecalibrationReport(GATKReport, SortedSet<String>) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport
- RecalibrationTables - Class in org.broadinstitute.hellbender.utils.recalibration
-
Utility class to facilitate base quality score recalibration.
- RecalibrationTables(StandardCovariateList) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
- RecalibrationTables(StandardCovariateList, int) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
- RecalUtils - Class in org.broadinstitute.hellbender.utils.recalibration
-
This helper class holds the data HashMap as well as submaps that represent the marginal distributions collapsed over all needed dimensions.
- RecalUtils() - Constructor for class org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- reciprocialOverlapFraction(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
reciprocialOverlap: what is the min.
- reconstructContigFromBestConfiguration(Set<String>, double) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
-
Reconstructs (possibly more than one)
AssemblyContigWithFineTunedAlignmentsbased on the best-scored configuration(s). - record(int[], double[], List<Double>, List<Double>, VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel
-
Adds data to the model for every alternate allele
- Record(int, int, Float, Float, float, IlluminaGenotype) - Constructor for class picard.arrays.illumina.IlluminaAdpcFileWriter.Record
- recordAllValuesInStorage(GATKRead, SAMFileHeader, ReadCovariates, boolean) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList
-
For each covariate compute the values for all positions in this read and record the values in the provided storage object.
- recordCall(ErrorProbabilities, double) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteringOutputStats
- RECORDS_ONLY - Variable in class picard.sam.ViewSam
- recordValues(GATKRead, SAMFileHeader, ReadCovariates, boolean) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ContextCovariate
- recordValues(GATKRead, SAMFileHeader, ReadCovariates, boolean) - Method in interface org.broadinstitute.hellbender.utils.recalibration.covariates.Covariate
-
Calculates covariate values for all positions in the read.
- recordValues(GATKRead, SAMFileHeader, ReadCovariates, boolean) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.CycleCovariate
- recordValues(GATKRead, SAMFileHeader, ReadCovariates, boolean) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.QualityScoreCovariate
- recordValues(GATKRead, SAMFileHeader, ReadCovariates, boolean) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadGroupCovariate
- RECOVER_ALL_DANGLING_BRANCHES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
- RECOVER_DANGLING_HEADS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerReadThreadingAssemblerArgumentCollection
- RECOVER_SWAPPED_REF_ALT - Variable in class picard.vcf.LiftoverVcf
- recoverAllDanglingBranches - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
By default, the read threading assembler does not recover dangling branches that fork after splitting from the reference.
- recoverDanglingHeads(int, int, boolean, SmithWatermanAligner, SWParameters) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Try to recover dangling heads
- recoverDanglingTails(int, int, boolean, SmithWatermanAligner, SWParameters) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Try to recover dangling tails
- RED - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
-
The red intensity value for the control.
- reduce(FindBreakpointEvidenceSpark.IntPair, FindBreakpointEvidenceSpark.IntPair) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark.IntPair
- reduce(ReadMetadata.LibraryRawStatistics, ReadMetadata.LibraryRawStatistics) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.LibraryRawStatistics
- REDUCED_DELIM - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
- ReducibleAnnotation - Interface in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
An interface for annotations that are calculated using raw data across samples, rather than the median (or median of median) of samples values The Raw annotation keeps some summary (one example might be a histogram of the raw values for each sample) of the individual sample (or allele) level annotation.
- ReducibleAnnotationData<T> - Class in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
A class to encapsulate the raw data for classes compatible with the ReducibleAnnotation interface
- ReducibleAnnotationData(String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData
-
Create a new ReducibleAnnotationData using the raw data string from a VCF
- ref - Variable in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- ref() - Method in enum class picard.analysis.artifacts.Transition
-
Gets the reference for the transition.
- REF - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants.ValidationType
-
Check whether the reported reference base in the VCF is the same as the corresponding base in the actual reference.
- REF_AND_ALT - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection.Type
- REF_BASE - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
-
The reference base (or it's complement).
- REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The (upper-case) original base on the reference strand.
- REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The (upper-case) original base on the reference strand.
- REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The (upper-case) original base on the reference strand.
- REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The (upper-case) original base on the reference strand.
- REF_CONTEXT_PADDING - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterConstants
- REF_COUNT - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
-
The number of reference bases observed.
- REF_DICTIONARY_FILE_NAME - Static variable in class org.broadinstitute.hellbender.utils.dragstr.STRTableFile
- REF_FLAT - Variable in class picard.analysis.CollectMultipleMetrics
- REF_FLAT - Variable in class picard.analysis.CollectRnaSeqMetrics
- REF_HIST_EXTENSION - Static variable in class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2CountsCollector
- REF_MODEL_DELETION_QUAL - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
-
Surrogate quality score for no base calls.
- REF_NONOXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of reference alleles observed as C in read 1 and G in read 2.
- REF_OXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of reference alleles observed as G in read 1 and C in read 2.
- REF_RECORD_LEN - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBadGenomicKmersSpark
- REF_RECORDS_PER_PARTITION - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBadGenomicKmersSpark
- REF_STRAND_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- REF_TOTAL_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The total number of reference alleles observed
- refactorNDNtoN(Cigar) - Static method in class org.broadinstitute.hellbender.transformers.NDNCigarReadTransformer
-
Refactor cigar strings that contain N-D-N elements to one N element (with total length of the three refactored elements).
- refAllele - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- refBases - Variable in class org.broadinstitute.hellbender.utils.baq.BAQ.BAQCalculationResult
- refDepth - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceResult
- reference - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.TensorType
- reference - Variable in class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations
- reference - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
- reference - Variable in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.Splice
- reference() - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- REFERENCE - Enum constant in enum class org.broadinstitute.hellbender.utils.read.FlowBasedRead.Direction
- REFERENCE - Variable in class picard.analysis.CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
- REFERENCE - Variable in class picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
- REFERENCE - Variable in class picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
- REFERENCE_BASES_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- REFERENCE_DICTIONARY_COMPANION - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- REFERENCE_GENOME_ERROR - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
locus overlaps a sequence error or an assembly error in the reference genome that affects its annotation (e.g., 1 or
- REFERENCE_GENOTYPE_QUALITY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- REFERENCE_INDEX_COMPANION - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- REFERENCE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- REFERENCE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
- REFERENCE_PADDING_FOR_ASSEMBLY - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- REFERENCE_SEQUENCE - Variable in class org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram
- REFERENCE_SEQUENCE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
- REFERENCE_SEQUENCE - Variable in class picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection
- REFERENCE_SEQUENCE - Variable in class picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection
- REFERENCE_SEQUENCE - Variable in class picard.cmdline.CommandLineProgram
- REFERENCE_SEQUENCE_BUFFER_SIZE_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFile
- REFERENCE_SHARD_SIZE - Static variable in class org.broadinstitute.hellbender.engine.ReferenceShard
- REFERENCE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- REFERENCE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
- REFERENCE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- REFERENCE_VERSION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- REFERENCE_WINDOW_PADDING - Static variable in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
- ReferenceArgumentCollection - Interface in picard.cmdline.argumentcollections
-
Base interface for a reference argument collection.
- referenceArguments - Variable in class org.broadinstitute.hellbender.engine.GATKTool
- referenceArguments - Variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- referenceArguments - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
- ReferenceBases - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Local reference context at a variant position.
- ReferenceBases - Class in org.broadinstitute.hellbender.utils.reference
-
ReferenceBases stores the bases of the reference genome for a particular interval.
- ReferenceBases() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.ReferenceBases
- ReferenceBases(byte[], SimpleInterval) - Constructor for class org.broadinstitute.hellbender.utils.reference.ReferenceBases
- referenceBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies a base onto the reference base that it covers, possibly reverse complemented if the read has been reversed by the aligner.
- ReferenceBlockConcordance - Class in org.broadinstitute.hellbender.tools.walkers.validation
-
Evaluate GVCF reference block concordance of an input GVCF against a truth GVCF.
- ReferenceBlockConcordance() - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance
- ReferenceConfidenceMode - Enum Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Reference confidence emission modes.
- referenceConfidenceModel - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- ReferenceConfidenceModel - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Code for estimating the reference confidence This code can estimate the probability that the data for a single sample is consistent with a well-determined REF/REF diploid genotype.
- ReferenceConfidenceModel(SampleList, SAMFileHeader, int, int, byte, boolean, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
-
Create a new ReferenceConfidenceModel
- ReferenceConfidenceResult - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Holds information about a genotype call of a single sample reference vs.
- ReferenceConfidenceResult() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceResult
- ReferenceConfidenceUtils - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
- ReferenceConfidenceUtils() - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceUtils
- ReferenceConfidenceVariantContextMerger - Class in org.broadinstitute.hellbender.tools.walkers
-
Variant context utilities related to merging variant-context instances.
- ReferenceConfidenceVariantContextMerger(VariantAnnotatorEngine, VCFHeader) - Constructor for class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
- ReferenceConfidenceVariantContextMerger(VariantAnnotatorEngine, VCFHeader, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
- ReferenceConfidenceVariantContextMerger(VariantAnnotatorEngine, VCFHeader, boolean, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
- ReferenceConfidenceVariantContextMerger(VariantAnnotatorEngine, VCFHeader, boolean, boolean, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
- ReferenceConfidenceVariantContextMerger.VCWithNewAlleles - Class in org.broadinstitute.hellbender.tools.walkers
- ReferenceContext - Class in org.broadinstitute.hellbender.engine
-
Wrapper around ReferenceDataSource that presents data from a specific interval/window to a client, without improperly exposing the entire ReferenceDataSource interface.
- ReferenceContext() - Constructor for class org.broadinstitute.hellbender.engine.ReferenceContext
-
Create a ReferenceContext with no backing data source.
- ReferenceContext(ReferenceContext, SimpleInterval) - Constructor for class org.broadinstitute.hellbender.engine.ReferenceContext
-
Create a windowed ReferenceContext set up to lazily query the provided interval.
- ReferenceContext(ReferenceDataSource, SimpleInterval) - Constructor for class org.broadinstitute.hellbender.engine.ReferenceContext
-
Create a windowless ReferenceContext set up to lazily query the bases spanning just the provided interval (with no extra bases of context)
- ReferenceContext(ReferenceDataSource, SimpleInterval, int, int) - Constructor for class org.broadinstitute.hellbender.engine.ReferenceContext
-
Create a windowed ReferenceContext set up to lazily query the provided interval, expanded by the specified number of bases in each direction.
- ReferenceContext(ReferenceDataSource, SimpleInterval, SimpleInterval) - Constructor for class org.broadinstitute.hellbender.engine.ReferenceContext
-
Create a windowed ReferenceContext set up to lazily query the provided interval, expanded by the specified number of bases in each direction.
- ReferenceDataSource - Interface in org.broadinstitute.hellbender.engine
-
Manages traversals and queries over reference data.
- referenceFasta - Variable in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
- referenceFasta - Variable in class picard.sam.AbstractAlignmentMerger
- ReferenceFileSource - Class in org.broadinstitute.hellbender.engine
-
Manages traversals and queries over reference data (for now, fasta files only) Supports targeted queries over the reference by interval, but does not yet support complete iteration over the entire reference.
- ReferenceFileSource(Path) - Constructor for class org.broadinstitute.hellbender.engine.ReferenceFileSource
-
Initialize this data source using a fasta file.
- ReferenceFileSource(Path, boolean) - Constructor for class org.broadinstitute.hellbender.engine.ReferenceFileSource
-
Initialize this data source using a fasta file.
- ReferenceFileSparkSource - Class in org.broadinstitute.hellbender.engine.spark.datasources
-
Class to load a reference sequence from a fasta file on Spark.
- ReferenceFileSparkSource(GATKPath) - Constructor for class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceFileSparkSource
- ReferenceHadoopSparkSource - Class in org.broadinstitute.hellbender.engine.spark.datasources
-
Class to load a reference sequence from a fasta file on HDFS.
- ReferenceHadoopSparkSource(GATKPath) - Constructor for class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceHadoopSparkSource
- ReferenceInputArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
An abstract ArgumentCollection for specifying a reference sequence file
- ReferenceInputArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.ReferenceInputArgumentCollection
- ReferenceMemorySource - Class in org.broadinstitute.hellbender.engine
-
Manages traversals and queries over in-memory reference data.
- ReferenceMemorySource(ReferenceBases, SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.engine.ReferenceMemorySource
-
Initialize this data source using ReferenceBases and corresponding sequence dictionary.
- referenceModelForNoVariation(AssemblyRegion, boolean, List<VariantContext>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
-
Create an ref model result (ref model or no calls depending on mode) for an active region without any variation (not is active, or assembled to just ref)
- ReferenceMultiSparkSource - Class in org.broadinstitute.hellbender.engine.spark.datasources
-
Wrapper to load a reference sequence from a file stored on HDFS, GCS, or locally.
- ReferenceMultiSparkSource() - Constructor for class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource
- ReferenceMultiSparkSource(GATKPath, SerializableFunction<GATKRead, SimpleInterval>) - Constructor for class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource
- ReferencePair - Class in org.broadinstitute.hellbender.tools.reference
-
Class representing a pair of references and their differences.
- ReferencePair(ReferenceSequenceTable, GATKPath, GATKPath) - Constructor for class org.broadinstitute.hellbender.tools.reference.ReferencePair
- ReferencePair.Status - Enum Class in org.broadinstitute.hellbender.tools.reference
- referencePath - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
- ReferenceProgramGroup - Class in picard.cmdline.programgroups
-
Tools that analyze and manipulate FASTA format references
- ReferenceProgramGroup() - Constructor for class picard.cmdline.programgroups.ReferenceProgramGroup
- referenceReader - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- referenceSequence - Variable in class picard.cmdline.CommandLineProgram
- ReferenceSequenceTable - Class in org.broadinstitute.hellbender.tools.reference
-
Table utilized by CompareReferences tool to compare and analyze sequences found in specified references.
- ReferenceSequenceTable(Map<GATKPath, SAMSequenceDictionary>) - Constructor for class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
-
Constructs a ReferenceSequenceTable from a collection of sequence dictionaries.
- ReferenceSequenceTable(Map<GATKPath, ReferenceDataSource>, CompareReferences.MD5CalculationMode) - Constructor for class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
-
Returns a ReferenceSequenceTable object.
- ReferenceSequenceTable.TableEntry - Class in org.broadinstitute.hellbender.tools.reference
-
Minimal class representing a table entry within a row of the ReferenceSequenceTable.
- ReferenceSequenceTable.TableRow - Class in org.broadinstitute.hellbender.tools.reference
-
Class representing a row of the ReferenceSequenceTable.
- ReferenceShard - Class in org.broadinstitute.hellbender.engine
-
ReferenceShard is section of the reference genome that's used for sharding work for pairing things with the reference.
- ReferenceShard(int, String) - Constructor for class org.broadinstitute.hellbender.engine.ReferenceShard
- referenceSpan - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- ReferenceSparkSource - Interface in org.broadinstitute.hellbender.engine.spark.datasources
-
Internal interface to load a reference sequence.
- ReferenceTwoBitSparkSource - Class in org.broadinstitute.hellbender.engine.spark.datasources
-
A ReferenceSource impl that is backed by a .2bit representation of a reference genome.
- ReferenceTwoBitSparkSource(GATKPath) - Constructor for class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceTwoBitSparkSource
- ReferenceUtils - Class in org.broadinstitute.hellbender.utils.reference
-
A collection of static methods for dealing with references.
- referenceVersion - Variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
- ReferenceWalker - Class in org.broadinstitute.hellbender.engine
-
A reference walker is a tool which processes each base in a given reference.
- ReferenceWalker() - Constructor for class org.broadinstitute.hellbender.engine.ReferenceWalker
- ReferenceWindowFunctions - Class in org.broadinstitute.hellbender.engine.spark.datasources
-
A library of reference window functions suitable for passing in to transforms such as AddContextDataToRead.
- ReferenceWindowFunctions() - Constructor for class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceWindowFunctions
- ReferenceWindowFunctions.FixedWindowFunction - Class in org.broadinstitute.hellbender.engine.spark.datasources
-
A function for requesting a fixed number of extra bases of reference context on either side of each read.
- referenceWindowPadding - Variable in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
- RefFlatReader - Class in picard.annotation
-
Loads gene annotations from a refFlat file into an OverlapDetector
. - RefFlatReader.RefFlatColumns - Enum Class in picard.annotation
- ReflectionUtil - Class in picard.util
-
Class which contains utility functions that use reflection.
- ReflectionUtil() - Constructor for class picard.util.ReflectionUtil
- reflectiveCopy(TargetMetrics, MT, String[], String[]) - Static method in class picard.analysis.directed.TargetMetricsCollector
-
Since the targeted metrics (HsMetrics, TargetedPcrMetrics,...) share many of the same values as TargetMetrics, this copy will copy all public attributes in targetMetrics to the outputMetrics' attributes of the same name.
- refModelDelQual - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
-
This parameter is determining the deletion quality in the reference confidence model.
- refQual - Variable in class org.broadinstitute.hellbender.tools.walkers.ReadAnonymizer
- REFSEQ_CATALOG_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
- REFSEQ_CATALOG_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
- refseqCatalogPath - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
- RefSeqCodec - Class in org.broadinstitute.hellbender.utils.codecs.refseq
-
Allows for reading in RefSeq information TODO this header needs to be rewritten
- RefSeqCodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- RefSeqFeature - Class in org.broadinstitute.hellbender.utils.codecs.refseq
-
The ref seq feature.
- RefSeqFeature(SimpleInterval) - Constructor for class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
- RefSeqTranscript - Interface in org.broadinstitute.hellbender.utils.codecs.refseq
-
Created by IntelliJ IDEA.
- RefuseNegativeContigAndCoordinates - Static variable in interface org.broadinstitute.hellbender.utils.SVInterval.SVIntervalConstructorArgsValidator
- RefuseNegativeContigs - Static variable in interface org.broadinstitute.hellbender.utils.SVInterval.SVIntervalConstructorArgsValidator
- RefuseNegativeCoordinates - Static variable in interface org.broadinstitute.hellbender.utils.SVInterval.SVIntervalConstructorArgsValidator
- RefVsAnyResult - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Holds information about a genotype call of a single sample reference vs.
- RefVsAnyResult(int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RefVsAnyResult
-
Creates a new ref-vs-alt result indicating the genotype likelihood vector capacity.
- regenerateVariationEvents(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
- regionStartLoc - Variable in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
- regionStopLoc - Variable in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
- regionWithHigherCoordOnContig - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera
- regionWithLowerCoordOnContig - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera
- registerClasses(Kryo) - Method in class org.broadinstitute.hellbender.engine.spark.GATKRegistrator
- registerFuncotationMapDependencies(Kryo) - Static method in class org.broadinstitute.hellbender.engine.spark.GATKRegistrator
-
Make sure that all FuncotationMap (which incl.
- REGULATION - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- REINTERPRETED_1_SEG_CALL_VCF_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark
- REINTERPRETED_MULTI_SEG_CALL_VCF_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark
- reInterpretMultiSegmentComplexVarThroughAlignmentPairIteration(JavaRDD<VariantContext>, SvDiscoveryInputMetaData, JavaRDD<GATKRead>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor
-
Send relevant contigs for re-interpretation via the pair-iteration way of scanning the alignments for interpretation.
- REJECT - Variable in class picard.util.LiftOverIntervalList
- REJECT - Variable in class picard.vcf.LiftoverVcf
- rejectSet(ReadsWithSameUMI) - Method in class org.broadinstitute.hellbender.engine.DuplicateSetWalker
-
Returns true for duplicate sets that does not meet required criteria for further processing.
- relearnThresholdAndClearAcumulatedProbabilities() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ThresholdCalculator
- RelevantAttributes(VariantContext) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor.RelevantAttributes
- remap(Allele) - Method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.AlleleMapper
- remap(List<Allele>) - Method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.AlleleMapper
- remapALengthList(List<T>, int[], T) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
-
Given a list of per-alt-allele attributes, subset to relevant alt alleles
- remapAlleles(VariantContext, Allele) - Static method in class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
-
This method does a couple of things: remaps the vc alleles considering the differences between the final reference allele and its own reference, collects alternative alleles present in variant context and add them to the
finalAllelesset. - remapRLengthList(List<T>, int[], T) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
-
Given a list of per-allele attributes including the reference allele, subset to relevant alleles
- remove() - Method in class org.broadinstitute.hellbender.engine.ActivityProfileStateIterator
- remove() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionFromActivityProfileStateIterator
- remove() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionIterator
- remove() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.PairedStrandedIntervalTreeIterator
- remove() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.PairedStrandedIntervalTreeOverlapperIterator
- remove() - Method in interface org.broadinstitute.hellbender.tools.spark.utils.LongIterator
- remove() - Method in class org.broadinstitute.hellbender.utils.iterators.AllLocusIterator
- remove() - Method in class org.broadinstitute.hellbender.utils.iterators.CloseAtEndIterator
- remove() - Method in class org.broadinstitute.hellbender.utils.iterators.PushToPullIterator
- remove() - Method in class org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator
- remove() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- remove() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.MultiHitAlignedReadIterator
-
Unsupported operation.
- remove() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree.OverlapIterator
- remove() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree.ValuesIterator
- remove() - Method in class org.broadinstitute.hellbender.utils.text.XReadLines
- remove() - Method in class picard.illumina.parser.MultiTileParser
- remove() - Method in class picard.illumina.parser.MultiTileBclParser
- remove() - Method in class picard.illumina.parser.PerTileParser
- remove() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
- remove() - Method in class picard.illumina.parser.readers.BarcodeFileReader
- remove() - Method in class picard.illumina.parser.readers.BclReader
- remove() - Method in class picard.illumina.parser.readers.FilterFileReader
- remove() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
- remove() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- remove() - Method in class picard.util.AsyncIterator
- remove() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- remove() - Method in class picard.vcf.ByIntervalListVariantContextIterator
- remove() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
- remove() - Method in class picard.vcf.PairedVariantSubContextIterator
- remove() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
- remove(int) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigListRC
- remove(int, String) - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
- remove(int, String) - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
- remove(int, String) - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
-
Remove element with given key from the map.
- remove(long) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- remove(long) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- remove(long, int) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- remove(Object) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- remove(Object) - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
- remove(Object) - Method in class org.broadinstitute.hellbender.utils.collections.IndexedSet
-
Removes an element from the set.
- remove(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
a simple removal of an interval contained in this list.
- remove(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Remove an interval from the tree.
- remove(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
Removes the end from this set, if present
- REMOVE_ALIGNMENT_INFORMATION - Variable in class picard.sam.RevertSam
- REMOVE_ALL_DUPLICATE_READS - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- REMOVE_DEFAULT_ATTRIBUTE_TO_CLEAR_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- REMOVE_DUPLICATE_INFORMATION - Variable in class picard.sam.PositionBasedDownsampleSam
- REMOVE_DUPLICATE_INFORMATION - Variable in class picard.sam.RevertSam
- REMOVE_DUPLICATES - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- REMOVE_FILTERED_VARIANTS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- REMOVE_LONGER_THAN_ONE_INDELS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- REMOVE_ONE_TO_ZERO_PROBS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- REMOVE_SEQUENCING_DUPLICATE_READS - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- REMOVE_SEQUENCING_DUPLICATES - Variable in class picard.sam.markduplicates.MarkDuplicates
- removeAll(long[]) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- removeAll(long[]) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- removeAll(Collection<?>) - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
-
unlike the AbstractCollection implementation, this one iterates over the supplied collection
- removeAll(Collection<GATKRead>) - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Remove all of the reads in readsToRemove from this region
- removeAll(LongHopscotchSet) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- removeAllDuplicates - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- removeAllelesToSubset(Collection<A>) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Removes subset of alleles
- removeChild(int) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- removeClipsAndPadding(Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
Removes all clipping and padding operators from the cigar.
- removeDataForSymbolicAlleles(VariantContext, List<T>) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- removeDataForSymbolicAlleles(VariantContext, List<T>, boolean) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- removeDataForSymbolicAltAlleles(VariantContext, List<T>) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- removeDefaults - Variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- removeDuplicates(List<VariantContext>, List<VariantContext>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor
-
Exist because the two ways to re-interpret simple variants via
SegmentedCpxVariantSimpleVariantExtractor.MultiSegmentsCpxVariantExtractorand viaSegmentedCpxVariantSimpleVariantExtractor.reInterpretMultiSegmentComplexVarThroughAlignmentPairIteration(JavaRDD, SvDiscoveryInputMetaData, JavaRDD)could give essentially the same variants. - removeEach(Object) - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
-
remove each of the elements equivalent to the key
- removeEldestEntry(Map.Entry<K, V>) - Method in class org.broadinstitute.hellbender.utils.LRUCache
- removeExtension(Path, List<String>) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Strips extension from the given path, if it has one.
- removeFilteredVariants - Variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorVariantArgumentCollection
- removeIncompleteTrios() - Method in class picard.pedigree.PedFile
-
Scans through the pedigrees and removes all entries that do not have both paternal and maternal ids set.
- removeItemsByIndex(List<T>, List<Integer>) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- removeLocationSet() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
- removeLongerThanOneIndels - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- RemoveNearbyIndels - Class in org.broadinstitute.hellbender.tools.walkers.validation
-
Remove indels that are close to another indel from a vcf file.
- RemoveNearbyIndels() - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.RemoveNearbyIndels
- removeOneToZeroProbs - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- removePathsNotConnectedToRef() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Remove all vertices in the graph that aren't on a path from the reference source vertex to the reference sink vertex More aggressive reference pruning algorithm than removeVerticesNotConnectedToRefRegardlessOfEdgeDirection, as it requires vertices to not only be connected by a series of directed edges but also prunes away paths that do not also meet eventually with the reference sink vertex
- removePLsAndAD(Genotype) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- removePredecessor(int, LocalAssembler.KmerSet<LocalAssembler.KmerAdjacency>) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- removePredecessor(int, LocalAssembler.KmerSet<LocalAssembler.KmerAdjacency>) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- removePredecessor(int, LocalAssembler.KmerSet<LocalAssembler.KmerAdjacency>) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- removeReadsFromAllSamplesExcept(String, AssemblyRegion) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- removeSequencingDuplicates - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- removeShadowedContigs - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- removeSingletonOrphanVertices() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Remove all vertices in the graph that have in and out degree of 0
- removeSingletonOrphanVertices() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
- removeStaleAttributesAfterMerge(Map<String, Object>) - Static method in class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
-
Remove the stale attributes from the merged set
- removeStatus(ReferencePair.Status) - Method in class org.broadinstitute.hellbender.tools.reference.ReferencePair
-
Given a Status, remove it from the ReferencePair's analysis, if present
- removeSuccessor(int, LocalAssembler.KmerSet<LocalAssembler.KmerAdjacency>) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- removeSuccessor(int, LocalAssembler.KmerSet<LocalAssembler.KmerAdjacency>) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- removeSuccessor(int, LocalAssembler.KmerSet<LocalAssembler.KmerAdjacency>) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- removeTag(String, int) - Method in class org.broadinstitute.hellbender.utils.SATagBuilder
-
Method that searches supplementaryReads for every read matching contig and start and removes them from the list.
- removeTag(GATKRead) - Method in class org.broadinstitute.hellbender.utils.SATagBuilder
-
Method that removes all SATag units from the list corresponding to the provided read based on start location
- removeTag(SATagBuilder) - Method in class org.broadinstitute.hellbender.utils.SATagBuilder
-
Method that removes all SATag units from the list corresponding to the provided read based on start location
- removeTrailingDeletions(Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Removing a trailing deletion from the incoming cigar if present
- removeUnreachableNodes() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
-
Deletes nodes unreachable from the root and returns the set of deleted nodes.
- removeVertex(MultiDeBruijnVertex) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
- removeVerticesNotConnectedToRefRegardlessOfEdgeDirection() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Remove all vertices on the graph that cannot be accessed by following any edge, regardless of its direction, from the reference source vertex
- RenameSampleInVcf - Class in picard.vcf
-
Renames a sample within a VCF or BCF.
- RenameSampleInVcf() - Constructor for class picard.vcf.RenameSampleInVcf
- renderPhasingMetricsFilesFromBasecallingDirectory(File) - Static method in class picard.illumina.parser.TileMetricsUtil
- renderProteinChangeString(SequenceComparison, Locatable) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Creates the string representation of the protein change for the given
SequenceComparison. - renderSamFileHeader() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
-
Create a SAM File Header from the preamble.
- renderSanitizedFuncotationForVcf(Funcotation, List<String>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
- REORDER_INPUT_BY_FIRST_VARIANT - Variable in class picard.vcf.GatherVcfs
- ReorderSam - Class in picard.sam
-
Reorders a SAM/BAM input file according to the order of contigs in a second reference file.
- ReorderSam() - Constructor for class picard.sam.ReorderSam
- repairSupplementaryTags(List<GATKRead>, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads
-
A method that repairs the NH and NM tags for a group of reads
- REPEAT_TOLERANCE - Variable in class picard.util.BaitDesigner
- REPEAT_UNIT_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- repeatBytes(byte, int) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
makes an array filled with n copies of the given byte.
- repeatChars(char, int) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
makes an array filled with n copies of the given char.
- repeatLength(int) - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrReferenceAnalyzer
-
Returns the number of consecutive repeated units for a position
- REPEATS_PER_ALLELE_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- repeatUnit(int) - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrReferenceAnalyzer
-
Return a new array with a copy of the repeat unit bases starting at a particular position
- repeatUnitAsString(int) - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrReferenceAnalyzer
- replace(ReadEndsForMateCigar, ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
Replaces a given end with the other end.
- REPLACE_ARGUMENT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionary
- replaceAllHaplotypes(Set<Haplotype>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
- replaceAllHaplotypes(AssemblyResultSet, Set<Haplotype>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LongHomopolymerHaplotypeCollapsingEngine
-
Replace the haplotypes contained in the assembly result set with a fresh set.
- replaceExtension(File, String) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
- replaceExtension(String, String) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
- ReplaceSamHeader - Class in picard.sam
- ReplaceSamHeader() - Constructor for class picard.sam.ReplaceSamHeader
- replaceSpanDels(List<VariantContext>, Allele, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine
- replicationRateFromReplicateSets - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
An estimate of the duplication rate that is based on the duplicate sets we observed.
- REPORT_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- REPORT_INS_OR_DEL_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- REPORTED_GENDER - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The sex, as reported by the collaborator
- ReportTypeCounts() - Constructor for class org.broadinstitute.hellbender.tools.AnalyzeSaturationMutagenesis.ReportTypeCounts
- REPRESENTATIVE - Enum constant in enum class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser.BreakpointSummaryStrategy
-
Picks a single representative call closest to the overall cluster
- RepresentativeReadIndexer - Class in picard.sam.util
-
Little struct-like class to hold a record index, the index of the corresponding representative read, and duplicate set size information.
- RepresentativeReadIndexer() - Constructor for class picard.sam.util.RepresentativeReadIndexer
- RepresentativeReadIndexerCodec - Class in picard.sam.markduplicates.util
-
Codec for read names and integers that outputs the primitive fields and reads them back.
- RepresentativeReadIndexerCodec() - Constructor for class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- representativeReadIndexInFile - Variable in class picard.sam.util.RepresentativeReadIndexer
- representativeReadIndicesForDuplicates - Variable in class picard.sam.markduplicates.MarkDuplicates
- REQUIRE_INDEX - Variable in class picard.vcf.VcfFormatConverter
- REQUIRE_INDEX_FILES - Variable in class picard.fingerprint.CrosscheckFingerprints
- REQUIRE_UNIQUE - Enum constant in enum class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.GenotypeMergeType
-
Require that all samples/genotypes be unique between all inputs.
- RequiredFeatureInputArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
An argument collection for use with tools that accept one or more input files containing Feature records (eg., BED files, hapmap files, etc.), and require at least one such input.
- RequiredFeatureInputArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredFeatureInputArgumentCollection
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.BaseQualityFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ClusteredEventsFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ContaminationFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.DuplicatedAltReadFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteredHaplotypeFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FragmentLengthFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.GermlineFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MappingQualityFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MinAlleleFractionFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MultiallelicFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2Filter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NormalArtifactFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NRatioFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.PanelOfNormalsFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.PolymeraseSlippageFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadOrientationFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadPositionFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrictStrandBiasFilter
- requiredInfoAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.TumorEvidenceFilter
- RequiredIntervalArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
An ArgumentCollection that requires one or more intervals be specified with -L at the command line
- RequiredIntervalArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredIntervalArgumentCollection
- RequiredOutputArgumentCollection - Class in picard.cmdline.argumentcollections
- RequiredOutputArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
- RequiredOutputArgumentCollection(File) - Constructor for class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
- RequiredReadInputArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
An argument collection for use with tools that accept one or more input files containing reads (eg., BAM/SAM/CRAM files), and require at least one such input.
- RequiredReadInputArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredReadInputArgumentCollection
- RequiredReferenceArgumentCollection - Class in picard.cmdline.argumentcollections
-
Argument collection for references that are required (and not common).
- RequiredReferenceArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection
- RequiredReferenceInputArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
An argument collection for use with tools that require a reference file as input.
- RequiredReferenceInputArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredReferenceInputArgumentCollection
- RequiredStratification - Interface in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
- RequiredVariantInputArgumentCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
An argument collection for use with tools that accept one or more input files containing VariantContext records (eg., VCF files), and require at least one such input.
- RequiredVariantInputArgumentCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredVariantInputArgumentCollection
- requiresCoordinateSortOrder() - Method in class org.broadinstitute.hellbender.utils.downsampling.FractionalDownsampler
- requiresCoordinateSortOrder() - Method in class org.broadinstitute.hellbender.utils.downsampling.MutectDownsampler
- requiresCoordinateSortOrder() - Method in class org.broadinstitute.hellbender.utils.downsampling.PassThroughDownsampler
- requiresCoordinateSortOrder() - Method in class org.broadinstitute.hellbender.utils.downsampling.PositionalDownsampler
- requiresCoordinateSortOrder() - Method in class org.broadinstitute.hellbender.utils.downsampling.ReadsDownsampler
-
Does this downsampler require that reads be fed to it in coordinate order?
- requiresCoordinateSortOrder() - Method in class org.broadinstitute.hellbender.utils.downsampling.ReservoirDownsampler
- requiresFeatures() - Method in class org.broadinstitute.hellbender.engine.FeatureWalker
- requiresFeatures() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Does this tool require features? Traversals types and/or tools that do should override to return true.
- requiresFeatures() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker
- requiresFeatures() - Method in class org.broadinstitute.hellbender.engine.VariantWalkerBase
- requiresFeatures() - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
- requiresFeatures() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory
- requiresFeatures() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory
- requiresFeatures() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- requiresFeatures() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactData
- requiresIntervals() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Does this tool require intervals? Traversals types and/or tools that do should override to return true.
- requiresIntervals() - Method in class org.broadinstitute.hellbender.engine.IntervalWalker
- requiresIntervals() - Method in class org.broadinstitute.hellbender.engine.LocusWalkerByInterval
- requiresIntervals() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Does this tool require intervals? Tools that do should override to return true.
- requiresIntervals() - Method in class org.broadinstitute.hellbender.engine.spark.IntervalWalkerSpark
- requiresIntervals() - Method in class org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervals
- requiresIntervals() - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCounts
- requiresIntervals() - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSpark
- requiresIntervals() - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts
- requiresIntervals() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler
- requiresIntervals() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- requiresIntervals() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactData
- requiresIntervals() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.CountFalsePositives
- requiresOverlapAndProximity() - Method in class org.broadinstitute.hellbender.tools.sv.cluster.ClusteringParameters
- requiresReads() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionWalker
- requiresReads() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Does this tool require reads? Traversals types and/or tools that do should override to return true.
- requiresReads() - Method in class org.broadinstitute.hellbender.engine.LocusWalker
-
LocusWalkers requires read sources
- requiresReads() - Method in class org.broadinstitute.hellbender.engine.ReadWalker
- requiresReads() - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Does this tool require reads? Tools that do should override to return true.
- requiresReads() - Method in class org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.engine.spark.ReadWalkerSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.AnalyzeSaturationMutagenesis
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.GetSampleName
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.PrintDistantMates
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.PrintReadsHeader
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.ApplyBQSRSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.bwa.BwaSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.PileupSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.BwaAndMarkDuplicatesPipelineSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.CountBasesSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.FlagStatSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSparkTool
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.SortSamSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.DiscoverVariantsFromContigAlignmentsSAMSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantReInterpreterSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.CalcMetadataSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ExtractSVEvidenceSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryPipelineSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.ExtractOriginalAlignmentRecordsByNameSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.StructuralVariantDiscoverer
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactData
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.walkers.PairWalker
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.PostProcessReadsForRSEM
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- requiresReads() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- requiresReference() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionWalker
- requiresReference() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Does this tool require reference data? Traversals types and/or tools that do should override to return true.
- requiresReference() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
- requiresReference() - Method in class org.broadinstitute.hellbender.engine.ReferenceWalker
- requiresReference() - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark
- requiresReference() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Does this tool require reference data? Tools that do should override to return true.
- requiresReference() - Method in class org.broadinstitute.hellbender.engine.VariantLocusWalker
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.AnalyzeSaturationMutagenesis
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervals
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCounts
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSpark
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervals
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegions
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEvents
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFile
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceSpark
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.funcotator.FuncotateSegments
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.funcotator.Funcotator
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.LeftAlignIndels
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.reference.CompareReferences
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.spark.bwa.BwaSpark
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.BwaAndMarkDuplicatesPipelineSpark
- requiresReference() - Method in interface org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSpark
-
Return whether or not this collector requires a reference.
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.DiscoverVariantsFromContigAlignmentsSAMSpark
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantReInterpreterSpark
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBadGenomicKmersSpark
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryPipelineSpark
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.StructuralVariantDiscoverer
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyper
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.MethylationTypeCaller
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactData
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.CheckPileup
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.ReadAnonymizer
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2Counts
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
-
Reference is required for left alignment
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- requiresReference() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants
- requiresReference() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- requiresReference() - Method in class picard.analysis.CollectOxoGMetrics
- requiresReference() - Method in class picard.analysis.CollectWgsMetrics
- requiresReference() - Method in class picard.arrays.GtcToVcf
- requiresReference() - Method in class picard.cmdline.CommandLineProgram
- requiresReference() - Method in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
- requiresReference() - Method in class picard.fingerprint.ExtractFingerprint
- requiresReference() - Method in class picard.fingerprint.IdentifyContaminant
- requiresReference() - Method in class picard.reference.ExtractSequences
- requiresReference() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
- requiresReference() - Method in class picard.sam.MergeBamAlignment
- requiresReference() - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- requiresReference() - Method in class picard.sam.SetNmMdAndUqTags
- requiresReference() - Method in class picard.util.BaitDesigner
- requiresTerritoryToBeSpecified() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- requiresTerritoryToBeSpecified() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- requiresTerritoryToBeSpecified() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
-
Subclasses must overload this to return true if they require an input to include a calling territory, either an interval list or a reference.
- requiresTerritoryToBeSpecified() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- requireStrictAlleleMatch - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- RESERVOIR_SAMPLING_RANDOM_SEED_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations
- ReservoirDownsampler - Class in org.broadinstitute.hellbender.utils.downsampling
-
Reservoir Downsampler: Selects n reads out of a stream whose size is not known in advance, with every read in the stream having an equal chance of being selected for inclusion.
- ReservoirDownsampler(int) - Constructor for class org.broadinstitute.hellbender.utils.downsampling.ReservoirDownsampler
-
Construct a ReservoirDownsampler
- ReservoirDownsampler(int, boolean) - Constructor for class org.broadinstitute.hellbender.utils.downsampling.ReservoirDownsampler
-
Construct a ReservoirDownsampler
- reset() - Method in class org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile
-
Resets the ReferenceSequenceFile so that the next call to nextSequence() will return the first sequence in the file.
- reset() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- reset() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator
- resetCount() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.TransitPairCount
- resetFilteredCount() - Method in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter.CountingAndReadFilter
- resetFilteredCount() - Method in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter
- resetFilteredCount() - Method in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter.CountingAndVariantFilter
- resetFilteredCount() - Method in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter
- resetOriginalBaseQualities(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Resets the quality scores of the reads to the orginal (pre-BQSR) ones.
- resetRandomGenerator() - Static method in class org.broadinstitute.hellbender.utils.Utils
- resetReadsDataSource() - Method in class org.broadinstitute.hellbender.engine.ReadWalker
-
Reset the reads data source so the caller can iterate through the reads again.
- resetRefSeqFileWalker() - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
- resetRefSeqFileWalker() - Method in class picard.sam.AbstractAlignmentMerger
- resetSeveritiesToDefault() - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Reset the severities of all
GencodeFuncotation.VariantClassifications to their default values. - resetStats() - Method in class org.broadinstitute.hellbender.utils.downsampling.Downsampler
-
Reset stats in the downsampler such as the number of discarded items *without* clearing the downsampler of items
- resolveFilePathStringFromKnownPath(String, Path) - Static method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
-
Resolves the path string to a full path object using the given knownPath as a sibling file.
- resolveIncompatibleAlleles(Allele, VariantContext) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- resolveIntervals(String, IntervalArgumentCollection, Logger) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
-
Resolve intervals from an
IntervalArgumentCollectionand a read-count path. - resolveSameLocusFeatures() - Method in class org.broadinstitute.hellbender.tools.sv.AbstractEvidenceSortMerger
- resolveVariantContexts(Set<String>, int, SampleDB, SortedSet<String>, List<VariantContext>) - Method in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
-
Correct genotype calls for overlapping variant contexts Note that we assume that a sample will not occur twice with the same copy number because it should have been defragmented
- Resource - Class in org.broadinstitute.hellbender.utils.io
-
Stores a resource by path and a relative class.
- Resource(String, Class<?>) - Constructor for class org.broadinstitute.hellbender.utils.io.Resource
-
Create a resource with a path and a relative class.
- RESOURCE_LABEL_INFO_HEADER_LINE_FORMAT_STRING - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
- RESOURCE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- RESOURCE_MATCHING_STRATEGY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
- resources - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
-
An external resource VCF file or files from which to annotate.
- RESTORE_HARDCLIPS - Variable in class picard.sam.RevertSam
- RESTORE_ORIGINAL_QUALITIES - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- RESTORE_ORIGINAL_QUALITIES - Variable in class picard.sam.RevertSam
- restoreHeaderIfNecessary(GATKRead, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Checks whether read is a headerless SAMRecordToGATKReadAdapter, and if it is, sets its header to the provided header.
- result() - Method in class picard.vcf.CallingMetricAccumulator
- result() - Method in interface picard.vcf.processor.VariantProcessor.Accumulator
- Result(double, double, double, double) - Constructor for class org.broadinstitute.hellbender.utils.MannWhitneyU.Result
- Result(Cigar, int, int) - Constructor for class org.broadinstitute.hellbender.utils.read.CigarBuilder.Result
- Result(AssemblyRegion, SimpleInterval, SimpleInterval) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer.Result
-
Creates a trimming result given all its properties.
- RESULT - Variable in class picard.fingerprint.CrosscheckMetric
-
The overall result of the match.
- results - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelLengthHistogram
- RETAIN_MAX_N_PROBS_BASE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- RETAINED_INTRON - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- RETAINED_INTRON_CDS - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
internal intron of CDS portion of transcript is retained.
- RETAINED_INTRON_FINAL - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
final intron of CDS portion of transcript is retained.
- RETAINED_INTRON_FIRST - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
first intron of CDS portion of transcript is retained.
- retainEvidence(Predicate<? super EVIDENCE>) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Remove those reads that do not comply with a requirement.
- retainMaxNProbs - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- retainNodes(Set<Integer>) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
-
Removes all nodes not in the given set
- retrieveAllHeaderInfo() - Method in interface org.broadinstitute.hellbender.tools.funcotator.metadata.FuncotationMetadata
- retrieveAllHeaderInfo() - Method in class org.broadinstitute.hellbender.tools.funcotator.metadata.VcfFuncotationMetadata
- retrieveConfiguration(File) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Create a configuration instance from a properties file, where key names are ordered.
- retrieveHeaderInfo(String) - Method in interface org.broadinstitute.hellbender.tools.funcotator.metadata.FuncotationMetadata
- retrieveHeaderInfo(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.metadata.VcfFuncotationMetadata
- RETROGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
protein-coding locus created via retrotransposition.
- RETROTRANSPOSED - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- REV - Enum constant in enum class org.broadinstitute.hellbender.tools.LocalAssembler.ContigOrientation
- REV_COMPED_ALLELES - Static variable in class picard.util.LiftoverUtils
- REV_CXT_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The number of ~REF_BASE:~ALT_BASE alignments at sites complementary to the given reference context.
- REV_CXT_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The number of ~REF_BASE:~REF_BASE alignments at sites complementary to the given reference context.
- REV_ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The substitution rate of ~REF_BASE:~ALT_BASE, calculated as max(1e-10, REV_CXT_ALT_BASES / (REV_CXT_ALT_BASES + REV_CXT_REF_BASES)).
- REVERSE - Enum constant in enum class org.broadinstitute.hellbender.engine.AlignmentContext.ReadOrientation
- REVERSE - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
- REVERSE - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils
- REVERSE_TO_FORWARD - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.StrandSwitch
- reverseComplement() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Modify this read by reverse complementing its bases and reversing its quality scores.
- reverseComplement() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- reverseComplement(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer
- reverseComplement(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
-
Returns a new SVKmerLong that's the reverse-complement of this one.
- reverseComplement(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
-
Returns a new SVKmerShort that's the reverse-complement of this one.
- reverseComplement(long) - Static method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- reverseComplement(long) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer
- reverseComplementByteValueAsLong(int) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer
- reverseComplementVariantContext(VariantContext, Interval, ReferenceSequence) - Static method in class picard.util.LiftoverUtils
- reverseIterator() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Return an iterator over the entire tree that returns intervals in reverse order.
- reverseIterator(SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Return an iterator over all intervals less than or equal to the specified interval, in reverse order.
- reverseTrimAlleles(VariantContext) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Trim the alleles in inputVC from the reverse direction
- REVERT_SOFTCLIPPED_BASES - Enum constant in enum class org.broadinstitute.hellbender.utils.clipping.ClippingRepresentation
-
Turn all soft-clipped bases into matches
- RevertBaseQualityScores - Class in org.broadinstitute.hellbender.tools.walkers
- RevertBaseQualityScores() - Constructor for class org.broadinstitute.hellbender.tools.walkers.RevertBaseQualityScores
- RevertOriginalBaseQualitiesAndAddMateCigar - Class in picard.sam
-
This tool reverts the original base qualities (if specified) and adds the mate cigar tag to mapped SAM, BAM or CRAM files.
- RevertOriginalBaseQualitiesAndAddMateCigar() - Constructor for class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile - Enum Class in picard.sam
-
Used as a return for the canSkipSAMFile function.
- revertReads(JavaRDD<GATKRead>, List<String>) - Method in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
-
Takes an individual SAMRecord and applies the set of changes/reversions to it that have been requested by program level options.
- RevertSam - Class in picard.sam
-
Reverts a SAM file by optionally restoring original quality scores and by removing all alignment information.
- RevertSam() - Constructor for class picard.sam.RevertSam
- RevertSam.FileType - Enum Class in picard.sam
- revertSamRecord(SAMRecord) - Method in class picard.sam.RevertSam
-
Takes an individual SAMRecord and applies the set of changes/reversions to it that have been requested by program level options.
- RevertSamSpark - Class in org.broadinstitute.hellbender.tools.spark
-
Reverts a SAM file by optionally restoring original quality scores and by removing all alignment information.
- RevertSamSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- RevertSamSpark.FileType - Enum Class in org.broadinstitute.hellbender.tools.spark
- revertSoftClippedBases(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
-
Reverts ALL soft-clipped bases
- revertSoftClips(Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.CigarUtils
-
replace soft clips (S) with match (M) operators, normalizing the result by all the transformations of the
CigarBuilderclass: merging consecutive identical operators and removing zero-length elements. - reviseAndConditionallyLogQuality(byte) - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
-
Accepts a quality read from a BCL file and (1) returns a 1 if the value was 0 and (2) makes a note of the provided quality if it is low.
- RevIterator(SVIntervalTree.Node<V>) - Constructor for class org.broadinstitute.hellbender.utils.SVIntervalTree.RevIterator
- RExecutor - Class in picard.util
-
Util class for executing R scripts.
- RExecutor() - Constructor for class picard.util.RExecutor
- RF - Static variable in class picard.sam.markduplicates.util.ReadEnds
- RG_TAG - Variable in class picard.sam.SamToFastq
- RGCN - Variable in class picard.sam.AddOrReplaceReadGroups
- RGDS - Variable in class picard.sam.AddOrReplaceReadGroups
- RGDT - Variable in class picard.sam.AddOrReplaceReadGroups
- RGFO - Variable in class picard.sam.AddOrReplaceReadGroups
- RGID - Variable in class picard.sam.AddOrReplaceReadGroups
- RGKS - Variable in class picard.sam.AddOrReplaceReadGroups
- RGLB - Variable in class picard.sam.AddOrReplaceReadGroups
- RGPG - Variable in class picard.sam.AddOrReplaceReadGroups
- RGPI - Variable in class picard.sam.AddOrReplaceReadGroups
- RGPL - Variable in class picard.sam.AddOrReplaceReadGroups
- RGPM - Variable in class picard.sam.AddOrReplaceReadGroups
- RGPU - Variable in class picard.sam.AddOrReplaceReadGroups
- RGQ_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- RGQ_THRESHOLD_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- rgqThreshold - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- RGSM - Variable in class picard.sam.AddOrReplaceReadGroups
- rhs - Variable in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter.CountingAndReadFilter
- rhs - Variable in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter.CountingAndVariantFilter
- rhs - Variable in class org.broadinstitute.hellbender.engine.filters.ReadFilter.ReadFilterBinOp
- RIBOSOMAL - Enum constant in enum class picard.annotation.LocusFunction
- RIBOSOMAL_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Number of bases in primary alignments that align to ribosomal sequence.
- RIBOSOMAL_INTERVALS - Variable in class picard.analysis.CollectRnaSeqMetrics
- ribosomalInitialValue - Variable in class picard.analysis.directed.RnaSeqMetricsCollector
- RIBOZYME - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- RIGHT - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportColumnFormat.Alignment
- RIGHT - Enum constant in enum class org.broadinstitute.hellbender.utils.Tail
- RIGHT_FILE - Variable in class picard.fingerprint.CrosscheckMetric
-
The RIGHT file from which the fingerprint was obtained.
- RIGHT_FILE - Variable in class picard.sam.SamComparisonMetric
-
Right file used in comparison
- RIGHT_GROUP_VALUE - Variable in class picard.fingerprint.CrosscheckMetric
-
The RIGHT group value.
- RIGHT_LANE - Variable in class picard.fingerprint.CrosscheckMetric
-
The RIGHT lane.
- RIGHT_LIBRARY - Variable in class picard.fingerprint.CrosscheckMetric
-
The RIGHT library identifier.
- RIGHT_MOLECULAR_BARCODE_SEQUENCE - Variable in class picard.fingerprint.CrosscheckMetric
-
The RIGHT molecular (sample) barcode.
- RIGHT_PRIMER - Variable in class picard.util.BaitDesigner
- RIGHT_RUN_BARCODE - Variable in class picard.fingerprint.CrosscheckMetric
-
The RIGHT run barcode (PU field) expected to look like : D047KACXX110901.1.ACCAACTG.
- RIGHT_SAMPLE - Variable in class picard.fingerprint.CrosscheckMetric
-
The RIGHT sample identifier.
- rightMedianDeviation(int) - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.CDF
- rightVariantContext - Variable in class picard.vcf.PairedVariantSubContextIterator.VcfTuple
- RIlmn - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- RMS_MAPPING_QUALITY_OLD_BEHAVIOR_OVERRIDE_ARGUMENT - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
- RMSMappingQuality - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Root Mean Square of the mapping quality of reads across all samples.
- RMSMappingQuality() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
- RNA - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Variant lies on one of the RNA transcripts.
- RNA_SEQ_SUPPORTED_ONLY - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Transcript supported by RNAseq data and not supported by mRNA or EST evidence.
- RNA_SEQ_SUPPORTED_PARTIAL - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Transcript annotated based on mixture of RNA-seq data and EST/mRNA/protein evidence.
- RNAME - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestField
- RnaSeqMetrics - Class in picard.analysis
-
Metrics about the alignment of RNA-seq reads within a SAM file to genes, produced by the CollectRnaSeqMetrics program and usually stored in a file with the extension ".rna_metrics".
- RnaSeqMetrics - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- RnaSeqMetrics() - Constructor for class picard.analysis.RnaSeqMetrics
- RnaSeqMetricsCollector - Class in picard.analysis.directed
- RnaSeqMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, Long, OverlapDetector<Gene>, OverlapDetector<Interval>, HashSet<Integer>, int, RnaSeqMetricsCollector.StrandSpecificity, double, boolean) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector
- RnaSeqMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, Long, OverlapDetector<Gene>, OverlapDetector<Interval>, HashSet<Integer>, int, RnaSeqMetricsCollector.StrandSpecificity, double, boolean, int) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector
- RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector - Class in picard.analysis.directed
- RnaSeqMetricsCollector.StrandSpecificity - Enum Class in picard.analysis.directed
- RNEXT - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestField
- round(double...) - Static method in class picard.util.MathUtil
-
returns a long array containing the rounded values of the input array
- round(double, int) - Static method in class picard.util.MathUtil
-
Round off the value to the specified precision.
- ROUND_DOWN_QUANTIZED_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.validation.CompareBaseQualities
- roundDown - Variable in class org.broadinstitute.hellbender.tools.ApplyBQSRUniqueArgumentCollection
-
Round down quantized only works with the static_quantized_quals option, and should not be used with the dynamic binning option provided by quantize_quals.
- roundDown - Variable in class org.broadinstitute.hellbender.tools.validation.CompareBaseQualities
-
Round down quantized only works with the
CompareBaseQualities.STATIC_QUANTIZED_QUALS_LONG_NAMEoption. - roundFinitePrecisionErrors(double) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- roundToNDecimalPlaces(double, int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Rounds the double to the given number of decimal places.
- row() - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup.Element
- ROWS - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.TableDataHeaderFields
- RP_SUPPORTED_TIS - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Transcript that contains a CDS that has a translation initiation site supported by Ribosomal Profiling data.
- RPL - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera
- RR - Static variable in class picard.sam.markduplicates.util.ReadEnds
- RrbsCpgDetailMetrics - Class in picard.analysis
-
Holds information about CpG sites encountered for RRBS processing QC
- RrbsCpgDetailMetrics() - Constructor for class picard.analysis.RrbsCpgDetailMetrics
- RrbsMetricsCollector - Class in picard.analysis
- RrbsMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, int, int, int, double) - Constructor for class picard.analysis.RrbsMetricsCollector
- RrbsSummaryMetrics - Class in picard.analysis
-
Holds summary statistics from RRBS processing QC
- RrbsSummaryMetrics() - Constructor for class picard.analysis.RrbsSummaryMetrics
- RRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- RRNA_FRAGMENT_PERCENTAGE - Variable in class picard.analysis.CollectRnaSeqMetrics
- RRNA_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- RS_ID - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- RScriptExecutor - Class in org.broadinstitute.hellbender.utils.R
-
Generic service for executing RScripts
- RScriptExecutor() - Constructor for class org.broadinstitute.hellbender.utils.R.RScriptExecutor
- RScriptExecutor(boolean) - Constructor for class org.broadinstitute.hellbender.utils.R.RScriptExecutor
- RScriptExecutorException - Exception in org.broadinstitute.hellbender.utils.R
- RScriptExecutorException(String) - Constructor for exception org.broadinstitute.hellbender.utils.R.RScriptExecutorException
- RScriptLibrary - Enum Class in org.broadinstitute.hellbender.utils.R
-
Libraries embedded in the StingUtils package.
- rsNames - Variable in class picard.arrays.illumina.InfiniumEGTFile
- rsNameToIndex - Variable in class picard.arrays.illumina.InfiniumEGTFile
- RTABLE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter.OUTPUT_FORMAT
- run() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
-
run method which extracts barcodes and accumulates metrics for an entire tile
- run() - Method in class picard.Test
- RUN_BARCODE - Variable in class picard.fastq.BamToBfq
- RUN_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToFastq
- RUN_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToSam
- RUN_DATE - Variable in class picard.sam.FastqToSam
- RUN_DIRECTORY - Variable in class picard.illumina.CollectIlluminaLaneMetrics
- RUN_MODE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller
- RUN_START_DATE - Variable in class picard.illumina.IlluminaBasecallsToSam
- RUN_WITHOUT_DBSNP - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
- runCommandLineProgram(CommandLineProgram, String[]) - Static method in class org.broadinstitute.hellbender.Main
-
Run the given command line program with the raw arguments from the command line
- runEamssForReadInPlace(byte[], byte[]) - Static method in class picard.illumina.parser.MultiTileBclParser
-
EAMSS is an Illumina Developed Algorithm for detecting reads whose quality has deteriorated towards their end and revising the quality to the masking quality (2) if this is the case.
- runInDebugMode - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- runInParallel(int, Supplier<T>) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Runs a task in parallel returning it returned result.
- runLocalAssembly(AssemblyRegion, Haplotype, byte[], SimpleInterval, ReadErrorCorrector, SAMFileHeader, SmithWatermanAligner, LongHomopolymerHaplotypeCollapsingEngine, SWParameters, SWParameters) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
-
Main entry point into the assembly engine.
- runMCMC() - Method in class org.broadinstitute.hellbender.utils.mcmc.GibbsSampler
-
Runs the Monte Carlo Markov Chain, using the state of the model provided in the constructor to initialize.
- running - Static variable in class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase
- RunningAverage() - Constructor for class org.broadinstitute.hellbender.utils.MathUtils.RunningAverage
- runningOn64BitX86Architecture() - Static method in class org.broadinstitute.hellbender.utils.NativeUtils
- runningOnArchitecture(String) - Static method in class org.broadinstitute.hellbender.utils.NativeUtils
- runningOnLinux() - Static method in class org.broadinstitute.hellbender.utils.NativeUtils
- runningOnMac() - Static method in class org.broadinstitute.hellbender.utils.NativeUtils
- runningOnPPCArchitecture() - Static method in class org.broadinstitute.hellbender.utils.NativeUtils
-
boolean : returns whether the current platform is PowerPC, LE only
- runPipeline(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- runPipeline(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram
-
Runs the pipeline.
- runPipeline(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.VariantWalkerSpark
- runPipeline(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormals
- runShellCommand(String[], Map<String, String>, File, boolean) - Static method in class org.broadinstitute.hellbender.utils.alignment.MummerExecutor
-
Method to run shell commands from GATK.
- RuntimeUtils - Class in org.broadinstitute.hellbender.utils.runtime
- RuntimeUtils() - Constructor for class org.broadinstitute.hellbender.utils.runtime.RuntimeUtils
- runTool() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
-
Template method that runs the startup hook, doWork and then the shutdown hook.
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Runs the tool itself after initializing and validating inputs.
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.IntervalWalkerSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.ReadWalkerSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.engine.spark.VariantWalkerSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.HaplotypeCallerSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.ApplyBQSRSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.bwa.BwaSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.ParallelCopyGCSDirectoryIntoHDFSSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.BwaAndMarkDuplicatesPipelineSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.CountBasesSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.CountVariantsSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.FlagStatSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectBaseDistributionByCycleSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MeanQualityByCycleSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSparkTool
-
The runTool method used when metrics collector tools are run "standalone".
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityScoreDistributionSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.SortSamSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.DiscoverVariantsFromContigAlignmentsSAMSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantReInterpreterSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.CalcMetadataSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ExtractSVEvidenceSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBadGenomicKmersSpark
-
Get the list of high copy number kmers in the reference, and write them to a file.
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryPipelineSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.ExtractOriginalAlignmentRecordsByNameSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- runTool(JavaSparkContext) - Method in class org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark
- runWithoutGapsAnnotation - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- runWithoutUmapS100Annotation - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
S
- S - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier.AlnModType.ModTypeString
- S - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- S - Enum constant in enum class picard.illumina.parser.ReadType
- S_LOCS_FILE - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
- SA_TAG_FIELD_SEPARATOR - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
String used to separate fields in an alignment-interval string representation.
- SA_TAG_INTERVAL_SEPARATOR_STR - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
String used to separate several alignment-intervals in a SA Tag like string.
- safeCombine(RecalibrationTables, RecalibrationTables) - Static method in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
-
Combines the two tables into a new table (allocating a new table in the process)
- sam - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.RevertSamSpark.FileType
- sam - Enum constant in enum class picard.sam.RevertSam.FileType
- SAM_DUPLICATE_READ_FLAG - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- SAM_FILE_HEADER_LINE_START - Static variable in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
- SAM_FILE_HEADER_START - Static variable in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
- SAM_FILES - Variable in class picard.sam.CompareSAMs
- SAM_FIRST_OF_PAIR_FLAG - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- SAM_MATE_STRAND_FLAG - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- SAM_MATE_UNMAPPED_FLAG - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- SAM_NOT_PRIMARY_ALIGNMENT_FLAG - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- SAM_PILEUP_FILE_EXTENSIONS - Static variable in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupCodec
- SAM_PROPER_PAIR_FLAG - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- SAM_READ_FAILS_VENDOR_QUALITY_CHECK_FLAG - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- SAM_READ_PAIRED_FLAG - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- SAM_READ_STRAND_FLAG - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- SAM_READ_UNMAPPED_FLAG - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- SAM_SECOND_OF_PAIR_FLAG - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- SAM_SUPPLEMENTARY_ALIGNMENT_FLAG - Static variable in class org.broadinstitute.hellbender.utils.read.ReadUtils
- SamAlignmentMerger - Class in org.broadinstitute.hellbender.utils.read.mergealignment
-
Class that takes in a set of alignment information in SAM format and merges it with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
- SamAlignmentMerger - Class in picard.sam
-
Class that takes in a set of alignment information in SAM format and merges it with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
- SamAlignmentMerger(File, File, File, SAMProgramRecord, boolean, boolean, boolean, List<File>, int, List<String>, List<String>, Integer, Integer, List<File>, List<File>, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean) - Constructor for class org.broadinstitute.hellbender.utils.read.mergealignment.SamAlignmentMerger
-
Constructor
- SamAlignmentMerger(File, File, File, SAMProgramRecord, boolean, boolean, boolean, List<File>, int, List<String>, List<String>, Integer, Integer, List<File>, List<File>, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean, int) - Constructor for class picard.sam.SamAlignmentMerger
-
Constructor with a default value for unmappingReadStrategy
- SamAlignmentMerger(File, File, File, SAMProgramRecord, boolean, boolean, boolean, List<File>, int, List<String>, List<String>, Integer, Integer, List<File>, List<File>, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean, int, AbstractAlignmentMerger.UnmappingReadStrategy, List<String>) - Constructor for class picard.sam.SamAlignmentMerger
-
Constructor
- SamComparison - Class in picard.sam.util
-
Compare two SAM/BAM files.
- SamComparison(SamReader, SamReader) - Constructor for class picard.sam.util.SamComparison
-
Note: the caller must make sure the SamReaders are closed properly.
- SamComparison(SamReader, SamReader, String, String, SAMComparisonArgumentCollection) - Constructor for class picard.sam.util.SamComparison
- SamComparison.AlignmentComparison - Enum Class in picard.sam.util
- samComparisonArgumentCollection - Variable in class picard.sam.CompareSAMs
- SAMComparisonArgumentCollection - Class in picard.sam.util
-
Argument collection for SAM comparison
- SAMComparisonArgumentCollection() - Constructor for class picard.sam.util.SAMComparisonArgumentCollection
- SamComparisonMetric - Class in picard.sam
-
Metric for results of SamComparison.
- SamComparisonMetric() - Constructor for class picard.sam.SamComparisonMetric
- same(byte, byte) - Static method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Checks whether two base encodings make reference to the same
Nucleotide(org.broadinstitute.hellbender.utils.Nucleotide...)instance regardless of their case. - same(Nucleotide) - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Checks whether this and another
Nucleotide(org.broadinstitute.hellbender.utils.Nucleotide...)make reference to the same nucleotide(s). - sameLocusQueue - Variable in class org.broadinstitute.hellbender.tools.sv.AbstractEvidenceSortMerger
- SAMFileDestination - Class in org.broadinstitute.hellbender.utils.haplotype
-
Class used to direct output from a HaplotypeBAMWriter to a bam/sam file.
- SAMFileDestination(Path, boolean, boolean, SAMFileHeader, Optional<String>) - Constructor for class org.broadinstitute.hellbender.utils.haplotype.SAMFileDestination
-
Create a new file destination.
- SAMFileGATKReadWriter - Class in org.broadinstitute.hellbender.utils.read
-
A GATKRead writer that writes to a SAM/BAM file.
- SAMFileGATKReadWriter(SAMFileWriter) - Constructor for class org.broadinstitute.hellbender.utils.read.SAMFileGATKReadWriter
- samFiles - Variable in class org.broadinstitute.hellbender.tools.validation.CompareBaseQualities
- SamFormatConverter - Class in picard.sam
-
Converts a BAM file to human-readable SAM output or vice versa
- SamFormatConverter() - Constructor for class picard.sam.SamFormatConverter
- SAMFormattedContigAlignmentParser(JavaRDD<GATKRead>, SAMFileHeader, boolean) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigAlignmentsRDDProcessor.SAMFormattedContigAlignmentParser
- samHeader - Variable in class org.broadinstitute.hellbender.engine.filters.ReadFilter
- samHeader - Variable in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
- SamHeaderAndIterator(SAMFileHeader, CloseableIterator<SAMRecord>) - Constructor for class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
- samjdk_compression_level() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- samjdk_use_async_io_read_samtools() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- samjdk_use_async_io_write_samtools() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- samjdk_use_async_io_write_tribble() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- SAMPileupCodec - Class in org.broadinstitute.hellbender.utils.codecs.sampileup
-
Decoder for single sample SAM pileup data.
- SAMPileupCodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupCodec
- SAMPileupElement - Class in org.broadinstitute.hellbender.utils.codecs.sampileup
-
Simple representation of a single base with associated quality from a SAM pileup
- SAMPileupFeature - Class in org.broadinstitute.hellbender.utils.codecs.sampileup
-
A tribble feature representing a SAM pileup.
- sample - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Partition
- sample - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.AlleleFrequencyQC
- sample - Variable in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods.BestAllele
-
The containing sample.
- sample(double) - Method in class org.broadinstitute.hellbender.utils.mcmc.MinibatchSliceSampler
-
Generate a single sample, given an initial value to use in slice construction.
- sample(double, int) - Method in class org.broadinstitute.hellbender.utils.mcmc.MinibatchSliceSampler
-
Generate multiple samples from the probability density function, given an initial value to use in slice construction.
- sample(RandomGenerator, Function<Double, Double>) - Method in class org.broadinstitute.hellbender.utils.mcmc.AdaptiveMetropolisSampler
- sample(RandomGenerator, Function<Double, Double>, int, int) - Method in class org.broadinstitute.hellbender.utils.mcmc.AdaptiveMetropolisSampler
-
Generate multiple samples from the probability density function.
- sample(RandomGenerator, S, T) - Method in interface org.broadinstitute.hellbender.utils.mcmc.ParameterSampler
-
Returns a random sample of a value that is dependent on an
ParameterizedStateand aDataCollection. - Sample - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies the eval RODs by each sample in the eval ROD.
- Sample - Class in org.broadinstitute.hellbender.utils.samples
-
Represents an individual under study.
- Sample(String, String, String, String, Sex) - Constructor for class org.broadinstitute.hellbender.utils.samples.Sample
- Sample(String, String, String, String, Sex, Affection) - Constructor for class org.broadinstitute.hellbender.utils.samples.Sample
- Sample(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Sample
- SAMPLE - Enum constant in enum class org.broadinstitute.hellbender.metrics.MetricAccumulationLevel
- SAMPLE - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.Metadata.Type
- SAMPLE - Enum constant in enum class picard.analysis.MetricAccumulationLevel
- SAMPLE - Enum constant in enum class picard.fingerprint.CrosscheckMetric.DataType
- SAMPLE - Variable in class org.broadinstitute.hellbender.metrics.analysis.AlleleFrequencyQCMetric
- SAMPLE - Variable in class org.broadinstitute.hellbender.metrics.MultiLevelMetrics
-
The sample to which these metrics apply.
- SAMPLE - Variable in class org.broadinstitute.hellbender.tools.SplitReads
- SAMPLE - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The name of the sample who's genotypes the sequence data was compared to.
- SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The sample whose known genotypes the sequence data was compared to.
- SAMPLE - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- SAMPLE - Variable in class picard.arrays.BafRegressMetrics
-
The sample name
- SAMPLE - Variable in class picard.metrics.MultilevelMetrics
-
The sample to which these metrics apply.
- SAMPLE - Variable in class picard.vcf.MakeSitesOnlyVcf
- SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
- SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The name of the sample being assayed.
- SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The name of the sample being assayed.
- SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The name of the sample being assayed.
- SAMPLE_ALIAS - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The name of the sample being assayed.
- SAMPLE_ALIAS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The name of the sample
- SAMPLE_ALIAS - Variable in class picard.arrays.GtcToVcf
- SAMPLE_ALIAS - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- SAMPLE_ALIAS - Variable in class picard.fingerprint.ExtractFingerprint
- SAMPLE_ALIAS - Variable in class picard.fingerprint.FingerprintMetrics
-
The Sample alias taken from RG header or #CHROME line
- SAMPLE_ALIAS - Variable in class picard.fingerprint.IdentifyContaminant
- SAMPLE_ALIAS - Variable in class picard.illumina.IlluminaBasecallsToSam
- SAMPLE_ALIAS - Variable in class picard.sam.RevertSam
- SAMPLE_ALIAS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
-
The name of the sample being assayed
- SAMPLE_ALIAS_ARG - Static variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- SAMPLE_ALIAS_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- SAMPLE_ALIAS_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- sample_by_center - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Partition
- sample_by_platform - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Partition
- sample_by_platform_by_center - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Partition
- SAMPLE_INDEX_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- SAMPLE_INDIVIDUAL_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
- SAMPLE_LIST_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- SAMPLE_LOCATABLE - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.Metadata.Type
- SAMPLE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.SplitReads
- SAMPLE_METADATA_TAG - Static variable in class org.broadinstitute.hellbender.utils.tsv.TableUtils
- SAMPLE_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- SAMPLE_NAME - Variable in class picard.sam.FastqToSam
- SAMPLE_NAME_ARGUMENT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- SAMPLE_NAME_DISCOVERY_VCF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- SAMPLE_NAME_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- SAMPLE_NAME_MAP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- SAMPLE_NAME_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- SAMPLE_NAME_TXT_FILE - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVNamingConstants
- SAMPLE_NAME_VALIDATION_CASE - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- SAMPLE_NAME_VALIDATION_CONTROL - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- SAMPLE_NAMES_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.PrintSVEvidence
- SAMPLE_NAMES_NAME - Static variable in class org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAF
- SAMPLE_PLOIDY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- SAMPLE_PLOIDY_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- SAMPLE_PREFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVNamingConstants
- SAMPLE_PSI_SCALE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineContigPloidyModelArgumentCollection
- SAMPLE_PSI_SCALE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
- SAMPLE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.SplitReads
- SAMPLE_SIZE - Variable in class picard.analysis.CollectWgsMetrics
- SAMPLE_SIZE - Variable in class picard.analysis.directed.CollectTargetedMetrics
- SAMPLE_SIZE - Variable in class picard.analysis.TheoreticalSensitivityMetrics
-
Number of samples drawn at each depth in the depth distribution.
- sampleAlias - Variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- sampleBarcodes - Variable in class picard.illumina.parser.ReadStructure
- sampleCount() - Method in class org.broadinstitute.hellbender.utils.samples.SampleDB
-
Get number of sample objects
- sampleCumulativeSums(int, int, boolean) - Method in class picard.analysis.TheoreticalSensitivity.RouletteWheel
- SampleDB - Class in org.broadinstitute.hellbender.utils.samples
-
Simple database for managing samples
- SampleDBBuilder - Class in org.broadinstitute.hellbender.utils.samples
-
Class for creating a temporary in memory database of samples.
- SampleDBBuilder(PedigreeValidationType) - Constructor for class org.broadinstitute.hellbender.utils.samples.SampleDBBuilder
- sampleEvidence(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Returns the units of evidence that belong to a sample sorted by their index (within that sample).
- sampleEvidenceCount(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Returns the quantity of evidence that belongs to a sample in the evidence-likelihood collection.
- sampleExpressions - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- sampleIndicesWithoutReplacement(int, int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Creates a new sample of k ints from [0..n-1], without duplicates.
- sampleLikelihoods(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingLikelihoods
-
Returns the genotype-likelihoods of the sample given its index in the collection.
- SampleList - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
List samples that are non-reference at a given variant site
- SampleList - Interface in org.broadinstitute.hellbender.utils.genotyper
-
An immutable, indexed set of samples.
- SampleList() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.SampleList
- SampleLocatableMetadata - Interface in org.broadinstitute.hellbender.tools.copynumber.formats.metadata
-
Interface for marking objects that contain metadata associated with a collection of locatables associated with a single sample.
- sampleMatrix(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Returns an evidence vs allele likelihood matrix corresponding to a sample.
- SampleMetadata - Interface in org.broadinstitute.hellbender.tools.copynumber.formats.metadata
-
Interface for marking objects that contain metadata associated with a single sample.
- sampleName - Variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVVariantComposer
- SampleNameMap - Class in org.broadinstitute.hellbender.tools.genomicsdb
-
A class to hold the mappings of sample names to VCF / VCF index paths.
- SampleNameMap() - Constructor for class org.broadinstitute.hellbender.tools.genomicsdb.SampleNameMap
-
Create an empty SampleNameMap.
- SampleNameMap(Path) - Constructor for class org.broadinstitute.hellbender.tools.genomicsdb.SampleNameMap
-
Create a SampleNameMap from a textual file containing the sample mappings.
- SampleNameMap(Path, boolean) - Constructor for class org.broadinstitute.hellbender.tools.genomicsdb.SampleNameMap
-
Create a SampleNameMap from a textual file containing the sample mappings.
- SampleNameSplitter - Class in org.broadinstitute.hellbender.tools.readersplitters
-
Splits readers sample names.
- SampleNameSplitter() - Constructor for class org.broadinstitute.hellbender.tools.readersplitters.SampleNameSplitter
- sampleNameToUse - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
-
You can use this argument to specify that HC should process a single sample out of a multisample BAM file.
- SamplePairExtractor - Class in org.broadinstitute.hellbender.tools.funcotator.metadata
-
Utility class to determine the tumor normal pairs that makeup a VCF Header
- samplePloidy - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
-
Sample ploidy - equivalent to number of chromoso mes per pool.
- samplePloidy(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingLikelihoods
-
Returns the ploidy of the sample given its index in the collection.
- samplePloidy(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.HeterogeneousPloidyModel
- samplePloidy(int) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.HomogeneousPloidyModel
- samplePloidy(int) - Method in interface org.broadinstitute.hellbender.tools.walkers.genotyper.PloidyModel
-
Return the assumed ploidy for a sample given its index.
- SampleReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only reads for a given sample.
- SampleReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.SampleReadFilter
- SampleReadFilter(SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.engine.filters.SampleReadFilter
- samples - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
- samples - Variable in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Sample list.
- samples() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Returns the samples in this evidence-likelihood collection.
- SAMPLES_FILE - Variable in class picard.arrays.VcfToAdpc
- samplesList - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- SampleSpecificData(String, Broadcast<SVIntervalTree<VariantContext>>, List<SVInterval>, PairedStrandedIntervalTree<EvidenceTargetLink>, ReadMetadata, Broadcast<SAMFileHeader>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData.SampleSpecificData
- samplesToKeep - Variable in class org.broadinstitute.hellbender.engine.filters.SampleReadFilter
- SAMPLING_MIN_MQ_ARGUMENT_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- SAMPLING_PADDING_ARGUMENT_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- SamReaderQueryingIterator - Class in org.broadinstitute.hellbender.utils.iterators
-
An iterator that allows for traversals over a SamReader restricted to a set of intervals, unmapped reads, or both.
- SamReaderQueryingIterator(SamReader, List<SimpleInterval>, boolean) - Constructor for class org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator
-
Create a SamReaderQueryingIterator given a SamReader, query intervals, and a flag indicating whether unmapped reads with no position assigned should be returned.
- SamReaderQueryingIterator(SamReader, TraversalParameters) - Constructor for class org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator
-
Create a SamReaderQueryingIterator given a SamReader and a set of traversal parameters governing which reads are to be returned during iteration.
- SAMRecordAndReference - Class in org.broadinstitute.hellbender.metrics
- SAMRecordAndReference - Class in picard.metrics
- SAMRecordAndReference(SAMRecord, ReferenceSequence) - Constructor for class org.broadinstitute.hellbender.metrics.SAMRecordAndReference
- SAMRecordAndReference(SAMRecord, ReferenceSequence) - Constructor for class picard.metrics.SAMRecordAndReference
- SAMRecordAndReferenceMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,
HKEY extends Comparable<HKEY>> - Class in org.broadinstitute.hellbender.metrics - SAMRecordAndReferenceMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,
HKEY extends Comparable> - Class in picard.metrics - SAMRecordAndReferenceMultiLevelCollector() - Constructor for class org.broadinstitute.hellbender.metrics.SAMRecordAndReferenceMultiLevelCollector
- SAMRecordAndReferenceMultiLevelCollector() - Constructor for class picard.metrics.SAMRecordAndReferenceMultiLevelCollector
- SAMRecordMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,
HKEY extends Comparable<HKEY>> - Class in org.broadinstitute.hellbender.metrics -
Defines a MultilevelPerRecordCollector using the argument type of SAMRecord so that this doesn't have to be redefined for each subclass of MultilevelPerRecordCollector
- SAMRecordMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,
HKEY extends Comparable> - Class in picard.metrics -
Defines a MultilevelPerRecordCollector using the argument type of SAMRecord so that this doesn't have to be redefined for each subclass of MultilevelPerRecordCollector
- SAMRecordMultiLevelCollector() - Constructor for class org.broadinstitute.hellbender.metrics.SAMRecordMultiLevelCollector
- SAMRecordMultiLevelCollector() - Constructor for class picard.metrics.SAMRecordMultiLevelCollector
- SAMRecordSerializer - Class in org.broadinstitute.hellbender.engine.spark
-
Efficient serializer for SAMRecords that uses SAMRecordSparkCodec for encoding/decoding.
- SAMRecordSerializer() - Constructor for class org.broadinstitute.hellbender.engine.spark.SAMRecordSerializer
- SAMRecordSparkCodec - Class in htsjdk.samtools
-
A class that uses a slightly adapted version of BAMRecordCodec for serialization/deserialization of SAMRecords.
- SAMRecordSparkCodec() - Constructor for class htsjdk.samtools.SAMRecordSparkCodec
- SAMRecordSparkCodec(SAMRecordFactory) - Constructor for class htsjdk.samtools.SAMRecordSparkCodec
- SAMRecordToGATKReadAdapter - Class in org.broadinstitute.hellbender.utils.read
-
Implementation of the
GATKReadinterface for theSAMRecordclass. - SAMRecordToGATKReadAdapter(SAMRecord) - Constructor for class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- SAMRecordToGATKReadAdapterSerializer - Class in org.broadinstitute.hellbender.engine.spark
-
Efficient serializer for SAMRecordToGATKReadAdapters that uses SAMRecordSparkCodec for encoding/decoding.
- SAMRecordToGATKReadAdapterSerializer() - Constructor for class org.broadinstitute.hellbender.engine.spark.SAMRecordToGATKReadAdapterSerializer
- SAMRecordToReadIterator - Class in org.broadinstitute.hellbender.utils.iterators
-
Wraps a SAMRecord iterator within an iterator of GATKReads.
- SAMRecordToReadIterator(Iterator<SAMRecord>) - Constructor for class org.broadinstitute.hellbender.utils.iterators.SAMRecordToReadIterator
- samRecordWithOrdinal - Variable in class picard.sam.markduplicates.util.ReadEndsForMateCigar
- SamRecordWithOrdinalAndSetDuplicateReadFlag - Class in picard.sam.markduplicates.util
-
This class sets the duplicate read flag as the result state when examining sets of records.
- SamRecordWithOrdinalAndSetDuplicateReadFlag() - Constructor for class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
- SamRecordWithOrdinalAndSetDuplicateReadFlag(SAMRecord, long) - Constructor for class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
- SamSequenceRecordsIterator(File, boolean) - Constructor for class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
- SamToBfqWriter - Class in picard.fastq
-
Class to take unmapped reads in SAM/BAM/CRAM file format and create Maq binary fastq format file(s) -- one or two of them, depending on whether it's a paired-end read.
- SamToBfqWriter(File, File, String, Integer, Integer, boolean, String, boolean, boolean, Integer) - Constructor for class picard.fastq.SamToBfqWriter
-
Constructor
- SamToBfqWriter(File, String, boolean, String, boolean) - Constructor for class picard.fastq.SamToBfqWriter
-
Constructor
- SamToFastq - Class in picard.sam
-
Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger FASTQ format.
- SamToFastq() - Constructor for class picard.sam.SamToFastq
- SamToFastqWithTags - Class in picard.sam
-
Extracts read sequences and qualities from the input SAM/BAM file and SAM/BAM tags and writes them into output files in Sanger FASTQ format.
- SamToFastqWithTags() - Constructor for class picard.sam.SamToFastqWithTags
- SAMTOOLS_OVERLAP_LOW_CONFIDENCE - Static variable in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Constant used by samtools to downgrade a quality for overlapping reads that disagrees in their base.
- sanitize - Variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- SANITIZE - Variable in class picard.sam.RevertSam
- sanitizeFuncotationFieldForMaf(String) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Make sure that an individual funcotation field (i.e.
- SATagBuilder - Class in org.broadinstitute.hellbender.utils
-
A builder class that expands functionality for SA tags.
- SATagBuilder(GATKRead) - Constructor for class org.broadinstitute.hellbender.utils.SATagBuilder
- saveMetrics(MetricsFile<?, ?>, String) - Static method in class org.broadinstitute.hellbender.metrics.MetricsUtils
-
Write a
MetricsFileto the given path, can be any destination supported byBucketUtils.createFile(String) - saveMetrics(MetricsFile<ExampleMultiMetrics, Integer>) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollector
-
Finish the metrics collection and save any results to the metrics file.
- saveMetrics(String) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleCollectMultiMetricsSpark
-
Finish the collection process and save any results.
- saveMetrics(String) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollectorSpark
-
Save the metrics out to a file.
- saveMetrics(String) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleCollectSingleMetricsSpark
-
Finish the collection process and save any results.
- saveMetrics(String) - Method in class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetricsCollectorSpark
-
Write out the results of the metrics collection
- saveMetrics(String) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectInsertSizeMetricsSpark
- saveMetrics(String) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark
- saveMetrics(String) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.InsertSizeMetricsCollectorSpark
- saveMetrics(String) - Method in interface org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSpark
-
This method is called after collectMetrics has returned and all Spark partitions have completed metrics collection.
- saveMetrics(String) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSparkTool
- saveMetrics(String) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityYieldMetricsCollectorSpark
-
Write out the results of the metrics collection
- saveMetricsRDD(MetricsFile<GATKDuplicationMetrics, Double>, SAMFileHeader, JavaPairRDD<String, GATKDuplicationMetrics>, String) - Static method in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils
-
Saves the metrics to a file.
- saveResults(MetricsFile<?, Integer>, SAMFileHeader, String) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectBaseDistributionByCycleSpark
- SB_TABLE_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- scaledEvidenceProbabilityUsingGenotypeFrequencies(double[]) - Method in class picard.fingerprint.HaplotypeProbabilities
-
This function returns the scaled probability of the evidence collected given a vector of priors on the haplotype using the internal likelihood, which may be scaled by an unknown factor.
- scaleLogSpaceArrayForNumericalStability(double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Given an array of log space (log or log10) values, subtract all values by the array maximum so that the max element in log space is zero.
- scan() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.util.AnalysisModuleScanner
-
scan the class and find all appropriate fields and tables
- SCAN_WINDOW_SIZE - Variable in class picard.analysis.CollectGcBiasMetrics
- SCANNER_NAME - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The name of the scanner used for this sample
- SCANNER_NAME - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- SCARNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- scatter(IntervalList, int) - Method in interface picard.util.IntervalList.IntervalListScatterer
-
Scatter an
IntervalListinto several IntervalLists. - SCATTER_CONTENT - Variable in class picard.util.IntervalListTools
- SCATTER_COUNT - Variable in class picard.util.IntervalListTools
- SCATTER_COUNT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- SCATTER_COUNT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- scatterContigIntervals(SAMFileHeader, List<GenomeLoc>, List<File>) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Splits an interval list into multiple files.
- scatterFixedIntervals(SAMFileHeader, List<List<GenomeLoc>>, List<File>) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Splits an interval list into multiple files.
- ScatterIntervalsByNReferenceArgumentCollection() - Constructor for class picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
- ScatterIntervalsByNs - Class in picard.util
-
A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.
- ScatterIntervalsByNs() - Constructor for class picard.util.ScatterIntervalsByNs
- ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection - Class in picard.util
- SCHEMA_HEADER_KEY - Static variable in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVSegmentVariantComposer
- scheme - Variable in class picard.vcf.GenotypeConcordanceScheme
-
The underlying scheme
- sChr - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- score - Variable in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.FlowModeFragment
- score - Variable in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Fragment
- score - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- score() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotype
- score(File, File) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.BGMMVariantAnnotationsScorer
- score(File, File) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.PythonSklearnVariantAnnotationsScorer
- score(File, File) - Method in interface org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsScorer
- score(GATKRead) - Method in enum class org.broadinstitute.hellbender.utils.read.markduplicates.MarkDuplicatesScoringStrategy
-
Given a read, compute the reads's score for mark duplicates.
- SCORE - Variable in class picard.util.IntervalListToBed
- SCORE_GENOME_LENGTH_UNITS - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScorer
- SCORE_KEY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- SCORE_METRICS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- SCORE_METRICS_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- SCORE_READS_PER_PARTITION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- SCORE_READS_PER_PARTITION_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- SCORE_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection
- SCORE_WARNINGS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- SCORE_WARNINGS_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- scoreArgs - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark
- scoreArgs - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreSpark
- scoreMetricsFileUri - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
-
If specified, records the following metrics: Number of reads mapped to the microbial reference Number of unmapped reads
- scoreReads(JavaSparkContext, JavaRDD<GATKRead>, JavaRDD<GATKRead>, SAMFileHeader) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScorer
- SCORES_HDF5_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- SCORES_OUTPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- SCORES_OUTPUT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- SCORES_PATH - Static variable in interface org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsScorer
- scoresPath - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- scoreThreshold - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection
-
This parameter controls the minimum quality of the BWA alignments for the output.
- ScoreVariantAnnotations - Class in org.broadinstitute.hellbender.tools.walkers.vqsr.scalable
-
Scores variant calls in a VCF file based on site-level annotations using a previously trained model.
- ScoreVariantAnnotations() - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- ScriptExecutor - Class in org.broadinstitute.hellbender.utils.runtime
-
Base class for executors that find and run scripts in an external script engine process (R, Python, etc).
- ScriptExecutor(String) - Constructor for class org.broadinstitute.hellbender.utils.runtime.ScriptExecutor
- ScriptExecutorException - Exception in org.broadinstitute.hellbender.utils.runtime
-
Base type for exceptions thrown by the ScriptExecutor.
- ScriptExecutorException(String) - Constructor for exception org.broadinstitute.hellbender.utils.runtime.ScriptExecutorException
- SCRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- SCRNA_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- SD_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The standard deviation of clusters per tile.
- SD_COVERAGE - Variable in class picard.analysis.WgsMetrics
-
The standard deviation of coverage of the genome after all filters are applied.
- SD_PCT_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The standard deviation in percentage of pf clusters per tile.
- SD_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The standard deviation in number of pf clusters per tile.
- SD_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The standard deviation of the read lengths.
- sDUST(GATKRead, int, double) - Static method in class org.broadinstitute.hellbender.transformers.DUSTReadTransformer
-
Wrapper method for runDUST so that we don't have to expose the IntTuple class.
- SECOND - Enum constant in enum class picard.illumina.parser.TileTemplateRead
- SECOND - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
- second_best_allele - Variable in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods.BestAllele
- SECOND_DOMINATES - Enum constant in enum class org.broadinstitute.hellbender.utils.MannWhitneyU.TestType
- SECOND_END_FASTQ - Variable in class picard.sam.SamToFastq
- SECOND_IN_MS - Static variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- SECOND_INPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
- SECOND_INPUT - Variable in class picard.util.IntervalListTools
- SECOND_INPUT_INDEX_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
- SECOND_INPUT_SAMPLE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
- SECOND_OF_PAIR - Enum constant in enum class picard.analysis.AlignmentSummaryMetrics.Category
- SECOND_OF_PAIR - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- SECOND_READ_TRANSCRIPTION_STRAND - Enum constant in enum class picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
- SECONDARY_OR_SUPPLEMENTARY_RDS - Variable in class picard.sam.DuplicationMetrics
-
The number of reads that were either secondary or supplementary
- secondBestLikelihood - Variable in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods.BestAllele
- secondIntervalFile - Variable in class org.broadinstitute.hellbender.tools.CompareIntervalLists
- SecondOfPairReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.SecondOfPairReadFilter
- secondPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.engine.TwoPassVariantWalker
- secondPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalker
- secondPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations
- secondPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MTLowHeteroplasmyFilterTool
- secondPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants
- secondPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.FilterVariantTranches
- SECONDS_BETWEEN_PROGRESS_UPDATES_NAME - Static variable in class org.broadinstitute.hellbender.engine.GATKTool
- secondSmallestMinusSmallest(int[], int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Given an int array returns the difference between the second smallest element and the smallest element.
- seedLength - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection
-
This parameter controls the sensitivity of the BWA-MEM aligner.
- seek(int) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Changes the index of the next value to set using
appendoperations. - seek(Enum<?>) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Changes the index of the next value to set using
appendoperations. - seek(String) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Changes the index of the next value to set using
appendoperations. - seek(List<File>, TileIndex, int) - Method in class picard.illumina.parser.readers.BclReader
- seeked - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator
- seekStream(long) - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader
- seekToTile(int) - Method in class picard.illumina.parser.MultiTileParser
- seekToTile(int) - Method in class picard.illumina.parser.MultiTileBclParser
-
Clear the current set of cycleFileParsers and replace them with the ones for the tile indicated by oneBasedTileNumber
- seekToTile(int) - Method in class picard.illumina.parser.PerTileParser
- SEG - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.OutputFormatType
- SEGMENT_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- SEGMENT_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- SEGMENT_GERMLINE_CNV_CALLS_PYTHON_SCRIPT - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- SEGMENT_MEANS - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioParameter
- SEGMENT_SIZE_ARG_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- SEGMENTAL_DUPLICATION_CONTENT - Static variable in class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.CopyNumberAnnotations
- SEGMENTAL_DUPLICATION_TRACK_PATH_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervals
- segmentationRecords() - Method in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel
- SegmentedCpxVariantSimpleVariantExtractor - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
For extracting simple variants from input GATK-SV complex variants.
- SegmentedCpxVariantSimpleVariantExtractor() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor
- SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- SegmentedCpxVariantSimpleVariantExtractor.MultiSegmentsCpxVariantExtractor - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- SegmentedCpxVariantSimpleVariantExtractor.RelevantAttributes - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- SegmentedCpxVariantSimpleVariantExtractor.ZeroAndOneSegmentCpxVariantExtractor - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- SegmentExonOverlaps - Class in org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment
-
Class that represents the exon numbers overlapped by a genomic region.
- SegmentExonOverlaps(String, String) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment.SegmentExonOverlaps
- SegmentExonUtils - Class in org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment
- SEGMENTS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument
- SEGMENTS_FILE_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.ModelSegments
- SELECT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
-
See example commands above for detailed usage examples.
- selectAlleleBiasedEvidence(Map<A, List<EVIDENCE>>, double) - Static method in class org.broadinstitute.hellbender.utils.downsampling.AlleleBiasedDownsamplingUtils
-
Computes reads to remove based on an allele biased down-sampling
- selectExps - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- SelectionMetric(String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager.SelectionMetric
- selectNames - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- SelectVariants - Class in org.broadinstitute.hellbender.tools.walkers.variantutils
-
Select a subset of variants from a VCF file
- SelectVariants() - Constructor for class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
- selectWorstVariants() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- SELENO - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
contains a selenocysteine.
- SELENOCYSTEINE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureType
- SEMI_PROCESSED - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
a processed pseudogene with one or more introns still present.
- sendAsynchronousCommand(String) - Method in class org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor
-
Send a command to the remote process without waiting for a response.
- sendSynchronousCommand(String) - Method in class org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor
-
Send a command to Python, and wait for an ack, returning all accumulated output since the last call to either <link #sendSynchronousCommand/> or <line #getAccumulatedOutput/> This is a blocking call - if no acknowledgment is received from the remote process, it will block indefinitely.
- sense - Variable in class org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation.SingleStrandFeatureCoverage
- SENSE_INTRONIC - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- SENSE_OVERLAPPING - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- sensitivity - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- SENSITIVITY_METADATA_TAG - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterStats
- sensitivityAtConstantDepth(int, Histogram<Integer>, double, int, double, long) - Static method in class picard.analysis.TheoreticalSensitivity
-
Calculates the theoretical sensitivity with a given Phred-scaled quality score distribution at a constant depth.
- separator - Variable in class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter
- seq - Variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- seq(double, double, double) - Static method in class picard.util.MathUtil
-
Mimic's R's seq() function to produce a sequence of equally spaced numbers.
- SEQ - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestField
- SEQ_ALT_HAPLOTYPE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- SEQ_IS_STORED - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- seqEquals(BaseVertex) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
-
Are b and this equal according to their base sequences?
- SeqGraph - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
-
A graph that contains base sequence at each node
- SeqGraph(int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqGraph
-
Construct an empty SeqGraph where we'll add nodes based on a kmer size of kmer The kmer size is purely information.
- SeqIsStoredReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.SeqIsStoredReadFilter
- seqLength() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- sequence - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
- SEQUENCE_DICTIONARY - Variable in class picard.annotation.SortGff
- SEQUENCE_DICTIONARY - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
- SEQUENCE_DICTIONARY - Variable in class picard.fingerprint.LiftOverHaplotypeMap
- SEQUENCE_DICTIONARY - Variable in class picard.sam.ReorderSam
- SEQUENCE_DICTIONARY - Variable in class picard.util.BedToIntervalList
- SEQUENCE_DICTIONARY - Variable in class picard.util.LiftOverIntervalList
- SEQUENCE_DICTIONARY - Variable in class picard.vcf.CollectVariantCallingMetrics
- SEQUENCE_DICTIONARY - Variable in class picard.vcf.MergeVcfs
- SEQUENCE_DICTIONARY - Variable in class picard.vcf.SortVcf
- SEQUENCE_DICTIONARY - Variable in class picard.vcf.SplitVcfs
- SEQUENCE_DICTIONARY - Variable in class picard.vcf.UpdateVcfSequenceDictionary
- SEQUENCE_DICTIONARY_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- SEQUENCE_DICTIONARY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- SEQUENCE_ERROR - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Transcript contains at least 1 non-canonical splice junction that is associated with a known or novel genome sequence
- SEQUENCE_MISMATCH - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Deprecated.- but used in existing extended manifest files.
- SEQUENCE_NAME - Variable in class picard.analysis.RrbsCpgDetailMetrics
-
Sequence the CpG is seen in
- SEQUENCE_NAMES - Variable in class picard.analysis.CollectRrbsMetrics
- SEQUENCE_TAG_GROUP - Variable in class picard.sam.SamToFastqWithTags
- SequenceComparison - Class in org.broadinstitute.hellbender.tools.funcotator
-
A simple data object to hold a comparison between a reference sequence and an alternate allele.
- SequenceComparison() - Constructor for class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- SequenceDictionaryIsMissingContigLengths(String, SAMSequenceDictionary) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.SequenceDictionaryIsMissingContigLengths
- SequenceDictionaryUtils - Class in org.broadinstitute.hellbender.utils
-
A series of utility functions that enable the GATK to compare two sequence dictionaries -- from the reference, from BAMs, or from feature sources -- for consistency.
- SequenceDictionaryUtils - Class in picard.util
-
Class with helper methods for generating and writing SequenceDictionary objects.
- SequenceDictionaryUtils() - Constructor for class picard.util.SequenceDictionaryUtils
- SequenceDictionaryUtils.SamSequenceRecordsIterator - Class in picard.util
- SequenceDictionaryUtils.SequenceDictionaryCompatibility - Enum Class in org.broadinstitute.hellbender.utils
- SequenceDictionaryValidationArgumentCollection - Interface in org.broadinstitute.hellbender.cmdline.argumentcollections
-
interface for argument collections that control how sequence dictionary validation should be handled
- SequenceDictionaryValidationArgumentCollection.NoValidationCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
doesn't provide a configuration argument, and always returns false, useful for tools that do not want to perform sequence dictionary validation, like aligners
- SequenceDictionaryValidationArgumentCollection.StandardValidationCollection - Class in org.broadinstitute.hellbender.cmdline.argumentcollections
-
most tools will want to use this, it defaults to performing sequence dictionary validation but provides the option to disable it
- sequenceDictionaryValidationArguments - Variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- SequenceRC(CharSequence) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.SequenceRC
- sequenceRecordsAreEquivalent(SAMSequenceRecord, SAMSequenceRecord) - Static method in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
-
Helper routine that returns whether two sequence records are equivalent, defined as having the same name and lengths.
- SequencerFlowClass - Enum Class in org.broadinstitute.hellbender.utils
-
In broad terms, each sequencing platform can be classified by whether it flows nucleotides in some order such that homopolymers get sequenced in a single event (ie 454 or Ion) or it reads each position in the sequence one at a time, regardless of base composition (Illumina or Solid).
- sequencerType - Variable in enum class org.broadinstitute.hellbender.utils.NGSPlatform
- SEQUENCING - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorType
- SEQUENCING - Enum constant in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateType
- SEQUENCING_CENTER - Variable in class picard.illumina.IlluminaBasecallsToSam
- SEQUENCING_CENTER - Variable in class picard.sam.FastqToSam
- SEQUENCING_QUAL_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- SequencingArtifactMetrics - Class in picard.analysis.artifacts
- SequencingArtifactMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics
- SequencingArtifactMetrics.BaitBiasDetailMetrics - Class in picard.analysis.artifacts
-
Bait bias artifacts broken down by context.
- SequencingArtifactMetrics.BaitBiasSummaryMetrics - Class in picard.analysis.artifacts
-
Summary analysis of a single bait bias artifact, also known as a reference bias artifact.
- SequencingArtifactMetrics.PreAdapterDetailMetrics - Class in picard.analysis.artifacts
-
Pre-adapter artifacts broken down by context.
- SequencingArtifactMetrics.PreAdapterSummaryMetrics - Class in picard.analysis.artifacts
-
Summary analysis of a single pre-adapter artifact.
- seqValidationArguments - Variable in class org.broadinstitute.hellbender.engine.GATKTool
- SeqVertex - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
-
A graph vertex containing a sequence of bases and a unique ID that allows multiple distinct nodes in the graph to have the same sequence.
- SeqVertex(byte[]) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqVertex
-
Create a new SeqVertex with sequence and the next available id
- SeqVertex(String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqVertex
-
Create a new SeqVertex having bases of sequence.getBytes()
- SerializableConsumer<T> - Interface in org.broadinstitute.hellbender.utils
- SerializableFunction<T,
R> - Interface in org.broadinstitute.hellbender.utils -
Represents a
Functionthat isSerializable. - SerializablePredicate<T> - Interface in org.broadinstitute.hellbender.utils
- SerializableSupplier<T> - Interface in org.broadinstitute.hellbender.utils
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTaxonomyDatabase
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.IntraChrStrandSwitchBreakpointComplications
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.InvertedDuplicationBreakpointComplications
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantCanonicalRepresentation
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInducingAssemblyContig
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.DiscordantReadPairEvidence
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.LargeIndel
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.OutiesPair
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SplitRead
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.TemplateSizeAnomaly
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.WeirdTemplateSize
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerAndInterval
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.KmerAndCount
- serialize(Kryo, Output) - Method in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.Strand
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchCollectionSpark
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- serialize(Kryo, Output) - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair
- serialize(File) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.BGMMVariantAnnotationsScorer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerBloomFilter.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSTaxonomyDatabase.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedAssembly.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.IntraChrStrandSwitchBreakpointComplications.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.InvertedDuplicationBreakpointComplications.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantCanonicalRepresentation.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInducingAssemblyContig.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ExternalEvidence.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.InterContigPair.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.LargeIndel.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.MateUnmapped.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.OutiesPair.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SameStrandPair.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SplitRead.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.TemplateSizeAnomaly.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.WeirdTemplateSize.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerAndInterval.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.LibraryRawStatistics.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionBounds.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionStatistics.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.KmerAndCount.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.Strand.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchCollectionSpark.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMapSpark.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMultiMapSpark.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchSetSpark.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.HopscotchUniqueMultiMapSpark.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.CDF.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.utils.SVInterval.Serializer
- Serializer() - Constructor for class org.broadinstitute.hellbender.utils.SVIntervalTree.Serializer
- serializeToString() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
-
Serializes all data in
GencodeGtfFeatureto a string. - serialVersionUID - Static variable in interface org.broadinstitute.hellbender.engine.filters.VariantFilter
- serialVersionUID - Static variable in class org.broadinstitute.hellbender.metrics.QualityYieldMetricsArgumentCollection
- serialVersionUID - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticGenotypingArgumentCollection
- serialVersionUID - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- serialVersionUID - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- serialVersionUID - Static variable in class org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsArgumentCollection
- serialVersionUID - Static variable in class org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetricsArgumentCollection
- serialVersionUID - Static variable in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedAllele
- serialVersionUID - Static variable in interface org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSpark
- serialVersionUID - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleAndContext
- serialVersionUID - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.InverseAllele
- serialVersionUID - Static variable in class org.broadinstitute.hellbender.transformers.DUSTReadTransformer
- serialVersionUID - Static variable in interface org.broadinstitute.hellbender.transformers.ReadTransformer
- serialVersionUID - Static variable in class org.broadinstitute.hellbender.transformers.StripMateNumberTransformer
- serialVersionUID - Static variable in interface org.broadinstitute.hellbender.transformers.VariantTransformer
- serialVersionUID - Static variable in interface org.broadinstitute.hellbender.utils.recalibration.covariates.Covariate
- SERINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- set(int, double) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the value for a column to a double given its index.
- set(int, double, int) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the value for a column to a double given its index.
- set(int, int) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the int value of a column given its index.
- set(int, int, double) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix
- set(int, int, double) - Method in interface org.broadinstitute.hellbender.utils.genotyper.LikelihoodMatrix
-
Set the likelihood of a unit of evidence given an allele through their indices.
- set(int, int, double, double, double) - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParamsBuilder
- set(int, int, Object) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Set the value for a given position in the table.
- set(int, long) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the long value of a column given its index.
- set(int, VariantContext, List<List<Allele>>, List<VariantType>, List<TreeSet<String>>) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
-
Sets the element at a specified index in the underlying
LabeledVariantAnnotationsData.datacollection. - set(int, String) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the string value of a column given its index.
- set(int, IntRange, double, double, double) - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParamsBuilder
- set(int, LocalAssembler.Contig) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigListRC
- set(int, V) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- set(Allele, X) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection
-
Take an allele, REF or ALT, and update its value appropriately
- set(Object, String, Object) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportTable
-
Set the value for a given position in the table.
- set(String, boolean) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the boolean value in the data-line that correspond to a column by its name.
- set(String, double) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the double value in the data-line that correspond to a column by its name.
- set(String, double, int) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the double value in the data-line that correspond to a column by its name.
- set(String, int) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the int value in the data-line that correspond to a column by its name.
- set(String, long) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the long value in the data-line that correspond to a column by its name.
- set(String, String) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets the string value in the data-line that correspond to a column by its name.
- set(Collection<Allele>, Function<Allele, X>) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection
- set(ArtifactPrior) - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPriorCollection
-
Add an artifact prior to the collection.
- SET_ONLY_UQ - Variable in class picard.sam.SetNmMdAndUqTags
- SET_TO_NO_CALL - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod
-
set all of the genotype GT values to NO_CALL
- SET_TO_NO_CALL_NO_ANNOTATIONS - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod
-
set all of the genotype GT values to NO_CALL and remove annotations
- setAdditionalInfo(String) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
-
Set additional debugging information for this vertex
- setAddPGTagToReads(boolean) - Method in class picard.sam.AbstractAlignmentMerger
-
Set addPGTagToReads.
- setAddSpecialTag(boolean) - Method in class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter
- setAFScale(VariantEvalArgumentCollection.StratifyingScale) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- setAlignedAlternateAllele(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setAlignedAlternateAlleleStop(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setAlignedCodingSequenceAlleleStart(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setAlignedCodingSequenceAlternateAllele(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setAlignedCodingSequenceReferenceAllele(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setAlignedReferenceAllele(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setAlignedReferenceAlleleStop(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setAlignmentStart(int) - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- setAlignmentStartHapwrtRef(int) - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- setAll(String...) - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Sets all the data-line values at once.
- setAlleleStart(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setAllowDuplicateReads(boolean) - Method in class picard.fingerprint.FingerprintChecker
-
Sets whether duplicate reads should be allowed when calling genotypes from SAM files.
- setAlreadyBuilt() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
- setAlt(Allele, X) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection
- setAlternateAllele(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setAndInitializeDebugOutputStream(OutputStreamWriter) - Method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
-
Attach a debugOuputStream to this HMM instance
- setAnnotationEngine(VariantAnnotatorEngine) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
-
Changes the annotation engine for this genotyping-engine.
- setAnnotationTranscript(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setAnnotationTranscript(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Transcript ID in the
GencodeFuncotation. - setApplyEamssFiltering(boolean) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Sets whether or not EAMSS filtering will be applied if parsing BCL files for bases and quality scores.
- setApprisRank(GencodeGtfFeature.FeatureTag) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setApprisRank(GencodeGtfFeature.FeatureTag) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Appris Rank in the
GencodeFuncotation. - setArgValues(CommandLineParser, String[], String) - Static method in class org.broadinstitute.hellbender.cmdline.ModeArgumentUtils
-
Set a group of arguments (and associated fields) to the specified values - thereby implementing a mode The method does not overwrite arguments already set on the command line (as indicated by the parser) Additionally, the method emits a warning message indicating which argument were set by the mode and to which values.
- setArtificialHaplotypeRecoveryMode(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- setAssayFormat(String) - Method in class picard.arrays.illumina.IlluminaManifest
- setAttribute(String, byte[]) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Set a byte array attribute on the read.
- setAttribute(String, byte[]) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setAttribute(String, Integer) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Set an integer-valued attribute on the read.
- setAttribute(String, Integer) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setAttribute(String, String) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Set a String-valued attribute on the read.
- setAttribute(String, String) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setAttributeMap(Map<Allele, T>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AlleleSpecificAnnotationData
- setAttributeMap(Map<Allele, T>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData
-
Assign all of the per-allele raw data at once
- setAttributesToReverse(Set<String>) - Method in class picard.sam.AbstractAlignmentMerger
-
Sets the set of attributes to be reversed on reads marked as negative strand.
- setAttributesToReverseComplement(Set<String>) - Method in class picard.sam.AbstractAlignmentMerger
-
Sets the set of attributes to be reverse complemented on reads marked as negative strand.
- setBaitSetName(String) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Sets the name of the bait set explicitly instead of inferring it from the bait file.
- setBaseQualities(byte[]) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Set the read's base qualities.
- setBaseQualities(byte[]) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setBaseQualityString(GATKRead, String) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Set the base qualities from a string of ASCII encoded values
- setBases(byte[]) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Set the read's sequence.
- setBases(byte[]) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setBases(byte[]) - Method in class picard.illumina.parser.ReadData
- setBigDuplicateSetSize(int) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
-
Sets the size of a set that is big enough to log progress about.
- setBufferSize(int) - Method in class org.broadinstitute.hellbender.utils.runtime.OutputStreamSettings
- setcDnaChange(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setcDnaChange(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the CDNA Change
Stringin theGencodeFuncotation. - setCds(GencodeGtfCDSFeature) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfExonFeature
- setChecksumAlgorithmAndExpectedChecksum(String, String) - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
-
Sets the
NioFileCopierWithProgressMeter.messageDigestand expected checksum to be used by thisNioFileCopierWithProgressMeterto validate the copied file. - setChromosome(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setChromosome(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Chromosome name in the
GencodeFuncotation. - setCigar(Cigar) - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
-
Set the cigar of this haplotype to cigar.
- setCigar(Cigar) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Set the read's Cigar using an existing
Cigarobject describing how the read aligns to the reference. - setCigar(Cigar) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setCigar(String) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Set the read's Cigar using a textual cigar String describing how the read aligns to the reference.
- setCigar(String) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setClipOverlappingReads(boolean) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
- setClipOverlappingReads(boolean) - Method in class picard.sam.AbstractAlignmentMerger
- setCodingSequenceAlleleStart(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setCodonChange(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setCodonChange(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Codon Change
Stringin theGencodeFuncotation. - setCollapsed(boolean) - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- setCollectorsToRun(List<CollectMultipleMetricsSpark.SparkCollectorProvider>) - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark
-
Use this method when invoking CollectMultipleMetricsSpark programmatically to run programs other than the ones available via enum.
- setColumn(int, String) - Method in class org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter.LineBuilder
- setColumn(String, String) - Method in class org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter.LineBuilder
- setCommand(String[]) - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- setContainsSuspectHaplotypes(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult
- setContig(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setContigOffset(LocalAssembler.Contig, int) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- setContigOffset(LocalAssembler.Contig, int) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyImpl
- setContigOffset(LocalAssembler.Contig, int) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacencyRC
- setConverter(BasecallsConverter.ClusterDataConverter<CLUSTER_OUTPUT_RECORD>) - Method in class picard.illumina.BasecallsConverter
-
Must be called before doTileProcessing.
- setCounter(long) - Method in class picard.analysis.AbstractWgsMetricsCollector
-
Sets the counter to the current number of processed loci.
- setCovariateIndex(int) - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.ReadCovariates
- setData(double, int, long, int, int, String, double, double) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MetricsCollection
- setData(List<VariantDatum>) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- setData(ClipReads.ClippingData) - Method in class org.broadinstitute.hellbender.tools.ClipReads.ReadClipperWithData
- setDataClass(HtsgetClass) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- setDataSourceName(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setDataSourceName(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Data Source Name
Stringin theGencodeFuncotation. - setDateManufactured(String) - Method in class picard.arrays.illumina.IlluminaManifest
- setDebug(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
- setDebug(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- setDebugGraphOutputPath(File) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
-
Set where to write debug graph files if
ReadThreadingAssembler.debugGraphTransformations== true - setDebugGraphTransformations(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- setDebugHistogramOutput(File) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- setDefaultHeaders(List<Header>) - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
-
Replaces the set of default metrics headers by the given argument.
- setDefaultHeaders(List<Header>) - Method in class picard.cmdline.CommandLineProgram
- setDefaultSampleID(String) - Method in class picard.fingerprint.FingerprintChecker
- setDeletionBaseQualities(GATKRead, byte[]) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
- setDepthOnlyParams(ClusteringParameters) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- setDescriptorFileName(String) - Method in class picard.arrays.illumina.IlluminaManifest
- setDirection(FlowBasedRead.Direction) - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- setDirectory(File) - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- setDiscoveredHaplotypes(Set<Haplotype>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult
- setDownsampler(ReadsDownsampler) - Method in class org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard
-
Reads in this shard will be downsampled using this downsampler before being returned.
- setDownsamplingInfo(LIBSDownsamplingInfo) - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentContextIteratorBuilder
- setDupe(boolean) - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- setEmitEmptyLoci(boolean) - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentContextIteratorBuilder
- setEmpiricalQuality(double) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- setEnabled(boolean) - Static method in class org.broadinstitute.hellbender.utils.logging.BunnyLog
-
Pass false to disable all logging via bunnylog (it's enabled by default).
- setEnd(int) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setEnd(int) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the end position (1-based, inclusive) in the
GencodeFuncotation. - setEnvironment(Map<String, String>) - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- setEstimatedQReported(double) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- setEventMap(EventMap) - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- setEventMapOut(File) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- setEvidenceParams(ClusteringParameters) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- setExon_frames(List<Integer>) - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
- setExonPosition(SimpleInterval) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setExons(List<SimpleInterval>) - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
- setFailsVendorQualityCheck(boolean) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Mark the read as failing platform/vendor quality checks
- setFailsVendorQualityCheck(boolean) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setFeatureCodecClass(Class<FeatureCodec<T, ?>>) - Method in class org.broadinstitute.hellbender.engine.FeatureInput
-
Remember the FeatureCodec class for this input the first time it is discovered so we can bypass dynamic codec discovery when multiple FeatureDataSources are created for the same input.
- setFeatureOrderNumber(int) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- setFieldSerializationOverrideValue(String, String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setFieldSerializationOverrideValue(String, String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
- setFieldSerializationOverrideValue(String, String) - Method in interface org.broadinstitute.hellbender.tools.funcotator.Funcotation
-
Override the given field with a given value for when it comes time to serialize and write this
Funcotation. - setFieldSerializationOverrideValues(Map<String, String>) - Method in interface org.broadinstitute.hellbender.tools.funcotator.Funcotation
-
Override fields with values as specified by the input map (for when it comes time to serialize and write this
Funcotation). - setFilteredGenotypesToNocall - Variable in class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
-
If this argument is provided, set filtered genotypes to no-call (./.).
- setFilteredGenotypeToNocall(VariantContextBuilder, VariantContext, boolean, BiFunction<VariantContext, Genotype, List<String>>) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Set the builder's filtered genotypes to no-call and update AC, AN and AF
- setFilteredHaplotypeCount(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
- setFinalized(boolean) - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
- setFlowOrder(List<String>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- setFormat(HtsgetFormat) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- setFormatTimeRemainingAsTimestamp() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
-
Sets the logger to log the time remaining in timestamp format ala 'DD:HH:MM:ss.SS'.
- setFormatTimeRemainingAsWords() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
-
Sets the logger to log the time remaining in word format ala 'D days, H hours, M minutes, s seconds'.
- setFounderIds(List<String>) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation
- setFragmentLength(int) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Set the observed length of the read's fragment (equivalent to TLEN in SAM).
- setFragmentLength(int) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setFullReferenceWithPadding(byte[]) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Sets the full reference with padding base sequence.
- setGcCacheSize(int) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
- setGcContent(Double) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setGcContent(Double) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the GC Content
Doublein theGencodeFuncotation. - setGcContent(Double) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setGene_name(String) - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
- setGeneTranscriptType(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setGeneTranscriptType(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the GeneTranscriptType in the
GencodeFuncotation. - setGenomeAssembly(String) - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
- setGenomeChange(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setGenomeChange(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Genome Change in the
GencodeFuncotation. - setGenomeLocation(Locatable) - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- setGenotypingErrorRate(double) - Method in class picard.fingerprint.FingerprintChecker
-
Sets the assumed genotyping error rate used when accurate error rates are not available.
- setGlobalNIODefaultOptions(int, String) - Static method in class org.broadinstitute.hellbender.utils.gcs.BucketUtils
-
Sets max_reopens, requester_pays, and generous timeouts as the global default.
- setGraphWriter(File) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- setHaplotypeCollapsingEngine(LongHomopolymerHaplotypeCollapsingEngine) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
- setHardClipOverlappingReads(boolean) - Method in class picard.sam.AbstractAlignmentMerger
- setHeader(SAMFileHeader) - Method in class org.broadinstitute.hellbender.engine.filters.flow.WellformedFlowBasedReadFilter
- setHeader(SAMFileHeader) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilter.ReadFilterBinOp
- setHeader(SAMFileHeader) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilter
- setHeader(SAMFileHeader) - Method in class org.broadinstitute.hellbender.engine.filters.ReadGroupBlackListReadFilter
- setHeader(SAMFileHeader) - Method in class org.broadinstitute.hellbender.engine.filters.WellformedReadFilter
- setHeader(SAMFileHeader) - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- setHeader(SAMFileHeader) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setHeader(VCFHeader) - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter
- setHeader(VCFHeader) - Method in class org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter
-
Defines header for the writer.
- setHeaderLine(List<String>) - Method in class org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter
-
Provides a header line to the XSV output file.
- setHgGenomeBuild(String) - Method in class picard.arrays.illumina.IlluminaManifestRecord
- sethInfo(VCFInfoHeaderLine) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.VAExpression
- setHugoSymbol(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setHugoSymbol(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Hugo Symbol / Gene Name in the
GencodeFuncotation. - setIdentifier(String) - Method in class picard.arrays.illumina.InfiniumDataFile
- setIgnoreExceptions(boolean) - Method in class org.broadinstitute.hellbender.utils.runtime.ScriptExecutor
-
Set to true to have the ScriptExecutor catch and ignore GATK exceptions.
- setIncludeDeletions(boolean) - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentContextIteratorBuilder
- setIncludeNs(boolean) - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentContextIteratorBuilder
- setIncludeSecondaryAlignments(boolean) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
- setIncludeSecondaryAlignments(boolean) - Method in class picard.sam.AbstractAlignmentMerger
- setInputBuffer(String) - Method in class org.broadinstitute.hellbender.utils.runtime.InputStreamSettings
- setInputFile(File) - Method in class org.broadinstitute.hellbender.utils.runtime.InputStreamSettings
- setInputStream(InputStream) - Method in class htsjdk.samtools.SAMRecordSparkCodec
-
Sets the input stream that records will be read from.
- setInputStream(InputStream) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- setInputStream(InputStream) - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- setInputStream(InputStream, String) - Method in class htsjdk.samtools.SAMRecordSparkCodec
-
Sets the input stream that records will be read from.
- setInsertionBaseQualities(GATKRead, byte[]) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
- setInterval(SimpleInterval) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- setIntervalsForTraversal(List<SimpleInterval>) - Method in class org.broadinstitute.hellbender.engine.FeatureDataSource
-
Restricts traversals of this data source via
FeatureDataSource.iterator()to only return Features that overlap the provided intervals. - setIntervalsForTraversal(List<SimpleInterval>) - Method in class org.broadinstitute.hellbender.engine.MultiVariantDataSource
-
Restricts traversals of this data source via
MultiVariantDataSource.iterator()to only return variants that overlap the provided intervals. - setIsActiveProb(double) - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState
-
Set the probability that this site is active.
- setIsCycleMember(boolean) - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- setIsCycleMember(boolean) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- setIsCycleMember(boolean) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- setIsDuplicate(boolean) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Mark the read as a PCR or optical duplicate.
- setIsDuplicate(boolean) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setIsFirstOfPair() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Mark the read as the first read of a pair.
- setIsFirstOfPair() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setIsPaired(boolean) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Mark the read as paired (having a mate) or not paired.
- setIsPaired(boolean) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setIsProperlyPaired(boolean) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Mark the read as properly paired (or not properly paired).
- setIsProperlyPaired(boolean) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setIsRef(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge
-
Indicate that this edge follows the reference sequence, or not
- setIsReverseStrand(boolean) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Mark the read as being on the reverse (or forward) strand.
- setIsReverseStrand(boolean) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setIsSecondaryAlignment(boolean) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Mark the read as a secondary alignment (an alternative to the primary alignment)
- setIsSecondaryAlignment(boolean) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setIsSecondOfPair() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Mark the read as the second read of a pair.
- setIsSecondOfPair() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setIsSupplementaryAlignment(boolean) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Mark the read as a supplementary alignment (used in the representation of a chimeric alignment)
- setIsSupplementaryAlignment(boolean) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setIsUnmapped() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Mark the read as unmapped (lacking a defined position on the genome).
- setIsUnmapped() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setIsUnplaced() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Mark the read as unmapped, and also removes mapping information from the read (i.e.
- setIsUnplaced() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setJunctionTreeEvidenceWeightThreshold(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
- setKeepAlignerProperPairFlags(boolean) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
-
If true, keep the aligner's idea of proper pairs rather than letting alignment merger decide.
- setKeepAlignerProperPairFlags(boolean) - Method in class picard.sam.AbstractAlignmentMerger
-
If true, keep the aligner's idea of proper pairs rather than letting alignment merger decide.
- setKingdomTaxonId(int) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- setKmerSize(int) - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- setLane(int) - Method in class picard.illumina.parser.ClusterData
- setLength(long) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- setLengthOf(int, long) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- setLibraryId(short) - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- setLibraryId(short) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
- setLibraryId(short) - Method in class picard.sam.markduplicates.util.ReadEnds
- setLibraryId(short) - Method in interface picard.sam.util.PhysicalLocation
- setLibraryId(short) - Method in class picard.sam.util.PhysicalLocationInt
- setLocationBinSize(int) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
-
defaults to 2500
- setLocationSet(PhysicalLocationForMateCigarSet) - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
- setLociCount(int) - Method in class picard.arrays.illumina.IlluminaManifest
- setLocusLevel(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setLocusLevel(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the LocusLevel
Integerin theGencodeFuncotation. - setLocusMaxReads(int) - Method in class picard.fingerprint.FingerprintChecker
- setLogger(Logger) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
-
Changes the logger for this genotyper engine.
- setLoggingLevel(Log.LogLevel) - Static method in class org.broadinstitute.hellbender.utils.LoggingUtils
-
Propagate the verbosity level to Picard, log4j, the java built in logger, and Kryo's MinLog
- setLogLikelihoods(double[]) - Method in class picard.fingerprint.CappedHaplotypeProbabilities
- setLongHomopolymer(int) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
-
defaults to 6
- setManifestFileParser(CsvInputParser) - Method in class picard.arrays.illumina.IlluminaManifest
- setMappingQuality(int) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Set the mapping quality of this alignment, representing how likely the read maps to this position as opposed to other locations.
- setMappingQuality(int) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setMarked(boolean) - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- setMarked(boolean) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- setMarked(boolean) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- setMatchedBarcode(String) - Method in class picard.illumina.parser.ClusterData
- setMateChanged() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.SplitRead
- setMateIsReverseStrand(boolean) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Mark the read's mate as being on the reverse (or forward) strand.
- setMateIsReverseStrand(boolean) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setMateIsUnmapped() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Mark the read's mate as unmapped (lacking a defined position on the genome).
- setMateIsUnmapped() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setMateIsUnplaced() - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Mark the read's mate as unmapped (lacking a defined position on the genome).
- setMateIsUnplaced() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setMatePosition(Locatable) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Set the position of the read's mate using the position of an existing
Locatable. - setMatePosition(Locatable) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setMatePosition(String, int) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Set the position of the read's mate (the contig and the start position).
- setMatePosition(String, int) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setMaxDuplicateSetSize(long) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
-
Sets the size of a set that is too big to process.
- setMaxPairErrorRate(double) - Method in class picard.util.AdapterMarker
- setMaxRecordsInRam(int) - Method in class picard.sam.AbstractAlignmentMerger
-
Allows the caller to override the maximum records in RAM.
- setMaxSingleEndErrorRate(double) - Method in class picard.util.AdapterMarker
- setMetadata(FuncotationMetadata) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setMinBaseQualityToUseInAssembly(byte) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- setMinDanglingBranchLength(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- setMinimalReadLength(int) - Static method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- setMinimumBaseQuality(int) - Method in class picard.fingerprint.FingerprintChecker
-
Sets the minimum base quality for bases used when computing a fingerprint from sequence data.
- setMinimumMappingQuality(int) - Method in class picard.fingerprint.FingerprintChecker
-
Sets the minimum mapping quality for reads used when computing fingerprints from sequence data.
- setMinimumSeriesLengthForNormalApproximation(int) - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU
-
Sets the minimum number of values in each data series to use the normal distribution approximation.
- setMinPairMatchBases(int) - Method in class picard.util.AdapterMarker
- setMinSingleEndMatchBases(int) - Method in class picard.util.AdapterMarker
- setMixedParams(ClusteringParameters) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
- setMultiplicity(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge
-
Set the multiplicity of this edge to value
- setName(String) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
- setName(String) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- setName(String) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.OptionalField
- setName(String) - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
- setName(String) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Set the name of the read (equivalent to QNAME in SAM), or set to
nullif the read has no name. - setName(String) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setNameOf(int, String) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- setNcbiBuild(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setNcbiBuild(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the NCBI build in the
GencodeFuncotation. - setNearProbeDistance(int) - Method in class picard.analysis.directed.TargetMetricsCollector
-
Sets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.
- SetNmAndUqTags - Class in picard.sam
-
Deprecated.
- SetNmAndUqTags() - Constructor for class picard.sam.SetNmAndUqTags
-
Deprecated.
- SetNmMdAndUqTags - Class in picard.sam
-
Fixes the NM, MD, and UQ tags in a SAM or BAM file.
- SetNmMdAndUqTags() - Constructor for class picard.sam.SetNmMdAndUqTags
- setNonRandomReplacementMode(boolean) - Method in class org.broadinstitute.hellbender.utils.downsampling.ReservoirDownsampler
- setNormalization(Map<String, Double>, Map<String, Double>) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- setNoSideEffects(boolean) - Method in class picard.analysis.directed.TargetMetricsCollector
-
In the case of ignoring bases in overlapping reads from the same template, we choose to internally modify the SAM record's CIGAR to clip overlapping bases.
- setNumAdaptersToKeep(int) - Method in class picard.util.AdapterMarker
-
After seeing the thresholdForSelectingAdapters number of adapters, keep up to this many of the original adapters.
- setNumAssays(int) - Method in class picard.arrays.illumina.IlluminaManifest
- setNumMismatches(double) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- setNumObservations(long) - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- setNumSamplesPerLogEntry(int) - Method in class org.broadinstitute.hellbender.utils.mcmc.GibbsSampler
-
Changes the number of samples per log entry.
- setOffset(int) - Method in class picard.arrays.illumina.InfiniumFileTOC
- setOffsetX(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setOffsetY(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setOrCheckLane(int) - Method in class picard.illumina.parser.ClusterData
-
Either set this value if not already set, or if already set, throw an exception if new value != current value.
- setOrCheckPf(boolean) - Method in class picard.illumina.parser.ClusterData
-
Either set this value if not already set, or if already set, throw an exception if new value != current value.
- setOrCheckTile(int) - Method in class picard.illumina.parser.ClusterData
-
Either set this value if not already set, or if already set, throw an exception if new value != current value.
- setOrCheckX(int) - Method in class picard.illumina.parser.ClusterData
-
Either set this value if not already set, or if already set, throw an exception if new value != current value.
- setOrCheckY(int) - Method in class picard.illumina.parser.ClusterData
-
Either set this value if not already set, or if already set, throw an exception if new value != current value.
- setOtherTranscripts(List<String>) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setOtherTranscripts(List<String>) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the list of other Transcript IDs in the
GencodeFuncotation. - setOutputFile(File) - Method in class org.broadinstitute.hellbender.utils.runtime.OutputStreamSettings
-
Overwrites the outputFile with the process output.
- setOutputFile(File, boolean) - Method in class org.broadinstitute.hellbender.utils.runtime.OutputStreamSettings
- setOutputStream(OutputStream) - Method in class htsjdk.samtools.SAMRecordSparkCodec
-
Sets the output stream that records will be written to.
- setOutputStream(OutputStream) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- setOutputStream(OutputStream) - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- setOutputStream(OutputStream, String) - Method in class htsjdk.samtools.SAMRecordSparkCodec
-
Sets the output stream that records will be written to.
- setOverallGCP(byte[]) - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- setOverrideValuesInFuncotations(List<Funcotation>) - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
Apply the override values in
DataSourceFuncotationFactory.annotationOverrideMapto everyFuncotationin the givenoutputFuncotations. - setOverwriteExisting(boolean) - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
-
Sets whether this
NioFileCopierWithProgressMeterwill overwriteNioFileCopierWithProgressMeter.destwhen copying. - setPaddedReferenceLoc(SimpleInterval) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Changes the padded reference location.
- setParent(int) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
- setParent(int) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- setPedigreeFile(GATKPath) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation
-
Setter for pedigree file and founderIDs to be used by the GATKAnnotationPluginDescriptor to handle duplicated annotation arguments between InbreedingCoeff and ExcessHet
- setPerBaseOutput(File) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Sets the (optional) File to write per-base coverage information to.
- setPerTargetOutput(File) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Sets the (optional) File to write per-target coverage information to.
- setPf(boolean) - Method in class picard.illumina.parser.ClusterData
- setpLossofHet(double) - Method in class picard.fingerprint.FingerprintChecker
- setPosition(Locatable) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Set the position of the read using the position of an existing
Locatable. - setPosition(Locatable) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setPosition(String, int) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Set the position of the read (the contig and the start position).
- setPosition(String, int) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setPositionInfo(AbstractIlluminaPositionFileReader.PositionInfo) - Method in class picard.illumina.parser.CbclData
- setPostReadFilterTransformer(ReadTransformer) - Method in class org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard
-
Reads in this shard will be transformed after filtering and before downsampling
- setPredictedMateInformation(GATKRead) - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager
-
Will edit the mate MC tag and mate start position field for given read if that read has been recorded being edited by the OverhangFixingManager before.
- setPreReadFilterTransformer(ReadTransformer) - Method in class org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard
-
Reads in this shard will be transformed before filtering
- setPrimaryAlignment(int) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
-
Set all alignments to not primary, except for the one specified by the argument.
- setPriorError(double) - Static method in class picard.sam.SamErrorMetric.ErrorMetric
- setProgramRecord(SAMProgramRecord) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
- setProgramRecord(SAMProgramRecord) - Method in class picard.sam.AbstractAlignmentMerger
- setProgramsToRun(Collection<CollectMultipleMetrics.ProgramInterface>) - Method in class picard.analysis.CollectMultipleMetrics
-
Use this method when invoking CollectMultipleMetrics programmatically to run programs other than the ones available via enum.
- setProteinChange(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setProteinChange(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Protein Change
Stringin theGencodeFuncotation. - setProteinChangeInfo(ProteinChangeInfo) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setQualities(byte[]) - Method in class picard.illumina.parser.ReadData
- setRank(String) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
- setRank(String) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- setRankOf(int, String) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- setRead(GATKRead) - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.SplitRead
- setReadDelQuals(byte[]) - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- setReadFilter(CountingReadFilter) - Method in class org.broadinstitute.hellbender.tools.walkers.variantrecalling.TrimmedReadsReader
- setReadFilter(ReadFilter) - Method in class org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard
-
Reads in this shard will be filtered using this filter before being returned.
- setReadGroup(short) - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- setReadGroup(short) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
- setReadGroup(short) - Method in class picard.sam.markduplicates.util.ReadEnds
- setReadGroup(short) - Method in interface picard.sam.util.PhysicalLocation
- setReadGroup(short) - Method in class picard.sam.util.PhysicalLocationInt
- setReadGroup(String) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
Set the ID of the read group this read belongs to, or
nullfor none. - setReadGroup(String) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- setReadInsQuals(byte[]) - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- setReadLength(int) - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- setReadsAsSupplemental(GATKRead, List<GATKRead>) - Static method in class org.broadinstitute.hellbender.utils.SATagBuilder
-
Sets a collection of GATKReads as supplemental reads of the primary read, This tool will set the isSupplemental attribute as well as the 'SA:' tag properly according to the Samspec (example: SA:rname,position,strand,Cigar,mapQ,NM;...) Note: this tool will not unset the primary read as supplemental, futhermore it will simply add to any existing SA tags on the given reads.
- setReadType(ReadType) - Method in class picard.illumina.parser.ReadData
- setRecordLabel(String) - Method in class org.broadinstitute.hellbender.engine.ProgressMeter
-
Change the label used for records in logger messages.
- setRecordsBetweenTimeChecks(long) - Method in class org.broadinstitute.hellbender.engine.ProgressMeter
-
Set the number of records we need to process before we check the current time
- setRecoverAllDanglingBranches(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- setRecoverDanglingBranches(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- setRedirectErrorStream(boolean) - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- setRef(Allele, X) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection
- setRefAllele(Allele) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Reference Allele in the
GencodeFuncotation. - setRefAllele(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setReferenceAllele(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setReferenceBases(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setReferenceContext(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
-
Set the reference context string.
- setReferenceContext(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Reference Context
Stringin theGencodeFuncotation. - setReferenceContext(ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine
- setReferenceFasta(File) - Method in class picard.fingerprint.FingerprintChecker
- setReferenceLength(long) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- setReferenceSequence(File) - Method in class picard.analysis.SinglePassSamProgram
-
Set the reference File.
- setReferenceWindow(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setRegionForGenotyping(AssemblyRegion) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Sets the region for genotyping.
- setRemovePathsNotConnectedToRef(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- setReserved1(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setReserved2(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setReserved3(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setReserved4(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setReserved5(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setReserved6(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setResultState(boolean) - Method in class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
- setRow(String[]) - Method in class org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter.LineBuilder
- setRow(List<String>) - Method in class org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter.LineBuilder
- setRsId(String) - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- setSampleContamination(Map<String, Double>) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection
-
Set the sample contamination map using the provided map.
- setSATag() - Method in class org.broadinstitute.hellbender.utils.SATagBuilder
-
Sets the stored SA tag information into the SA attribute field of the read encapsulated by the SATagBuilder
- setScaleX(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setScaleY(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setScore(double) - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
-
Set the score (an estimate of the support) of this haplotype.
- setSecondaryVariantClassification(GencodeFuncotation.VariantClassification) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setSecondaryVariantClassification(GencodeFuncotation.VariantClassification) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Secondary Variant Classification in the
GencodeFuncotation. - setSentinel(V) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Set the special sentinel value that will be used to signal novelty when putting a new interval into the tree, or to signal "not found" when removing an interval.
- setSeverity(int) - Method in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Set the
GencodeFuncotation.VariantClassification.relativeSeverityofthisGencodeFuncotation.VariantClassification. - setShear(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setSize - Variable in class picard.sam.util.RepresentativeReadIndexer
- setSize() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet
- SetSizeUtils - Class in org.broadinstitute.hellbender.utils.collections
-
Set size utility
- SetSizeUtils() - Constructor for class org.broadinstitute.hellbender.utils.collections.SetSizeUtils
- setSkipBlankLines(boolean) - Method in class picard.util.AbstractInputParser
- setSkipNLoci(int) - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- setSparkVerbosity(String) - Method in class org.broadinstitute.hellbender.engine.spark.SparkCommandLineArgumentCollection
- setSpecies(String) - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
- setStart(int) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setStart(int) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the start position (1-based, inclusive) in the
GencodeFuncotation. - setStart(GenomeLoc, int) - Static method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
create a new genome loc from an existing loc, with a new start position Note that this function will NOT explicitly check the ending offset, in case someone wants to set the start of a new GenomeLoc pertaining to a read that goes off the end of the contig.
- setStartCodon(GencodeGtfStartCodonFeature) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfExonFeature
- setStatePrior(double[], double, ArtifactState) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- setStop(GenomeLoc, int) - Static method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
create a new genome loc from an existing loc, with a new stop position Note that this function will NOT explicitly check the ending offset, in case someone wants to set the stop of a new GenomeLoc pertaining to a read that goes off the end of the contig.
- setStopCodon(GencodeGtfStopCodonFeature) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfExonFeature
- setStrand(int) - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
- setStrand(Strand) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Strand in the
GencodeFuncotation. - setStrand(Strand) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setSupportedFuncotationFields(Path) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.LocatableXsvFuncotationFactory
-
Set the field names that this
LocatableXsvFuncotationFactorycan create. - setTag(String) - Method in class org.broadinstitute.hellbender.engine.GATKPath
- setTagAttributes(Map<String, String>) - Method in class org.broadinstitute.hellbender.engine.GATKPath
- setTheta(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setThreadingStartOnlyAtExistingVertex(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Changes the threading start location policy.
- setThresholdForSelectingAdaptersToKeep(int) - Method in class picard.util.AdapterMarker
-
When this number of adapters have been matched, discard the least-frequently matching ones.
- setTile(int) - Method in class picard.illumina.parser.ClusterData
- setTile(short) - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- setTile(short) - Method in interface picard.sam.util.PhysicalLocation
- setTile(short) - Method in class picard.sam.util.PhysicalLocationInt
- setTileLimits(Integer, Integer) - Method in class picard.illumina.BasecallsConverter
-
Uses the firstTile and tileLimit parameters to set which tiles will be processed.
- setTiles(List<Integer>) - Method in class picard.illumina.parser.ParameterizedFileUtil
- setTilesForPerRunFile(List<Integer>) - Method in class picard.illumina.parser.ParameterizedFileUtil
- setTilesForPerRunFile(List<Integer>) - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
- setToMarkQueueMinimumDistance(int) - Method in class picard.sam.markduplicates.util.MarkQueue
-
Sets the minimum genomic distance such that we can be assured that all duplicates have been considered.
- setTranscript_coding_interval(SimpleInterval) - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
- setTranscript_id(String) - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
- setTranscript_interval(SimpleInterval) - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
- setTranscriptAlleleStart(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setTranscriptCodingSequence(ReferenceSequence) - Method in class org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- setTranscriptEndPos(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setTranscriptEndPos(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the end position (1-based, inclusive) relative to the start of the transcript of a the variant in the
GencodeFuncotation. - setTranscriptExonNumber(int) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the transcript exon number in the
GencodeFuncotation. - setTranscriptExonNumber(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setTranscriptLength(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setTranscriptLength(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Transcript Length
Integerin theGencodeFuncotation. - setTranscriptStartPos(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setTranscriptStartPos(Integer) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the start position (1-based, inclusive) relative to the start of the transcript of a the variant in the
GencodeFuncotation. - setTranscriptStrand(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setTransientAttribute(Object, Object) - Method in interface org.broadinstitute.hellbender.utils.read.GATKRead
-
This is used to access the transient attribute store in the underlying data type.
- setTransientAttribute(Object, Object) - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
-
This is used to access the transient attribute store in the underlying SAMRecord.
- setTraversalBounds(List<SimpleInterval>) - Method in interface org.broadinstitute.hellbender.engine.ReadsDataSource
-
Restricts a traversal of this data source via
Iterable.iterator()to only return reads which overlap the given intervals. - setTraversalBounds(List<SimpleInterval>, boolean) - Method in interface org.broadinstitute.hellbender.engine.ReadsDataSource
-
Restricts a traversal of this data source via
Iterable.iterator()to only return reads that overlap the given intervals, and to unmapped reads if specified. - setTraversalBounds(List<SimpleInterval>, boolean) - Method in class org.broadinstitute.hellbender.engine.ReadsPathDataSource
-
Restricts a traversal of this data source via
ReadsPathDataSource.iterator()to only return reads that overlap the given intervals, and to unmapped reads if specified. - setTraversalBounds(TraversalParameters) - Method in interface org.broadinstitute.hellbender.engine.ReadsDataSource
-
Restricts a traversal of this data source via
Iterable.iterator()to only return reads that overlap the given intervals, and to unmapped reads if specified. - setTreatGroupedDelimitersAsOne(boolean) - Method in class picard.util.AbstractInputParser
- setTumorSeqAllele2(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setTumorSeqAllele2(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the bases of tumorSeqAllele2 in the
GencodeFuncotation. - setUcscGenomeVersion(String) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- setUniquenessValue(int) - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- setup(SAMFileHeader, File) - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectAlignmentSummaryMetrics
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectBaseDistributionByCycle
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectGcBiasMetrics
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectInsertSizeMetrics
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectQualityYieldMetrics
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectRnaSeqMetrics
- setup(SAMFileHeader, File) - Method in class picard.analysis.MeanQualityByCycle
- setup(SAMFileHeader, File) - Method in class picard.analysis.QualityScoreDistribution
- setup(SAMFileHeader, File) - Method in class picard.analysis.SinglePassSamProgram
-
Should be implemented by subclasses to do one-time initialization work.
- setup(SAMFileHeader, File) - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
- setup(VCFHeader) - Method in class picard.vcf.CallingMetricAccumulator
- setup(VCFHeader) - Method in class picard.vcf.GvcfMetricAccumulator
- setup(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelCollector
-
Use an init method so that overloaded methods in subclasses can pass use parameters that are initialized in their constructor
- setup(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>) - Method in class org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector
-
Use an init method so that overloaded methods in subclasses can pass use parameters that are initialized in their constructor
- setup(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>) - Method in class picard.metrics.MultiLevelCollector
-
Use an init method so that overloaded methods in subclasses can pass use parameters that are initialized in their constructor
- setupConfigAndExtractProgram(String[], List<String>, List<Class<? extends CommandLineProgram>>, String) - Method in class org.broadinstitute.hellbender.Main
-
Set up the configuration file store and create the
CommandLineProgramto run. - setupOpticalDuplicateFinder() - Method in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- setupVCFWriter(Set<VCFHeaderLine>, boolean, DbsnpArgumentCollection, VariantContextWriter) - Method in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine
-
Create a VCF header in the writer
- setUri(String) - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
- setUseCompAFStratifier(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- setUseOriginalQualities(boolean) - Method in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
- setValidated(boolean) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
- setValidationStringency(ValidationStringency) - Method in class picard.fingerprint.FingerprintChecker
- setValue(Integer) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerAndInterval
- setValue(Integer) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval
- setValue(Integer) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.KmerAndCount
- setValue(T) - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.OptionalField
- setValue(V1) - Method in interface org.broadinstitute.hellbender.utils.SVIntervalTree.Entry
- setValuesFromAlignment(SAMRecord, SAMRecord) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
-
Sets the values from the alignment record on the unaligned BAM record.
- setValuesFromAlignment(SAMRecord, SAMRecord, boolean) - Method in class picard.sam.AbstractAlignmentMerger
-
Sets the values from the alignment record on the unaligned BAM record.
- setVariantCallingSubsetUsed(SimpleInterval) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
- setVariantClassification(GencodeFuncotation.VariantClassification) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setVariantClassification(GencodeFuncotation.VariantClassification) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Variant Classification in the
GencodeFuncotation. - setVariantClassificationCustomSeverity(GATKPath) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
-
Set the severity for
GencodeFuncotation.VariantClassifications as specified in a given input file. - setVariantType(GencodeFuncotation.VariantType) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setVariantType(GencodeFuncotation.VariantType) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Variant Type (1-based, inclusive) in the
GencodeFuncotation. - setVerbosity(NioFileCopierWithProgressMeter.Verbosity) - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
-
Sets the progress meter
NioFileCopierWithProgressMeter.verbosityof thisNioFileCopierWithProgressMeter. - setVersion(int) - Method in class picard.arrays.illumina.InfiniumTransformation
- setVersion(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
- setVersion(String) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
-
Set the Version
Stringin theGencodeFuncotation. - setWalkerType(String) - Method in class org.broadinstitute.hellbender.utils.help.GATKGSONWorkUnit
- setWasPoorlyRecovered(boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JTBestHaplotype
-
Add a flag of graph that based on this haplotype we think we should expand the kmer size
- setWindow(int, int) - Method in class org.broadinstitute.hellbender.engine.ReferenceContext
-
Set expanded window boundaries, subject to cropping at contig boundaries Allows the client to request a specific number of extra reference bases to include before and after the bases within our interval.
- setWordCount(int) - Method in class picard.util.AbstractInputParser
- setX(int) - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- setX(int) - Method in class picard.illumina.parser.ClusterData
- setX(int) - Method in interface picard.sam.util.PhysicalLocation
- setX(int) - Method in class picard.sam.util.PhysicalLocationInt
- setX(int) - Method in class picard.sam.util.PhysicalLocationShort
- setY(int) - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- setY(int) - Method in class picard.illumina.parser.ClusterData
- setY(int) - Method in interface picard.sam.util.PhysicalLocation
- setY(int) - Method in class picard.sam.util.PhysicalLocationInt
- setY(int) - Method in class picard.sam.util.PhysicalLocationShort
- Sex - Enum Class in org.broadinstitute.hellbender.utils.samples
-
ENUM of possible human sexes: male, female, or unknown
- Sex - Enum Class in picard.pedigree
-
Represents the sex of an individual.
- shard(JavaSparkContext, JavaRDD<L>, Class<L>, SAMSequenceDictionary, List<SB>, int) - Static method in class org.broadinstitute.hellbender.engine.spark.SparkSharder
-
Create an RDD of
Shardfrom an RDD of coordinate sortedLocatablewithout using a shuffle. - shard(JavaSparkContext, JavaRDD<L>, Class<L>, SAMSequenceDictionary, List<SB>, int, boolean) - Static method in class org.broadinstitute.hellbender.engine.spark.SparkSharder
-
Create an RDD of
Shardfrom an RDD of coordinate sortedLocatable, optionally using a shuffle. - shard(JavaSparkContext, JavaRDD<L>, Class<L>, SAMSequenceDictionary, JavaRDD<SB>, int) - Static method in class org.broadinstitute.hellbender.engine.spark.SparkSharder
-
Create an RDD of
Shardfrom an RDD of coordinate sortedLocatablewithout using a shuffle, and where the intervals for shards are specified as an RDD, rather than a list. - Shard<T> - Interface in org.broadinstitute.hellbender.engine
-
A Shard of records of type T covering a specific genomic interval, optionally expanded by a configurable amount of padded data, that provides the ability to iterate over its records.
- SHARD_INDEX_PREFIX - Static variable in class org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter
- SHARD_INDEX_SUFFIX - Static variable in class org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter
- SHARD_MAX_OUTPUT_COUNT - Static variable in class org.broadinstitute.hellbender.tools.SplitCRAM
- SHARD_RECORDS_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.SplitCRAM
- SHARD_SIZE_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- ShardBoundary - Class in org.broadinstitute.hellbender.engine
-
Holds the bounds of a
Shard, both with and without padding - ShardBoundary(SimpleInterval, SimpleInterval) - Constructor for class org.broadinstitute.hellbender.engine.ShardBoundary
-
Create a new ShardBoundary from the given intervals
- ShardBoundary(SimpleInterval, SimpleInterval, boolean) - Constructor for class org.broadinstitute.hellbender.engine.ShardBoundary
- ShardBoundaryShard<T> - Class in org.broadinstitute.hellbender.engine
-
A
Shardbacked by aShardBoundaryand a collection of records. - ShardBoundaryShard(ShardBoundary, Iterable<T>) - Constructor for class org.broadinstitute.hellbender.engine.ShardBoundaryShard
-
Create a new
ShardBoundaryShardfrom the givenShardBoundaryand records. - SHARDED - Enum constant in enum class org.broadinstitute.hellbender.utils.read.ReadsWriteFormat
-
Write reads to a sharded set of BAM files
- SHARDED_OUTPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- ShardedIntervalIterator - Class in org.broadinstitute.hellbender.utils.iterators
-
Iterator that will break up each input interval into shards.
- ShardedIntervalIterator(Iterator<SimpleInterval>, int) - Constructor for class org.broadinstitute.hellbender.utils.iterators.ShardedIntervalIterator
- shardedOutput - Variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- shardedPartsDir - Variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- shardIndex(int, int) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
number of the shard this offset is in.
- shardingArgs - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark
- shardingArgs - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- ShardingVCFWriter - Class in org.broadinstitute.hellbender.utils.variant.writers
-
Variant writer tha splits output to multiple VCFs given the maximum records per file.
- ShardingVCFWriter(Path, int, SAMSequenceDictionary, boolean, Options...) - Constructor for class org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter
-
Create a new sharding VCF writer
- ShardToMultiIntervalShardAdapter<T> - Class in org.broadinstitute.hellbender.engine
-
adapts a normal Shard into a MultiIntervalShard that contains only the single wrapped shard this is a temporary shim until we can fully adopt MultiIntervalShard in HaplotypeCallerSpark
- ShardToMultiIntervalShardAdapter(Shard<T>) - Constructor for class org.broadinstitute.hellbender.engine.ShardToMultiIntervalShardAdapter
- SHARED_POSIXFS_OPTIMIZATIONS - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection
- SHARED_POSIXFS_OPTIMIZATIONS - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- sharedPosixFSOptimizations - Variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection
- sharedPosixFSOptimizations() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBOptions
- SharedSequenceMerger - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
-
Merges the incoming vertices of a vertex V of a graph Looks at the vertices that are incoming to V (i.e., have an outgoing edge connecting to V).
- SharedVertexSequenceSplitter - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
-
Split a collection of middle nodes in a graph into their shared prefix and suffix values This code performs the following transformation.
- SharedVertexSequenceSplitter(SeqGraph, Collection<SeqVertex>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SharedVertexSequenceSplitter
-
Create a utility that will change the given graph so that the vertices in toSplitsArg (with their shared suffix and prefix sequences) are extracted out.
- shift(int) - Method in class org.broadinstitute.hellbender.utils.IndexRange
- SHIFT_BACK_OUTPUT - Static variable in class org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta
- SHIFT_OFFSET_LIST - Static variable in class org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta
- shiftBackOutput - Variable in class org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta
- shiftContig(SAMSequenceRecord, ListIterator<Integer>) - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta
-
This method adds to a new fasta ref file that has been shifted by the amount indicated in the shiftOffsetsIt.
- shiftedLogEvidenceProbability() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns log (p(evidence)) + c assuming that the prior on haplotypes is given by the internal haplotypeFrequencies
- shiftedLogEvidenceProbabilityGivenOtherEvidence(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilities
-
returns the log-probability the evidence, using as priors the posteriors of another object
- shiftedLogEvidenceProbabilityUsingGenotypeFrequencies(double[]) - Method in class picard.fingerprint.HaplotypeProbabilities
- shiftEnd(int) - Method in class org.broadinstitute.hellbender.utils.IndexRange
- shiftEndLeft(int) - Method in class org.broadinstitute.hellbender.utils.IndexRange
- ShiftFasta - Class in org.broadinstitute.hellbender.tools.walkers.fasta
-
Create a fasta with the bases shifted by offset delta1 = offset - 1 delta2 = total - delta1 To shift forward: if you are given a position in the regular fasta (pos_r) and want the position in the shifted fasta (pos_s): if pos_r > delta1 => pos_s = pos_r - delta1 == pos_r - offset +1 otherwise pos_s = pos_r + delta2 == pos_r + total - offset + 1 To shift back: if you are given a position in the shifted fasta (pos_s) and want the position in the regular fasta (pos_r): if pos_s > delta2 => pos_r = pos_s - delta2 == pos_s - total + offset - 1 otherwise pos_r = pos_s + delta1 == pos_s + offset - 1 Example command line: ShiftFasta -R "<CIRCURLAR_REFERENCE.fasta>" // the reference to shift -O "<SHIFTED_REFERENCE.fasta>" // output; the shifted fasta --shift-back-output "<SHIFT_BACK.chain>" // output; the shiftback chain file to use when lifting over --shift-offset-list "
" // optional; Specifies the offset to shift for each contig in the reference. - ShiftFasta() - Constructor for class org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta
- shiftLeft(int) - Method in class org.broadinstitute.hellbender.utils.IndexRange
- shiftStart(int) - Method in class org.broadinstitute.hellbender.utils.IndexRange
- shiftStartLeft(int) - Method in class org.broadinstitute.hellbender.utils.IndexRange
- SHORT_HOMOPOLYMER - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
- shortToByteArray(short) - Static method in class picard.arrays.illumina.InfiniumDataFile
-
Utility method to convert a short to a byte array
- ShortVariantDiscoveryProgramGroup - Class in org.broadinstitute.hellbender.cmdline.programgroups
-
Tools that perform variant calling and genotyping for short variants (SNPs, SNVs and Indels)
- ShortVariantDiscoveryProgramGroup() - Constructor for class org.broadinstitute.hellbender.cmdline.programgroups.ShortVariantDiscoveryProgramGroup
- shouldBeCalled(Genotype) - Static method in class org.broadinstitute.hellbender.utils.GenotypeUtils
- shouldBeInLocations(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.MarkQueue
-
Returns true if we should track this for optical duplicate detection, false otherwise
- shouldExitEarly(GATKRead) - Method in class org.broadinstitute.hellbender.engine.PartialReadWalker
-
Method to be overridden by the implementation class to determine when to stop the read stream traversal
- shouldExitEarly(GATKRead) - Method in class org.broadinstitute.hellbender.tools.examples.ExamplePartialReadWalker
- shouldExitEarly(GATKRead) - Method in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- shouldIncludeInterval(long, double, long) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
- shouldIncludeInterval(long, double, long) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivisionWithOverflow
- ShouldNeverReachHereException(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.GATKException.ShouldNeverReachHereException
- ShouldNeverReachHereException(String, Throwable) - Constructor for exception org.broadinstitute.hellbender.exceptions.GATKException.ShouldNeverReachHereException
- ShouldNeverReachHereException(Throwable) - Constructor for exception org.broadinstitute.hellbender.exceptions.GATKException.ShouldNeverReachHereException
- shouldRemoveReadsAfterGraphConstruction() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
- shouldRemoveReadsAfterGraphConstruction() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
- shouldRemoveReadsAfterGraphConstruction() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
- shouldTrackPileupsForAssemblyRegions() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionWalker
-
Allows implementing tools to decide whether pileups must be tracked and attached to assembly regions for later processing.
- shouldTrackPileupsForAssemblyRegions() - Method in class org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalker
- shouldTrackPileupsForAssemblyRegions() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
- shouldTrackPileupsForAssemblyRegions() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- showVerbose - Variable in class org.broadinstitute.hellbender.tools.spark.PileupSpark
-
In addition to the standard pileup output, adds 'verbose' output too.
- showVerbose - Variable in class org.broadinstitute.hellbender.tools.walkers.qc.Pileup
-
In addition to the standard pileup output, adds 'verbose' output too.
- shuffle - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark
- shuffle - Variable in class org.broadinstitute.hellbender.engine.spark.IntervalWalkerSpark
- shuffle - Variable in class org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark
- shuffle - Variable in class org.broadinstitute.hellbender.engine.spark.VariantWalkerSpark
- shutdown() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
-
Shutdown this HC engine, closing resources as appropriate
- shutdown() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerEngine
-
Shutdown this HC engine, closing resources as appropriate
- signalEndOfInput() - Method in class org.broadinstitute.hellbender.utils.downsampling.Downsampler
-
Used to tell the downsampler that no more items will be submitted to it, and that it should finalize any pending items.
- signalEndOfInput() - Method in class org.broadinstitute.hellbender.utils.downsampling.FractionalDownsampler
- signalEndOfInput() - Method in class org.broadinstitute.hellbender.utils.downsampling.LevelingDownsampler
- signalEndOfInput() - Method in class org.broadinstitute.hellbender.utils.downsampling.MutectDownsampler
- signalEndOfInput() - Method in class org.broadinstitute.hellbender.utils.downsampling.PassThroughDownsampler
- signalEndOfInput() - Method in class org.broadinstitute.hellbender.utils.downsampling.PositionalDownsampler
- signalEndOfInput() - Method in class org.broadinstitute.hellbender.utils.downsampling.ReservoirDownsampler
- signalEndOfInput() - Method in interface org.broadinstitute.hellbender.utils.iterators.PushPullTransformer
-
Used to tell the transformer that no more items will be submitted to it, and that it should finalize any pending items.
- signalEndOfInput() - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlockCombiner
- signalEndOfInput() - Method in class org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFBlockCombiner
- signalNoMoreReadsBefore(GATKRead) - Method in class org.broadinstitute.hellbender.utils.downsampling.FractionalDownsampler
- signalNoMoreReadsBefore(GATKRead) - Method in class org.broadinstitute.hellbender.utils.downsampling.MutectDownsampler
- signalNoMoreReadsBefore(GATKRead) - Method in class org.broadinstitute.hellbender.utils.downsampling.PassThroughDownsampler
- signalNoMoreReadsBefore(GATKRead) - Method in class org.broadinstitute.hellbender.utils.downsampling.PositionalDownsampler
- signalNoMoreReadsBefore(GATKRead) - Method in class org.broadinstitute.hellbender.utils.downsampling.ReadsDownsampler
-
Tell this downsampler that no more reads located before the provided read (according to the sort order of the read stream) will be fed to it.
- signalNoMoreReadsBefore(GATKRead) - Method in class org.broadinstitute.hellbender.utils.downsampling.ReservoirDownsampler
- silent - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.FunctionalClass.FunctionalType
- SILENT - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Variant is in coding region of the chosen transcript, but protein structure is identical (i.e.
- SILENT - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectFunctionalClass
- SILENT - Enum constant in enum class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter.Verbosity
-
Output no logging messages whatsoever.
- SILENT - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.PedigreeValidationType
-
Do not enforce any overlap between the VCF/BAM samples and the pedigree data
- Simple - Enum constant in enum class picard.util.BaitDesigner.DesignStrategy
-
Ultra simple bait design algorithm that just lays down baits starting at the target start position until either the bait start runs off the end of the target or the bait would run off the sequence
- SIMPLE_CHIMERA - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments.AlignmentSignatureBasicType
- SIMPLE_CHIMERA_VCF_FILE_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark
- SIMPLE_COUNT_CODEC_EXTENSIONS - Static variable in class org.broadinstitute.hellbender.utils.codecs.copynumber.SimpleCountCodec
- SIMPLE_DEL - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera
- SIMPLE_INS - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera
- SIMPLE_XSV - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.DataSourceType
-
This value indicates a simple arbitrary separated value (XSV) file that can be annotated on records via matching by gene name or transcript ID.
- SimpleAnnotatedIntervalWriter - Class in org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
- SimpleAnnotatedIntervalWriter(File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.SimpleAnnotatedIntervalWriter
-
Initialize this writer to the given output file.
- simpleBaseToBaseIndex(byte) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
-
Converts a simple base to a base index
- SimpleChimera - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
Conceptually, a simple chimera represents the junction on
AssemblyContigWithFineTunedAlignmentsthat have exactly two good alignments. - SimpleChimera(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera
- SimpleChimera(String, AlignmentInterval, AlignmentInterval, StrandSwitch, boolean, List<String>, String) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera
- SimpleChimera(AlignmentInterval, AlignmentInterval, List<String>, String, String, SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera
-
Construct a new SimpleChimera from two alignment intervals.
- SimpleChimera.DistancesBetweenAlignmentsOnRefAndOnRead - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
Struct to represent the (distance - 1) between boundaries of the two alignments represented by this CA, on reference, and on read.
- SimpleChimera.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- simpleChimeraWithStichableAlignments(AlignmentInterval, AlignmentInterval) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
-
See the funny alignment signature described in ticket 4951 on GATK github
- simpleComplement(byte) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
-
Return the complement (A <-> T or C <-> G) of a base, or the specified base if it can't be complemented (i.e.
- SimpleCopyRatioCaller - Class in org.broadinstitute.hellbender.tools.copynumber.caller
-
This caller is loosely based on the legacy ReCapSeg caller that was originally implemented in ReCapSeg v1.4.5.0, but introduces major changes.
- SimpleCopyRatioCaller(CopyRatioSegmentCollection, double, double, double, double) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.caller.SimpleCopyRatioCaller
- SimpleCount - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records
-
Represents a count at an interval.
- SimpleCount(SimpleInterval, int) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount
- SimpleCountCodec - Class in org.broadinstitute.hellbender.utils.codecs.copynumber
- SimpleCountCodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.copynumber.SimpleCountCodec
- SimpleCountCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
Simple data structure to pass and read/write a List of
SimpleCountobjects. - SimpleCountCollection(SampleLocatableMetadata, List<SimpleCount>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection
- SimpleCountCollection.SimpleCountTableColumn - Enum Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
CONTIG, START, END, COUNT Note: Unlike the package-private enums in other collection classes, this enum and its
TableColumnCollectionare public so that they can be accessed bySimpleCountCodec, which must be in org.broadinstitute.hellbender.utils.codecs to be discovered as a codec. - SimpleErrorCalculator - Class in picard.sam.SamErrorMetric
-
A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.
- SimpleErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.SimpleErrorCalculator
- SimpleGermlineTagger - Class in org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging
-
This utility class performs a simple tagging of germline segments in a tumor segments file.
- SimpleInsDelOrReplacementBreakpointComplications(String, String) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications
- SimpleInterval - Class in org.broadinstitute.hellbender.utils
-
Minimal immutable class representing a 1-based closed ended genomic interval SimpleInterval does not allow null contig names.
- SimpleInterval(Locatable) - Constructor for class org.broadinstitute.hellbender.utils.SimpleInterval
-
Create a new SimpleInterval from a
Locatable - SimpleInterval(String) - Constructor for class org.broadinstitute.hellbender.utils.SimpleInterval
-
Makes an interval by parsing the string.
- SimpleInterval(String, int, int) - Constructor for class org.broadinstitute.hellbender.utils.SimpleInterval
-
Create a new immutable 1-based interval of the form [start, end]
- SimpleIntervalCollection - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
-
Represents a collection of
SimpleInterval. - SimpleIntervalCollection(File) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleIntervalCollection
- SimpleIntervalCollection(LocatableMetadata, List<SimpleInterval>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleIntervalCollection
- SimpleKeyXsvFuncotationFactory - Class in org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv
-
Factory for creating
TableFuncotations by handling `Separated Value` files with arbitrary delimiters (e.g. - SimpleKeyXsvFuncotationFactory(String, Path, String, String, int, SimpleKeyXsvFuncotationFactory.XsvDataKeyType) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory
- SimpleKeyXsvFuncotationFactory(String, Path, String, String, int, SimpleKeyXsvFuncotationFactory.XsvDataKeyType, LinkedHashMap<String, String>) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory
- SimpleKeyXsvFuncotationFactory(String, Path, String, String, int, SimpleKeyXsvFuncotationFactory.XsvDataKeyType, LinkedHashMap<String, String>, int) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory
- SimpleKeyXsvFuncotationFactory(String, Path, String, String, int, SimpleKeyXsvFuncotationFactory.XsvDataKeyType, LinkedHashMap<String, String>, int, boolean) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory
- SimpleKeyXsvFuncotationFactory(String, Path, String, String, int, SimpleKeyXsvFuncotationFactory.XsvDataKeyType, LinkedHashMap<String, String>, int, boolean, boolean) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory
- SimpleKeyXsvFuncotationFactory(String, Path, String, String, int, SimpleKeyXsvFuncotationFactory.XsvDataKeyType, LinkedHashMap<String, String>, int, boolean, boolean, int) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory
- SimpleKeyXsvFuncotationFactory.XsvDataKeyType - Enum Class in org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv
- SimpleLocatableMetadata - Class in org.broadinstitute.hellbender.tools.copynumber.formats.metadata
-
Metadata associated with a collection of locatables.
- SimpleLocatableMetadata(SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleLocatableMetadata
- SimpleLocatableMetadata(LocatableMetadata) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleLocatableMetadata
- SimpleMarkDuplicatesWithMateCigar - Class in picard.sam.markduplicates
-
This is a simple tool to mark duplicates using the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator.
- SimpleMarkDuplicatesWithMateCigar() - Constructor for class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
- simpleMerge(Collection<VariantContext>, List<String>, int, GATKVariantContextUtils.FilteredRecordMergeType, GATKVariantContextUtils.GenotypeMergeType, boolean) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Merges VariantContexts into a single hybrid.
- simpleMerge(Collection<VariantContext>, List<String>, GATKVariantContextUtils.FilteredRecordMergeType, GATKVariantContextUtils.GenotypeMergeType, boolean) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Merges VariantContexts into a single hybrid.
- SimpleNovelAdjacencyAndChimericAlignmentEvidence - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
Simply a wrapper to link together
NovelAdjacencyAndAltHaplotypeand evidenceSimpleChimera's. - SimpleNovelAdjacencyAndChimericAlignmentEvidence(NovelAdjacencyAndAltHaplotype, Iterable<SimpleChimera>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence
- SimpleNovelAdjacencyAndChimericAlignmentEvidence.ChimericContigAlignmentEvidenceAnnotations - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
Utility structs for extraction information from the consensus NovelAdjacencyAndAltHaplotype out of multiple ChimericAlignments, to be later added to annotations of the VariantContext extracted.
- SimpleNovelAdjacencyAndChimericAlignmentEvidence.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- SimpleNovelAdjacencyInterpreter - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
-
This deals with the special case where a contig has exactly two alignments and seemingly has the complete alt haplotype assembled.
- SimpleNovelAdjacencyInterpreter() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyInterpreter
- SimplePosteriorSummary(double, double, double) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment.SimplePosteriorSummary
- SimplePosteriorSummary(List<Double>) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment.SimplePosteriorSummary
- SimpleRepeatMaskTransformer - Class in org.broadinstitute.hellbender.transformers
-
Masks read bases with a supra-threshold number of A/T's or G/C's within a given window size.
- SimpleRepeatMaskTransformer(int, int, int) - Constructor for class org.broadinstitute.hellbender.transformers.SimpleRepeatMaskTransformer
- simpleReverseComplement(byte[]) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
-
Reverse complement a byte array of bases (that is, chars casted to bytes, *not* base indices in byte form)
- SimpleSampleLocatableMetadata - Class in org.broadinstitute.hellbender.tools.copynumber.formats.metadata
-
Metadata associated with a collection of locatables associated with a single sample.
- SimpleSampleLocatableMetadata(String, SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleLocatableMetadata
- SimpleSampleMetadata - Class in org.broadinstitute.hellbender.tools.copynumber.formats.metadata
-
Metadata associated with a single sample.
- SimpleSampleMetadata(String) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleMetadata
- SimpleSVD - Class in org.broadinstitute.hellbender.utils.svd
-
Simple implementation of the SVD interface for storing the matrices (and vector) of a SVD result.
- SimpleSVD(RealMatrix, double[], RealMatrix, RealMatrix) - Constructor for class org.broadinstitute.hellbender.utils.svd.SimpleSVD
- SimpleSVType - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- SimpleSVType(String, int, int, String, Allele, Allele, int, Map<String, Object>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType
- SimpleSVType.Deletion - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- SimpleSVType.DuplicationInverted - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- SimpleSVType.DuplicationTandem - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- SimpleSVType.ImpreciseDeletion - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- SimpleSVType.Insertion - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- SimpleSVType.Inversion - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- SimpleSVType.SupportedType - Enum Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- SimpleTsvOutputRenderer - Class in org.broadinstitute.hellbender.tools.funcotator.simpletsvoutput
-
This class is very versatile, but as a result, it must do some lazy loading after it receives the first write command.
- SIMPLEX_CONSENSUS - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
-
Read which had multiple observations, but all from the same strand (or the strand could not be determined).
- SIMPLEX_SINGLETON - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
-
Read which only one observation is made.
- SimpleXSVWriter - Class in org.broadinstitute.hellbender.utils.tsv
-
A simple TSV/CSV/XSV writer with support for writing in the cloud with configurable delimiter.
- SimpleXSVWriter(Writer, char) - Constructor for class org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter
-
Creates a new table writer given an initialized writer and column names.
- SimpleXSVWriter(Path, char) - Constructor for class org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter
-
Creates a new table writer given the file and column names.
- SimpleXSVWriter.LineBuilder - Class in org.broadinstitute.hellbender.utils.tsv
-
Helper to allow for incremental construction of a body line using either indexes or column headings
- simplifiedAssignGenotypeLikelihood(List<Haplotype>, AlleleLikelihoods<GATKRead, Haplotype>, byte[], SimpleInterval, SimpleInterval) - Method in class org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeBasedVariantRecaller
- simplifyGraph() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqGraph
-
Simplify this graph, merging vertices together and restructuring the graph in an effort to minimize the number of overall vertices in the graph without changing in any way the sequences implied by a complex enumeration of all paths through the graph.
- SINGLE - Enum constant in enum class org.broadinstitute.hellbender.utils.read.ReadsWriteFormat
-
Write reads to a single BAM file
- SINGLE_END - Enum constant in enum class org.broadinstitute.hellbender.utils.illumina.IlluminaAdapterPair
- SINGLE_END - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- SINGLE_END_ALIGNMENT_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.bwa.BwaArgumentCollection
- SINGLE_END_ALIGNMENT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.bwa.BwaArgumentCollection
- SINGLE_END_READS_CLIPPING_IS_END_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- SINGLE_END_READS_END_POSITION_SIGNIFICANT - Static variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- SINGLE_EST_SUPPORT - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.TranscriptSupportLevel
-
the only support is from a single EST
- SINGLE_LINKAGE - Enum constant in enum class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine.CLUSTERING_TYPE
- SINGLE_SAMPLE - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.ModelSegments.RunMode
- SingleBarcodeDistanceMetric - Class in picard.util
-
A class for finding the distance between a single barcode and a barcode-read (with base qualities)
- SingleBarcodeDistanceMetric(byte[], byte[], byte[], int, int) - Constructor for class picard.util.SingleBarcodeDistanceMetric
- singleEndAlignment - Variable in class org.broadinstitute.hellbender.tools.spark.bwa.BwaArgumentCollection
-
Run single-end instead of paired-end alignment.
- SingleFileLocationTranslator - Class in org.broadinstitute.hellbender.tools.walkers.groundtruth
- singleNewtonArgmaxUpdate(Function<Double, Double>, double, double, double) - Static method in class org.broadinstitute.hellbender.utils.OptimizationUtils
- singleNewtonArgmaxUpdate(Function<Double, Double>, double, double, double, double, double) - Static method in class org.broadinstitute.hellbender.utils.OptimizationUtils
-
One iteration of Newton's method for univariate optimization (i.e.
- SinglePassSamProgram - Class in picard.analysis
-
Super class that is designed to provide some consistent structure between subclasses that simply iterate once over a coordinate sorted BAM and collect information from the records as the go in order to produce some kind of output.
- SinglePassSamProgram() - Constructor for class picard.analysis.SinglePassSamProgram
- SingleSequenceReferenceAligner<T,
U> - Class in org.broadinstitute.hellbender.tools.spark.sv.utils -
Encompasses an aligner to a single-sequence reference.
- SingleSequenceReferenceAligner(String, byte[], Function<? super T, List<byte[]>>, SingleSequenceReferenceAligner.TriFunction<? super T, List<List<BwaMemAlignment>>, List<String>, ? extends U>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SingleSequenceReferenceAligner
- SingleSequenceReferenceAligner(String, byte[], Function<? super T, List<byte[]>>, SingleSequenceReferenceAligner.TriFunction<? super T, List<List<BwaMemAlignment>>, List<String>, ? extends U>, Predicate<? super BwaMemAlignment>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SingleSequenceReferenceAligner
- SingleSequenceReferenceAligner.TriFunction<T,
U, V, W> - Interface in org.broadinstitute.hellbender.tools.spark.sv.utils - singletonIterator(T) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
- singletonSampleList(String) - Static method in interface org.broadinstitute.hellbender.utils.genotyper.SampleList
-
Creates a list with a single sample.
- SingularValueDecomposer - Interface in org.broadinstitute.hellbender.utils.svd
-
Perform singular value decomposition (and pseudoinverse calculation).
- SITE_DEPTH_INPUT_ARGUMENT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- SITE_DEPTH_INPUT_ARGUMENT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- SITE_DEPTH_OUTPUT_ARGUMENT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- SITE_DEPTH_OUTPUT_ARGUMENT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- SITE_FREQUENCY_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- SITE_LEVEL_FILTERS - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- SiteDepth - Class in org.broadinstitute.hellbender.tools.sv
-
The read depth of each base call for a sample at some locus.
- SiteDepth(Locatable, String) - Constructor for class org.broadinstitute.hellbender.tools.sv.SiteDepth
- SiteDepth(String, int, String, int, int, int, int) - Constructor for class org.broadinstitute.hellbender.tools.sv.SiteDepth
- SiteDepthBCICodec - Class in org.broadinstitute.hellbender.utils.codecs
-
Codec to handle SiteDepths in BlockCompressedInterval files
- SiteDepthBCICodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.SiteDepthBCICodec
- SiteDepthCodec - Class in org.broadinstitute.hellbender.utils.codecs
-
Codec to handle SiteDepths in tab-delimited text files
- SiteDepthCodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.SiteDepthCodec
- siteDepthInputFilename - Variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- siteDepthOutputFilename - Variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- SiteDepthSortMerger - Class in org.broadinstitute.hellbender.tools.sv
-
Imposes additional ordering of same-locus SiteDepth records by sample.
- SiteDepthSortMerger(SAMSequenceDictionary, FeatureSink<SiteDepth>) - Constructor for class org.broadinstitute.hellbender.tools.sv.SiteDepthSortMerger
- SiteDepthtoBAF - Class in org.broadinstitute.hellbender.tools.sv
-
Merges locus-sorted SiteDepth evidence files, and calculates the bi-allelic frequency (baf) for each sample and site, and writes these values as a BafEvidence output file.
- SiteDepthtoBAF() - Constructor for class org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAF
- siteOverlapsBuffer(VariantContext) - Method in class org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFWriter
- SITES_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- SITES_FILE_NAME - Static variable in class org.broadinstitute.hellbender.utils.dragstr.STRTableFile
- SITES_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- SITES_INDEX_FILE_NAME - Static variable in class org.broadinstitute.hellbender.utils.dragstr.STRTableFile
- SITES_ONLY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- SITES_TEXT_FILE_NAME - Static variable in class org.broadinstitute.hellbender.utils.dragstr.STRTableFile
- SIXTY_FOUR_MIB - Static variable in class org.broadinstitute.hellbender.tools.spark.ParallelCopyGCSDirectoryIntoHDFSSpark
- size() - Method in class org.broadinstitute.hellbender.engine.AlignmentContext
-
How many reads cover this locus?
- size() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Get the number of reads currently in this region
- size() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractRecordCollection
- size() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection
- size() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCases
- size() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
- size() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- size() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- size() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigListRC
- size() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- size() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree
- size() - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.CDF
- size() - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet
- size() - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet
- size() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
-
How many states are held in this stratification manager?
- size() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- size() - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
-
How many profile results are in this profile?
- size() - Method in class org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature
-
Return the number of observed bases over the genomic location
- size() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
- size() - Method in class org.broadinstitute.hellbender.utils.collections.AutoCloseableCollection
- size() - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
- size() - Method in class org.broadinstitute.hellbender.utils.collections.IndexedSet
-
Returns number of elements in the set.
- size() - Method in class org.broadinstitute.hellbender.utils.Dirichlet
- size() - Method in class org.broadinstitute.hellbender.utils.downsampling.Downsampler
-
Get the current number of items in this downsampler This should be the best estimate of the total number of elements that will come out of the downsampler were consumeFinalizedItems() to be called immediately after this call.
- size() - Method in class org.broadinstitute.hellbender.utils.downsampling.FractionalDownsampler
- size() - Method in class org.broadinstitute.hellbender.utils.downsampling.LevelingDownsampler
- size() - Method in class org.broadinstitute.hellbender.utils.downsampling.MutectDownsampler
- size() - Method in class org.broadinstitute.hellbender.utils.downsampling.PassThroughDownsampler
- size() - Method in class org.broadinstitute.hellbender.utils.downsampling.PositionalDownsampler
- size() - Method in class org.broadinstitute.hellbender.utils.downsampling.ReservoirDownsampler
- size() - Method in class org.broadinstitute.hellbender.utils.dragstr.DoubleSequence
-
Number of elements in the sequence.
- size() - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
How many BPs are covered by this locus?
- size() - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
return the size of the collection
- size() - Method in class org.broadinstitute.hellbender.utils.IndexRange
-
Returns number indexes expanded by this range.
- size() - Method in class org.broadinstitute.hellbender.utils.IntToDoubleFunctionCache
- size() - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
The number of elements in this pileup.
- size() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.CovariateKeyCache
-
Returns the size of this cache.
- size() - Method in class org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList
-
Returns the size of the list of standard covariates.
- size() - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
- size() - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree
-
Return the number of intervals in the tree.
- size() - Method in class picard.fingerprint.HaplotypeBlock
-
Returns the number of SNPs within the haplotype block.
- size() - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
- size() - Method in class picard.sam.markduplicates.util.MarkQueue
-
The number of records currently in this queue.
- size() - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
- size() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
The number of records in this set
- size() - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
- SIZE - Static variable in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ReadOrientation
- SIZE_AND_BASE_ORDER - Static variable in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
-
Compares two haplotypes first by their lengths and then by lexicographic order of their bases.
- SIZE_OF - Static variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- sizeBeforeLoc(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
Return the number of bps before loc in the sorted set
- sizeInRam() - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
- sizeInRam() - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
- sizeInRam() - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
- skimArray(T, boolean[]) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Skims out positions of an array returning a shorter one with the remaning positions in the same order.
- skimArray(T, int, T, int, boolean[], int) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Skims out positions of an array returning a shorter one with the remaining positions in the same order.
- skimArray(T, int, T, int, boolean[], int, int) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Skims out positions of an array returning a shorter one with the remaning positions in the same order.
- skip(int) - Method in class org.broadinstitute.hellbender.utils.recalibration.ReadRecalibrationInfo
-
Should offset in this read be skipped (because it's covered by a known variation site?)
- Skip - Static variable in enum class picard.illumina.parser.ReadType
- SKIP_CHROMS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- SKIP_FILTERS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- SKIP_MATE_VALIDATION - Variable in class picard.sam.ValidateSamFile
- SKIP_PRE_BWA_REPARTITION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- skipEmptyFiles - Variable in class picard.illumina.parser.ParameterizedFileUtil
- skipFamilyPriors - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
-
Skip application of family-based priors.
- skipFilters - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
- SKIPPED - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations.Judgment
- skipPopulationPriors - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
-
Skip application of population-based priors
- skipPreBwaRepartition - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection
-
Advanced optimization option that should be used only in the case of inputs with a high proportion of microbial reads that are not host-aligned/coordinate-sorted.
- skipRecords(int) - Method in class picard.illumina.parser.readers.FilterFileReader
- skipRecords(int) - Method in class picard.illumina.parser.readers.LocsFileReader
- skips - Variable in class picard.illumina.parser.ReadStructure
- SliceSampler - Class in org.broadinstitute.hellbender.utils.mcmc
-
Implements slice sampling of a continuous, univariate, unnormalized probability density function (PDF), which is assumed to be unimodal.
- SliceSampler(RandomGenerator, Function<Double, Double>, double) - Constructor for class org.broadinstitute.hellbender.utils.mcmc.SliceSampler
-
Creates a new sampler for an unbounded univariate random variable, given a random number generator, a continuous, univariate, unimodal, unnormalized log probability density function, and a step width.
- SliceSampler(RandomGenerator, Function<Double, Double>, double, double, double) - Constructor for class org.broadinstitute.hellbender.utils.mcmc.SliceSampler
-
Creates a new sampler for a bounded univariate random variable, given a random number generator, a continuous, univariate, unimodal, unnormalized log probability density function, hard limits on the random variable, and a step width.
- slippageRate - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- SMALL_DUP_CPX - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera
- SMALL_DUP_EXPANSION - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera
- SMITH_WATERMAN_DANGLING_END_GAP_EXTEND_PENALTY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SMITH_WATERMAN_DANGLING_END_GAP_OPEN_PENALTY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SMITH_WATERMAN_DANGLING_END_MATCH_VALUE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SMITH_WATERMAN_DANGLING_END_MISMATCH_PENALTY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_GAP_EXTEND_PENALTY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_GAP_OPEN_PENALTY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_MATCH_VALUE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_MISMATCH_PENALTY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SMITH_WATERMAN_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SMITH_WATERMAN_READ_TO_HAPLOTYPE_GAP_EXTEND_PENALTY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SMITH_WATERMAN_READ_TO_HAPLOTYPE_GAP_OPEN_PENALTY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SMITH_WATERMAN_READ_TO_HAPLOTYPE_MATCH_VALUE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SMITH_WATERMAN_READ_TO_HAPLOTYPE_MISMATCH_PENALTY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SmithWatermanAligner - Interface in org.broadinstitute.hellbender.utils.smithwaterman
-
Interface and factory for Smith-Waterman aligners
- SmithWatermanAligner.Implementation - Enum Class in org.broadinstitute.hellbender.utils.smithwaterman
- SmithWatermanAlignment - Interface in org.broadinstitute.hellbender.utils.smithwaterman
- SmithWatermanAlignmentConstants - Class in org.broadinstitute.hellbender.utils.smithwaterman
-
This class collects the various
SWParametersthat are used for various alignment procedures. - smithWatermanDanglingEndGapExtendPenalty - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- smithWatermanDanglingEndGapOpenPenalty - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- smithWatermanDanglingEndMatchValue - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- smithWatermanDanglingEndMismatchPenalty - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- smithWatermanHaplotypeToReferenceGapExtendPenalty - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- smithWatermanHaplotypeToReferenceGapOpenPenalty - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- smithWatermanHaplotypeToReferenceMatchValue - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- smithWatermanHaplotypeToReferenceMismatchPenalty - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- smithWatermanImplementation - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- smithWatermanImplementation - Variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
- SmithWatermanIntelAligner - Class in org.broadinstitute.hellbender.utils.smithwaterman
-
SmithWatermanIntelAligner class that converts instance of
SWAlignerNativeBindinginto aSmithWatermanIntelAlignerThis is optimized for Intel Architectures and can fail if Machine does not support AVX and will throwUserException - SmithWatermanIntelAligner() - Constructor for class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanIntelAligner
-
Create a new SW pairwise aligner, which is implementation of smith waterman aligner that's takes advantage of intel hardware optimizations.
- SmithWatermanJavaAligner - Class in org.broadinstitute.hellbender.utils.smithwaterman
-
Pairwise discrete smith-waterman alignment implemented in pure java ************************************************************************ **** IMPORTANT NOTE: **** **** This class assumes that all bytes come from UPPERCASED chars! **** ************************************************************************
- SmithWatermanJavaAligner.State - Enum Class in org.broadinstitute.hellbender.utils.smithwaterman
-
The state of a trace step through the matrix
- smithWatermanReadToHaplotypeGapExtendPenalty - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- smithWatermanReadToHaplotypeGapOpenPenalty - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- smithWatermanReadToHaplotypeMatchValue - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- smithWatermanReadToHaplotypeMismatchPenalty - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SMOOTHING_CREDIBLE_INTERVAL_THRESHOLD_ALLELE_FRACTION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- SMOOTHING_CREDIBLE_INTERVAL_THRESHOLD_COPY_RATIO_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- smoothingCredibleIntervalThresholdAlleleFraction - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- smoothingCredibleIntervalThresholdCopyRatio - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- smoothSegments(int, int, double, double) - Method in class org.broadinstitute.hellbender.tools.copynumber.models.MultidimensionalModeller
- SNORNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- SNORNA_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- Snp - Class in picard.fingerprint
-
Class to represent a SNP in context of a haplotype block that is used in fingerprinting.
- Snp(String, String, int, byte, byte, double, List<String>) - Constructor for class picard.fingerprint.Snp
- SNP - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantType
- SNP - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary.Type
- SNP - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary.Type
- SNP - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.VariantType
- SNP - Enum constant in enum class org.broadinstitute.hellbender.utils.variant.DbSnpVariantType
- SNP - Enum constant in enum class picard.util.VariantType
- SNP - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The name of a representative SNP within the haplotype that was compared.
- SNP_ALLELES - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The possible alleles for the SNP.
- SNP_CALIBRATION_SENSITIVITY_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- SNP_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord
- SNP_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- SNP_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- SNP_FPR_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord
- SNP_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- SNP_het_to_hom_ratio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- SNP_HETEROZYGOSITY - Static variable in class org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants
-
Standard heterozygous rate for SNP variation.
- SNP_KEY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
- SNP_LABEL - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- SNP_MASK_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker
- SNP_MASK_PRIORITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker
- SNP_OUTPUT - Variable in class picard.vcf.SplitVcfs
- SNP_PADDING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- SNP_REFERENCE_BIAS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The rate at which reference bases are observed at ref/alt heterozygous SNP sites.
- SNP_to_indel_ratio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- SNP_to_indel_ratio_for_singletons - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- snpAdajacentToAssemblyIndel - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- snpCounter - Variable in class picard.vcf.GenotypeConcordance
- SNPDPPerSample - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- SnpEffPositionModifier - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies variants as genes or coding regions, according to the effect modifier, as indicated by snpEff.
- SnpEffPositionModifier(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.SnpEffPositionModifier
- SnpEffPositionModifier.PositionModifier - Enum Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
- SnpEffUtil - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.util
-
Created with IntelliJ IDEA.
- SnpEffUtil() - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil
- SnpEffUtil.EffectFunctionalClass - Enum Class in org.broadinstitute.hellbender.tools.walkers.varianteval.util
- SnpEffUtil.EffectType - Enum Class in org.broadinstitute.hellbender.tools.walkers.varianteval.util
- snpHeterozygosity - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
-
The expected heterozygosity value used to compute prior probability that a locus is non-reference.
- snpHeterozygosity - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine
- snpmask - Variable in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker
-
SNPs from this file are used as a mask (inserting N's in the sequence) when constructing the alternate reference
- snpmaskPriority - Variable in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker
-
Gives priority to a SNP mask over an input VCF for a site.
- SNPNoveltyRate - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- SNPNoveltyRate - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- snpPaddingForGenotyping - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- snps - Variable in class org.broadinstitute.hellbender.utils.variant.DbSnpBitSetUtil.DbSnpBitSets
- snps - Variable in class picard.util.DbSnpBitSetUtil.DbSnpBitSets
- SNPSubstitutionType(byte, byte) - Static method in class org.broadinstitute.hellbender.utils.BaseUtils
-
Returns the base substitution type of the 2 state SNP
- snpThreshold - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
-
Percentage of reads required to support the alt for a variant to be considered
- SNRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- SNRNA_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- snvIdenticalBases - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
number of bases that need to be identical before the snv
- snvIdenticalBasesAfter - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
number of bases that need to be identical after the snv
- SNVMapper - Class in org.broadinstitute.hellbender.tools.walkers.featuremapping
-
An implementation of a feature mapper that finds SNPs (SVN) This class only finds SNP that are surrounded by a specific number of bases identical to the reference.
- SNVMapper(FlowFeatureMapperArgumentCollection) - Constructor for class org.broadinstitute.hellbender.tools.walkers.featuremapping.SNVMapper
- SOFT_CLIP_LOW_QUALITY_ENDS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SOFT_CLIPPED_LEADING_TRAILING_RATIO_THRESHOLD - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- SOFT_CLIPPED_RATIO_THRESHOLD - Static variable in class org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- SOFTCLIP_BASES - Enum constant in enum class org.broadinstitute.hellbender.utils.clipping.ClippingRepresentation
-
Change the read's cigar string to soft clip (S, see sam-spec) away the bases.
- SOFTCLIP_FILL_VALUE - Static variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- softClipBothEndsByReferenceCoordinates(GATKRead, int, int) - Static method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
- softClipByReadCoordinates(GATKRead, int, int) - Static method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
- softClipByReferenceCoordinates(int, int) - Method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
-
Generic functionality to soft clip a read (is analogous to hardClipByReferenceCoordinates()) Note, it REQUIRES you to give the directionality of your soft clip (i.e.
- softClipLowQualEnds(GATKRead, byte) - Static method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
- softClipLowQualityEnds - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- SoftClippedReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out reads where the ratio of soft-clipped bases to total bases exceeds some given value.
- SoftClippedReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.SoftClippedReadFilter
- softClipsLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into the number of soft-clipped bases that the read has in its alignment, or -1 if not aligned.
- softClipToRegionIncludingClippedBases(GATKRead, int, int) - Static method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
-
Soft clip the read to the variable region (from refStart to refStop) processing also the clipped bases
- SOLID - Enum constant in enum class org.broadinstitute.hellbender.utils.NGSPlatform
- SOLID_NOCALL_STRATEGY - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
- SOLID_RECAL_MODE - Static variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
- SOMATIC_ARG_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader
- SOMATIC_GCLOUD_DATASOURCES_BASEURL - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader
- SOMATIC_GCLOUD_DATASOURCES_PATH - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader
- SOMATIC_HET - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
- SOMATIC_INPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
- SomaticClusteringModel - Class in org.broadinstitute.hellbender.tools.walkers.mutect.clustering
-
A model for the allele fraction spectrum of somatic variation.
- SomaticClusteringModel(M2FiltersArgumentCollection, List<MutectStats>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel
- SomaticGenotypingArgumentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.arguments
- SomaticGenotypingArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticGenotypingArgumentCollection
- SomaticGenotypingEngine - Class in org.broadinstitute.hellbender.tools.walkers.mutect
- SomaticGenotypingEngine(M2ArgumentCollection, Set<String>, VariantAnnotatorEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine
- SomaticGVCFBlockCombiner - Class in org.broadinstitute.hellbender.utils.variant.writers
- SomaticGVCFBlockCombiner(List<Number>, int) - Constructor for class org.broadinstitute.hellbender.utils.variant.writers.SomaticGVCFBlockCombiner
- SomaticGVCFBlockCombiner(List<Number>, int, int) - Constructor for class org.broadinstitute.hellbender.utils.variant.writers.SomaticGVCFBlockCombiner
- SomaticGVCFWriter - Class in org.broadinstitute.hellbender.utils.variant.writers
-
Genome-wide VCF writer for somatic (Mutect2) output Merges reference blocks based on TLOD
- SomaticGVCFWriter(VariantContextWriter, List<Number>) - Constructor for class org.broadinstitute.hellbender.utils.variant.writers.SomaticGVCFWriter
-
Create a new GVCF writer Should be a non-empty list of boundaries.
- SomaticGVCFWriter(VariantContextWriter, List<Number>, int) - Constructor for class org.broadinstitute.hellbender.utils.variant.writers.SomaticGVCFWriter
- somaticInput - Variable in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
-
Merge somatic GVCFs, retaining LOD and haplotype event count information in FORMAT field Note that the Mutect2 reference confidence mode is in BETA -- the likelihoods model and output format are subject to change in subsequent versions.
- somaticInput - Variable in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
-
"Genotype" somatic GVCFs, outputting genotypes according to confidently called alt alleles, which may lead to inconsistent ploidy Note that the Mutect2 reference confidence mode is in BETA -- the likelihoods model and output format are subject to change in subsequent versions.
- SomaticLikelihoodsEngine - Class in org.broadinstitute.hellbender.tools.walkers.mutect
-
Created by David Benjamin on 3/9/17.
- SomaticLikelihoodsEngine() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticLikelihoodsEngine
- somaticLogOdds(LikelihoodMatrix<EVIDENCE, Allele>) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine
- SomaticModelingArgumentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.arguments
- SomaticModelingArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- SomaticReferenceConfidenceModel - Class in org.broadinstitute.hellbender.tools.walkers.mutect
- SomaticSegmentationArgumentCollection - Class in org.broadinstitute.hellbender.tools.copynumber.arguments
- SomaticSegmentationArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- SORT - Variable in class picard.illumina.IlluminaBasecallsToFastq
- SORT - Variable in class picard.illumina.IlluminaBasecallsToSam
- SORT - Variable in class picard.util.BedToIntervalList
- SORT - Variable in class picard.util.IntervalListToBed
- SORT - Variable in class picard.util.IntervalListTools
- SORT_BY_COLUMN - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.Sorting
- SORT_BY_ROW - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.Sorting
- SORT_ORDER - Variable in class picard.sam.AddOrReplaceReadGroups
- SORT_ORDER - Variable in class picard.sam.FastqToSam
- SORT_ORDER - Variable in class picard.sam.FilterSamReads
- SORT_ORDER - Variable in class picard.sam.FixMateInformation
- SORT_ORDER - Variable in class picard.sam.MergeBamAlignment
- SORT_ORDER - Variable in class picard.sam.MergeSamFiles
- SORT_ORDER - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- SORT_ORDER - Variable in class picard.sam.RevertSam
- SORT_ORDER - Variable in class picard.sam.SortSam
- SORT_ORDER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- SORT_ORDER_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- SORT_ORDER_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- SortableJexlVCMatchExp - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.util
- SortableJexlVCMatchExp(String, Expression) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SortableJexlVCMatchExp
-
Create a new matcher expression with name and JEXL expression exp
- sortAlleles(Collection<Allele>) - Static method in class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
- sortAndMergeIntervals(Collection<SimpleInterval>, SAMSequenceDictionary, IntervalMergingRule) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Given a collection of
SimpleIntervalinstances returns a map where the key is the enclosing contig name and the value is the list of the intervals on that contig that result from sorting and then merging those that are contiguous or overlap. - sortAndMergeIntervals(GenomeLocParser, List<GenomeLoc>, IntervalMergingRule) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Sorts and merges an interval list.
- SortedBasecallsConverter<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
-
SortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
- SortedBasecallsConverter(File, File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>, boolean, int, List<File>, int, Integer, Integer, Comparator<CLUSTER_OUTPUT_RECORD>, SortingCollection.Codec<CLUSTER_OUTPUT_RECORD>, Class<CLUSTER_OUTPUT_RECORD>, BclQualityEvaluationStrategy, boolean, boolean, boolean, AsyncWriterPool, BarcodeExtractor) - Constructor for class picard.illumina.SortedBasecallsConverter
-
Constructs a new SortedBaseCallsConverter.
- sortedIterator() - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Iterator over sorted by read start PileupElements.
- SortGff - Class in picard.annotation
-
Summary
- SortGff() - Constructor for class picard.annotation.SortGff
- SORTING_COLLECTION_SIZE_RATIO - Variable in class picard.sam.markduplicates.MarkDuplicates
- sortLocatablesBySequenceDictionary(Collection<T>, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Sort by the contig then position as specified by the index order in the given sequence dictionary.
- sortOrder - Variable in class org.broadinstitute.hellbender.tools.spark.RevertSamSpark
- sortReadsAccordingToHeader(JavaRDD<GATKRead>, SAMFileHeader, int) - Static method in class org.broadinstitute.hellbender.utils.spark.SparkUtils
-
Do a total sort of an RDD of
GATKReadaccording to the sort order in the header. - SortSam - Class in picard.sam
-
Sorts a SAM or BAM file.
- SortSam() - Constructor for class picard.sam.SortSam
- SortSamSpark - Class in org.broadinstitute.hellbender.tools.spark.pipelines
-
SortSam on Spark (works on SAM/BAM/CRAM)
- SortSamSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.pipelines.SortSamSpark
- sortUsingElementsAsKeys(JavaRDD<T>, Comparator<T>, int) - Static method in class org.broadinstitute.hellbender.utils.spark.SparkUtils
-
Do a global sort of an RDD using the given comparator.
- sortVariantConsequenceDict(Map<String, Set<String>>) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Create a copy of the variant consequence dictionary in which the feature names for each consequence are sorted in alphabetical order
- sortVariantContextsByPriority(Collection<VariantContext>, List<String>, GATKVariantContextUtils.GenotypeMergeType) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- sortVariantsByCoordinate(List<VariantContext>, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVVCFWriter
- SortVcf - Class in picard.vcf
-
Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then by coordinate.
- SortVcf() - Constructor for class picard.vcf.SortVcf
- source - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- SOURCE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- SOURCE - Variable in class picard.fingerprint.FingerprintMetrics
-
The originating file (if available) for this fingerprint
- SOURCE_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- SOURCE_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- SOURCE_SEQUENCE_INVALID - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Source sequence is invalid (contains invalid character).
- SOURCE_SEQUENCE_MISMATCH - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Deprecated.- but used in existing extended manifest files.
- SOURCE_SEQUENCE_STRAND_INVALID - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Deprecated.- but used in existing extended manifest files.
- SOURCE_STRAND_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- SOURCE_VERSION_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- sourceContigName - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera
- spanByKey(JavaPairRDD<K, V>) - Static method in class org.broadinstitute.hellbender.utils.spark.SparkUtils
-
Like
groupByKey, but assumes that values are already sorted by key, so no shuffle is needed, which is much faster. - SPANNING_DELETION_SYMBOLIC_ALLELE_DEPRECATED - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- SPANNING_DELETION_SYMBOLIC_ALLELE_NAME_DEPRECATED - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- spanWith(Locatable) - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
-
Returns a new SimpleInterval that represents the region between the endpoints of this and other.
- spark_driver_extraJavaOptions() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- spark_driver_maxResultSize() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- spark_driver_userClassPathFirst() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- spark_executor_extraJavaOptions() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- spark_executor_memoryOverhead() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- spark_io_compression_codec() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- spark_kryoserializer_buffer_max() - Method in interface org.broadinstitute.hellbender.utils.config.GATKConfig
- SPARK_MASTER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.SparkCommandLineArgumentCollection
- SPARK_PROGRAM_NAME_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram
- SPARK_PROPERTY_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- SPARK_VERBOSITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.SparkCommandLineArgumentCollection
- sparkArgs - Variable in class org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram
- SparkCommandLineArgumentCollection - Class in org.broadinstitute.hellbender.engine.spark
-
Command line arguments needed for configuring a spark context
- SparkCommandLineArgumentCollection() - Constructor for class org.broadinstitute.hellbender.engine.spark.SparkCommandLineArgumentCollection
- SparkCommandLineProgram - Class in org.broadinstitute.hellbender.engine.spark
- SparkCommandLineProgram() - Constructor for class org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram
- SparkContextFactory - Class in org.broadinstitute.hellbender.engine.spark
-
Manages creation of the Spark context.
- SparkConverter - Class in org.broadinstitute.hellbender.utils.spark
-
Class with helper methods to convert objects (mostly matrices) to/from Spark (particularly, in MLLib)
- sparkReadAdapter(AlignmentRecord) - Static method in class org.broadinstitute.hellbender.utils.read.BDGAlignmentRecordToGATKReadAdapter
- sparkReadAdapter(AlignmentRecord, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.utils.read.BDGAlignmentRecordToGATKReadAdapter
- SparkSharder - Class in org.broadinstitute.hellbender.engine.spark
-
Utility methods for sharding
Locatableobjects (such as reads) for given intervals, without using a shuffle. - SparkSharder() - Constructor for class org.broadinstitute.hellbender.engine.spark.SparkSharder
- SparkSingularValueDecomposer - Class in org.broadinstitute.hellbender.utils.svd
-
SVD using MLLib
- SparkSingularValueDecomposer(JavaSparkContext) - Constructor for class org.broadinstitute.hellbender.utils.svd.SparkSingularValueDecomposer
- SparkUtils - Class in org.broadinstitute.hellbender.utils.spark
-
Miscellaneous Spark-related utilities
- sparkVariantAdapter(VariantContext) - Static method in class org.broadinstitute.hellbender.utils.variant.VariantContextVariantAdapter
- specialArgumentsCollection - Variable in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- specialArgumentsCollection - Variable in class picard.cmdline.CommandLineProgram
- SPECIES - Variable in class picard.sam.CreateSequenceDictionary
- SPECIES_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- specificity - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- Splice(String, int, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.Splice
- SPLICE_SITE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
The variant is within a configurable number of bases (default=2) of a splice site.
- SPLICE_SITE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.SnpEffPositionModifier.PositionModifier
- SPLICE_SITE_ACCEPTOR - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- SPLICE_SITE_DONOR - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- split() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SharedVertexSequenceSplitter
-
Actually do the splitting up of the vertices Must be called before calling updateGraph
- split(int) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
-
Splits the contig into to regions: [start,split point) and [split point, end].
- split(String, char) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Splits a String using indexOf instead of regex to speed things up.
- split(String, String) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Splits a String using indexOf instead of regex to speed things up.
- split(String, String[], String) - Method in class picard.Test
- split(SeqGraph, SeqVertex) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.CommonSuffixSplitter
-
Simple single-function interface to split and then update a graph
- SPLIT_DELIM - Static variable in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
- SPLIT_MULTI_ALLELIC_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTable
- SPLIT_MULTI_ALLELIC_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTable
- SPLIT_MULTIALLELEICS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
- SPLIT_READ_FILE_ARGUMENT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- SPLIT_READ_FILE_ARGUMENT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- SPLIT_READ_SUPPORT - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- SPLIT_TO_N_FILES - Variable in class picard.sam.SplitSamByNumberOfReads
- SPLIT_TO_N_READS - Variable in class picard.sam.SplitSamByNumberOfReads
- splitAndUpdate(SeqVertex, SeqVertex) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SharedVertexSequenceSplitter
-
Simple single-function interface to split and then update a graph
- splitAnnotationArgsIntoMap(List<String>) - Static method in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine
-
Split each element of the given
Listinto a key and value. - splitASFilters(VariantContext, List<Map<String, Object>>) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- splitASSBTable(VariantContext, List<Map<String, Object>>) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- splitAttributesIntoPerAlleleLists(VariantContext, List<String>, VCFHeader) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- splitBySample(SAMFileHeader, String) - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
-
Splits the ReadPileup by sample
- splitContextBySampleName(SAMFileHeader) - Method in class org.broadinstitute.hellbender.engine.AlignmentContext
- splitContextBySampleName(String, SAMFileHeader) - Method in class org.broadinstitute.hellbender.engine.AlignmentContext
-
Splits the given AlignmentContext into a StratifiedAlignmentContext per sample, but referenced by sample name instead of sample object.
- splitContextBySampleName(ReadPileup, SAMFileHeader) - Static method in class org.broadinstitute.hellbender.engine.AlignmentContext
- SplitCRAM - Class in org.broadinstitute.hellbender.tools
-
SplitCRAM - split a cram file into smaller cram files (shards) containing a minimal number of records while still respecting container boundaries.
- SplitCRAM() - Constructor for class org.broadinstitute.hellbender.tools.SplitCRAM
- spliterator() - Method in class org.broadinstitute.hellbender.utils.nio.PathLineIterator
- spliterator() - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
- splitFactor - Variable in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
-
BWA-mem seed split factor
- splitFixedIntervals(List<GenomeLoc>, int) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Splits the genome locs up by size.
- splitFixedWidth(String, List<Integer>) - Static method in class org.broadinstitute.hellbender.utils.text.TextFormattingUtils
-
Parses a fixed width line of text.
- splitGappedAlignment(AlignmentInterval, int, int) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier
-
Splits a gapped alignment into multiple alignment regions, based on input sensitivity: i.e.
- SplitIntervals - Class in org.broadinstitute.hellbender.tools.walkers
-
This tool takes in intervals via the standard arguments of
IntervalArgumentCollectionand splits them into interval files for scattering. - SplitIntervals() - Constructor for class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- splitIntervalsToSubLists(List<GenomeLoc>, List<Integer>) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Splits an interval list into multiple sublists.
- splitIntoPrimitiveAlleles(VariantContext) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Splits the alleles for the provided variant context into its primitive parts.
- splitLocusIntervals(List<GenomeLoc>, int) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
- splitMultiAllelic - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTable
-
By default, a variant record with multiple ALT alleles will be summarized in one line, with per alt-allele fields (e.g.
- splitMultiallelics - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants
-
If this argument is set, split multiallelic records and left-align individual alleles.
- splitNCigarRead(GATKRead, OverhangFixingManager, boolean, SAMFileHeader, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads
-
Goes through the cigar string of the read and create new reads for each consecutive non-N elements (while soft clipping the rest of the read) that are supplemental to each other.
- SplitNCigarReads - Class in org.broadinstitute.hellbender.tools.walkers.rnaseq
-
Splits reads that contain Ns in their cigar string (e.g.
- SplitNCigarReads() - Constructor for class org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads
- splitPairStrongEnoughEvidenceForCA(AlignmentInterval, AlignmentInterval) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera
-
Roughly similar to ContigChimericAlignmentIterativeInterpreter#nextAlignmentMayBeInsertion(AlignmentInterval, AlignmentInterval, Integer, Integer, boolean): 1) either alignment may have very low mapping quality (a more relaxed mapping quality threshold); 2) either alignment may consume only a "short" part of the contig, or if assuming that the alignment consumes roughly the same amount of ref bases and read bases, has isAlignment that is too short
- SplitRead(GATKRead) - Constructor for class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.SplitRead
- SplitRead(GATKRead, ReadMetadata, boolean) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SplitRead
- SplitReadEvidence - Class in org.broadinstitute.hellbender.tools.sv
-
Documents evidence of reads (of some sample at some locus) that align well to reference for some portion of the read, and fails to align for another portion of the read.
- SplitReadEvidence(String, String, int, int, boolean) - Constructor for class org.broadinstitute.hellbender.tools.sv.SplitReadEvidence
- SplitReadEvidenceBCICodec - Class in org.broadinstitute.hellbender.utils.codecs
-
Codec to handle SplitReadEvidence in BlockCompressedInterval files
- SplitReadEvidenceBCICodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceBCICodec
- SplitReadEvidenceCodec - Class in org.broadinstitute.hellbender.utils.codecs
-
Codec to handle SplitReadEvidence in tab-delimited text files
- SplitReadEvidenceCodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceCodec
- SplitReadEvidenceSortMerger - Class in org.broadinstitute.hellbender.tools.sv
-
Imposes additional ordering of same-locus SplitReadEvidence by sample and strand.
- SplitReadEvidenceSortMerger(SAMSequenceDictionary, FeatureSink<SplitReadEvidence>) - Constructor for class org.broadinstitute.hellbender.tools.sv.SplitReadEvidenceSortMerger
- SplitReads - Class in org.broadinstitute.hellbender.tools
-
Outputs reads from a SAM/BAM/CRAM by read group, sample and library name
- SplitReads() - Constructor for class org.broadinstitute.hellbender.tools.SplitReads
- splitReadsBySample(Collection<GATKRead>) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- splitReadsBySample(SampleList, SAMFileHeader, Collection<GATKRead>) - Static method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- SplitSamByLibrary - Class in picard.sam
-
Command-line program to split a SAM/BAM/CRAM file into separate files based on library name.
- SplitSamByLibrary() - Constructor for class picard.sam.SplitSamByLibrary
- SplitSamByNumberOfReads - Class in picard.sam
-
Splits the input queryname sorted or query-grouped SAM/BAM/CRAM file and writes it into multiple BAM files, each with an approximately equal number of reads.
- SplitSamByNumberOfReads() - Constructor for class picard.sam.SplitSamByNumberOfReads
- splitSomaticVariantContextToBiallelics(VariantContext, boolean, VCFHeader) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- SPLITTING_INDEX_GRANULARITY - Static variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- SPLITTING_INDEX_GRANULARITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndex
- splittingIndexGranularity - Variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- splitVariantContextToBiallelics(VariantContext, boolean, GenotypeAssignmentMethod, boolean) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Split variant context into its biallelic components if there are more than 2 alleles
- SplitVcfs - Class in picard.vcf
-
Splits the input VCF file into two, one for indels and one for SNPs.
- SplitVcfs() - Constructor for class picard.vcf.SplitVcfs
- splitWhiteSpace(String) - Static method in class org.broadinstitute.hellbender.utils.text.TextFormattingUtils
-
Parses a line of text by whitespace.
- SPREADER - Static variable in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
- square(double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Calculate f(x) = x^2
- squatters() - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
- srcFileSize - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- srcFileSizeNumDigits - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- srFile - Variable in class org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
- SRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- Standard - Enum constant in enum class org.broadinstitute.hellbender.utils.runtime.StreamLocation
- STANDARD - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection.FlowMode
- STANDARD - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection.FlowMode
- STANDARD - Enum constant in enum class org.broadinstitute.hellbender.utils.GenomeLocParser.ValidationLevel
-
Do the standard amount of validation
- STANDARD_BASES - Static variable in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Set of the standard (non-redundant) nucleotide values in their preferred alphabetical order.
- STANDARD_DEVIATION - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
Standard deviation of insert sizes over the "core" of the distribution.
- STANDARD_DEVIATION - Variable in class picard.analysis.InsertSizeMetrics
-
Standard deviation of insert sizes over the "core" of the distribution.
- STANDARD_ENCODING - Static variable in class org.broadinstitute.hellbender.tools.GetSampleName
- STANDARD_MUTECT_INFO_FIELDS_FOR_FILTERING - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- STANDARD_NGS - Static variable in class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAlignmentConstants
-
STANDARD_NGSis the default forAbstractReadThreadingGraphmethods for the recovery of dangling heads/tails. - StandardAnnotation - Interface in org.broadinstitute.hellbender.tools.walkers.annotator
-
This is a marker interface used to indicate which annotations are "Standard".
- standardArgs - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- StandardArgumentDefinitions - Class in org.broadinstitute.hellbender.cmdline
-
A set of String constants in which the name of the constant (minus the _SHORT_NAME suffix) is the standard long Option name, and the value of the constant is the standard shortName.
- StandardCallerArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
-
This is pulled out so that every caller isn't exposed to the arguments from every other caller.
- StandardCallerArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection
- standardConfidenceForCalling - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
-
The minimum phred-scaled confidence threshold at which variants should be called.
- StandardCovariateList - Class in org.broadinstitute.hellbender.utils.recalibration.covariates
-
Represents the list of standard BQSR covariates.
- StandardCovariateList(RecalibrationArgumentCollection, SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList
-
Creates a new list of standard BQSR covariates and initializes each covariate.
- StandardCovariateList(RecalibrationArgumentCollection, List<String>) - Constructor for class org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList
-
Creates a new list of standard BQSR covariates and initializes each covariate.
- standardDeviation(double, int, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- StandardEval - Interface in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
- StandardFlowBasedAnnotation - Interface in org.broadinstitute.hellbender.tools.walkers.annotator.flow
-
This is a marker interface used to indicate which annotations are part of the standard flow based group
- StandardHCAnnotation - Interface in org.broadinstitute.hellbender.tools.walkers.annotator
-
This is a marker interface used to indicate which annotations are "Standard" for the HaplotypeCaller only.
- STANDARDIZED_COPY_RATIOS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument
- StandardMutectAnnotation - Interface in org.broadinstitute.hellbender.tools.walkers.annotator
-
This is a marker interface used to indicate which annotations are "Standard" for Mutect2 only.
- StandardOptionDefinitions - Class in picard.cmdline
-
A set of String constants in which the name of the constant (minus the _SHORT_NAME suffix) is the standard long Option name, and the value of the constant is the standard shortName.
- StandardOptionDefinitions() - Constructor for class picard.cmdline.StandardOptionDefinitions
- StandardPairHMMInputScoreImputator - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller
-
Standard or classic pair-hmm score imputator.
- StandardStratification - Interface in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
- StandardValidationCollection() - Constructor for class org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection.StandardValidationCollection
- start - Variable in class org.broadinstitute.hellbender.utils.clipping.ClippingOp
- start - Variable in class org.broadinstitute.hellbender.utils.GenomeLoc
- start - Variable in class picard.annotation.Gene.Transcript.Exon
- start - Variable in class picard.illumina.parser.Range
- start() - Method in class org.broadinstitute.hellbender.engine.ProgressMeter
-
Start the progress meter and produce preliminary output such as column headings.
- start() - Method in class org.broadinstitute.hellbender.utils.runtime.StreamingProcessController
-
Starts the remote process running based on the setting specified in the constructor.
- start() - Method in class picard.annotation.Gene.Transcript
- start() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
- start() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
-
Starts the work of the executor, returning immediately.
- start() - Method in class picard.vcf.processor.VcfFileSegment
-
Deprecated.
- start() - Method in class picard.vcf.processor.VcfPathSegment
- start(String) - Method in class org.broadinstitute.hellbender.utils.logging.BunnyLog
- start(List<String>) - Method in class org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor
-
Start the Python process.
- start(List<String>, boolean, File) - Method in class org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor
-
Start the Python process.
- START - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection.SimpleCountTableColumn
- START_BREAKPOINT - Enum constant in enum class org.broadinstitute.hellbender.utils.IntervalUtils.IntervalBreakpointType
- START_CODON - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureType
- START_CODON_DEL - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Deletion that overlaps the start codon.
- START_CODON_INS - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Insertion that overlaps the start codon.
- START_CODON_SNP - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Point mutation that overlaps the start codon.
- START_COL_COMMENT - Static variable in class org.broadinstitute.hellbender.utils.codecs.AnnotatedIntervalCodec
- START_END_SEPARATOR - Static variable in class org.broadinstitute.hellbender.utils.SimpleInterval
- START_EXON_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
Used when generating start exon field name for segment funcotations.
- START_GAINED - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- START_GENE_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
Since gencode funcotation field names are generated dynamically, we have to search the incoming funcotation fields for the proper gencode funcotations.
- START_LOST - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- START_TRANSCRIPT_DELIMITER - Static variable in class org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer
-
The delimiter to use when starting the information regarding a transcript.
- startBatchWrite(String, List<T>) - Method in class org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor
-
Request that a batch of items be written to the stream on a background thread.
- startBatchWrite(List<T>) - Method in class org.broadinstitute.hellbender.utils.runtime.AsynchronousStreamWriter
-
Request that a batch of items be written to the stream on a background thread.
- started() - Method in class org.broadinstitute.hellbender.engine.ProgressMeter
-
Returns whether the meter has been started.
- startInAssembledContig - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- startingChr - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator
- startingVC - Variable in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- startPos - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator
- startsAtBeginning() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.PathPart
- startsOrEndsWithInsertionOrDeletion(Cigar) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Does cigar start or end with a deletion operation? WARNING: there is usually no good reason to use this method, because one should handle the leading and trailing deletion via the
CigarBuilderclass. - startTime - Variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- state - Variable in class org.broadinstitute.hellbender.utils.baq.BAQ.BAQCalculationResult
- state() - Method in class org.broadinstitute.hellbender.utils.mcmc.ParameterizedModel
-
Returns a copy of the
ParameterizedStateheld internally. - stateAlignedPosition(int) - Static method in class org.broadinstitute.hellbender.utils.baq.BAQ
-
decode the bit encoded state array values
- stateIsIndel(int) - Static method in class org.broadinstitute.hellbender.utils.baq.BAQ
-
decode the bit encoded state array values
- stateList - Variable in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
- states - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier
- STATIC_QUANTIZED_QUALS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.validation.CompareBaseQualities
- staticQuantizationQuals - Variable in class org.broadinstitute.hellbender.tools.ApplyBQSRUniqueArgumentCollection
-
Static quantized quals are entirely separate from the quantize_qual option which uses dynamic binning.
- staticQuantizationQuals - Variable in class org.broadinstitute.hellbender.tools.validation.CompareBaseQualities
-
Return value is 0 if the two files have identical base qualities and non-zero otherwise.
- statistics - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.FileType
- statusAsString() - Method in class org.broadinstitute.hellbender.tools.reference.ReferencePair
-
Displays a ReferencePair's status set
- stddev() - Method in class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistribution
- stddev() - Method in class org.broadinstitute.hellbender.utils.MathUtils.RunningAverage
- stddev(double[], double) - Static method in class picard.util.MathUtil
-
Calculated the standard deviation of an array of doubles.
- stddev(double[], int, int) - Static method in class picard.util.MathUtil
-
Calculated the standard deviation of an array of doubles.
- stddev(double[], int, int, double) - Static method in class picard.util.MathUtil
-
Calculated the standard deviation of an array of doubles.
- STDERR - Enum constant in enum class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase.ProcessStream
- STDERR - Variable in class picard.arrays.BafRegressMetrics
-
The standard error of the estimate
- stdErrFuture - Variable in class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase
- STDOUT - Enum constant in enum class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase.ProcessStream
- stdOutFuture - Variable in class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase
- step() - Method in class org.broadinstitute.hellbender.utils.dragstr.DoubleSequence
-
Returns the step in the sequence.
- STEP_DECRIPTION_PATTERN - Static variable in class org.broadinstitute.hellbender.utils.dragstr.DoubleSequence
-
Currently the only supported format for the string descriptor is: start:step:end.
- stepEnd(String) - Method in class org.broadinstitute.hellbender.utils.logging.BunnyLog
- stepForwardOnGenome() - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
-
Step the state machine forward one unit Takes the current state of this machine, and advances the state until the next on-genome cigar element (M, X, =, D) is encountered, at which point this function returns with the cigar operator of the current element.
- STEPWISE_FITLERING_ARGUMENT - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- stepwiseFiltering - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- stop - Variable in class org.broadinstitute.hellbender.utils.clipping.ClippingOp
- stop - Variable in class org.broadinstitute.hellbender.utils.GenomeLoc
- stop() - Method in class org.broadinstitute.hellbender.engine.ProgressMeter
-
Stop the progress meter and output summary statistics to the logger
- stop() - Method in class picard.vcf.processor.VcfFileSegment
-
Deprecated.
- stop() - Method in class picard.vcf.processor.VcfPathSegment
- STOP_AFTER - Variable in class picard.analysis.CollectMultipleMetrics
- STOP_AFTER - Variable in class picard.analysis.CollectOxoGMetrics
- STOP_AFTER - Variable in class picard.analysis.CollectWgsMetrics
- STOP_AFTER - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- STOP_AFTER - Variable in class picard.analysis.SinglePassSamProgram
- STOP_AFTER - Variable in class picard.sam.PositionBasedDownsampleSam
- STOP_CODON - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- STOP_CODON - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureType
- STOP_CODON_READTHROUGH - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Transcript whose coding sequence contains an internal stop codon that does not cause the translation termination.
- STOP_GAINED - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.SnpEffPositionModifier.PositionModifier
- STOP_GAINED - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- STOP_LOST - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.SnpEffPositionModifier.PositionModifier
- STOP_LOST - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- stopOnReadName - Variable in class org.broadinstitute.hellbender.tools.examples.ExamplePartialReadWalker
- stopped() - Method in class org.broadinstitute.hellbender.engine.ProgressMeter
-
Returns whether the meter has been stopped.
- stopsAtEnd() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.PathPart
- stopSparkContext(JavaSparkContext) - Static method in class org.broadinstitute.hellbender.engine.spark.SparkContextFactory
-
Stop a
JavaSparkContext, unless it is the test context. - StorageAPIAvroReader - Class in org.broadinstitute.hellbender.utils.bigquery
- StorageAPIAvroReader(TableReference) - Constructor for class org.broadinstitute.hellbender.utils.bigquery.StorageAPIAvroReader
- StorageAPIAvroReader(TableReference, String) - Constructor for class org.broadinstitute.hellbender.utils.bigquery.StorageAPIAvroReader
- store(GATKPath) - Method in class org.broadinstitute.hellbender.utils.dragstr.STRTableFileBuilder
- STR_PADDING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- STR_PRESENT_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- STR_TABLE_PATH_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- STR_TABLE_PATH_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- Strand - Enum Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- STRAND - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- STRAND_ARTIFACT_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- STRAND_BALANCE - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of PF reads aligned to the positive strand of the genome divided by the number of PF reads aligned to the genome.
- STRAND_BIAS_BY_SAMPLE_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- STRAND_COUNT_BY_SAMPLE_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- STRAND_INDEX - Static variable in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- STRAND_MINUS - Static variable in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- STRAND_MINUS - Static variable in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceCodec
- STRAND_ODDS_RATIO_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- STRAND_PLUS - Static variable in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- STRAND_PLUS - Static variable in class org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceCodec
- STRAND_QUAL_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- STRAND_SPECIFICITY - Variable in class picard.analysis.CollectRnaSeqMetrics
- Strand.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- StrandArtifactFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- StrandArtifactFilter() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter
- StrandArtifactFilter.EStep - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- StrandBiasBySample - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Number of forward and reverse reads that support REF and ALT alleles
- StrandBiasBySample() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasBySample
- StrandBiasTest - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Class of tests to detect strand bias.
- StrandBiasTest() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest
- StrandBiasUtils - Class in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
-
Common strand bias utilities used by allele specific strand bias annotators
- StrandBiasUtils() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils
- StrandCorrectedAllele - Class in org.broadinstitute.hellbender.tools.funcotator
-
Class to represent a strand-corrected
Allele. - StrandCorrectedReferenceBases - Class in org.broadinstitute.hellbender.tools.funcotator
-
Simple container class to represent bases that have been corrected for strandedness already.
- StrandCorrectedReferenceBases(byte[], Strand) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedReferenceBases
- StrandCorrectedReferenceBases(String, Strand) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedReferenceBases
- StrandedInterval - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
-
Represents an interval and strand from the reference genome.
- StrandedInterval(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval
- StrandedInterval(SVInterval, boolean) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval
- StrandedInterval.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- StrandOddsRatio - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Strand bias estimated by the Symmetric Odds Ratio test
- StrandOddsRatio() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.StrandOddsRatio
- STRANDS_ATTRIBUTE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- strandsMatch(SVCallRecord, SVCallRecord) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
-
Test if breakend strands match.
- StrandSwitch - Enum Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
-
For symbolizing the change of strand from one alignment to the next of an assembly contig.
- STRATEGY - Variable in class picard.sam.DownsampleSam
- StratificationManager<K extends Stratifier<Object>,
V> - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager -
Represents the full state space of all stratification combinations
- StratificationManager(List<K>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
-
Create a new StratificationManager with nodes to store data for all combinations of the ordered list of strats
- StratificationManager.Combiner<V> - Interface in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager
- stratificationsToUse - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- Stratifier<T> - Interface in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager
-
A basic interface for a class to be used with the StratificationManager system
- STRATIFIER_VALUE - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CigarOperatorsInReadStratifier
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.ConsensusStratifier
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellTileStratifier
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellYStratifier
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.GCContentStratifier
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
-
Returns the number of bases associated with I and D CIGAR elements.
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.NsInReadStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.BinnedReadCycleStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CollectionStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelLengthStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymerStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.MismatchesInReadStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.PairStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in interface picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
- stratify(AlignmentContext.ReadOrientation) - Method in class org.broadinstitute.hellbender.engine.AlignmentContext
-
Returns a potentially derived subcontext containing only forward, reverse, or in fact all reads in alignment context context.
- STRDecimationTable - Class in org.broadinstitute.hellbender.tools.dragstr
-
Represents a decimation table.
- STRDecimationTable(String) - Constructor for class org.broadinstitute.hellbender.tools.dragstr.STRDecimationTable
-
Creates a decimation table from its string representation.
- stream() - Method in class org.broadinstitute.hellbender.utils.BinaryTableReader
- stream() - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Returns an stream on the reaming records in the source.
- stream(byte[], int, int, SVKmer) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVDUSTFilteredKmerizer
- stream(byte[], int, int, SVKmer) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- stream(byte[], int, SVKmer) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- stream(CharSequence, int, int, SVKmer) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVDUSTFilteredKmerizer
- stream(CharSequence, int, int, SVKmer) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- stream(Iterable<T>) - Static method in class org.broadinstitute.hellbender.utils.Utils
- stream(Enumeration<T>) - Static method in class org.broadinstitute.hellbender.utils.Utils
- stream(Iterator<T>) - Static method in class org.broadinstitute.hellbender.utils.Utils
- STREAM_BLOCK_TRANSFER_SIZE - Static variable in class org.broadinstitute.hellbender.utils.runtime.CapturedStreamOutput
- STREAMING_ACK_MESSAGE - Static variable in class org.broadinstitute.hellbender.utils.runtime.StreamingToolConstants
-
Command acknowledgement messages used to signal positive acknowledgement ('ack'), negative acknowledgement ('nck'), and negative acknowledgement with an accompanying message ('nkm').
- STREAMING_ACK_MESSAGE_SIZE - Static variable in class org.broadinstitute.hellbender.utils.runtime.StreamingToolConstants
- STREAMING_NCK_MESSAGE - Static variable in class org.broadinstitute.hellbender.utils.runtime.StreamingToolConstants
- STREAMING_NCK_WITH_MESSAGE_MAX_MESSAGE_LENGTH - Static variable in class org.broadinstitute.hellbender.utils.runtime.StreamingToolConstants
- STREAMING_NCK_WITH_MESSAGE_MESSAGE - Static variable in class org.broadinstitute.hellbender.utils.runtime.StreamingToolConstants
- STREAMING_NCK_WITH_MESSAGE_MESSAGE_LEN_SIZE - Static variable in class org.broadinstitute.hellbender.utils.runtime.StreamingToolConstants
-
Number of characters used to represent the length of the serialized message, fixed at a constant 4 characters to ensure we can deterministically know how much input to wait for when looking for a message length in the incoming stream.
- StreamingProcessController - Class in org.broadinstitute.hellbender.utils.runtime
-
Facade to Runtime.exec() and java.lang.Process.
- StreamingProcessController(ProcessSettings) - Constructor for class org.broadinstitute.hellbender.utils.runtime.StreamingProcessController
- StreamingProcessController(ProcessSettings, boolean) - Constructor for class org.broadinstitute.hellbender.utils.runtime.StreamingProcessController
-
Create a controller using the specified settings.
- StreamingPythonScriptExecutor<T> - Class in org.broadinstitute.hellbender.utils.python
-
Python executor used to interact with a cooperative, keep-alive Python process.
- StreamingPythonScriptExecutor(boolean) - Constructor for class org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor
-
The start method must be called to actually start the remote executable.
- StreamingPythonScriptExecutor(PythonExecutorBase.PythonExecutableName, boolean) - Constructor for class org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor
-
The start method must be called to actually start the remote executable.
- StreamingToolConstants - Class in org.broadinstitute.hellbender.utils.runtime
-
Various constants used by StreamingProcessController that require synchronized equivalents in the companion process, i.e., if the streaming process is written in Python, there must be equivalent Python constants for use by the Python code.
- StreamingToolConstants() - Constructor for class org.broadinstitute.hellbender.utils.runtime.StreamingToolConstants
- StreamLocation - Enum Class in org.broadinstitute.hellbender.utils.runtime
-
Where to read/write a stream
- streamOfSubsettedAndValidatedReadCounts(List<String>, SimpleIntervalCollection, Logger) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
-
Common method for subsetting and validating read counts in both
DetermineGermlineContigPloidyandGermlineCNVCaller. - StreamOutput - Class in org.broadinstitute.hellbender.utils.runtime
-
The content of stdout or stderr.
- StreamOutput() - Constructor for class org.broadinstitute.hellbender.utils.runtime.StreamOutput
- strict - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark
- strict - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- STRICT - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.PedigreeValidationType
-
Require if a pedigree file is provided at all samples in the VCF or BAM files have a corresponding entry in the pedigree file(s).
- STRICT - Variable in class picard.vcf.SplitVcfs
- STRICT_STRAND_BIAS_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- StrictStrandBiasFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- StrictStrandBiasFilter(int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrictStrandBiasFilter
- String - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportDataType
-
Used for string values.
- stringForCSV() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- stringRep(ReadMetadata, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
-
All ReadEvidence has basic BreakpointEvidence.stringRep() with appended info: templateName/fragmentOrdinal forwardStrand cigarString mappingQuality Child classes may extend stringRep() by appending class-specific tab-separated info
- stringRep(ReadMetadata, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
-
Returns string representation of BreakpointEvidence in tab-separated form: Contig[begin:end] weight validated EvidenceType distal_targets distal_targets is a (; separated) list of string representations (.toString()) for each distal target it is empty if there are no distal targets Child classes may extend stringRep() by appending class-specific tab-separated info
- stringRep(ReadMetadata, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.TemplateSizeAnomaly
- stringSeqsToString(String[], String) - Static method in class picard.util.IlluminaUtil
- stringSerializer - Static variable in class org.broadinstitute.hellbender.utils.runtime.AsynchronousStreamWriter
-
Convenience function that can be provided to an
AsynchronousStreamWriterto serialize String objects. - STRIP_UNPAIRED_MATE_NUMBER - Variable in class picard.sam.FastqToSam
-
Deprecated.
- StripMateNumberTransformer - Class in org.broadinstitute.hellbender.transformers
-
Removes /1 or /2 and any whitespace from the end of the read name if present
- StripMateNumberTransformer() - Constructor for class org.broadinstitute.hellbender.transformers.StripMateNumberTransformer
- stripPLsAndAD(GenotypesContext) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- STRONG - Static variable in enum class org.broadinstitute.hellbender.utils.Nucleotide
- strPadding - Variable in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- strPaddingForGenotyping - Variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- STRTableFile - Class in org.broadinstitute.hellbender.utils.dragstr
-
Class to create and access STR table file contents.
- STRTableFileBuilder - Class in org.broadinstitute.hellbender.utils.dragstr
-
Utility class to compose the contents of the STR Table file.
- STRUCTURAL_VARIANT_SIZE_LOWER_BOUND - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection
- StructuralVariantDiscoverer - Class in org.broadinstitute.hellbender.tools
- StructuralVariantDiscoverer() - Constructor for class org.broadinstitute.hellbender.tools.StructuralVariantDiscoverer
- StructuralVariantDiscoveryProgramGroup - Class in org.broadinstitute.hellbender.cmdline.programgroups
-
Tools that detect structural variants
- StructuralVariantDiscoveryProgramGroup() - Constructor for class org.broadinstitute.hellbender.cmdline.programgroups.StructuralVariantDiscoveryProgramGroup
- StructuralVariantFilter - Interface in org.broadinstitute.hellbender.tools.spark.sv.discovery
- StructuralVariationDiscoveryArgumentCollection - Class in org.broadinstitute.hellbender.tools.spark.sv
- StructuralVariationDiscoveryArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection
- StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection - Class in org.broadinstitute.hellbender.tools.spark.sv
- StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection - Class in org.broadinstitute.hellbender.tools.spark.sv
- StructuralVariationDiscoveryPipelineSpark - Class in org.broadinstitute.hellbender.tools.spark.sv
-
Runs the structural variation discovery workflow on a single sample
- StructuralVariationDiscoveryPipelineSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryPipelineSpark
- StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser - Class in org.broadinstitute.hellbender.tools.spark.sv
- subComputekeayLikelihoodGivenHaplotypeKeysLog10(int, int[], byte[], int[], byte[], FlowBasedRead, byte[], byte[], byte[], boolean) - Method in class org.broadinstitute.hellbender.utils.pairhmm.FlowBasedPairHMM
- subComputeReadLikelihoodGivenHaplotypeLog10(byte[], byte[], byte[], byte[], byte[], byte[], int, boolean, int) - Method in class org.broadinstitute.hellbender.utils.pairhmm.FlowBasedPairHMM
- subComputeReadLikelihoodGivenHaplotypeLog10(byte[], byte[], byte[], byte[], byte[], byte[], int, boolean, int) - Method in class org.broadinstitute.hellbender.utils.pairhmm.Log10PairHMM
-
To be implemented by subclasses to do calculation for #computeReadLikelihoodGivenHaplotypeLog10
- subComputeReadLikelihoodGivenHaplotypeLog10(byte[], byte[], byte[], byte[], byte[], byte[], int, boolean, int) - Method in class org.broadinstitute.hellbender.utils.pairhmm.LoglessPairHMM
-
To be implemented by subclasses to do calculation for #computeReadLikelihoodGivenHaplotypeLog10
- subComputeReadLikelihoodGivenHaplotypeLog10(byte[], byte[], byte[], byte[], byte[], byte[], int, boolean, int) - Method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
-
To be implemented by subclasses to do calculation for #computeReadLikelihoodGivenHaplotypeLog10
- SUBDIVISION_MODE - Variable in class picard.util.IntervalListTools
- SUBDIVISION_MODE_lONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- SUBDIVISION_MODE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- subKmer(int, int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.Kmer
-
Create a derived shallow kmer that starts at newStart and has newLength bases
- submit(VariantContext) - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlockCombiner
- submit(VariantContext) - Method in class org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFBlockCombiner
-
Add the input as a new reference block or write and remove ref blocks that end before the variantContext if it is variant Trim ref block if the variant occurs in the middle of a block
- submit(Collection<T>) - Method in class org.broadinstitute.hellbender.utils.downsampling.Downsampler
-
Submit a collection of items to the downsampler for consideration.
- submit(Collection<T>) - Method in class org.broadinstitute.hellbender.utils.downsampling.LevelingDownsampler
- submit(Collection<T>) - Method in interface org.broadinstitute.hellbender.utils.iterators.PushPullTransformer
- submit(GATKRead) - Method in class org.broadinstitute.hellbender.utils.downsampling.FractionalDownsampler
- submit(GATKRead) - Method in class org.broadinstitute.hellbender.utils.downsampling.MutectDownsampler
- submit(GATKRead) - Method in class org.broadinstitute.hellbender.utils.downsampling.PassThroughDownsampler
- submit(GATKRead) - Method in class org.broadinstitute.hellbender.utils.downsampling.PositionalDownsampler
- submit(GATKRead) - Method in class org.broadinstitute.hellbender.utils.downsampling.ReservoirDownsampler
- submit(T) - Method in class org.broadinstitute.hellbender.utils.downsampling.Downsampler
-
Submit one item to the downsampler for consideration.
- submit(T) - Method in class org.broadinstitute.hellbender.utils.downsampling.LevelingDownsampler
- submit(T) - Method in interface org.broadinstitute.hellbender.utils.iterators.PushPullTransformer
-
Submit one item to the transformer for consideration.
- subsamplingRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- subSequence(int, int) - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.SequenceRC
- subSequence(int, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer.ASCIICharSequence
- SUBSET - Enum constant in enum class org.broadinstitute.hellbender.tools.reference.ReferencePair.Status
- subsetAlleles(GenotypesContext, int, List<Allele>, List<Allele>, GenotypePriorCalculator, GenotypeAssignmentMethod) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
- subsetAlleles(GenotypesContext, int, List<Allele>, List<Allele>, GenotypePriorCalculator, GenotypeAssignmentMethod, List<String>) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
-
Create the new GenotypesContext with the subsetted PLs and ADs Will reorder subsetted alleles according to the ordering provided by the list allelesToKeep
- subsetAlleles(GenotypesContext, List<Allele>, List<Allele>) - Static method in class picard.util.AlleleSubsettingUtils
-
Create the new GenotypesContext with the subsetted PLs and ADs Expects allelesToKeep to be in the same order in which they are in originalAlleles.
- subsetAlleles(VariantContext, List<Allele>) - Static method in class picard.util.AlleleSubsettingUtils
- subsetAnnotationsToTemporaryFile(List<String>, double[][], List<Boolean>) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
-
Subsets annotation data according to a boolean filter and writes a limited representation to a temporary HDF5 file.
- subsetSomaticAlleles(VCFHeader, GenotypesContext, List<Allele>, int[]) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
-
Remove alternate alleles from a set of genotypes turning removed alleles to no-call and dropping other per-allele attributes
- SubsettedLikelihoodMatrix<EVIDENCE extends htsjdk.samtools.util.Locatable,
A extends htsjdk.variant.variantcontext.Allele> - Class in org.broadinstitute.hellbender.tools.walkers.mutect -
Fast wrapper for a LikelihoodMatrix that uses only a subset of alleles.
- SubsettedLikelihoodMatrix(LikelihoodMatrix<EVIDENCE, A>, List<A>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix
- subsettedPLIndices(int, List<Allele>, List<Allele>) - Static method in class org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
-
Given a list of original alleles and a subset of new alleles to retain, find the array of old PL indices that correspond to new PL indices i.e.
- subsettedPLIndices(List<Allele>, List<Allele>) - Static method in class picard.util.AlleleSubsettingUtils
-
Given a list of original alleles and a subset of new alleles to retain, find the array of old PL indices that correspond to new PL indices i.e.
- subsetToNeighbors(V, int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Get a graph containing only the vertices within distance edges of target
- subsetToRefOnly(VariantContext, int) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Subset the samples in VC to reference only information with ref call alleles Preserves DP if present
- subsetToRefSource(int) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Get a subgraph of graph that contains only vertices within a given number of edges of the ref source vertex
- subsetVCToMatchSnp(VariantContext, Snp) - Static method in class picard.util.AlleleSubsettingUtils
-
Method to subset the alleles in the VariantContext to those in the input snp.
- SUBSTITUTION - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
-
A single string representing the substition from REF_BASE to ALT_BASE for convenience.
- SUBSTITUTION_RATE - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
-
The rate of the substitution in question.
- Substructure(List<Integer>, List<Range>) - Constructor for class picard.illumina.parser.ReadStructure.Substructure
-
Indices into the ReadStructure.descriptors for this specific substructure, indices must be in the order they appear in the descriptors list (but the indices do NOT have to be continuous)
- subtract(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- SUBTRACT - Enum constant in enum class picard.util.IntervalListTools.Action
- subtractMax(double[]) - Static method in class picard.util.MathUtil
- subtractRegions(GenomeLocSortedSet) - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
- successor(SVKmer.Base, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer
- successor(SVKmer.Base, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
-
Returns a new SVKmerLong that's like this one, but with its leading base discarded and a new one added to the end.
- successor(SVKmer.Base, int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
-
Returns a new SVKmerShort that's like this one, but with its leading base discarded and a new one added to the end.
- sum() - Method in class org.broadinstitute.hellbender.utils.Nucleotide.Counter
-
Return the total count of all nucleotide constants.
- sum(double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- sum(double...) - Method in class picard.util.MathUtil.LogMath
-
Computes the sum of the provided log values.
- sum(double[]) - Static method in class picard.util.MathUtil
-
Returns the sum of the elements in the array.
- sum(double[], double) - Static method in class picard.util.MathUtil
-
calculates the sum of an array and a double.
- sum(double[], double[]) - Static method in class picard.util.MathUtil
-
calculates the sum of the arrays as a third array.
- sum(double[], int, int) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Returns the sum of the elements in the array starting with start and ending before stop.
- sum(int[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- sum(long[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- sum(long[], int, int) - Static method in class picard.util.MathUtil
-
Returns the sum of the elements in the array starting with start and ending before stop.
- sum(IntToDoubleFunction) - Method in class org.broadinstitute.hellbender.utils.IndexRange
-
Sums the values of an int -> double function applied to this range
- SUM_GL_THRESH_NOCALL - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- SUM_OF_BASE_QUALITIES - Enum constant in enum class org.broadinstitute.hellbender.utils.read.markduplicates.MarkDuplicatesScoringStrategy
- sumADsOverSamples(VariantContext, boolean, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- sumArrayFunction(int, int, MathUtils.IntToDoubleArrayFunction) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- sumDoubleFunction(Collection<E>, ToDoubleFunction<E>) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- sumHistogramsFromFiles(List<MetricsFile<?, Integer>>, boolean) - Static method in class org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel
- sumIntFunction(Collection<E>, ToIntFunction<E>) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- sumLog10(double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Returns the sum of values whose log10s we have.
- summary - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.FileType
- summary - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- summary - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- summary - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance
- SUMMARY - Enum constant in enum class picard.sam.ValidateSamFile.Mode
- SUMMARY - Variable in class picard.metrics.GcBiasMetrics
- SUMMARY_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
- SUMMARY_FILE_NAME - Static variable in class org.broadinstitute.hellbender.utils.dragstr.STRTableFile
- SUMMARY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- SUMMARY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance
- SUMMARY_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
- SUMMARY_OUTPUT - Variable in class picard.analysis.CollectGcBiasMetrics
- SUMMARY_OUTPUT - Variable in class picard.fingerprint.CheckFingerprint
- SUMMARY_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- SUMMARY_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance
- summaryMetricsExtension - Static variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- sumOfBaseQualities(GATKRead) - Static method in enum class org.broadinstitute.hellbender.utils.read.markduplicates.MarkDuplicatesScoringStrategy
-
Computes the sum of base qualities of the given read.
- sumOfSquares(Collection<Integer>) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Computes the sum of squares of the given collection of ints or 0.0 if the collection is empty.
- sumOverAlleleIndicesAndCounts(IntToDoubleBiFunction) - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
- SUPERSET - Enum constant in enum class org.broadinstitute.hellbender.tools.reference.ReferencePair.Status
- SUPERSET - Enum constant in enum class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.SequenceDictionaryCompatibility
- SUPPORTED_ALLELES_TAG - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- SUPPORTED_BUILD - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- SUPPORTED_CHAIN_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- SUPPORTED_REFERENCE_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- supportedTypes() - Method in class picard.illumina.parser.MultiTileBclParser
- supportedTypes() - Method in class picard.illumina.parser.PerTileParser
-
The DataTypes that this parser can provide
- supportedTypes() - Method in class picard.illumina.parser.MultiTileParser
- supportedTypes() - Method in class picard.illumina.parser.PosParser
- SUPPORTING_CALLSET_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- SUPPORTING_CALLSET_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- SUPPORTING_CALLSETS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
- SUPPORTING_CALLSETS_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
- supportsCombine() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
-
Must be overloaded to return true for evaluation modules that support the combine operation
- supportsMetricAccumulationLevel() - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
- supportsSerialIteration() - Method in interface org.broadinstitute.hellbender.engine.ReadsDataSource
- supportsSerialIteration() - Method in class org.broadinstitute.hellbender.engine.ReadsPathDataSource
- supportsVariant(GATKRead, VariantContext, int) - Static method in class org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentEngine
- supportVariants - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
-
Supporting external panel.
- supportVariants - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
-
Supporting external panels.
- surroundingMeanQualitySize - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
surrounding mean quality (size) - if not specified, this feature is off
- surroundingMediaQualitySize - Variable in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
-
surrounding media quality (size) - if not specified, this feature is off
- SVAlignmentLengthFilter - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- SVAlignmentLengthFilter(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SVAlignmentLengthFilter
- SVAlleleCounter - Class in org.broadinstitute.hellbender.tools.sv
-
Simple allele counter for SVs.
- SVAlleleCounter(List<Allele>, List<Genotype>) - Constructor for class org.broadinstitute.hellbender.tools.sv.SVAlleleCounter
- SVAnnotate - Class in org.broadinstitute.hellbender.tools.walkers.sv
-
Adds gene overlap, predicted functional consequence, and noncoding element overlap annotations to a structural variant (SV) VCF from the GATK-SV pipeline.
- SVAnnotate() - Constructor for class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate
- SVAnnotateEngine - Class in org.broadinstitute.hellbender.tools.walkers.sv
- SVAnnotateEngine(SVAnnotateEngine.GTFIntervalTreesContainer, SVIntervalTree<String>, SAMSequenceDictionary, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
- SVAnnotateEngine.GTFIntervalTreesContainer - Class in org.broadinstitute.hellbender.tools.walkers.sv
- SVAnnotateEngine.SVSegment - Class in org.broadinstitute.hellbender.tools.walkers.sv
- SVCallRecord - Class in org.broadinstitute.hellbender.tools.sv
- SVCallRecord(String, String, int, Boolean, String, int, Boolean, GATKSVVCFConstants.StructuralVariantAnnotationType, GATKSVVCFConstants.ComplexVariantSubtype, Integer, List<String>, List<Allele>, List<Genotype>, Map<String, Object>) - Constructor for class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- SVCallRecord(String, String, int, Boolean, String, int, Boolean, GATKSVVCFConstants.StructuralVariantAnnotationType, GATKSVVCFConstants.ComplexVariantSubtype, Integer, List<String>, List<Allele>, List<Genotype>, Map<String, Object>, SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- SVCallRecordUtils - Class in org.broadinstitute.hellbender.tools.sv
- SVCallRecordUtils() - Constructor for class org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
- SVCluster - Class in org.broadinstitute.hellbender.tools.walkers.sv
-
Clusters structural variants based on coordinates, event type, and supporting algorithms.
- SVCluster() - Constructor for class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- SVClusterEngine - Class in org.broadinstitute.hellbender.tools.sv.cluster
-
Base class for clustering items that possess start/end genomic coordinates.
- SVClusterEngine(SVClusterEngine.CLUSTERING_TYPE, Function<SVClusterEngine.OutputCluster, SVCallRecord>, SVClusterLinkage<SVCallRecord>, SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine
- SVClusterEngine.CLUSTERING_TYPE - Enum Class in org.broadinstitute.hellbender.tools.sv.cluster
-
Available clustering algorithms
- SVClusterEngine.OutputCluster - Class in org.broadinstitute.hellbender.tools.sv.cluster
- SVClusterEngineArgumentsCollection - Class in org.broadinstitute.hellbender.tools.sv.cluster
-
Arguments for use with
SVClusterEngine. - SVClusterEngineArgumentsCollection() - Constructor for class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection
- SVClusterEngineFactory - Class in org.broadinstitute.hellbender.tools.sv.cluster
-
Some useful functions for creating different kinds of
SVClusterEngine. - SVClusterEngineFactory() - Constructor for class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineFactory
- SVClusterLinkage<T extends SVLocatable> - Class in org.broadinstitute.hellbender.tools.sv.cluster
- SVClusterLinkage() - Constructor for class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterLinkage
- SVConcordance - Class in org.broadinstitute.hellbender.tools.walkers.sv
-
This tool calculates SV genotype concordance between an "evaluation" VCF and a "truth" VCF.
- SVConcordance() - Constructor for class org.broadinstitute.hellbender.tools.walkers.sv.SVConcordance
- SVConcordanceAnnotator - Class in org.broadinstitute.hellbender.tools.sv.concordance
-
Generates SV records annotated with concordance metrics given a pair of "evaluation" and "truth" SVs.
- SVConcordanceAnnotator(boolean) - Constructor for class org.broadinstitute.hellbender.tools.sv.concordance.SVConcordanceAnnotator
- SVConcordanceLinkage - Class in org.broadinstitute.hellbender.tools.sv.concordance
- SVConcordanceLinkage(SAMSequenceDictionary) - Constructor for class org.broadinstitute.hellbender.tools.sv.concordance.SVConcordanceLinkage
- SVContext - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
-
Variant context with additional method to mine the structural variant specific information from structural variant records.
- SVD - Interface in org.broadinstitute.hellbender.utils.svd
-
Interface for SVD implementation.
- SVDDenoisedCopyRatioResult - Class in org.broadinstitute.hellbender.tools.copynumber.denoising
-
Represents copy ratios for a sample that has been standardized and denoised by an
SVDReadCountPanelOfNormals. - SVDDenoisedCopyRatioResult(SampleLocatableMetadata, List<SimpleInterval>, RealMatrix, RealMatrix) - Constructor for class org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisedCopyRatioResult
- SVDDenoisingUtils - Class in org.broadinstitute.hellbender.tools.copynumber.denoising
-
Utility class for package-private methods for performing SVD-based denoising and related operations.
- SVDFactory - Class in org.broadinstitute.hellbender.utils.svd
-
Entry point for creating an instance of SVD.
- SVDFactory() - Constructor for class org.broadinstitute.hellbender.utils.svd.SVDFactory
- SvDiscoverFromLocalAssemblyContigAlignmentsSpark - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
-
(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints
- SvDiscoverFromLocalAssemblyContigAlignmentsSpark() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark
- SvDiscoverFromLocalAssemblyContigAlignmentsSpark.AssemblyContigsClassifiedByAlignmentSignatures - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- SvDiscoveryInputMetaData - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- SvDiscoveryInputMetaData(JavaSparkContext, StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection, String, String, ReadMetadata, List<SVInterval>, PairedStrandedIntervalTree<EvidenceTargetLink>, Broadcast<SVIntervalTree<VariantContext>>, SAMFileHeader, ReferenceMultiSparkSource, Set<VCFHeaderLine>, Logger) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData
- SvDiscoveryInputMetaData.ReferenceData - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- SvDiscoveryInputMetaData.SampleSpecificData - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- SvDiscoveryUtils - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- SvDiscoveryUtils() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryUtils
- SVDReadCountPanelOfNormals - Interface in org.broadinstitute.hellbender.tools.copynumber.denoising
-
Interface for the panel of normals (PoN) for SVD-based coverage denoising.
- SVDUSTFilteredKmerizer - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
-
An iterator over kmers with a specified maximum DUST-style, low-complexity score.
- SVDUSTFilteredKmerizer(byte[], int, int, SVKmer) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVDUSTFilteredKmerizer
- SVDUSTFilteredKmerizer(CharSequence, int, int, SVKmer) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVDUSTFilteredKmerizer
- svEvidenceFilterModelFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- svEvidenceFilterThresholdProbability - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- SVFastqUtils - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
-
Memory-economical utilities for producing a FASTQ file.
- SVFastqUtils() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils
- SVFastqUtils.FastqRead - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- SVFastqUtils.FastqRead.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- SVFastqUtils.Mapping - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- SVFeature - Interface in org.broadinstitute.hellbender.tools.sv
- SVFeaturesHeader - Class in org.broadinstitute.hellbender.tools.sv
- SVFeaturesHeader(String, String, SAMSequenceDictionary, List<String>) - Constructor for class org.broadinstitute.hellbender.tools.sv.SVFeaturesHeader
- SVFileUtils - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- SVFileUtils() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFileUtils
- svGenomeGapsFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- svGenomeUmapS100File - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- SVInterval - Class in org.broadinstitute.hellbender.utils
-
Naturally collating, simple interval WARNING: THIS IS NOT THE SAME AS THE BED COORDINATE SYSTEM OR
SimpleInterval!!!!! - SVInterval(int, int, int) - Constructor for class org.broadinstitute.hellbender.utils.SVInterval
-
This constructor uses the
SVInterval.SVIntervalConstructorArgsValidator.RefuseNegativeContigAndCoordinatesas the validator. - SVInterval(int, int, int, SVInterval.SVIntervalConstructorArgsValidator) - Constructor for class org.broadinstitute.hellbender.utils.SVInterval
- SVInterval.Serializer - Class in org.broadinstitute.hellbender.utils
- SVInterval.SVIntervalConstructorArgsValidator - Interface in org.broadinstitute.hellbender.utils
- SVIntervalTree<V> - Class in org.broadinstitute.hellbender.utils
-
A Red-Black tree with intervals for keys.
- SVIntervalTree() - Constructor for class org.broadinstitute.hellbender.utils.SVIntervalTree
- SVIntervalTree.Entry<V1> - Interface in org.broadinstitute.hellbender.utils
- SVIntervalTree.FwdIterator - Class in org.broadinstitute.hellbender.utils
- SVIntervalTree.OverlapIterator - Class in org.broadinstitute.hellbender.utils
- SVIntervalTree.RevIterator - Class in org.broadinstitute.hellbender.utils
- SVIntervalTree.Serializer<T> - Class in org.broadinstitute.hellbender.utils
- SVIntervalTree.ValuesIterator<V1> - Class in org.broadinstitute.hellbender.utils
- SVKmer - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- SVKmer() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer
- SVKmer.Base - Enum Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- SVKmerizer - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
-
Iterator over successive Kmers from a sequence of characters.
- SVKmerizer(byte[], int, int, SVKmer) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- SVKmerizer(byte[], int, SVKmer) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- SVKmerizer(int, int, CharSequence) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- SVKmerizer(int, CharSequence) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- SVKmerizer(CharSequence, int, int, SVKmer) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- SVKmerizer(CharSequence, int, SVKmer) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- SVKmerizer.ASCIICharSequence - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- SVKmerLong - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
-
An immutable SVKmerLong.
- SVKmerLong() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
- SVKmerLong(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
-
Makes an empty SVKmerLong.
- SVKmerLong(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
- SVKmerLong(SVKmer) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
- SVKmerLong(SVKmerLong) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
- SVKmerLong.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- SVKmerShort - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
-
An immutable SVKmerShort.
- SVKmerShort() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
-
Makes an empty SVKmerShort.
- SVKmerShort(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
-
Makes an empty SVKmerShort.
- SVKmerShort(long) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
- SVKmerShort(SVKmerShort) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
- SVKmerShort.Serializer - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- svLen - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- SVLEN - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- SVLocatable - Interface in org.broadinstitute.hellbender.tools.sv
-
Any class with loci that are potentially on different chromosomes should implement this interface.
- SVLocation - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- SVLocation(int, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVLocation
- SVMappingQualityFilter - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
- SVMappingQualityFilter(int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SVMappingQualityFilter
- SVNoveltyRate - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- SVReadFilter - Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
- SVReadFilter(StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter
- SVReferenceUtils - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- SVReferenceUtils() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVReferenceUtils
- SVSegment(GATKSVVCFConstants.StructuralVariantAnnotationType, SimpleInterval) - Constructor for class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine.SVSegment
- SvType - Class in org.broadinstitute.hellbender.tools.spark.sv.discovery
-
Various types of structural variations.
- SvType(String, int, int, String, Allele, Allele, int, Map<String, Object>) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- SVTYPE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- SVUtils - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
-
Useful scraps of this and that.
- SVUtils() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
- SVUtils.IteratorFilter<T> - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- SVVCFReader - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- SVVCFReader() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVVCFReader
- SVVCFWriter - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
-
A utility class that writes out variants to a VCF file.
- SVVCFWriter() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.SVVCFWriter
- swapAlleles(VariantContext, Allele, Allele) - Static method in class picard.util.AlleleSubsettingUtils
-
Swaps one of the alleles in a VC (and its genotypes) with another.
- SWAPPED_ALLELES - Static variable in class picard.util.LiftoverUtils
-
Attribute used to store the fact that the alt and ref alleles of the variant have been swapped, while all the INFO annotations have not.
- swapRefAlt(VariantContext, Collection<String>, Collection<String>) - Static method in class picard.util.LiftoverUtils
-
method to swap the reference and alt alleles of a bi-allelic, SNP
- switchToNaturalLog() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
- SWNativeAlignerWrapper - Class in org.broadinstitute.hellbender.utils.smithwaterman
-
A wrapper that converts instances of
SWAlignerNativeBindinginto aSmithWatermanAligner - SWNativeAlignerWrapper(SWAlignerNativeBinding) - Constructor for class org.broadinstitute.hellbender.utils.smithwaterman.SWNativeAlignerWrapper
- SYMB_ALT_STRING_DEL - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- SYMB_ALT_STRING_DUP - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- SYMB_ALT_STRING_INS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- SYMB_ALT_STRING_INV - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- SYMB_ALT_STRING_INVDUP - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- SYMBOLIC_ALLELE_DEFINITION_HEADER_TAG - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- SYMBOLIC_UNASSEMBLED_EVENT_ALLELE - Static variable in class org.broadinstitute.hellbender.utils.haplotype.EventMap
- SYMDIFF - Enum constant in enum class picard.util.IntervalListTools.Action
- SYMMETRIC_INDELS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- symmetricDirichlet(int, double) - Static method in class org.broadinstitute.hellbender.utils.Dirichlet
-
Create a symmetric distribution Dir(a/K, a/K, a/K .
- symmetricIndels - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- SYNONYMOUS_CODING - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- SYNONYMOUS_START - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- SYNONYMOUS_STOP - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- SYNTAX_TRANSITION_URL - Static variable in class picard.cmdline.CommandLineProgram
- SYNTHESIS - Enum constant in enum class org.broadinstitute.hellbender.utils.read.FlowBasedRead.Direction
- SYNTHETIC_PHASESET_PREFIX - Static variable in class picard.fingerprint.HaplotypeMap
- SYSTEM_SUGGESTED_THREAD_NUMBER - Static variable in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- SystemProperty - Annotation Interface in org.broadinstitute.hellbender.utils.config
-
An annotation to denote Configuration options that should be injected into the Java System Properties.
T
- T - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer.Base
- T - Enum constant in enum class org.broadinstitute.hellbender.utils.BaseUtils.Base
- T - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- T - Enum constant in enum class picard.analysis.artifacts.Transition.Base
- T - Enum constant in enum class picard.illumina.parser.IntensityChannel
- T - Enum constant in enum class picard.illumina.parser.ReadType
- T_FOLLOWED_BY_INSERTION_BASE - Static variable in class org.broadinstitute.hellbender.utils.pileup.PileupElement
- TAB_MODE - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- TabbedInputParser - Class in picard.util
-
Parser for tab-delimited files
- TabbedInputParser(boolean, File...) - Constructor for class picard.util.TabbedInputParser
-
Constructor
- TabbedInputParser(boolean, InputStream...) - Constructor for class picard.util.TabbedInputParser
-
Constructor
- TabbedTextFileWithHeaderParser - Class in picard.util
-
Parse a tabbed text file in which columns are found by looking at a header line rather than by position.
- TabbedTextFileWithHeaderParser(File) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
- TabbedTextFileWithHeaderParser(File, String[]) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
- TabbedTextFileWithHeaderParser(TabbedInputParser) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
- TabbedTextFileWithHeaderParser.Row - Class in picard.util
- TABLE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter.DEPTH_OF_COVERAGE_OUTPUT_FORMAT
- TABLE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter.OUTPUT_FORMAT
- TableCodec - Class in org.broadinstitute.hellbender.utils.codecs.table
-
Reads tab deliminated tabular text files
- TableCodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.table.TableCodec
-
Create a TableCodec for IGV track data.
- TableCodec(String) - Constructor for class org.broadinstitute.hellbender.utils.codecs.table.TableCodec
-
Create a TableCodec with a configured header line delimiter
- TableColumnCollection - Class in org.broadinstitute.hellbender.utils.tsv
-
Represents a list of table columns.
- TableColumnCollection(Class<? extends Enum<?>>) - Constructor for class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Creates a new table-column collection from a set of enum constants.
- TableColumnCollection(Iterable<String>) - Constructor for class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Creates a new table-column names collection.
- TableColumnCollection(Object...) - Constructor for class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Creates a new table-column names collection.
- TableColumnCollection(String...) - Constructor for class org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
-
Creates a new table-column names collection.
- tableDataset - Variable in class org.broadinstitute.hellbender.utils.bigquery.TableReference
- TableEntry(String, String) - Constructor for class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableEntry
- TableFeature - Class in org.broadinstitute.hellbender.utils.codecs.table
-
Feature representing a row in a text table.
- TableFeature(Locatable, List<String>, List<String>) - Constructor for class org.broadinstitute.hellbender.utils.codecs.table.TableFeature
-
Public constructor.
- TableFuncotation - Class in org.broadinstitute.hellbender.tools.funcotator.dataSources
-
A
Funcotationto hold data from simple tabular data. - tableName - Variable in class org.broadinstitute.hellbender.utils.bigquery.TableReference
- tableProject - Variable in class org.broadinstitute.hellbender.utils.bigquery.TableReference
- TableReader<R> - Class in org.broadinstitute.hellbender.utils.tsv
-
Reads the contents of a tab separated value formatted text input into records of an arbitrary type
TableReader. - TableReader(Reader) - Constructor for class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Creates a new table reader given an input
Reader. - TableReader(String, Reader) - Constructor for class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Creates a new table reader given an input
Reader. - TableReader(Path) - Constructor for class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Creates a new table reader given the input file path.
- TableReference - Class in org.broadinstitute.hellbender.utils.bigquery
-
A reference to a BigQuery table by project, dataset, and table name, along with the contained fields.
- TableReference(String, String, String, List<String>) - Constructor for class org.broadinstitute.hellbender.utils.bigquery.TableReference
- TableReference(String, List<String>) - Constructor for class org.broadinstitute.hellbender.utils.bigquery.TableReference
-
TableReference from fully qualified table name.
- TableRow(String, int, List<GATKPath>) - Constructor for class org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableRow
- TableUtils - Class in org.broadinstitute.hellbender.utils.tsv
-
Common constants for table readers and writers.
- TableWriter<R> - Class in org.broadinstitute.hellbender.utils.tsv
-
Class to write tab separated value files.
- TableWriter(Writer, TableColumnCollection) - Constructor for class org.broadinstitute.hellbender.utils.tsv.TableWriter
-
Creates a new table writer given the destination writer and column names.
- TableWriter(Path, TableColumnCollection) - Constructor for class org.broadinstitute.hellbender.utils.tsv.TableWriter
-
Creates a new table writer given the file and column names.
- TAG - Variable in class picard.sam.FilterSamReads
- TAG_DUPLICATE_SET_MEMBERS - Variable in class picard.sam.markduplicates.MarkDuplicates
- TAG_GROUP_SEPERATOR - Variable in class picard.sam.SamToFastqWithTags
- TAG_PER_MOLECULAR_INDEX - Variable in class picard.illumina.IlluminaBasecallsToSam
- TAG_VALUE - Variable in class picard.sam.FilterSamReads
- TAGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Transcript created or extended using assembled RNA-seq long reads.
- TagGermlineEvents - Class in org.broadinstitute.hellbender.tools.copynumber.utils
- TagGermlineEvents() - Constructor for class org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEvents
- TAGGING_POLICY - Variable in class picard.sam.markduplicates.MarkDuplicates
- taggingPolicy - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- TAGS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.HtsgetReader
- TAGS_TO_DROP - Variable in class picard.vcf.LiftoverVcf
- TAGS_TO_REVERSE - Variable in class picard.vcf.LiftoverVcf
- tagTumorSegmentsWithGermlineActivity(List<AnnotatedInterval>, List<AnnotatedInterval>, String, SAMSequenceDictionary, String, int, double) - Static method in class org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging.SimpleGermlineTagger
-
Look for concordant endpoints for determining whether an event in the tumor regions are in the germline regions.
- Tail - Enum Class in org.broadinstitute.hellbender.utils
-
Enum for two-sided things, for example which end of a read has been clipped, which end of a chain within an assembly graph etc.
- TAIL_LIMIT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
- takeSome(Interval, long, long, double) - Method in interface picard.util.IntervalList.IntervalListScatterer
-
Figure out how much of the input interval to put into current list and how much to leave for the next interval list.
- takeSome(Interval, long, long, double) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
- takeSome(Interval, long, long, double) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCountWithDistributedRemainder
- takeSome(Interval, long, long, double) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
- takeSome(Interval, long, long, double) - Method in class picard.util.IntervalList.IntervalListScattererWithSubdivision
- tallyPrimaryAlignments(boolean) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
- TANDEM_READS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- TandemRepeat - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Tandem repeat unit composition and counts per allele
- TandemRepeat - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies the evals into sites that are tandem repeats
- TandemRepeat() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.TandemRepeat
- TandemRepeat(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.TandemRepeat
- TANGENT_NORMALIZED_COUNTS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- TANGENT_NORMALIZED_COUNTS_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- target - Variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.DiscordantReadPairEvidence
- TARGET_BUILD - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- TARGET_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- TARGET_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- TARGET_INTERVALS - Variable in class picard.analysis.directed.CollectTargetedMetrics
- TARGET_INTERVALS - Variable in class picard.vcf.CollectVariantCallingMetrics
- TARGET_TERRITORY - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of unique bases covered by the intervals of all targets that should be covered
- TARGET_TERRITORY_COLUMN_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord
- TargetedPcrMetrics - Class in picard.analysis.directed
-
Metrics class for the analysis of reads obtained from targeted pcr experiments e.g.
- TargetedPcrMetrics() - Constructor for class picard.analysis.directed.TargetedPcrMetrics
- TargetedPcrMetricsCollector - Class in picard.analysis.directed
-
Calculates HS metrics for a given SAM or BAM file.
- TargetedPcrMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, boolean, boolean, int, int) - Constructor for class picard.analysis.directed.TargetedPcrMetricsCollector
- TargetedPcrMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, int, int) - Constructor for class picard.analysis.directed.TargetedPcrMetricsCollector
- targetForwardStrand - Variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.DiscordantReadPairEvidence
- targetLinkFile - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- TargetMetrics - Class in picard.analysis.directed
-
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
- TargetMetrics() - Constructor for class picard.analysis.directed.TargetMetrics
- TargetMetricsBase - Class in picard.analysis.directed
-
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
- TargetMetricsBase() - Constructor for class picard.analysis.directed.TargetMetricsBase
- TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics> - Class in picard.analysis.directed
-
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
- TargetMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, boolean, boolean, int, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector
- TargetMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, int, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector
- TargetMetricsCollector.Coverage - Class in picard.analysis.directed
-
A simple class that is used to store the coverage information about an interval.
- TargetMetricsCollector.PerUnitTargetMetricCollector - Class in picard.analysis.directed
-
Collect the Target Metrics for one unit of "accumulation" (i.e.
- targetQuality - Variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.DiscordantReadPairEvidence
- TARGETS - Variable in class picard.util.BaitDesigner
- TAX_DUMP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
- TAX_DUMP_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
- taxdumpPath - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
- taxIDs - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenAlignmentHit
- TAXONOMIC_DATABASE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- TAXONOMIC_DATABASE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- taxonomyDatabasePath - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection
- TEC - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- Template - Static variable in enum class picard.illumina.parser.ReadType
- TemplateFragmentOrdinal - Enum Class in org.broadinstitute.hellbender.tools.spark.sv.evidence
-
Indicates the ordinal of a fragment in a paired sequenced template.
- templateLengthMean - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- templateLengthStd - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- templates - Variable in class picard.illumina.parser.ReadStructure
- TemplateSizeAnomaly(Kryo, Input) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.TemplateSizeAnomaly
- TemplateSizeAnomaly(SVInterval, int, int) - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.TemplateSizeAnomaly
- TensorType - Enum Class in org.broadinstitute.hellbender.tools.walkers.vqsr
-
TensorType documents the tensors available and what information they encode.
- terminate() - Method in class org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor
-
Terminate the remote process, closing the fifo if any.
- terminate() - Method in class org.broadinstitute.hellbender.utils.runtime.AsynchronousStreamWriter
-
Terminate the async writer, cancelling any outstanding work.
- terminate() - Method in class org.broadinstitute.hellbender.utils.runtime.StreamingProcessController
-
Close the input stream, close the FIFO, and wait for the remote process to terminate destroying it if necessary.
- test(double[], double[], MannWhitneyU.TestType) - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU
-
Constructs a new rank sum test with the given data.
- test(Cigar, int) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.HostAlignmentReadFilter
- test(VariantContext) - Method in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter.CountingAndVariantFilter
- test(VariantContext) - Method in class org.broadinstitute.hellbender.engine.filters.CountingVariantFilter
- test(VariantContext) - Method in class org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary.AllowAllVariantsVariantFilter
- test(VariantContext) - Method in class org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary.NotSymbolicOrSVVariantFilter
- test(VariantContext) - Method in class org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary.PassesFiltersVariantFilter
- test(VariantContext) - Method in class org.broadinstitute.hellbender.engine.filters.VariantIDsVariantFilter
- test(VariantContext) - Method in class org.broadinstitute.hellbender.engine.filters.VariantTypesVariantFilter
- test(VariantContext) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SVAlignmentLengthFilter
- test(VariantContext) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SVMappingQualityFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.AlignmentAgreesWithHeaderReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.AmbiguousBaseReadFilter
-
Test read for a given maximum threshold of allowable ambiguous bases
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter.CountingAndReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ExcessiveEndClippedReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.flow.FlowBasedTPAttributeSymetricReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.flow.FlowBasedTPAttributeValidReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.flow.HmerQualitySymetricReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.flow.ReadGroupHasFlowOrderReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.flow.WellformedFlowBasedReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.FragmentLengthReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.IntervalOverlapReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.JexlExpressionReadTagValueFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.LibraryReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.MappingQualityReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.MateDistantReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.MetricsReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.NotOpticalDuplicateReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.OverclippedReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.PlatformReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.PlatformUnitReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilter.ReadFilterAnd
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.AllowAllReadsReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.CigarContainsNoNOperator
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.FirstOfPairReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.GoodCigarReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.HasReadGroupReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.MappedReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.MappingQualityAvailableReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.MappingQualityNotZeroReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.MatchingBasesAndQualsReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.MateDifferentStrandReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.MateOnSameContigOrNoMappedMateReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.MateUnmappedAndUnmappedReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.NonChimericOriginalAlignmentReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.NonZeroFragmentLengthReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.NonZeroReferenceLengthAlignmentReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.NotDuplicateReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.NotProperlyPairedReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.NotSecondaryAlignmentReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.NotSupplementaryAlignmentReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.PairedReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.PassesVendorQualityCheckReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.PrimaryLineReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.ProperlyPairedReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.ReadLengthEqualsCigarLengthReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.SecondOfPairReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.SeqIsStoredReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.ValidAlignmentEndReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.ValidAlignmentStartReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadGroupBlackListReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadGroupReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadLengthReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadNameReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadStrandFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.ReadTagValueFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.SampleReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.SoftClippedReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.engine.filters.WellformedReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.ContainsKmerReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.HostAlignmentReadFilter
- test(GATKRead) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.MarkedOpticalDuplicateReadFilter
- Test - Class in picard
- Test() - Constructor for class picard.Test
- TEST - Enum constant in enum class org.broadinstitute.hellbender.utils.clustering.BayesianGaussianMixtureModeller.InitMethod
- TEST_INPUT_READABILITY - Variable in class picard.fingerprint.CalculateFingerprintMetrics
- TEST_INPUT_READABILITY - Variable in class picard.fingerprint.CrosscheckFingerprints
- TEST_INPUT_READABILITY - Variable in class picard.fingerprint.ExtractFingerprint
- TEST_INPUT_READABILITY - Variable in class picard.fingerprint.IdentifyContaminant
- testHmer(byte[], int, int) - Method in class org.broadinstitute.hellbender.engine.filters.flow.FlowBasedTPAttributeSymetricReadFilter
- testHmer(byte[], int, int) - Method in class org.broadinstitute.hellbender.engine.filters.flow.FlowBasedTPAttributeValidReadFilter
- testHmer(byte[], int, int) - Method in class org.broadinstitute.hellbender.engine.filters.flow.HmerQualitySymetricReadFilter
- Testing - Class in picard.cmdline.programgroups
-
For internal test purposes only.
- Testing() - Constructor for class picard.cmdline.programgroups.Testing
- TestingReadThreadingGraph - Class in org.broadinstitute.hellbender.testutils
- TestingReadThreadingGraph(String) - Constructor for class org.broadinstitute.hellbender.testutils.TestingReadThreadingGraph
-
Constructs a read-threading-graph for a string representation.
- TestProgramGroup - Class in org.broadinstitute.hellbender.cmdline
-
Program group for use with internal test CommandLinePrograms only.
- TestProgramGroup() - Constructor for class org.broadinstitute.hellbender.cmdline.TestProgramGroup
- testReadAndGatherEvidence(GATKRead, List<BreakpointEvidence>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
-
Used in production to gather evidence derived from K-S calculation on windows.
- TestStatistic(double, double) - Constructor for class org.broadinstitute.hellbender.utils.MannWhitneyU.TestStatistic
- TestStatistic(double, double, double) - Constructor for class org.broadinstitute.hellbender.utils.MannWhitneyU.TestStatistic
- testValueAsJSON(String, ArgumentDefinition, String, String) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLWorkUnitHandler
-
Return a test input value for use in the WDL validation test inputs.
- TextFormattingUtils - Class in org.broadinstitute.hellbender.utils.text
-
Common utilities for dealing with text formatting.
- TextMDCodec - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- TextMDCodec() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec
- TextMDCodec.DeletionMDElement - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- TextMDCodec.MatchMDElement - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- TextMDCodec.MDElement - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- TextMDCodec.MismatchMDElement - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
- textWriter(OutputStream, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.dragstr.DragstrLocusUtils
-
Returns a tab separated text format writer.
- THEORETICAL_SENSITIVITY - Variable in class picard.analysis.TheoreticalSensitivityMetrics
-
Estimation of sensitivity at a particular allele fraction.
- THEORETICAL_SENSITIVITY_OUTPUT - Variable in class picard.analysis.CollectWgsMetrics
- THEORETICAL_SENSITIVITY_OUTPUT - Variable in class picard.analysis.directed.CollectTargetedMetrics
- THEORETICAL_SENSITIVITY_Q - Variable in class picard.analysis.TheoreticalSensitivityMetrics
-
Phred-scaled value of 1-THEORETICAL_SENSITIVITY.
- theoreticalHetSensitivitySampleSize - Variable in class picard.analysis.WgsMetrics
-
The sample size used for theoretical het sensitivity.
- theoreticalSensitivity(Histogram<Integer>, Histogram<Integer>, int, double, double) - Static method in class picard.analysis.TheoreticalSensitivity
-
Calculates the theoretical sensitivity with a given Phred-scaled quality score distribution and depth distribution.
- TheoreticalSensitivity - Class in picard.analysis
-
Created by David Benjamin on 5/13/15.
- TheoreticalSensitivity() - Constructor for class picard.analysis.TheoreticalSensitivity
- TheoreticalSensitivity.RouletteWheel - Class in picard.analysis
- TheoreticalSensitivityMetrics - Class in picard.analysis
-
TheoreticalSensitivityMetrics, are metrics calculated from TheoreticalSensitivity and parameters used in the calculation.
- TheoreticalSensitivityMetrics() - Constructor for class picard.analysis.TheoreticalSensitivityMetrics
- THETA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- thetaIlmn - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- thetaRegionNumSites - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ThetaVariantEvaluator
- ThetaVariantEvaluator - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
- ThetaVariantEvaluator(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ThetaVariantEvaluator
- THREAD_COUNT - Variable in class picard.vcf.CollectVariantCallingMetrics
- THREAD_COUNT - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- threadLocalPairHMMComputeTimeDiff - Variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
- ThreadPoolExecutorUtil - Class in picard.util
- ThreadPoolExecutorUtil() - Constructor for class picard.util.ThreadPoolExecutorUtil
- ThreadPoolExecutorWithExceptions - Class in picard.util
-
This version of the thread pool executor will throw an exception if any of the internal jobs have throw exceptions while executing
- ThreadPoolExecutorWithExceptions(int) - Constructor for class picard.util.ThreadPoolExecutorWithExceptions
-
Creates a fixed size thread pool executor that will rethrow exceptions from submitted jobs.
- THREADS_FULL_NAME - Static variable in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- THREE - Enum constant in enum class picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
- THREE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToFastq
- THREE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToSam
- THREE_PRIME_ADAPTER - Variable in class picard.illumina.MarkIlluminaAdapters
- THREE_PRIME_ADAPTER_LOCATION_TAG - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- THREE_PRIME_FLANK - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
The variant is downstream of the chosen transcript
- THREE_PRIME_FLANK_SIZE_DEFAULT_VALUE - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- THREE_PRIME_FLANK_SIZE_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- THREE_PRIME_NESTED_SUPPORTED_EXTENSION - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
3' end extended based on RNA-seq data.
- THREE_PRIME_OVERLAPPING_NCRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- THREE_PRIME_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- THREE_PRIME_STANDARD_SUPPORTED_EXTENSION - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
3' end extended based on RNA-seq data.
- THREE_PRIME_TRIMMING_TAG - Static variable in class org.broadinstitute.hellbender.tools.ClipReads
- THREE_PRIME_UTR - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Variant is on the 3'UTR for the chosen transcript
- THREE_WAYS_DISAGREEMENT_ONLY_Q - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
-
The (phred) rate of bases that disagree with both the reference and their mate (which also disagree)
- threePrimeFlankSize - Variable in class org.broadinstitute.hellbender.tools.funcotator.FlankSettings
- threePrimeFlankSize - Variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorVariantArgumentCollection
- THREONINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- threshold - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.AlleleFrequencyQC
- THRESHOLD_FOR_ALLELE_COUNT_CONVERGENCE - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator
- THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- THRESHOLD_METADATA_TAG - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterStats
- THRESHOLD_STRATEGY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
-
meta-filtering parameters -- how we set the threshold on artifact probabilities
- ThresholdCalculator - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- ThresholdCalculator(ThresholdCalculator.Strategy, double, double, double) - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ThresholdCalculator
- ThresholdCalculator.Strategy - Enum Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- thresholdStrategy - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- THROW_ON_DIFF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark
- THROW_ON_DIFF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.validation.CompareBaseQualities
- throwOnDiff - Variable in class org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark
- throwOnDiff - Variable in class org.broadinstitute.hellbender.tools.validation.CompareBaseQualities
- THYMINE - Static variable in enum class org.broadinstitute.hellbender.utils.Nucleotide
- tile - Variable in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- tile - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
-
The tile, which is determined from the file name
- tile - Variable in class picard.sam.util.PhysicalLocationInt
- Tile - Class in picard.illumina.parser
-
Represents a tile from TileMetricsOut.bin.
- Tile(int, int, float, float, TilePhasingValue...) - Constructor for class picard.illumina.parser.Tile
- TILE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
The Tile that is described by this metric
- TILE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The Tile that is described by this metric.
- TILE_LIMIT - Variable in class picard.illumina.IlluminaBasecallsToFastq
- TILE_LIMIT - Variable in class picard.illumina.IlluminaBasecallsToSam
- TILE_METRICS_OUT_FILE_NAME - Static variable in class picard.illumina.parser.TileMetricsUtil
-
The expected name of the tile metrics output file.
- TILE_NUMBER_COMPARATOR - Static variable in class picard.illumina.BasecallsConverter
-
A comparator used to sort Illumina tiles in their proper order.
- TILE_NUMBERS - Variable in class picard.illumina.CheckIlluminaDirectory
- tileIndex - Variable in class picard.illumina.parser.MultiTileFileUtil
- TileIndex - Class in picard.illumina.parser
-
Load a file containing 8-byte records like this: tile number: 4-byte int number of clusters in tile: 4-byte int Number of records to read is determined by reaching EOF.
- TileIndex.TileIndexRecord - Class in picard.illumina.parser
- tileIsSet() - Method in class picard.illumina.parser.ClusterData
- tileLimit(Integer) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures the total number of tiles that the converter will process.
- tileMetricsOut() - Method in class picard.illumina.parser.IlluminaFileUtil
- TileMetricsOutReader - Class in picard.illumina.parser.readers
-
Reads a TileMetricsOut file commonly found in the InterOp directory of an Illumina Run Folder.
- TileMetricsOutReader(File) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader
-
Return a TileMetricsOutReader for the specified file
- TileMetricsOutReader.IlluminaLaneTileCode - Class in picard.illumina.parser.readers
-
Helper class which captures the combination of a lane, tile & metric code
- TileMetricsOutReader.IlluminaTileMetrics - Class in picard.illumina.parser.readers
-
IlluminaPhasingMetrics corresponds to a single record in a TileMetricsOut file
- TileMetricsOutReader.TileMetricsVersion - Enum Class in picard.illumina.parser.readers
- TileMetricsUtil - Class in picard.illumina.parser
-
Utility for reading the tile data from an Illumina run directory's TileMetricsOut.bin file
- TileMetricsUtil() - Constructor for class picard.illumina.parser.TileMetricsUtil
- TilePhasingValue - Class in picard.illumina.parser
-
Captures information about a phasing value - Which read it corresponds to, which phasing type and a median value
- TilePhasingValue(TileTemplateRead, float, float) - Constructor for class picard.illumina.parser.TilePhasingValue
- tiles - Variable in class picard.illumina.BasecallsConverter
- tiles - Variable in class picard.illumina.parser.ParameterizedFileUtil
- TileTemplateRead - Enum Class in picard.illumina.parser
-
Defines the first or second template read for a tile
- tiTvDerivedRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator
- tiTvRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MetricsCollection
- tiTvRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator
- TiTvRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- TiTvRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- TiTvRatioPerSample - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- TiTvRatioStandard - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator
- TiTvVariantEvaluator - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
- TiTvVariantEvaluator(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator
- TLEN - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestField
- tlodThreshold - Variable in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
-
Only variants with tumor LODs exceeding this threshold will be written to the VCF, regardless of filter status.
- TMP_DIR - Variable in class picard.cmdline.CommandLineProgram
- TMP_DIR_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- tmpDir - Variable in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- TMRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- TN - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
- TN - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- TN_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The TN (true negative) count across all variants
- TN_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
- TN_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
- TNP - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantType
- toAbsolute(int, int) - Method in class org.broadinstitute.hellbender.utils.reference.AbsoluteCoordinates
- toAbsolute(String, int) - Method in class org.broadinstitute.hellbender.utils.reference.AbsoluteCoordinates
- toAbsolute(SimpleInterval) - Method in class org.broadinstitute.hellbender.utils.reference.AbsoluteCoordinates
-
Obtains the absolute coordinate for the start position in an interval.
- toApplyBQSRArgumentCollection(RecalibrationArgumentCollection) - Method in class org.broadinstitute.hellbender.tools.ApplyBQSRUniqueArgumentCollection
-
Combine the extra arguments in
ApplyBQSRArgumentCollectionthat are not in thisApplyBQSRUniqueArgumentCollectionfrom the givenRecalibrationArgumentCollectionto create aApplyBQSRArgumentCollection. - toArray() - Method in class org.broadinstitute.hellbender.utils.tsv.DataLine
-
Returns the current values in a string array.
- toBedpeString(ReadMetadata) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
- toCode() - Method in enum class picard.pedigree.Sex
-
Returns the code used to encode this sex in a ped/fam file.
- toCoverage - Variable in class org.broadinstitute.hellbender.utils.downsampling.DownsamplingMethod
-
Actual downsampling target is specified as an integer number of reads.
- toDoubleArray() - Method in class org.broadinstitute.hellbender.utils.dragstr.DoubleSequence
-
Returns a new double array containing the elements of the sequence in the same order.
- toDownsamplingInfo(DownsamplingMethod) - Static method in class org.broadinstitute.hellbender.utils.locusiterator.LIBSDownsamplingInfo
- toFraction - Variable in class org.broadinstitute.hellbender.utils.downsampling.DownsamplingMethod
-
Actual downsampling target is specified as a fraction of total available reads.
- toHeader() - Method in interface org.broadinstitute.hellbender.tools.copynumber.formats.metadata.Metadata
- toHeader() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleLocatableMetadata
- toHeader() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleLocatableMetadata
- toHeader() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleMetadata
- toIndex(int) - Method in interface org.broadinstitute.hellbender.utils.collections.Permutation
-
Given an index on the original list, returns the position of tha element in the resulting list.
- toIndex(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.ActualPermutation
- toIndex(int) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.NonPermutation
- toIntExactOrThrow(long, Supplier<RuntimeException>) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Convert a long to the exact same int value.
- toIteratorActivityProfileState(Iterator<ActivityProfileStateRange>) - Static method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileStateRange
- toKey() - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMapSpark
-
getKey returns the key part of a Map.Entry
- toKey() - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMultiMapSpark
-
getKey returns the key part of a Map.Entry
- toKey() - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchCollection
-
in a general multiset, the entry is the key
- toKey() - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchMap
-
getKey returns the key part of a Map.Entry
- toKey() - Method in class org.broadinstitute.hellbender.utils.collections.HopscotchMultiMap
-
getKey returns the key part of a Map.Entry
- toKmer(byte[], SVKmer) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- toKmer(CharSequence, SVKmer) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer
- toList() - Method in interface org.broadinstitute.hellbender.utils.collections.Permutation
-
Returns an unmodifiable view to the original element list.
- toList() - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
-
convert this object to a list
- toList() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.ActualPermutation
- toList() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.NonPermutation
- toList() - Method in class org.broadinstitute.hellbender.utils.tsv.TableReader
-
Read the remaining records into a list.
- toLog10(double[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Converts a real space array of numbers (typically probabilities) into a log10 array
- TOO_MANY_SCAFFOLDS_DEFAULT - Static variable in class org.broadinstitute.hellbender.tools.LocalAssembler
- TOO_MANY_TRAVERSALS_DEFAULT - Static variable in class org.broadinstitute.hellbender.tools.LocalAssembler
- toolDisplayName(Class<?>) - Static method in class org.broadinstitute.hellbender.utils.runtime.RuntimeUtils
-
Given a Class that is a CommandLineProgram, either GATK or Picard, return a display name suitable for presentation to the user that distinguishes GATK tools from Picard tools by including a " (Picard)" suffix;
- toolVersion - Variable in class org.broadinstitute.hellbender.tools.funcotator.OutputRenderer
-
The version of the tool used to produce the output file.
- TOP - Enum constant in enum class picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
- TOP_GENOMIC_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- toPackedString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- toPath() - Method in class org.broadinstitute.hellbender.engine.GATKPath
- toPath() - Method in class picard.nio.PicardHtsPath
-
Resolve the URI of this object to a
Pathobject. - toPaths(Collection<PicardHtsPath>) - Static method in class picard.nio.PicardHtsPath
-
Create a
List<Path>fromPicardHtsPaths - toReadStructure() - Method in class picard.illumina.parser.ReadStructure.Substructure
-
Create a ReadStructure from this substructure composed of only the descriptors contained in this substructure, Any ReadDescriptors not in this substructure are treated as if they don't exist (e.g.
- toRef() - Method in interface org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- toRef() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- toRef() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- toRelative(long) - Method in class org.broadinstitute.hellbender.utils.reference.AbsoluteCoordinates
- toRelative(long, AbsoluteCoordinates.RelativeFactory<E>) - Method in class org.broadinstitute.hellbender.utils.reference.AbsoluteCoordinates
- toSAMRecord(SAMFileHeader, String, byte[], boolean, int, Collection<? extends SAMRecord.SAMTagAndValue>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
Returns a
SAMRecordinstance that reflects this alignment interval given the outputSAMFileHeaderand the enclosing sequence bases. - toSAMStreamForAlignmentsOfThisAssembly(SAMFileHeader, List<String>, SAMReadGroupRecord) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse
- toSAMStreamForRead(String, byte[], List<BwaMemAlignment>, SAMFileHeader, List<String>, SAMReadGroupRecord) - Static method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignmentUtils
- toSATagString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
-
Returns the SA tag string representation for this interval.
- toSequenceGraph() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
-
Convert this kmer graph to a simple sequence graph.
- toSequenceGraph() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
- toSequenceGraph() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
- toSimpleInterval(long, int) - Method in class org.broadinstitute.hellbender.utils.reference.AbsoluteCoordinates
- toSimpleInterval(SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.utils.SVInterval
-
Converts SVInterval to SimpleInterval Assumes half-open, 1-based SVInterval being converted to closed, 1-based SimpleInterval.
- toSimpleOrBNDTypes(BasicReference) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- toSize() - Method in interface org.broadinstitute.hellbender.utils.collections.Permutation
-
Length of the resulting element list.
- toSize() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.ActualPermutation
- toSize() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleList.NonPermutation
- toString() - Method in class org.broadinstitute.hellbender.engine.AlignmentContext
- toString() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
- toString() - Method in class org.broadinstitute.hellbender.engine.FeatureInput
-
Returns a String representation of this FeatureInput.
- toString() - Method in class org.broadinstitute.hellbender.engine.filters.MetricsReadFilter
- toString() - Method in class org.broadinstitute.hellbender.engine.GATKPath
- toString() - Method in class org.broadinstitute.hellbender.engine.ReadContextData
- toString() - Method in class org.broadinstitute.hellbender.engine.ReadlessAssemblyRegion
- toString() - Method in class org.broadinstitute.hellbender.engine.ReferenceShard
- toString() - Method in class org.broadinstitute.hellbender.engine.ShardBoundary
- toString() - Method in class org.broadinstitute.hellbender.engine.VariantShard
- toString() - Method in class org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractRecordCollection
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleLocatableMetadata
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleLocatableMetadata
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleMetadata
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.AnnotatedInterval
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationKey
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationMap
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledCopyRatioSegment
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledLegacySegment
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyNumberPosteriorDistribution
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatio
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatioSegment
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.IntervalCopyNumberGenotypingData
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.LegacySegment
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment.SimplePosteriorSummary
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.gcnv.IntegerCopyNumberState
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval
- toString() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection
- toString() - Method in class org.broadinstitute.hellbender.tools.dragstr.STRDecimationTable
- toString() - Method in class org.broadinstitute.hellbender.tools.FlagStat.FlagStatus
- toString() - Method in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- toString() - Method in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
- toString() - Method in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantType
- toString() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
- toString() - Method in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.DataSourceType
- toString() - Method in class org.broadinstitute.hellbender.tools.funcotator.metadata.TumorNormalPair
- toString() - Method in class org.broadinstitute.hellbender.tools.funcotator.metadata.VcfFuncotationMetadata
- toString() - Method in class org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo
- toString() - Method in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedAllele
- toString() - Method in class org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedReferenceBases
- toString() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl
- toString() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl
- toString() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.KmerAdjacency
- toString() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Path
- toString() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.SequenceRC
- toString() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.TransitPairCount
- toString() - Method in class org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- toString() - Method in class org.broadinstitute.hellbender.tools.reference.ReferencePair
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig.GoodAndBadMappings
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- toString() - Method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier.AlnModType
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.InvertedDuplicationBreakpointComplications
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantCanonicalRepresentation
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInducingAssemblyContig
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera.DistancesBetweenAlignmentsOnRefAndOnRead
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.Deletion
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.DuplicationInverted
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.DuplicationTandem
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.ImpreciseDeletion
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.Insertion
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.Inversion
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ExternalEvidence
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.InterContigPair
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.LargeIndel
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.MateUnmapped
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.OutiesPair
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SameStrandPair
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SplitRead
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.TemplateSizeAnomaly
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.WeirdTemplateSize
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval
- toString() - Method in enum class org.broadinstitute.hellbender.tools.spark.sv.evidence.TemplateFragmentOrdinal
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistribution
- toString() - Method in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.Strand
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.Mapping
-
Generates the mapping string as it would be included in the Fastq read header.
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer.ASCIICharSequence
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVLocation
- toString() - Method in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils.IndexPair
- toString() - Method in class org.broadinstitute.hellbender.tools.sv.BafEvidence
- toString() - Method in class org.broadinstitute.hellbender.tools.sv.DepthEvidence
- toString() - Method in class org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence
- toString() - Method in class org.broadinstitute.hellbender.tools.sv.SiteDepth
- toString() - Method in class org.broadinstitute.hellbender.tools.sv.SplitReadEvidence
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper.MappedFeature
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculationResult
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleAndContext
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqVertex
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.Kmer
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.KMerCounter
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph.ThreadingTree
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
- toString() - Method in interface org.broadinstitute.hellbender.tools.walkers.mutect.clustering.AlleleFractionCluster
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BetaBinomialCluster
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BinomialCluster
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier
- toString() - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VQSLODTranche
- toString() - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
- toString() - Method in class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState
- toString() - Method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
- toString() - Method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureType
- toString() - Method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.GenomicPhase
- toString() - Method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- toString() - Method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.LocusLevel
- toString() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.OptionalField
- toString() - Method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapStatus
- toString() - Method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapTargetStatus
- toString() - Method in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature
- toString() - Method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.TranscriptSupportLevel
- toString() - Method in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature
- toString() - Method in class org.broadinstitute.hellbender.utils.codecs.table.TableFeature
-
Format as a tab-delimited row.
- toString() - Method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
- toString() - Method in class org.broadinstitute.hellbender.utils.CompressedDataList
- toString() - Method in class org.broadinstitute.hellbender.utils.downsampling.DownsamplingMethod
- toString() - Method in class org.broadinstitute.hellbender.utils.dragstr.DoubleSequence
-
Return the original spec of the sequence
- toString() - Method in class org.broadinstitute.hellbender.utils.dragstr.DragstrParams
- toString() - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- toString() - Method in class org.broadinstitute.hellbender.utils.GenomeLocSortedSet
- toString() - Method in class org.broadinstitute.hellbender.utils.haplotype.EventMap
- toString() - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
- toString() - Method in class org.broadinstitute.hellbender.utils.Histogram
- toString() - Method in class org.broadinstitute.hellbender.utils.IndexRange
- toString() - Method in class org.broadinstitute.hellbender.utils.KV
- toString() - Method in class org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
- toString() - Method in class org.broadinstitute.hellbender.utils.pileup.PileupElement
- toString() - Method in class org.broadinstitute.hellbender.utils.pileup.ReadPileup
- toString() - Method in class org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- toString() - Method in class org.broadinstitute.hellbender.utils.read.BDGAlignmentRecordToGATKReadAdapter
- toString() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.ReadsKey.KeyForFragment
- toString() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.ReadsKey.KeyForPair
- toString() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.EmptyFragment
- toString() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.FlowModeFragment
- toString() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Fragment
- toString() - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair
- toString() - Method in class org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
- toString() - Method in enum class org.broadinstitute.hellbender.utils.recalibration.EventType
- toString() - Method in class org.broadinstitute.hellbender.utils.recalibration.QualQuantizer.QualInterval
- toString() - Method in class org.broadinstitute.hellbender.utils.recalibration.RecalDatum
- toString() - Method in class org.broadinstitute.hellbender.utils.reference.ReferenceBases
- toString() - Method in enum class org.broadinstitute.hellbender.utils.report.GATKReportDataType
- toString() - Method in enum class org.broadinstitute.hellbender.utils.report.GATKReportVersion
- toString() - Method in class org.broadinstitute.hellbender.utils.runtime.StreamOutput
- toString() - Method in class org.broadinstitute.hellbender.utils.samples.Sample
- toString() - Method in class org.broadinstitute.hellbender.utils.SimpleInterval
- toString() - Method in class org.broadinstitute.hellbender.utils.SVInterval
- toString() - Method in class org.broadinstitute.hellbender.utils.variant.MinimalVariant
- toString() - Method in class org.broadinstitute.hellbender.utils.variant.VariantContextVariantAdapter
- toString() - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
- toString() - Method in enum class picard.analysis.artifacts.Transition
- toString() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
- toString() - Method in class picard.arrays.illumina.ArraysControlInfo
- toString() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- toString() - Method in class picard.fingerprint.HaplotypeBlock
- toString() - Method in class picard.fingerprint.Snp
- toString() - Method in class picard.illumina.IlluminaBasecallingMetrics
- toString() - Method in class picard.illumina.parser.ClusterData
- toString() - Method in class picard.illumina.parser.Range
- toString() - Method in class picard.illumina.parser.ReadDescriptor
- toString() - Method in class picard.illumina.parser.ReadStructure
-
Converts this object into a String using rules complementary to the single string constructor above.
- toString() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- toString() - Method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
- toString() - Method in class picard.sam.util.Pair
- toString() - Method in class picard.vcf.processor.VcfFileSegment
-
Deprecated.
- toString() - Method in class picard.vcf.processor.VcfPathSegment
- toString(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer
- toString(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong
-
Not an override.
- toString(int) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort
-
Not an override.
- toString(PSTree) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- toString(GATKRead) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.Mapping
-
Generates the mapping string for a read.
- toSymbol() - Method in enum class picard.pedigree.Sex
-
Returns the single-character symbol used to encode sex in a VCF file
- TOTAL_BASES - Variable in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
-
The total number of bases in all reads
- TOTAL_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The total number of basecalls observed at all sites.
- TOTAL_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The total number of bases in all reads
- TOTAL_BASES - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of bases assigned to the index.
- TOTAL_BASES - Variable in class picard.sam.SamErrorMetric.ErrorMetric
-
The total number of bases included in the calculation of this metric
- TOTAL_CLUSTERS - Variable in class picard.analysis.GcBiasSummaryMetrics
-
The total number of clusters that were seen in the gc bias calculation.
- TOTAL_CLUSTERS - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of clusters assigned to the index.
- TOTAL_COMPLEX_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing complex indel calls that were examined
- TOTAL_GQ0_VARIANTS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
-
The total number of variants in a particular sample that have a GQ score of 0.
- TOTAL_HET_DEPTH - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
-
total number of reads (from AD field) for passing bi-allelic SNP hets for this sample
- TOTAL_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing indel calls that were examined
- TOTAL_MAPPED_REFERENCE_LENGTH - Enum constant in enum class org.broadinstitute.hellbender.utils.read.markduplicates.MarkDuplicatesScoringStrategy
- TOTAL_MAPPINGS - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- TOTAL_MENDELIAN_VIOLATIONS - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The total of all mendelian violations observed.
- TOTAL_MULTIALLELIC_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing multi-allelic SNP calls that were examined
- TOTAL_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The total Phred-scaled Q-score for this artifact.
- TOTAL_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The total Phred-scaled Q-score for this artifact.
- TOTAL_READS - Variable in class org.broadinstitute.hellbender.metrics.QualityYieldMetrics
-
The total number of reads in the input file
- TOTAL_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The total number of reads including all PF and non-PF reads.
- TOTAL_READS - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The total number of reads in the input file
- TOTAL_READS - Variable in class picard.analysis.directed.PanelMetricsBase
-
The total number of reads in the SAM or BAM file examined.
- TOTAL_READS - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of reads assigned to the index.
- TOTAL_READS_IN_INPUT - Variable in class picard.sam.SplitSamByNumberOfReads
- TOTAL_SITES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The total number of sites that had at least one base covering them.
- TOTAL_SITES - Variable in class picard.analysis.RrbsCpgDetailMetrics
-
Number of times this CpG site was encountered
- TOTAL_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing bi-allelic SNPs calls (i.e.
- totalAvgDiffs - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ThetaVariantEvaluator
- totalBytesRead - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- totalCalledSites - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantAFEvaluator
- totalCount - Variable in class org.broadinstitute.hellbender.engine.filters.CountingReadFilter.CountingAndReadFilter
- totalCounts() - Method in class org.broadinstitute.hellbender.tools.AnalyzeSaturationMutagenesis.ReportTypeCounts
- totalCycles - Variable in class picard.illumina.parser.ReadStructure
- totalDistance(SVCallRecord, SVCallRecord) - Static method in class org.broadinstitute.hellbender.tools.sv.concordance.ClosestSVFinder
-
Total distance between breakends, or
Integer.MAX_VALUEif one record is null. - totalHet - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ThetaVariantEvaluator
- totalHetSites - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantAFEvaluator
- totalHomRefSites - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantAFEvaluator
- totalHomVarSites - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantAFEvaluator
- totalKeyBases() - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
-
Number of total bases that the flow based key generates
- totalMappedReferenceLength(GATKRead) - Static method in enum class org.broadinstitute.hellbender.utils.read.markduplicates.MarkDuplicatesScoringStrategy
- totalPloidy() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.HeterogeneousPloidyModel
- totalPloidy() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.HomogeneousPloidyModel
- totalPloidy() - Method in interface org.broadinstitute.hellbender.tools.walkers.genotyper.PloidyModel
-
Sum of all ploidy across all samples.
- totalPloidy(VariantContext, int) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Calculates the total ploidy of a variant context as the sum of all plodies across genotypes.
- totalReadCount - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- totalScore - Variable in class picard.arrays.illumina.InfiniumEGTFile
- toUnphasedGenotypeString() - Method in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts
-
Generates a string that would represent the unphased genotype with this allele counts.
- toURI() - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
-
Convert request to a URI which can be used to make http request for data blocks
- toVariantAttributes() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationBreakpointComplications
- toVariantAttributes() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications
- toVariantAttributes() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications
- toVariantAttributes() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications
-
Intended to be overridden by sub classes when more complications are involved.
- toVariantContext(String, boolean) - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
-
Convert a HomRefBlock into a VariantContext
- toVariantContext(CpxVariantCanonicalRepresentation, Iterable<CpxVariantInducingAssemblyContig>, BasicReference) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInterpreter
- toVariantContexts(List<SvType>, String, SAMSequenceDictionary, SVIntervalTree<VariantContext>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence
-
This implementation is the 1st step going towards allowing re-interpretation, below we simply take the inferred type and turn it to a VC, future implementation may integrate other types of evidence and re-interpret if necessary
- TP - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
- TP - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- TP_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The TP (true positive) count across all variants
- TP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
- TP_FP - Static variable in class picard.vcf.GenotypeConcordanceScheme
- TP_FP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
- TP_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
- TP_TN - Static variable in class picard.vcf.GenotypeConcordanceScheme
- TR_C_GENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- TR_D_GENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- TR_J_GENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- TR_J_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- TR_V_GENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- TR_V_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- traceLinearChain(SeqVertex) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqGraph
-
Get all of the vertices in a linear chain of vertices starting at zipStart Build a list of vertices (in order) starting from zipStart such that each sequential pair of vertices in the chain A and B can be zipped together.
- TRACKING_PATH_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller
- trackKmer(Kmer, MultiDeBruijnVertex) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
-
Define the behavior for how the graph should keep track of a potentially new kmer.
- trackKmer(Kmer, MultiDeBruijnVertex) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
- trackKmer(Kmer, MultiDeBruijnVertex) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
- trackOpticalDuplicates(List<? extends ReadEnds>, ReadEnds, OpticalDuplicateFinder, LibraryIdGenerator) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
Looks through the set of reads and identifies how many of the duplicates are in fact optical duplicates, and stores the data in the instance level histogram.
- trainAndSerialize(File, String) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.BGMMVariantAnnotationsModel
- trainAndSerialize(File, String) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.PythonSklearnVariantAnnotationsModel
- trainAndSerialize(File, String) - Method in interface org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsModel
- TRAINING_LABEL - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- TRAINING_SCORES_HDF5_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
- TRAINING_SET_MEAN_COVERAGE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- TRAINING_SET_OPTIMAL_MIN_COHERENCE - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- TRAINING_SET_OPTIMAL_MIN_OVERLAP - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- TrainingSet - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
-
A set of training variants for use with VQSR.
- TrainingSet(FeatureInput<VariantContext>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.TrainingSet
-
A set of training variants for use with VQSR.
- trainingSets - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- TrainVariantAnnotationsModel - Class in org.broadinstitute.hellbender.tools.walkers.vqsr.scalable
-
Trains a model for scoring variant calls based on site-level annotations.
- TrainVariantAnnotationsModel() - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
- Tranche - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
-
Created by gauthier on 7/13/17.
- Tranche(String, double, long, double, VariantRecalibratorArgumentCollection.Mode, double, int, long, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- Tranche.TrancheComparator<T extends Tranche> - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
- Tranche.TrancheTruthSensitivityComparator - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
- TrancheComparator() - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche.TrancheComparator
- TrancheManager - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
- TrancheManager() - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager
- TrancheManager.SelectionMetric - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
- TrancheManager.TruthSensitivityMetric - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
- trancheOfVariants(List<VariantDatum>, int, double, VariantRecalibratorArgumentCollection.Mode) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- trancheOfVariants(List<VariantDatum>, int, double, VariantRecalibratorArgumentCollection.Mode) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VQSLODTranche
- tranchesString(List<? extends Tranche>) - Static method in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
-
Returns an appropriately formatted string representing the raw tranches file on disk.
- TrancheTruthSensitivityComparator() - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche.TrancheTruthSensitivityComparator
- TRANS_PROB_ARRAY_LENGTH - Static variable in class org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
-
Length of the standard transition probability array.
- TRANSCRIBED_PROCESSED_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- TRANSCRIBED_UNITARY_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- TRANSCRIBED_UNPROCESSED_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- Transcript(String, int, int, int, int, int) - Constructor for class picard.annotation.Gene.Transcript
- TRANSCRIPT - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- TRANSCRIPT - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureType
- TRANSCRIPT_ID - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory.XsvDataKeyType
-
The key specified is a Transcript ID which will be used to match and annotate a
VariantContext. - TRANSCRIPT_ID_INDEX - Static variable in class org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec
- TRANSCRIPT_LIST_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
-
Do not give this a static default value or the integration tests will get hosed.
- TRANSCRIPT_NAME - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- TRANSCRIPT_SELECTION_MODE_DEFAULT_VALUE - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- TRANSCRIPT_SELECTION_MODE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- TranscriptCodingSequenceException(String) - Constructor for exception org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.TranscriptCodingSequenceException
- TranscriptCodingSequenceException(String, Throwable) - Constructor for exception org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.TranscriptCodingSequenceException
- transcriptId - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
- transcriptionEnd - Variable in class picard.annotation.Gene.Transcript
- transcriptionStart - Variable in class picard.annotation.Gene.Transcript
- transcriptName - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
- transcriptSelectionMode - Variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
- TranscriptSelectionMode - Enum Class in org.broadinstitute.hellbender.tools.funcotator
-
The manner to select a single transcript from a set of transcripts to report as the "best" or main transcript.
- transcriptStatus - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
- transcriptType - Variable in class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
-
There are no formal definitions for what can be a valid transcriptType and the number of possible values seem to increase as new versions of Gencode are released.
- TransferReadTags - Class in org.broadinstitute.hellbender.tools.walkers.qc
-
This tool takes a pair of SAM files sharing the same read names (e.g.
- TransferReadTags() - Constructor for class org.broadinstitute.hellbender.tools.walkers.qc.TransferReadTags
- TRANSFORM_DRAGEN_MAPPING_QUALITY_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- transformDRAGENMapQ - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- transformFeatureQueryInterval(SimpleInterval) - Method in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
A Method to allow
DataSourceFuncotationFactoryobjects to adjust the query interval further for their own needs (e.g. - transformFeatureQueryInterval(SimpleInterval) - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
-
A Method to allow
DataSourceFuncotationFactoryobjects to adjust the query interval further for their own needs (e.g. - transformParallel(Iterator<F>, Function<F, T>, int) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Like Guava's
Iterators.transform(Iterator, com.google.common.base.Function), but runs a fixed number (numThreads) of transformations in parallel, while maintaining ordering of the output iterator. - transformTies(int, ArrayList<Integer>) - Method in class org.broadinstitute.hellbender.utils.MannWhitneyU
- transformToWDLCollectionType(Class<?>) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLWorkUnitHandler
-
Given a Java collection class, return a String pair representing the string that should be replaced (the Java type), and the string to substitute (the corresponding WDL type), i.e., for an argument with type Java List.class, return the Pair ("List", "Array") to convert from the Java type to the corresponding WDL collection type.
- transformToWDLType(Class<?>) - Method in class org.broadinstitute.hellbender.utils.help.GATKWDLWorkUnitHandler
-
Given an argument class, return a String pair representing the string that should be replaced (the Java type), and the string to substitute (the corresponding WDL type), i.e., for an argument with type Java Integer.class, return the Pair ("Integer", "Int") to convert from the Java type to the corresponding WDL type.
- transformTraversalIntervals(List<SimpleInterval>, SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.engine.GATKTool
- transformTraversalIntervals(List<SimpleInterval>, SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
-
Get the largest interval per contig that contains the intervals specified on the command line.
- transformTraversalIntervals(List<SimpleInterval>, SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
-
Get the largest interval per contig that contains the intervals specified on the command line.
- transformTraversalIntervals(List<SimpleInterval>, SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyper
-
Get the largest interval per contig that contains the intervals specified on the command line.
- transformTraversalIntervals(List<SimpleInterval>, SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.tools.walkers.PairWalker
- TransientFieldPhysicalLocation - Class in org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
-
A common class for holding the fields in PhysicalLocation that we don't want to be serialized by kryo.
- TransientFieldPhysicalLocation(int, String) - Constructor for class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- transition - Variable in class org.broadinstitute.hellbender.utils.pairhmm.FlowBasedPairHMM
- transition - Variable in class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM
- transition() - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns the instance that would include all possible transition mutations from this one.
- Transition - Enum Class in picard.analysis.artifacts
-
Enum representation of a transition from one base to any other.
- TRANSITION - Enum constant in enum class org.broadinstitute.hellbender.utils.BaseUtils.BaseSubstitutionType
- Transition.Base - Enum Class in picard.analysis.artifacts
- transitionOf(char, char) - Static method in enum class picard.analysis.artifacts.Transition
-
Gets a the enum representing the transition from a 'reference' to a 'call' base.
- TransitPairCount(LocalAssembler.Contig, LocalAssembler.Contig) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.TransitPairCount
- TRANSLATED_PROCESSED_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- TRANSLATED_UNPROCESSED_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- TRANSMISSION_PROBABILITY_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- transpose(List<List<T>>) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorProbabilities
- transversion() - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns the instance that would include all possible tranversion mutations from nucleotides included in this one.
- transversion(boolean) - Method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Transversion mutation toward a strong or a weak base.
- TRANSVERSION - Enum constant in enum class org.broadinstitute.hellbender.utils.BaseUtils.BaseSubstitutionType
- Traversal(Collection<LocalAssembler.Contig>) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- TraversalEndpointComparator() - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.TraversalEndpointComparator
- traversalIsBounded() - Method in interface org.broadinstitute.hellbender.engine.ReadsDataSource
- traversalIsBounded() - Method in class org.broadinstitute.hellbender.engine.ReadsPathDataSource
- traversalParameters - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
-
Full parameters for traversal, including our parsed intervals and a flag indicating whether unmapped records should be returned.
- TraversalParameters - Class in org.broadinstitute.hellbender.engine
-
A simple container class for parameters controlling which records get returned during traversals.
- TraversalParameters(List<SimpleInterval>, boolean) - Constructor for class org.broadinstitute.hellbender.engine.TraversalParameters
- TraversalSet(int) - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.TraversalSet
- traverse() - Method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
-
A complete traversal from start to finish.
- traverse() - Method in class org.broadinstitute.hellbender.engine.AssemblyRegionWalker
-
A complete traversal from start to finish.
- traverse() - Method in class org.broadinstitute.hellbender.engine.DuplicateSetWalker
- traverse() - Method in class org.broadinstitute.hellbender.engine.FeatureWalker
-
A complete traversal from start to finish.
- traverse() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
A complete traversal from start to finish.
- traverse() - Method in class org.broadinstitute.hellbender.engine.IntervalWalker
-
A complete traversal from start to finish.
- traverse() - Method in class org.broadinstitute.hellbender.engine.LocusWalker
-
A complete traversal from start to finish.
- traverse() - Method in class org.broadinstitute.hellbender.engine.LocusWalkerByInterval
-
Implementation of locus-based traversal.
- traverse() - Method in class org.broadinstitute.hellbender.engine.MultiFeatureWalker
-
A complete traversal from start to finish.
- traverse() - Method in class org.broadinstitute.hellbender.engine.MultiplePassReadWalker
- traverse() - Method in class org.broadinstitute.hellbender.engine.MultiplePassVariantWalker
-
Implementation of variant-based traversal.
- traverse() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalker
-
A complete traversal from start to finish.
- traverse() - Method in class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
-
A complete traversal from start to finish.
- traverse() - Method in class org.broadinstitute.hellbender.engine.PartialReadWalker
-
traverse is overridden to consult the implementation class whether to stop The stoppage is implemented using a custom forEach method to compensate for the lack of .takeWhile() in Java 8
- traverse() - Method in class org.broadinstitute.hellbender.engine.ReadWalker
-
A complete traversal from start to finish.
- traverse() - Method in class org.broadinstitute.hellbender.engine.ReferenceWalker
-
A complete traversal from start to finish.
- traverse() - Method in class org.broadinstitute.hellbender.engine.VariantLocusWalker
-
A complete traversal from start to finish.
- traverse() - Method in class org.broadinstitute.hellbender.engine.VariantWalker
-
Implementation of variant-based traversal.
- traverse() - Method in class org.broadinstitute.hellbender.tools.AnalyzeSaturationMutagenesis
- traverse() - Method in class org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervals
- traverse() - Method in class org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
- traverse() - Method in class org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervals
- traverse() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.CombineSegmentBreakpoints
- traverse() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegions
- traverse() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsByAnnotation
- traverse() - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEvents
- traverse() - Method in class org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel
- traverse() - Method in class org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFile
- traverse() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
-
A complete traversal from start to finish.
- traverse() - Method in class org.broadinstitute.hellbender.tools.GetSampleName
- traverse() - Method in class org.broadinstitute.hellbender.tools.PrintReadsHeader
- traverse() - Method in class org.broadinstitute.hellbender.tools.reference.CheckReferenceCompatibility
- traverse() - Method in class org.broadinstitute.hellbender.tools.reference.CompareReferences
- traverse() - Method in class org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta
- traverse() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.PostProcessReadsForRSEM
- traverse() - Method in class org.broadinstitute.hellbender.tools.walkers.qc.TransferReadTags
-
The traversal assumes that the aligned (target) reads is a subset of the unmapped reads.
- traverse() - Method in class org.broadinstitute.hellbender.tools.walkers.SplitIntervals
- traverse() - Method in class org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeBasedVariantRecaller
- traverseReads() - Method in class org.broadinstitute.hellbender.engine.MultiplePassReadWalker
-
Implemented by MultiplePassReadWalker-derived tools.
- traverseReads() - Method in class org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads
- traverseUnmappedReads() - Method in class org.broadinstitute.hellbender.engine.TraversalParameters
- TREAT_UNSORTED_AS_ORDERED - Static variable in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- treatUnsortedAsOrdered - Variable in class org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark
- tree - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTaxonomyDatabase
- TREE_SCORE - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- TREE_SCORE_THRESHOLD_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- TRIALLELIC - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- Trilean - Enum Class in org.broadinstitute.hellbender.utils
-
An enumeration to represent true, false, or unknown.
- trim() - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram
-
Returns a histogram with the smallest tracked maximum such that the fraction of untracked observations does not exceed 1/trackedMaximum.
- trim(Locatable) - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
-
Create a new Haplotype derived from this one that exactly spans the provided location Note that this haplotype must have a contain a genome loc for this operation to be successful.
- trim(Locatable, boolean) - Method in class org.broadinstitute.hellbender.utils.haplotype.Haplotype
-
Create a new Haplotype derived from this one that exactly spans the provided location Note that this haplotype must have a contain a genome loc for this operation to be successful.
- trim(AssemblyRegion, SortedSet<VariantContext>, ReferenceContext) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer
-
Returns a trimming result object from which the variant trimmed region and flanking non-variant sections can be recovered latter.
- trim(SimpleInterval, int) - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Trim this region to just the span, producing a new assembly region without any reads that has only the extent of newExtend intersected with the current extent
- trim(SimpleInterval, SimpleInterval) - Method in class org.broadinstitute.hellbender.engine.AssemblyRegion
-
Trim this region to no more than the span, producing a new assembly region with properly trimmed reads that attempts to provide the best possible representation of this region covering the span.
- trimAlleles(VariantContext, boolean, boolean) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Trim the alleles in inputVC forward and reverse, as requested
- trimAlleles(VariantContext, int, int) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
Trim up alleles in inputVC, cutting out all bases up to fwdTrimEnd inclusive and the last revTrim bases from the end
- trimCigarByBases(Cigar, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Trim cigar down to one that starts at start base in the cigar and extends to (inclusive) end base
- trimCigarByReference(Cigar, int, int) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Trim cigar down to one that starts at start reference on the left and extends to end on the reference
- trimIntervalToContig(String, int, int, int) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Create a new interval, bounding start and stop by the start and end of contig This function will return null if start and stop cannot be adjusted in any reasonable way to be on the contig.
- trimLegacy(AssemblyRegion, SortedSet<VariantContext>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer
-
Returns a trimming result object from which the variant trimmed region and flanking non-variant sections can be recovered latter.
- TrimmedReadsReader - Class in org.broadinstitute.hellbender.tools.walkers.variantrecalling
-
a service class for HaplotypeBasedVariableRecaller that reads SAM/BAM files.
- TrimmedReadsReader(List<Path>, Path, int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.variantrecalling.TrimmedReadsReader
- trimmer - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
- TRIMMING_QUALITY - Variable in class picard.illumina.IlluminaBasecallsToFastq
- trimTo(AssemblyRegion) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
-
Trims an assembly result set down based on a new set of trimmed haplotypes.
- Trio - Class in org.broadinstitute.hellbender.utils.samples
-
A class for imposing a trio structure on three samples; a common paradigm
- Trio(Sample, Sample, Sample) - Constructor for class org.broadinstitute.hellbender.utils.samples.Trio
- TRIOS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- triSiteHeterogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
the rate of heterogeneity within tripleton sets
- triSiteHomogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
the rate of homogeneity within tripleton sets.
- TRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- TRNA_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- TRUE - Enum constant in enum class org.broadinstitute.hellbender.utils.Trilean
- TRUE_POSITIVE - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceState
- TRUE_POSITIVES_AND_FALSE_NEGATIVES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- TRUE_POSITIVES_AND_FALSE_NEGATIVES_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- TRUE_POSITIVES_AND_FALSE_POSITIVES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- TRUE_POSITIVES_AND_FALSE_POSITIVES_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- truePositive(VariantContext, VariantContext) - Static method in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval
- truePositivesAndFalseNegativesVcf - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- truePositivesAndFalsePositivesVcf - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- trueProbToQual(double) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Convert a probability of being right to a phred-scaled quality score (0.99 => 20).
- trueProbToQual(double, byte) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
-
Convert a probability of being right to a phred-scaled quality score (0.99 => 20).
- trueProbToQual(double, int) - Static method in class org.broadinstitute.hellbender.utils.QualityUtils
- TRUNCATE_NAMES_AT_WHITESPACE - Variable in class picard.sam.CreateSequenceDictionary
- TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE - Variable in class picard.reference.NormalizeFasta
- TRUSEQ_SMALLRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.illumina.IlluminaAdapterPair
- TRUSEQ_SMALLRNA - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- TRUTH_ALLELE_COUNT_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- TRUTH_ALLELE_FREQUENCY_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- TRUTH_ALLELE_NUMBER_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- TRUTH_BLOCK_HISTOGRAM_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance
- TRUTH_BLOCK_HISTOGRAM_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance
- TRUTH_CN_EQUAL_FORMAT - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordance
- TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The name of the 'truth' sample
- TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The name of the 'truth' sample
- TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The name of the 'truth' sample
- TRUTH_STATE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The state of the 'truth' sample (i.e.
- TRUTH_STATUS_HEADER_LINE - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- TRUTH_STATUS_VCF_ATTRIBUTE - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.Concordance
- TRUTH_VARIANT_ID_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- TRUTH_VARIANTS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- TRUTH_VCF - Variable in class picard.vcf.GenotypeConcordance
- truthAllele1 - Variable in class picard.vcf.GenotypeConcordance.Alleles
- truthAllele2 - Variable in class picard.vcf.GenotypeConcordance.Alleles
- truthAlleles() - Method in class picard.vcf.GenotypeConcordance.Alleles
- TruthAndCallStates(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Constructor for class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
- truthBlockHistogramFile - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance
- truthIdToItemMap - Variable in class org.broadinstitute.hellbender.tools.sv.concordance.ClosestSVFinder
- truthInfoKey - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance
- truthIntervalPadding - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- TruthSensitivityMetric(int) - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager.TruthSensitivityMetric
- truthState - Variable in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
- truthVariantsFile - Variable in class org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
- truthVCF - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
- tryCleanShutdown() - Method in class org.broadinstitute.hellbender.utils.runtime.ProcessController
-
Stops the process from running and tries to ensure process is cleaned up properly.
- tryCleanShutdown() - Method in class org.broadinstitute.hellbender.utils.runtime.StreamingProcessController
-
Stops the process from running and tries to ensure the process is cleaned up properly.
- tryDelete(File) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Tries to delete a file.
- TRYPTOPHAN - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- TSS_DUP - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- TSV - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts.Format
- TT - Enum constant in enum class picard.fingerprint.DiploidGenotype
- TtoA - Enum constant in enum class picard.analysis.artifacts.Transition
- TtoC - Enum constant in enum class picard.analysis.artifacts.Transition
- TtoG - Enum constant in enum class picard.analysis.artifacts.Transition
- TtoT - Enum constant in enum class picard.analysis.artifacts.Transition
- TUMOR_ALLELIC_COUNTS_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- TUMOR_ALLELIC_COUNTS_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- TUMOR_BAM_FILE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- TUMOR_BAM_FILE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- TUMOR_EVIDENCE_FILTER_NAME - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- TUMOR_LOG_10_ODDS_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- TUMOR_SAMPLE_KEY_IN_VCF_HEADER - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- TUMOR_SAMPLE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- TUMOR_SAMPLE_NAME_LIST - Static variable in class org.broadinstitute.hellbender.tools.funcotator.metadata.SamplePairExtractor
- TUMOR_SAMPLE_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- TUMOR_SEGMENTATION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination
- TUMOR_SEGMENTATION_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- TUMOR_SEGMENTATION_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination
- TumorEvidenceFilter - Class in org.broadinstitute.hellbender.tools.walkers.mutect.filtering
- TumorEvidenceFilter() - Constructor for class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.TumorEvidenceFilter
- TumorNormalPair - Class in org.broadinstitute.hellbender.tools.funcotator.metadata
-
Convenience class for tumor normal pair.
- TumorNormalPair(String, String) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.metadata.TumorNormalPair
- tumorSample - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
- tumorSegmentationTables - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- TVAL - Variable in class picard.arrays.BafRegressMetrics
-
The test statistic for the estimate
- TWO - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.GenomicPhase
- TWO - Enum constant in enum class picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
- TWO_BIT_EXTENSION - Static variable in class org.broadinstitute.hellbender.engine.spark.datasources.ReferenceTwoBitSparkSource
- TWO_SIDED - Enum constant in enum class org.broadinstitute.hellbender.utils.MannWhitneyU.TestType
- twoBasePaddedContextStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into the two base context of the base, which includes two read-bases on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencer
- TwoPassFuncotationFilter - Class in org.broadinstitute.hellbender.tools.funcotator.filtrationRules
- TwoPassVariantWalker - Class in org.broadinstitute.hellbender.engine
- TwoPassVariantWalker() - Constructor for class org.broadinstitute.hellbender.engine.TwoPassVariantWalker
- twoSidedPValue(int[][]) - Static method in class org.broadinstitute.hellbender.utils.FisherExactTest
-
Computes the 2-sided pvalue of the Fisher's exact test on a normalized table that ensures that the sum of all four entries is less than 2 * 200.
- TX_END - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- TX_START - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- type - Variable in exception org.broadinstitute.hellbender.exceptions.UserException.FailsStrictValidation
- type - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase
- type - Variable in class org.broadinstitute.hellbender.utils.downsampling.DownsamplingMethod
-
Type of downsampling to perform.
- type - Variable in class picard.illumina.parser.ReadDescriptor
- TYPE_NAME - Variable in class picard.illumina.IlluminaPhasingMetrics
-
Defines an Illumina template read number (first or second)
- TypeInferredFromSimpleChimera - Enum Class in org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
- typeOfVariant(Allele, Allele) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
-
This is lifted directly from htsjdk with some minor modifications! However, it is a private method there.
- typesMatch(SVCallRecord, SVCallRecord) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage
-
Tests if SVTYPEs match, allowing for DEL/DUP/CNVs to match in some cases.
- typeSpecificAttributes - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- TYROSINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
U
- U - Static variable in enum class org.broadinstitute.hellbender.utils.Nucleotide
- uByteToInt(byte) - Static method in class org.broadinstitute.hellbender.utils.UnsignedTypeUtil
-
Convert an unsigned byte to a signed int
- uByteToInt(byte) - Static method in class picard.util.UnsignedTypeUtil
-
Convert an unsigned byte to a signed int
- uByteToShort(byte) - Static method in class org.broadinstitute.hellbender.utils.UnsignedTypeUtil
-
Convert an unsigned byte to a signed short
- uByteToShort(byte) - Static method in class picard.util.UnsignedTypeUtil
-
Convert an unsigned byte to a signed short
- uIntToFloat(int) - Static method in class picard.util.UnsignedTypeUtil
- uIntToLong(int) - Static method in class org.broadinstitute.hellbender.utils.UnsignedTypeUtil
-
Convert an unsigned int to a long
- uIntToLong(int) - Static method in class picard.util.UnsignedTypeUtil
-
Convert an unsigned int to a long
- UMI_BASE_QUALITIES - Variable in class picard.sam.markduplicates.UmiMetrics
-
Estimation of Phred scaled quality scores for UMIs
- UMI_METRICS_FILE - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
- UMI_TAG_NAME - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
- UmiAwareMarkDuplicatesWithMateCigar - Class in picard.sam.markduplicates
-
This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
- UmiAwareMarkDuplicatesWithMateCigar() - Constructor for class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
- UmiGraph - Class in picard.sam.markduplicates
-
UmiGraph is used to identify UMIs that come from the same original source molecule.
- UmiMetrics - Class in picard.sam.markduplicates
-
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.
- UmiMetrics() - Constructor for class picard.sam.markduplicates.UmiMetrics
- UmiMetrics(String) - Constructor for class picard.sam.markduplicates.UmiMetrics
- UmiMetrics(String, double, int, int, int, int, int, double, double, double, double) - Constructor for class picard.sam.markduplicates.UmiMetrics
- UNAFFECTED - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.Affection
-
Unaffected by the disease
- Unaligned - Enum constant in enum class picard.sam.ViewSam.AlignmentStatus
- unclippedLoc - Variable in class org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.SplitRead
- unclippedReadLength(GATKRead) - Static method in class org.broadinstitute.hellbender.utils.read.AlignmentUtils
-
Returns the number of bases in a read minus the number of softclipped bases.
- uncollapseHmersInHaplotypes(Collection<Haplotype>, boolean, byte[]) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LongHomopolymerHaplotypeCollapsingEngine
-
This method is the main functional part of the uncollapsing engine.
- UNCONVERTED_BASE_COVERAGE_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- UNDECODABLE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- UNDEFINED_LENGTH - Static variable in class org.broadinstitute.hellbender.tools.sv.SVCallRecord
- UNDERGONE_OVERLAP_REMOVAL - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier.AlnModType
- undoDistantMateAlterations(GATKRead) - Static method in class org.broadinstitute.hellbender.tools.PrintDistantMates
- UNEQUAL_COMMON_CONTIGS - Enum constant in enum class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.SequenceDictionaryCompatibility
- UNEXPECTED_MATCH - Enum constant in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
- UNEXPECTED_MISMATCH - Enum constant in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
- unfilteredBaseQHistogram - Variable in class picard.analysis.WgsMetrics
-
The count of bases observed with a given base quality.
- unfilteredBaseQHistogramArray - Variable in class picard.analysis.AbstractWgsMetricsCollector
-
Count of bases observed with a given base quality.
- unfilteredDepthHistogram - Variable in class picard.analysis.WgsMetrics
-
Count of sites with a given depth of coverage.
- unfilteredDepthHistogramArray - Variable in class picard.analysis.AbstractWgsMetricsCollector
-
Count of sites with a given depth of coverage.
- unfilteredEvidenceDir - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- UnimplementedFeature(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.UnimplementedFeature
- UNINFORMATIVE - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments.ReasonForAlignmentClassificationFailure
- union(GenomeLoc) - Method in class org.broadinstitute.hellbender.utils.GenomeLoc
- UNION - Enum constant in enum class org.broadinstitute.hellbender.utils.IntervalSetRule
-
Take the union of all intervals
- UNION - Enum constant in enum class picard.util.IntervalListTools.Action
- UNIQUE - Variable in class picard.util.BedToIntervalList
- UNIQUE - Variable in class picard.util.IntervalListTools
- UNIQUE_ALT_READ_COUNT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- uniqueAltReadCount - Variable in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- UniqueAltReadCount - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Finds a lower bound on the number of unique reads at a locus that support a non-reference allele.
- UniqueAltReadCount() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.UniqueAltReadCount
- UniqueIDWrapper<A> - Class in org.broadinstitute.hellbender.utils
-
Create a unique ID for an arbitrary object and wrap it.
- UniqueIDWrapper(A) - Constructor for class org.broadinstitute.hellbender.utils.UniqueIDWrapper
- uniquify(Collection<SVKmer>, Collection<SVKmer>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
- UNIQUIFY - Enum constant in enum class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.GenotypeMergeType
-
Make all sample genotypes unique by file.
- UNITARY_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- UNITIG_SIZES_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- Unknown - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportDataType
-
The default value when a format string is not present
- Unknown - Enum constant in enum class picard.pedigree.Sex
- UNKNOWN - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments.AlignmentSignatureBasicType
- UNKNOWN - Enum constant in enum class org.broadinstitute.hellbender.utils.NGSPlatform
- UNKNOWN - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.Affection
-
Status is unknown
- UNKNOWN - Enum constant in enum class org.broadinstitute.hellbender.utils.samples.Sex
- UNKNOWN - Enum constant in enum class org.broadinstitute.hellbender.utils.Trilean
- UNKNOWN - Enum constant in enum class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
- UNKNOWN - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
-
Read whose consensus status cannot be determined.
- UNKNOWN - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
- UNKNOWN - Static variable in class org.broadinstitute.hellbender.metrics.MultiLevelCollector
- UNKNOWN - Static variable in class picard.metrics.MultiLevelCollector
- UNKNOWN_DESCRIPTION - Static variable in class org.broadinstitute.hellbender.tools.funcotator.metadata.FuncotationMetadataUtils
- UNKNOWN_FILL_VALUE - Static variable in class org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
- UNKNOWN_LIBRARY - Static variable in class org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator
- UNKNOWN_OUT_PREFIX - Static variable in class org.broadinstitute.hellbender.tools.SplitReads
- UNKNOWN_SEX - Static variable in class picard.pedigree.PedFile
- UNKNOWN_VALUE_STRING - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorConstants
-
Value to insert into fields when the annotation is unspecified, but still required.
- UNLABELED_ANNOTATIONS_HDF5_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
- UNLABELED_SCORES_HDF5_SUFFIX - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
- UNLABELED_TAG - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations
- UNMAP_CONTAMINANT_READS - Variable in class picard.sam.MergeBamAlignment
- UNMAPPED - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionBounds
- UNMAPPED - Static variable in class org.broadinstitute.hellbender.utils.GenomeLoc
-
A static constant to use when referring to the unmapped section of a datafile file.
- UNMAPPED_BAM - Variable in class picard.sam.MergeBamAlignment
- UNMAPPED_BOTH - Enum constant in enum class picard.sam.util.SamComparison.AlignmentComparison
- UNMAPPED_BOTH - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records which are not mapped in either file.
- UNMAPPED_INSERTION - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantCanonicalRepresentation
- UNMAPPED_LEFT - Enum constant in enum class picard.sam.util.SamComparison.AlignmentComparison
- UNMAPPED_LEFT - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records which are mapped in right file and found but not mapped in left file
- UNMAPPED_LOC_NAME - Static variable in class org.broadinstitute.hellbender.utils.GenomeLocParser
- UNMAPPED_READ_STRATEGY - Variable in class picard.sam.MergeBamAlignment
- UNMAPPED_READS - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreMetrics
-
The number of non-host reads that could not be mapped to a pathogen
- UNMAPPED_READS - Variable in class picard.sam.DuplicationMetrics
-
The total number of unmapped reads examined.
- UNMAPPED_RIGHT - Enum constant in enum class picard.sam.util.SamComparison.AlignmentComparison
- UNMAPPED_RIGHT - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records which are mapped in left file and found but not mapped in right file
- unmappedReadCount - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- unmappedRemaining - Variable in class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
- unmappedSamFile - Variable in class org.broadinstitute.hellbender.tools.walkers.qc.TransferReadTags
- UnmarkDuplicates - Class in org.broadinstitute.hellbender.tools.walkers
-
Clears the 0x400 duplicate SAM flag from reads.
- UnmarkDuplicates() - Constructor for class org.broadinstitute.hellbender.tools.walkers.UnmarkDuplicates
- UNPAIRED - Enum constant in enum class org.broadinstitute.hellbender.tools.spark.sv.evidence.TemplateFragmentOrdinal
-
Ordinal for fragments in unpaired sequenced templates.
- UNPAIRED - Enum constant in enum class picard.analysis.AlignmentSummaryMetrics.Category
- UNPAIRED_DUP_RATE_WITH_TLEN - Variable in class picard.sam.FlowBasedDuplicationMetrics
-
The fraction of duplicated reads out of all reads with exact fragment length known
- UNPAIRED_DUP_RATE_WITHOUT_TLEN - Variable in class picard.sam.FlowBasedDuplicationMetrics
-
The fraction of duplicated reads out of all reads with exact fragment length unknown
- UNPAIRED_DUPS_WITH_TLEN - Variable in class picard.sam.FlowBasedDuplicationMetrics
- UNPAIRED_DUPS_WITHOUT_TLEN - Variable in class picard.sam.FlowBasedDuplicationMetrics
- UNPAIRED_END_UNCERTAINTY - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- UNPAIRED_FASTQ - Variable in class picard.sam.SamToFastq
- UNPAIRED_INPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSpark
- UNPAIRED_INPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreSpark
- UNPAIRED_OUTPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSpark
- UNPAIRED_OUTPUT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSpark
- UNPAIRED_READ_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
-
The number of fragments that were marked as duplicates.
- UNPAIRED_READS_EXAMINED - Variable in class picard.sam.DuplicationMetrics
-
The number of mapped reads examined which did not have a mapped mate pair, either because the read is unpaired, or the read is paired to an unmapped mate.
- UNPAIRED_WITH_TLEN - Variable in class picard.sam.FlowBasedDuplicationMetrics
- unpairedInput - Variable in class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreSpark
- unpersist() - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark.AssemblyContigsClassifiedByAlignmentSignatures
- UNPROCESSED_PSEUDOGENE - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- unsafeNextInfo() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
Returns the next position info.
- unsafeNextInfo() - Method in class picard.illumina.parser.readers.ClocsFileReader
-
Grab the next set of offset values, decompress them.
- unsafeNextInfo() - Method in class picard.illumina.parser.readers.LocsFileReader
- unsafeNextInfo() - Method in class picard.illumina.parser.readers.PosFileReader
-
Read a line of text and parse it into two float values, create a PositionInfo and return it
- UNSCRUPULOUS_HOM_REF_ALLELE_FRACTION - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel
- UNSCRUPULOUS_HOM_REF_FRACTION_TO_REMOVE_FOR_POSSIBLE_LOH - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel
- UNSCRUPULOUS_HOM_REF_PERCENTILE - Static variable in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel
- UNSET_CONTIG - Static variable in class org.broadinstitute.hellbender.utils.read.ReadConstants
-
Value used to represent the absence of a defined contig in a read
- UNSET_POSITION - Static variable in class org.broadinstitute.hellbender.utils.read.ReadConstants
-
Value used to represent the absence of a defined start/end position in a read
- UnsignedTypeUtil - Class in org.broadinstitute.hellbender.utils
-
A utility class for dealing with unsigned types.
- UnsignedTypeUtil - Class in picard.util
-
A utility class for dealing with unsigned types.
- UnsignedTypeUtil() - Constructor for class org.broadinstitute.hellbender.utils.UnsignedTypeUtil
- UnsignedTypeUtil() - Constructor for class picard.util.UnsignedTypeUtil
- UNSORTED - Enum constant in enum class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.GenotypeMergeType
-
Take the genotypes in any order.
- UnsortedBasecallsConverter<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
-
UnortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
- UnsortedBasecallsConverter(File, File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>, boolean, Integer, Integer, BclQualityEvaluationStrategy, boolean, boolean, boolean, AsyncWriterPool, BarcodeExtractor, Integer) - Constructor for class picard.illumina.UnsortedBasecallsConverter
-
Constructs a new BasecallsConverter object.
- UNSPECIFIED - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.Genus
-
Unspecified genus / genus not in this list.
- UNSUPPORTED_GENOME_BUILD - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
- UNVALIDATED - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations.Judgment
- unzip(GATKPath, File, String...) - Static method in class org.broadinstitute.hellbender.utils.ZipUtils
-
Unzips a file in a provided path into a destination directory.
- unzipToFolder(Path, Path) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
A simple helper method that reads a zipped archive and unzippes it to a file target, preserving the directory structure.
- update(Locatable) - Method in class org.broadinstitute.hellbender.engine.ProgressMeter
-
Signal to the progress meter that an additional record has been processed.
- update(Locatable, long) - Method in class org.broadinstitute.hellbender.engine.ProgressMeter
-
Signal to the progress meter that several additional records hav been processed.
- update(Map<String, int[]>) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
- update(RandomGenerator) - Method in class org.broadinstitute.hellbender.utils.mcmc.ParameterizedModel
-
Updates the
ParameterizedStateheld internally using theParameterSamplers and update method specified via the Builder pattern. - update(T, U) - Method in class org.broadinstitute.hellbender.utils.mcmc.ParameterizedState
-
Updates the value of a
Parametercontained in the collection held by theParameterizedState. - update1(VariantContext, VariantEvalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- update1(VariantContext, VariantEvalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.GenotypeFilterSummary
- update1(VariantContext, VariantEvalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelLengthHistogram
- update1(VariantContext, VariantEvalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- update1(VariantContext, VariantEvalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ThetaVariantEvaluator
- update1(VariantContext, VariantEvalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantAFEvaluator
- update1(VariantContext, VariantEvalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
- update2(VariantContext, VariantContext, VariantEvalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap
- update2(VariantContext, VariantContext, VariantEvalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
- update2(VariantContext, VariantContext, VariantEvalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- update2(VariantContext, VariantContext, VariantEvalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.PrintMissingComp
- update2(VariantContext, VariantContext, VariantEvalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator
- update2(VariantContext, VariantContext, VariantEvalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- update2(VariantContext, VariantContext, VariantEvalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
- update2(VariantContext, VariantContext, VariantEvalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- updateAlleleSpecificINFOFieldCombineOperation(GenomicsDBVidMapProto.VidMappingPB, Map<String, Integer>, String, String) - Static method in class org.broadinstitute.hellbender.tools.genomicsdb.GATKGenomicsDBUtils
-
Update vid Protobuf object with a new variable length descriptor, as for allele-specific annotations
- updateCigarForTrimmedOrClippedBases(SAMRecord, SAMRecord) - Method in class org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
- updateCigarForTrimmedOrClippedBases(SAMRecord, SAMRecord) - Method in class picard.sam.AbstractAlignmentMerger
- updateCopyProgress(int) - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- updateFieldSetDisableRemapMissingAlleleToNonRef(GenomicsDBVidMapProto.VidMappingPB, Map<String, Integer>, String, boolean) - Static method in class org.broadinstitute.hellbender.tools.genomicsdb.GATKGenomicsDBUtils
-
Update vid Protobuf field to set whether missing allele should be remapped with value from NON_REF
- updateFormatting(Object) - Method in class org.broadinstitute.hellbender.utils.report.GATKReportColumn
- updateGenotypes(Set<String>, int, SampleDB, SortedSet<String>, VariantContext, Map<String, JointGermlineCNVSegmentation.CopyNumberAndEndRecord>) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
-
For CNVs, i.e.
- updateGenotypesWithMappedAlleles(GenotypesContext, GATKVariantContextUtils.AlleleMapper) - Static method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- updateGraph(SeqVertex, SeqVertex) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SharedVertexSequenceSplitter
-
Update graph outer, replacing the previous middle vertices that were split out with the new graph structure of the split, linking this subgraph into the graph at top and bot (the vertex connecting the middle nodes and the vertex outgoing of all middle node)
- updateHeaderContigLines(Set<VCFHeaderLine>, Path, SAMSequenceDictionary, boolean) - Static method in class org.broadinstitute.hellbender.utils.variant.VcfUtils
-
Given a set of VCF header lines, update the set with contig lines from the provided reference dictionary.
- updateImportProtobufVidMapping(GenomicsDBImporter) - Static method in class org.broadinstitute.hellbender.tools.genomicsdb.GATKGenomicsDBUtils
-
Info and Allele-specific fields that need to be treated differently will have to be explicitly overridden in this method during import.
- updateINFOFieldCombineOperation(GenomicsDBVidMapProto.VidMappingPB, Map<String, Integer>, String, String) - Static method in class org.broadinstitute.hellbender.tools.genomicsdb.GATKGenomicsDBUtils
-
Update vid Protobuf object with new combine operation for field
- updateLengthHistogram(Allele, Allele) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelLengthHistogram
-
Update the histogram with the implied length of the indel allele between ref and alt (alt.len - ref.len).
- updateMessageDigest(byte[], int, int) - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- updateMetric(SamComparison.AlignmentComparison) - Method in class picard.sam.SamComparisonMetric
- updateMetrics(SAMRecord) - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.GATKDuplicationMetrics
-
Update metrics given a record or GATKRead
- updateMetrics(Map<String, BarcodeMetric>, BarcodeMetric) - Method in class picard.illumina.BasecallsConverter
- updateMetrics(GATKRead) - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.GATKDuplicationMetrics
- updateNonRefAlleleLikelihoods() - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Updates the likelihoods of the non-ref allele, if present, considering all non-symbolic alleles avaialble.
- updateNonRefAlleleLikelihoods(AlleleList<A>) - Method in class org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods
-
Updates the likelihood of the NonRef allele (if present) based on the likelihoods of a set of non-symbolic
- updateOutputPath(String) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData
- updateTiTv(VariantContext, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator
- updateVariantConsequenceDict(Map<String, Set<String>>, String, String) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Adds key:value pair to provided variant consequence dictionary
- UpdateVcfSequenceDictionary - Class in picard.vcf
-
Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.
- UpdateVcfSequenceDictionary() - Constructor for class picard.vcf.UpdateVcfSequenceDictionary
- UpdateVCFSequenceDictionary - Class in org.broadinstitute.hellbender.tools.walkers.variantutils
-
Updates the reference contigs in the header of the VCF format file, i.e.
- UpdateVCFSequenceDictionary() - Constructor for class org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionary
- updateViolations(String, String, String, String, VariantContext) - Method in class org.broadinstitute.hellbender.utils.samples.MendelianViolation
- UPSTREAM - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- UPSTREAM_ATG - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
an upstream ATG exists when a downstream ATG is better supported.
- UPSTREAM_UORF - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
a low confidence upstream ATG existing in other coding variant would lead to NMD in this trancript, that uses the high
- upstreamBreakpointRefContig - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference
- upstreamBreakpointRefPos - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference
- upwards - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph.TraversalDirection
- URACIL - Static variable in enum class org.broadinstitute.hellbender.utils.Nucleotide
- URI - Variable in class picard.sam.CreateSequenceDictionary
- URL_ENCODING_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.GetSampleName
- URL_ENCODING_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.tools.GetSampleName
- URL_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.HtsgetReader
- urlDecode(String) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
- urlEncode - Variable in class org.broadinstitute.hellbender.tools.GetSampleName
- urlEncode(String) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
- USAGE - Static variable in class picard.illumina.IlluminaBasecallsToSam
- USAGE - Variable in class picard.sam.ViewSam
- USAGE_ONE_LINE_SUMMARY - Static variable in class org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator
- USAGE_SUMMARY - Static variable in class org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator
- USAGE_SUMMARY - Static variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- USE_ALLELE_SPECIFIC_ANNOTATIONS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
- USE_BCF_CODEC_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection
- USE_CACHED_READ_INDEL_INFORMATIVENESS_VALUES - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
- USE_DICT - Enum constant in enum class org.broadinstitute.hellbender.tools.reference.CompareReferences.MD5CalculationMode
- USE_END_IN_UNPAIRED_READS - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- USE_FAST_ALGORITHM - Variable in class picard.analysis.CollectWgsMetrics
- USE_FILTERED_READS_FOR_ANNOTATIONS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- USE_FIRST - Enum constant in enum class picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
- USE_GCS_HDFS_CONNECTOR - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection
- USE_GCS_HDFS_CONNECTOR - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- USE_IUPAC_SAMPLE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker
- USE_JDK_DEFLATER - Variable in class picard.cmdline.CommandLineProgram
- USE_JDK_DEFLATER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- USE_JDK_DEFLATER_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- USE_JDK_INFLATER - Variable in class picard.cmdline.CommandLineProgram
- USE_JDK_INFLATER_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- USE_JDK_INFLATER_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- USE_NIO - Static variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- USE_OQ - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- USE_OQ - Variable in class picard.analysis.CollectOxoGMetrics
- USE_ORIGINAL_QUALITIES - Variable in class picard.analysis.CollectQualityYieldMetrics
- USE_ORIGINAL_QUALITIES_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- USE_ORIGINAL_QUALITIES_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- USE_ORIGINAL_QUALITIES_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- USE_PLS_TO_ASSIGN - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod
-
Use the subsetted PLs to greedily assign genotypes
- USE_POSTERIOR_PROBABILITIES - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod
-
Calculate posterior probabilities and use those to assign genotypes
- USE_POSTERIORS_ANNOTATION - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod
-
Use the existing, subsetted posteriors array to assign genotypes
- USE_POSTERIORS_TO_CALCULATE_QUAL_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- USE_SEQUENTIAL_FASTQS - Variable in class picard.sam.FastqToSam
- USE_THREADING - Variable in class picard.sam.MergeSamFiles
- USE_TRUTH_AF_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.SVConcordance
- USE_UNPAIRED_CLIPPED_END - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- USE_VCF_INDEX - Variable in class picard.vcf.GenotypeConcordance
- useAdaptivePruning - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerReadThreadingAssemblerArgumentCollection
-
A single edge multiplicity cutoff for pruning doesn't work in samples with variable depths, for example exomes and RNA.
- useBCFCodec - Variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection
-
Currently there is no support for 64-bit fields in BCF2Codec.
- useBCFCodec() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBOptions
- useBpResolution - Variable in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
- useFilteredReadMapForAnnotations - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
- useFlatPriorsForIndels - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors
-
Use flat priors for indels (can be used to replicate the legacy CalculateGenotypePosteriors behavior) If an input variant contains an indel allele, flat priors will be applied to that site.
- useFlowFragments - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
- useGcsHdfsConnector - Variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection
- useGcsHdfsConnector - Variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- useGcsHdfsConnector() - Method in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBOptions
- useJdkDeflater - Variable in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- useJdkInflater - Variable in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- useLegacyParser() - Static method in class picard.cmdline.CommandLineProgram
-
Return true if the legacy Picard command line parser should be used in place of the Barclay command line parser, otherwise, false.
- useLinkedDeBruijnGraph - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
-
Disables graph simplification into a seq graph, opts to construct a proper De Bruijn graph with potential loops NOTE: --linked-de-bruijn-graph is currently an experimental feature that does not directly match with the regular HaplotypeCaller.
- useNewAFCalculator - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
-
As of version 4.1.0.0, this argument is no longer needed because the new qual score is now on by default.
- useNio - Variable in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- useOriginalBaseQualities - Variable in class org.broadinstitute.hellbender.tools.ApplyBQSRArgumentCollection
-
This flag tells GATK to use the original base qualities (that were in the data before BQSR/recalibration) which are stored in the OQ tag, if they are present, rather than use the post-recalibration quality scores.
- useOriginalBaseQualities - Variable in class org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
-
This flag tells GATK to use the original base qualities (that were in the data before BQSR/recalibration) which are stored in the OQ tag, if they are present, rather than use the post-recalibration quality scores.
- useOriginalQualities - Variable in class org.broadinstitute.hellbender.metrics.QualityYieldMetricsArgumentCollection
- useOriginalQualities - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
- usePileupDetection - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
-
Enables pileup-based haplotype creation and variant detection NOTE: --pileup-detection is a beta feature.
- usePosteriorProbabilitiesToCalculateQual - Variable in class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
- USER_EXCEPTION_EXIT_VALUE - Static variable in class org.broadinstitute.hellbender.Main
-
Exit value when an unrecoverable
UserExceptionoccurs. - userCollectors - Variable in class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark
- userDisabledReadFilterNames - Variable in class org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKReadFilterArgumentCollection
- userEnabledReadFilterNames - Variable in class org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKReadFilterArgumentCollection
- UserException - Exception in org.broadinstitute.hellbender.exceptions
-
Class UserException.
- UserException() - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException
- UserException(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException
- UserException(String, Throwable) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException
- UserException.BadInput - Exception in org.broadinstitute.hellbender.exceptions
- UserException.BadTempDir - Exception in org.broadinstitute.hellbender.exceptions
- UserException.CannotExecuteScript - Exception in org.broadinstitute.hellbender.exceptions
- UserException.CannotHandleGzippedRef - Exception in org.broadinstitute.hellbender.exceptions
- UserException.CouldNotCreateOutputFile - Exception in org.broadinstitute.hellbender.exceptions
-
Class UserException.CouldNotCreateOutputFile
- UserException.CouldNotIndexFile - Exception in org.broadinstitute.hellbender.exceptions
- UserException.CouldNotReadInputFile - Exception in org.broadinstitute.hellbender.exceptions
-
Class UserException.CouldNotReadInputFile
- UserException.EmptyIntersection - Exception in org.broadinstitute.hellbender.exceptions
- UserException.FailsStrictValidation - Exception in org.broadinstitute.hellbender.exceptions
- UserException.HardwareFeatureException - Exception in org.broadinstitute.hellbender.exceptions
- UserException.HeaderMissingReadGroup - Exception in org.broadinstitute.hellbender.exceptions
- UserException.IncompatibleRecalibrationTableParameters - Exception in org.broadinstitute.hellbender.exceptions
- UserException.IncompatibleSequenceDictionaries - Exception in org.broadinstitute.hellbender.exceptions
- UserException.LexicographicallySortedSequenceDictionary - Exception in org.broadinstitute.hellbender.exceptions
- UserException.MalformedBAM - Exception in org.broadinstitute.hellbender.exceptions
- UserException.MalformedFile - Exception in org.broadinstitute.hellbender.exceptions
-
Class UserException.MalformedFile
- UserException.MalformedGenomeLoc - Exception in org.broadinstitute.hellbender.exceptions
- UserException.MalformedRead - Exception in org.broadinstitute.hellbender.exceptions
- UserException.MisencodedQualityScoresRead - Exception in org.broadinstitute.hellbender.exceptions
- UserException.MissingContigInSequenceDictionary - Exception in org.broadinstitute.hellbender.exceptions
- UserException.MissingIndex - Exception in org.broadinstitute.hellbender.exceptions
- UserException.MissingReference - Exception in org.broadinstitute.hellbender.exceptions
- UserException.MissingReferenceDictFile - Exception in org.broadinstitute.hellbender.exceptions
- UserException.MissingReferenceFaiFile - Exception in org.broadinstitute.hellbender.exceptions
- UserException.MissingReferenceGziFile - Exception in org.broadinstitute.hellbender.exceptions
- UserException.NoSuitableCodecs - Exception in org.broadinstitute.hellbender.exceptions
- UserException.ReadMissingReadGroup - Exception in org.broadinstitute.hellbender.exceptions
- UserException.SequenceDictionaryIsMissingContigLengths - Exception in org.broadinstitute.hellbender.exceptions
- UserException.UnimplementedFeature - Exception in org.broadinstitute.hellbender.exceptions
- UserException.ValidationFailure - Exception in org.broadinstitute.hellbender.exceptions
- UserException.VQSRNegativeModelFailure - Exception in org.broadinstitute.hellbender.exceptions
- UserException.VQSRPositiveModelFailure - Exception in org.broadinstitute.hellbender.exceptions
- UserException.WarnableAnnotationFailure - Exception in org.broadinstitute.hellbender.exceptions
- UserException.WrongFeatureType - Exception in org.broadinstitute.hellbender.exceptions
- userTranscriptIdSet - Variable in class org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
- useSimpleCigar - Variable in class org.broadinstitute.hellbender.tools.walkers.ReadAnonymizer
- usesNoRefReads() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- usesNoRefReads() - Method in class picard.analysis.CollectInsertSizeMetrics
- usesNoRefReads() - Method in class picard.analysis.CollectQualityYieldMetrics
-
Ensure that we get all reads regardless of alignment status.
- usesNoRefReads() - Method in class picard.analysis.SinglePassSamProgram
-
Can be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.
- usesNoRefReads() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
- useT0Tag - Variable in class org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection
- useVariantAnnotations() - Method in class org.broadinstitute.hellbender.engine.GATKTool
-
Must be overridden in order to add annotation arguments to the engine.
- useVariantAnnotations() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
- useVariantAnnotations() - Method in class org.broadinstitute.hellbender.tools.HaplotypeCallerSpark
- useVariantAnnotations() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- useVariantAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
- useVariantAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.CombineGVCFs
- useVariantAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs
- useVariantAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
- useVariantAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
- useVariantAnnotations() - Method in class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF
- uShortToInt(short) - Static method in class org.broadinstitute.hellbender.utils.UnsignedTypeUtil
-
Convert an unsigned short to an Int
- uShortToInt(short) - Static method in class picard.util.UnsignedTypeUtil
-
Convert an unsigned short to an Int
- usingGVCFIndexingArguments(GATKVCFIndexType, int) - Static method in class org.broadinstitute.hellbender.utils.variant.VcfUtils
-
Check if using the GCVF indexing arguments' values
- Utils - Class in org.broadinstitute.hellbender.utils
- UTR - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureType
- UTR - Enum constant in enum class picard.annotation.LocusFunction
- UTR - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- UTR_3_DELETED - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- UTR_3_PRIME - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- UTR_5_DELETED - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- UTR_5_PRIME - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
- UTR_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Number of bases in primary alignments that align to a UTR base for some gene, and not a coding base.
V
- V - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- V0_1 - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportVersion
-
Differences between other versions: - Does not allow spaces in cells.
- V0_2 - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportVersion
-
Differences between other versions: - Spaces allowed in cells, for example in sample names with spaces in them ex: "C507/FG-CR 6".
- V1_0 - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportVersion
- V1_1 - Enum constant in enum class org.broadinstitute.hellbender.utils.report.GATKReportVersion
- VAExpression(String, List<FeatureInput<VariantContext>>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.VAExpression
- VALID_ALIGNMENT_END - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- VALID_ALIGNMENT_START - Static variable in class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- VALID_ALLELES - Static variable in class picard.arrays.illumina.IlluminaManifest
- ValidAlignmentEndReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.ValidAlignmentEndReadFilter
- ValidAlignmentStartReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.ValidAlignmentStartReadFilter
- validate() - Method in class org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
- validate() - Method in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineContigPloidyModelArgumentCollection
- validate() - Method in class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
- validate() - Method in class org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
-
Performs some validation constraint changes on the values provided to this argument collection.
- validate() - Method in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection
-
Explicit call this method.
- validate() - Method in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
-
Explicit call this method.
- validate(boolean, String) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Check a condition that should always be true and throw an
IllegalStateExceptionif false. - validate(boolean, Supplier<String>) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Check a condition that should always be true and throw an
IllegalStateExceptionif false. - validate(CommandLineArgumentParser, GermlineCNVCaller.RunMode) - Method in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCallingArgumentCollection
- validate(CommandLineArgumentParser, GermlineCNVCaller.RunMode) - Method in class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
- validate(T) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationKey
- VALIDATE_INDEX - Variable in class picard.sam.ValidateSamFile
- VALIDATE_INTEGRITY_ARG_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader
- VALIDATE_SAMPLE_MAP_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- validateAllelesList() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData
- validateAndInitialize(Collection<String>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
-
Initialize the stratifications, evaluations, evaluation contexts, and reporting object
- validateAndPrepareOutputDirectories(File...) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
-
Validate that output directories are writeable.
- validateAndResolvePlugins() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
-
Validate the list of arguments and reduce the list of annotations to those actually seen on the command line.
- validateAndResolvePlugins() - Method in class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
-
Validate the list of arguments and reduce the list of read filters to those actually seen on the command line.
- validateAnnotatedIntervals(File, AbstractLocatableCollection<?, ?>, Logger) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
-
Checks equality of the sequence dictionary and intervals contained in an
locatableCollectionagainst those contained in anAnnotatedIntervalCollectionrepresented byannotatedIntervalsFile. - validateAnnotatedIntervalsSubset(File, AbstractLocatableCollection<?, ?>, Logger) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
-
Same as
CopyNumberArgumentValidationUtils.validateAnnotatedIntervals(java.io.File, org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractLocatableCollection<?, ?>, org.apache.logging.log4j.Logger), except we only require thatannotatedIntervalsFilecontains as a subset all the intervals contained inlocatableCollectionalong with equality of the sequence dictionaries. - validateArg(boolean, String) - Static method in class org.broadinstitute.hellbender.utils.Utils
- validateArg(boolean, Supplier<String>) - Static method in class org.broadinstitute.hellbender.utils.Utils
- validateArgs(String[]) - Method in class org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor
-
Validate command line arguments.
- validateArguments() - Method in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
- validateArguments() - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation
-
Provide input arguments so as to warn the user if they are providing an incorrect subset of pedigree inputs.
- ValidateBasicSomaticShortMutations - Class in org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
- ValidateBasicSomaticShortMutations() - Constructor for class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- ValidateBasicSomaticShortMutations.Judgment - Enum Class in org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
- validateCommandLine(String[]) - Method in class org.broadinstitute.hellbender.CommandLineArgumentValidatorMain
-
Call the command line program (specified in the input arguments) in command line validation mode only.
- validateCountsAgainstScheme(GenotypeConcordanceScheme) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Validates that there are no counts for NA states in the underlying scheme
- validateCRAMDictionaryAgainstReference(SAMSequenceDictionary, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
-
Tests for compatibility between a reference dictionary and a CRAM dictionary, using appropriate validation settings.
- VALIDATED - Enum constant in enum class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations.Judgment
- validateDictionaries(String, SAMSequenceDictionary, String, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
-
Tests for compatibility between two sequence dictionaries, using standard validation settings appropriate for the GATK.
- validateDictionaries(String, SAMSequenceDictionary, String, SAMSequenceDictionary, boolean, boolean) - Static method in class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
-
Tests for compatibility between two sequence dictionaries.
- validateExpectedSortOrder(SAMFileHeader.SortOrder, SAMFileHeader.SortOrder, boolean, String) - Static method in class org.broadinstitute.hellbender.utils.read.ReadUtils
-
Validate that the expected input sort order is either "unsorted", or that it matches the actualSortOrder.
- validateGenomeLoc(String, int, int, int, boolean) - Method in class org.broadinstitute.hellbender.utils.GenomeLocParser
-
validate a position or interval on the genome as valid Requires that contig exist in the master sequence dictionary, and that contig index be valid as well.
- validateInputs(File...) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
-
Validate that input files and/or directories are readable if they are not
null(i.e., optional inputs). - validateInputs(String...) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
-
Validate that input paths are readable if they are not
null(i.e., optional inputs). - validateIntervalArgumentCollection(IntervalArgumentCollection) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
-
Validate that the interval-argument collection parameters minimally modify the input intervals.
- validateIntervals(List<T>, SAMSequenceDictionary) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
-
Validate that a list of locatables is valid and sorted according to a sequence dictionary and contains no duplicates or overlaps.
- validateLocatableColumnName(String) - Static method in class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
-
Throw an exception if the given column name cannot be used for one of the locatable columns.
- validateNoOverlappingIntervals(List<T>) - Static method in class org.broadinstitute.hellbender.utils.IntervalUtils
-
Throws Bad Input exception if any overlaps are detected within the list of locatables.
- validateOutputFiles(File...) - Static method in class org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
-
Validate that output files are writeable, whether or not they already exist.
- validateRecords(Collection<SVCallRecord>) - Method in class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
-
Asserts that the given records are valid for collapsing.
- ValidateSamFile - Class in picard.sam
-
This tool reports on the validity of a SAM or BAM file relative to the SAM format specification.
- ValidateSamFile() - Constructor for class picard.sam.ValidateSamFile
- ValidateSamFile.Mode - Enum Class in picard.sam
- validateScheme() - Method in class picard.vcf.GenotypeConcordanceScheme
-
Check that all cells in the scheme exist.
- validateSequenceDictionaries() - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Validates standard tool inputs against each other.
- validateSequenceDictionaries() - Method in class org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark
- ValidateVariants - Class in org.broadinstitute.hellbender.tools.walkers.variantutils
-
Validate a VCF file with a strict set of criteria
- ValidateVariants() - Constructor for class org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants
- ValidateVariants.ValidationType - Enum Class in org.broadinstitute.hellbender.tools.walkers.variantutils
- VALIDATION_AD_HEADER_LINE - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- VALIDATION_AD_INFO_FIELD_KEY - Static variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- VALIDATION_STRINGENCY - Variable in class org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram
- VALIDATION_STRINGENCY - Variable in class picard.cmdline.CommandLineProgram
- validationCaseName - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- validationControlName - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
- ValidationFailure(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.ValidationFailure
- ValidationReport - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
- ValidationReport(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
- validIndex(int, int) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Checks whether an index is within bounds considering a collection or array of a particular size whose first position index is 0
- validIndex(int, int, String) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Checks whether an index is within bounds considering a collection or array of a particular size whose first position index is 0
- VALINE - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
- value - Variable in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer.Base
- value - Variable in class org.broadinstitute.hellbender.utils.collections.NestedIntegerArray.Leaf
- value - Variable in enum class picard.arrays.illumina.IlluminaGenotype
- VALUE_SEPARATOR - Static variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- VALUE1 - Variable in class picard.analysis.CompareMetrics.MetricComparisonDifferences
- VALUE2 - Variable in class picard.analysis.CompareMetrics.MetricComparisonDifferences
- value2bin(int) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
- valueCounts - Variable in class org.broadinstitute.hellbender.utils.CompressedDataList
- valueFormat() - Element in annotation interface org.broadinstitute.hellbender.tools.walkers.varianteval.util.Molten
- valueName() - Element in annotation interface org.broadinstitute.hellbender.tools.walkers.varianteval.util.Molten
-
The name to use for the molten value field in the output table.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.engine.AlignmentContext.ReadOrientation
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.engine.filters.ReadTagValueFilter.Operator
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.engine.spark.GATKSparkTool.ReadInputMergingPolicy
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.metrics.MetricAccumulationLevel
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection.CopyNumberPosteriorExpectationMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts.Format
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.RunMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection.SimpleCountTableColumn
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.Metadata.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledCopyRatioSegment.Call
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.RunMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionParameter
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioParameter
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.ModelSegments.RunMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.utils.segmentation.KernelSegmenter.ChangepointSortOrder
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory.XsvDataKeyType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations.AlleleFrequencyDataSource
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations.Reference
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.DataSourceType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.OutputFormatType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.Genus
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.TranscriptSelectionMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.GatherVcfsCloud.GatherType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetClass
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetFormat
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestField
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.LocalAssembler.ContigOrientation
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.reference.CompareReferences.BaseComparisonMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.reference.CompareReferences.MD5CalculationMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.reference.ReferencePair.Status
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark.SparkCollectors
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.RevertSamSpark.FileType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments.AlignmentSignatureBasicType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments.ReasonForAlignmentClassificationFailure
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier.AlnModType.ModTypeString
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier.AlnModType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.StrandSwitch
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.SupportedType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.SupportedType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.evidence.TemplateFragmentOrdinal
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistributionShape
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.ComplexVariantSubtype
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.StructuralVariantAnnotationType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.Strand
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer.Base
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser.AltAlleleSummaryStrategy
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser.BreakpointSummaryStrategy
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine.CLUSTERING_TYPE
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter.DEPTH_OF_COVERAGE_OUTPUT_FORMAT
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Aggregation
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.FileType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Partition
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.genotyper.OutputMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult.Status
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection.FlowMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.PCRErrorModel
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection.OffRampTypeEnum
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection.OnRampTypeEnum
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine.Implementation
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph.TraversalDirection
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ThresholdCalculator.Strategy
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection.FlowMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ReadOrientation
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter.CountPileupType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter.OUTPUT_FORMAT
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations.Judgment
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceState
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.FunctionalClass.FunctionalType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.SnpEffPositionModifier.PositionModifier
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectFunctionalClass
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection.StratifyingScale
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants.ValidationType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.VariantType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsModelBackend
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.TensorType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.baq.BAQ.CalculationMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.baq.BAQ.QualityMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.BaseUtils.Base
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.BaseUtils.BaseSubstitutionType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.clipping.ClippingRepresentation
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.clustering.BayesianGaussianMixtureModeller.InitMethod
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.AnnotationSource
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.GeneTranscriptStatus
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.GenomicPhase
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.LocusLevel
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapStatus
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapTargetStatus
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.TranscriptSupportLevel
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.downsampling.DownsampleType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.GenomeLocParser.ValidationLevel
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter.WriterType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.illumina.IlluminaAdapterPair
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.IntervalMergingRule
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.IntervalSetRule
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.IntervalUtils.IntervalBreakpointType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.MannWhitneyU.TestType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.mcmc.Decile
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterizedModel.UpdateMethod
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.NGSPlatform
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter.Verbosity
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.pairhmm.PairHMM.Implementation
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM.Implementation
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.python.PythonExecutorBase.PythonExecutableName
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.R.RScriptLibrary
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.read.FlowBasedRead.Direction
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.read.markduplicates.MarkDuplicatesScoringStrategy
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert.NumPrimaryAlignmentState
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.read.ReadsWriteFormat
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.recalibration.EventType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.report.GATKReportColumnFormat.Alignment
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.report.GATKReportDataType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.Sorting
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.TableDataHeaderFields
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.TableNameHeaderFields
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.report.GATKReportVersion
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase.ProcessStream
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.runtime.StreamLocation
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.samples.Affection
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.samples.PedigreeValidationType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.samples.PedReader.Field
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.samples.PedReader.MissingPedField
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.samples.Sex
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.SequenceDictionaryCompatibility
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.SequencerFlowClass
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner.Implementation
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner.State
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.Tail
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.Trilean
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.variant.DbSnpVariantType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.FilteredRecordMergeType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.GenotypeMergeType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.broadinstitute.hellbender.utils.variant.GATKVCFIndexType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.analysis.AlignmentSummaryMetrics.Category
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.analysis.artifacts.Transition.Base
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.analysis.artifacts.Transition
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.analysis.CollectMultipleMetrics.Program
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.analysis.MetricAccumulationLevel
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.annotation.LocusFunction
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.annotation.RefFlatReader.RefFlatColumns
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.arrays.illumina.IlluminaGenotype
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.fingerprint.CrosscheckMetric.DataType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.fingerprint.DiploidGenotype
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.fingerprint.DiploidHaplotype
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.fingerprint.HaplotypeProbabilities.Genotype
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.DistanceMetric
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.parser.IlluminaDataType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.parser.IlluminaMetricsCode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.parser.IntensityChannel
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.parser.ReadType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.parser.TileTemplateRead
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.nio.PathProvider
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.pedigree.Sex
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.FilterSamReads.Filter
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.markduplicates.CheckDuplicateMarking.Mode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.RevertSam.FileType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.util.SamComparison.AlignmentComparison
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.ValidateSamFile.Mode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.ViewSam.AlignmentStatus
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.ViewSam.PfStatus
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.util.BaitDesigner.DesignStrategy
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.util.IntervalList.IntervalListScatterMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.util.IntervalListTools.Action
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.util.VariantType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.vcf.GenotypeConcordanceStateCodes
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.vcf.GenotypeConcordanceStates.CallState
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.vcf.GenotypeConcordanceStates.TruthState
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
-
Returns the enum constant of this class with the specified name.
- values() - Static method in enum class org.broadinstitute.hellbender.engine.AlignmentContext.ReadOrientation
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.engine.filters.ReadTagValueFilter.Operator
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.engine.spark.GATKSparkTool.ReadInputMergingPolicy
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.metrics.MetricAccumulationLevel
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection.CopyNumberPosteriorExpectationMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.HybridADVIArgument
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts.Format
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.RunMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection.SimpleCountTableColumn
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.formats.metadata.Metadata.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledCopyRatioSegment.Call
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.RunMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionParameter
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioParameter
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.ModelSegments.RunMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.copynumber.utils.segmentation.KernelSegmenter.ChangepointSortOrder
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.AminoAcid
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Method in class org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
- values() - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory.XsvDataKeyType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations.AlleleFrequencyDataSource
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations.Reference
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.DataSourceType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.OutputFormatType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.Genus
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.funcotator.TranscriptSelectionMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.GatherVcfsCloud.GatherType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetClass
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetFormat
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestField
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.LocalAssembler.ContigOrientation
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.reference.CompareReferences.BaseComparisonMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.reference.CompareReferences.MD5CalculationMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.reference.ReferencePair.Status
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark.SparkCollectors
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.RevertSamSpark.FileType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments.AlignmentSignatureBasicType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments.ReasonForAlignmentClassificationFailure
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier.AlnModType.ModTypeString
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier.AlnModType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.StrandSwitch
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.SupportedType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.SupportedType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.evidence.TemplateFragmentOrdinal
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistributionShape
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.ComplexVariantSubtype
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.StructuralVariantAnnotationType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.Strand
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer.Base
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser.AltAlleleSummaryStrategy
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser.BreakpointSummaryStrategy
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine.CLUSTERING_TYPE
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter.DEPTH_OF_COVERAGE_OUTPUT_FORMAT
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Aggregation
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.FileType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.Partition
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.genotyper.OutputMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult.Status
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection.FlowMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.PCRErrorModel
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection.OffRampTypeEnum
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection.OnRampTypeEnum
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine.Implementation
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph.TraversalDirection
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ThresholdCalculator.Strategy
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection.FlowMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.readorientation.ReadOrientation
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter.CountPileupType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter.OUTPUT_FORMAT
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations.Judgment
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceState
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.FunctionalClass.FunctionalType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.SnpEffPositionModifier.PositionModifier
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectFunctionalClass
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.EffectType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection.StratifyingScale
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants.ValidationType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.VariantType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsModelBackend
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.tools.walkers.vqsr.TensorType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.baq.BAQ.CalculationMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.baq.BAQ.QualityMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.BaseUtils.Base
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.BaseUtils.BaseSubstitutionType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.clipping.ClippingRepresentation
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.clustering.BayesianGaussianMixtureModeller.InitMethod
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.AnnotationSource
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.GeneTranscriptStatus
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.GenomicPhase
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.LocusLevel
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapStatus
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapTargetStatus
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.TranscriptSupportLevel
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.downsampling.DownsampleType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.GenomeLocParser.ValidationLevel
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter.WriterType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.illumina.IlluminaAdapterPair
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.IntervalMergingRule
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.IntervalSetRule
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.IntervalUtils.IntervalBreakpointType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.MannWhitneyU.TestType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.mcmc.Decile
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterizedModel.UpdateMethod
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Method in class org.broadinstitute.hellbender.utils.mcmc.ParameterizedState
-
Returns a List of the
Parameterobjects that are held internally as values of the parameter map. - values() - Static method in enum class org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.NGSPlatform
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter.Verbosity
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.Nucleotide
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.pairhmm.PairHMM.Implementation
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM.Implementation
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.python.PythonExecutorBase.PythonExecutableName
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.R.RScriptLibrary
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.read.FlowBasedRead.Direction
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.read.markduplicates.MarkDuplicatesScoringStrategy
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert.NumPrimaryAlignmentState
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.read.ReadsWriteFormat
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.recalibration.EventType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.report.GATKReportColumnFormat.Alignment
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.report.GATKReportDataType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.Sorting
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.TableDataHeaderFields
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.report.GATKReportTable.TableNameHeaderFields
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.report.GATKReportVersion
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase.ProcessStream
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.runtime.StreamLocation
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.samples.Affection
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.samples.PedigreeValidationType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.samples.PedReader.Field
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.samples.PedReader.MissingPedField
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.samples.Sex
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.SequenceDictionaryCompatibility
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.SequencerFlowClass
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner.Implementation
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner.State
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.Tail
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.Trilean
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.variant.DbSnpVariantType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Method in class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.AlleleMapper
- values() - Static method in enum class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.FilteredRecordMergeType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.GenotypeMergeType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.broadinstitute.hellbender.utils.variant.GATKVCFIndexType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.analysis.AlignmentSummaryMetrics.Category
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.analysis.artifacts.Transition.Base
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.analysis.artifacts.Transition
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.analysis.CollectMultipleMetrics.Program
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.analysis.MetricAccumulationLevel
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.annotation.LocusFunction
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.annotation.RefFlatReader.RefFlatColumns
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.arrays.illumina.IlluminaGenotype
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.fingerprint.CrosscheckMetric.DataType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.fingerprint.DiploidGenotype
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.fingerprint.DiploidHaplotype
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.fingerprint.HaplotypeProbabilities.Genotype
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.DistanceMetric
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.parser.IlluminaDataType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.parser.IlluminaMetricsCode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.parser.IntensityChannel
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.parser.ReadType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.parser.TileTemplateRead
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.nio.PathProvider
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.pedigree.Sex
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.FilterSamReads.Filter
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.markduplicates.CheckDuplicateMarking.Mode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.RevertSam.FileType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.util.SamComparison.AlignmentComparison
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.ValidateSamFile.Mode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.ViewSam.AlignmentStatus
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.ViewSam.PfStatus
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.util.BaitDesigner.DesignStrategy
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.util.IntervalList.IntervalListScatterMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.util.IntervalListTools.Action
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.util.VariantType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.vcf.GenotypeConcordanceStateCodes
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.vcf.GenotypeConcordanceStates.CallState
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.vcf.GenotypeConcordanceStates.TruthState
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values(List<List<Object>>) - Method in class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager
- ValuesIterator(Iterator<SVIntervalTree.Entry<V1>>) - Constructor for class org.broadinstitute.hellbender.utils.SVIntervalTree.ValuesIterator
- var() - Method in class org.broadinstitute.hellbender.utils.MathUtils.RunningAverage
- VAR_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The ppv (positive predictive value) for all (heterozygous and homozygous) variants (PPV is the TP / (TP + FP))
- VAR_PPV_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- VAR_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The sensitivity for all (heterozygous and homozygous) variants (Sensitivity is TP / (TP + FN))
- VAR_SENSITIVITY_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- VAR_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The specificity for all (heterozygous and homozygous) variants (Specificity is TN / (FP + TN))
- VAR_SPECIFICITY_INFO - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- variableFormat() - Element in annotation interface org.broadinstitute.hellbender.tools.walkers.varianteval.util.Molten
- variableName() - Element in annotation interface org.broadinstitute.hellbender.tools.walkers.varianteval.util.Molten
-
The name to use for the molten variable field in the output table.
- variance() - Method in class org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistribution
- VARIANCE - Enum constant in enum class org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioParameter
- VARIANT_DEPTH_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- VARIANT_ID_METHOD - Static variable in class picard.vcf.VcfToIntervalList
- VARIANT_INDEX_COMPANION - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- VARIANT_LONG_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- VARIANT_PREFIX_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.walkers.sv.SVCluster
- VARIANT_SHARDSIZE - Static variable in class org.broadinstitute.hellbender.engine.VariantShard
- VARIANT_SHORT_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The type of the event (i.e.
- VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The type of the event (i.e.
- VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The type of the event (i.e.
- VariantAccumulatorExecutor<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,
RESULT> - Interface in picard.vcf.processor -
Describes the functionality for an executor that manages the delegation of work to
VariantProcessor.Accumulators. - VariantAccumulatorExecutor.MultiThreadedChunkBased<A extends VariantProcessor.Accumulator<R>,
R> - Class in picard.vcf.processor -
A
VariantAccumulatorExecutorthat breaks down work into chunks described by the providedVariantIteratorProducerand spreads them over the indicated number of threads. - VariantAFEvaluator - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
- VariantAFEvaluator(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantAFEvaluator
- VariantAnnotation - Interface in org.broadinstitute.hellbender.tools.walkers.annotator
-
Interface of all variant annotations.
- VariantAnnotationsModel - Interface in org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling
-
File interface for passing annotations to a modeling backend and indicating a path prefix for resulting output.
- VariantAnnotationsModelBackend - Enum Class in org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling
- VariantAnnotationsScorer - Interface in org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling
-
File interface for passing annotations to a scoring backend and returning scores.
- VariantAnnotator - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Annotate variant calls with context information
- VariantAnnotator() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
- VariantAnnotatorEngine - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
The class responsible for computing annotations for variants.
- VariantAnnotatorEngine(Collection<Annotation>, FeatureInput<VariantContext>, List<FeatureInput<VariantContext>>, boolean, boolean) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
- VariantAnnotatorEngine(Collection<Annotation>, FeatureInput<VariantContext>, List<FeatureInput<VariantContext>>, boolean, boolean, Collection<Annotation>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
-
Creates an annotation engine from a list of selected annotations output from command line parsing
- VariantAnnotatorEngine.VAExpression - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
A container object for storing the objects necessary for carrying over expression annotations.
- VariantCallingDetailMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
- VariantCallingSummaryMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
- variantChromosome - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- VariantContextGetters - Class in org.broadinstitute.hellbender.utils.variant
- VariantContextGetters() - Constructor for class org.broadinstitute.hellbender.utils.variant.VariantContextGetters
- VariantContextVariantAdapter - Class in org.broadinstitute.hellbender.utils.variant
-
VariantContextVariantAdapter wraps the existing htsjdk VariantContext class so it can be used with the
GATKVariantAPI. - VariantContextVariantAdapter(VariantContext) - Constructor for class org.broadinstitute.hellbender.utils.variant.VariantContextVariantAdapter
- VariantDataManager - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
- VariantDataManager(List<String>, VariantRecalibratorArgumentCollection) - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- VariantEval - Class in org.broadinstitute.hellbender.tools.walkers.varianteval
-
Given a variant callset, it is common to calculate various quality control metrics.
- VariantEval() - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval
- variantEvalArgs - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval
- VariantEvalArgumentCollection - Class in org.broadinstitute.hellbender.tools.walkers.varianteval
-
The collection of arguments for VariantEval
- VariantEvalArgumentCollection() - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- VariantEvalArgumentCollection.StratifyingScale - Enum Class in org.broadinstitute.hellbender.tools.walkers.varianteval
- VariantEvalContext - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.util
-
A wrapper used internally by VariantEval and related classes to pass information related to the evaluation/stratification context, without exposing the entire walker to the consumer.
- VariantEvalContext(ReferenceContext, FeatureContext, Map<FeatureInput<VariantContext>, List<VariantContext>>, VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.util.VariantEvalContext
- VariantEvalEngine - Class in org.broadinstitute.hellbender.tools.walkers.varianteval
-
This class allows other classes to replicate the behavior of VariantEval Usage: -Pass the genotype args into the constructor, which will the initialize the engine completely
- VariantEvalEngine() - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- VariantEvalEngine(VariantEvalArgumentCollection, FeatureManager, List<SimpleInterval>, SAMSequenceDictionary, Collection<String>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- VariantEvalReportWriter - Class in org.broadinstitute.hellbender.tools.walkers.varianteval
-
Class for writing the GATKReport for VariantEval Accepts a fulled evaluated (i.e., there's no more data coming) set of stratifications and evaluators and supports writing out the data in these evaluators to a GATKReport.
- VariantEvalReportWriter() - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalReportWriter
- VariantEvaluationProgramGroup - Class in picard.cmdline.programgroups
-
Tools that evaluate and refine variant calls, e.g.
- VariantEvaluationProgramGroup() - Constructor for class picard.cmdline.programgroups.VariantEvaluationProgramGroup
- VariantEvaluator - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
- VariantEvaluator(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
- VariantEvaluator(VariantEvalEngine, String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
- variantFiles - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalVariantInputArgumentCollection
- variantFiles - Variable in class org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredVariantInputArgumentCollection
- VariantFilter - Interface in org.broadinstitute.hellbender.engine.filters
- VariantFilter - Interface in picard.vcf.filter
-
Interface for classes that can generate filters for VariantContexts.
- VariantFilteringProgramGroup - Class in picard.cmdline.programgroups
-
Tools that filter variants
- VariantFilteringProgramGroup() - Constructor for class picard.cmdline.programgroups.VariantFilteringProgramGroup
- VariantFilterLibrary - Class in org.broadinstitute.hellbender.engine.filters
-
Collects common variant filters.
- VariantFilterLibrary() - Constructor for class org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary
- VariantFilterLibrary.AllowAllVariantsVariantFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Do not filter out any variants.
- VariantFilterLibrary.NotSymbolicOrSVVariantFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out any variants that are symbolic or SV.
- VariantFilterLibrary.PassesFiltersVariantFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Filter out any variants that fail (variant-level) filters.
- VariantFiltration - Class in org.broadinstitute.hellbender.tools.walkers.filters
-
Filter variant calls based on INFO and/or FORMAT annotations
- VariantFiltration() - Constructor for class org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
- variantId - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- VariantIDsVariantFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only variants with any of these IDs.
- VariantIDsVariantFilter(Set<String>) - Constructor for class org.broadinstitute.hellbender.engine.filters.VariantIDsVariantFilter
- VariantIteratorProducer - Class in picard.vcf.processor
-
A mechanism for iterating over
CloseableIteratorofVariantContexts in in some fashion, given VCF files and optionally an interval list. - VariantIteratorProducer() - Constructor for class picard.vcf.processor.VariantIteratorProducer
- VariantLocusWalker - Class in org.broadinstitute.hellbender.engine
-
VariantLocusWalker processes variants from a single source, grouped by locus overlap, or optionally one at a time in order, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features.
- VariantLocusWalker() - Constructor for class org.broadinstitute.hellbender.engine.VariantLocusWalker
- VariantManipulationProgramGroup - Class in picard.cmdline.programgroups
-
Tools that manipulate variant call format (VCF) data
- VariantManipulationProgramGroup() - Constructor for class picard.cmdline.programgroups.VariantManipulationProgramGroup
- variantMultiIndelRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- variantMultiSnpRatio - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
- VariantOverlapAnnotator - Class in org.broadinstitute.hellbender.tools.walkers.annotator
-
Annotate the ID field and attribute overlap FLAGs for a VariantContext against a FeatureContext or a list of VariantContexts.
- VariantOverlapAnnotator(FeatureInput<VariantContext>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator
-
Create a new VariantOverlapAnnotator
- VariantOverlapAnnotator(FeatureInput<VariantContext>, Map<FeatureInput<VariantContext>, String>) - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator
-
Create a new VariantOverlapAnnotator
- VariantProcessor<RESULT,
ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>> - Class in picard.vcf.processor -
Describes an object that processes variants and produces a result.
- VariantProcessor.Accumulator<RESULT> - Interface in picard.vcf.processor
-
Handles
VariantContexts, and accumulates their data in some fashion internally. - VariantProcessor.AccumulatorGenerator<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,
RESULT> - Interface in picard.vcf.processor -
Generates instances of
VariantProcessor.Accumulators. - VariantProcessor.Builder<A extends VariantProcessor.Accumulator<R>,
R> - Class in picard.vcf.processor -
Simple builder of
VariantProcessors. - VariantProcessor.ResultMerger<RESULT> - Interface in picard.vcf.processor
-
Takes a collection of results produced by
VariantProcessor.Accumulator.result()and merges them into a single RESULT. - variantRate - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- variantRatePerBp - Variable in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
- VariantRecalibrator - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
-
Build a recalibration model to score variant quality for filtering purposes
- VariantRecalibrator() - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator
- VariantRecalibratorEngine - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
- VariantRecalibratorEngine(VariantRecalibratorArgumentCollection) - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorEngine
- VariantRecallerResultWriter - Class in org.broadinstitute.hellbender.tools.walkers.variantrecalling
- VariantRecallerResultWriter(File) - Constructor for class org.broadinstitute.hellbender.tools.walkers.variantrecalling.VariantRecallerResultWriter
- variants - Variable in class org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
- variants - Variable in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker
-
Variants from this input file are used by this tool to construct an alternate reference.
- VariantShard - Class in org.broadinstitute.hellbender.engine
-
VariantShard is section of the genome that's used for sharding work for pairing things with variants.
- VariantShard(int, String) - Constructor for class org.broadinstitute.hellbender.engine.VariantShard
- variantShardSize - Variable in class org.broadinstitute.hellbender.engine.spark.VariantWalkerSpark
- variantSource - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.TrainingSet
- variantSpan - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer.Result
-
Holds the smaller range that contain all relevant callable variants in the input active region (not considering the extension).
- variantSpansFeature(SimpleInterval, SimpleInterval) - Static method in class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
-
Checks if a given variant interval spans (contains) a given feature interval
- VariantsSparkSink - Class in org.broadinstitute.hellbender.engine.spark.datasources
-
VariantsSparkSink writes variants to a VCF file in parallel using Hadoop-BAM.
- VariantsSparkSink() - Constructor for class org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSink
- VariantsSparkSource - Class in org.broadinstitute.hellbender.engine.spark.datasources
-
VariantsSparkSource loads Variants from files serially (using FeatureDataSource
) or in parallel using Hadoop-BAM. - VariantsSparkSource(JavaSparkContext) - Constructor for class org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSource
- variantStart - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- variantStop - Variable in class org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- VariantsToTable - Class in org.broadinstitute.hellbender.tools.walkers.variantutils
-
Extract fields from a VCF file to a tab-delimited table
- VariantsToTable() - Constructor for class org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTable
- VariantStratifier - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
- VariantStratifier(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier
- VariantSummary - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
- VariantSummary(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
- VariantSummary.Type - Enum Class in org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
- VariantTransformer - Interface in org.broadinstitute.hellbender.transformers
-
Classes which perform transformations from
VariantContext->VariantContextshould implement this interface by overriding< VariantContext ,VariantContext>#apply(VariantContext)Created by jonn on 6/26/18. - variantType(VariantContext, FlowAnnotatorBase.LocalContext) - Method in class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
- VariantType - Class in org.broadinstitute.hellbender.tools.walkers.annotator.flow
-
Flow Annotation: type of variant: SNP/NON-H-INDEL/H-INDEL
- VariantType - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
-
Stratifies the eval variants by their type (SNP, INDEL, ETC)
- VariantType - Enum Class in org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data
-
This code and logic for determining variant types was mostly retained from VQSR.
- VariantType - Enum Class in picard.util
-
Enum to hold the possible types of dbSnps.
- VariantType() - Constructor for class org.broadinstitute.hellbender.tools.walkers.annotator.flow.VariantType
- VariantType(VariantEvalEngine) - Constructor for class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantType
- variantTypes - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
- VariantTypesVariantFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Keep only variants with any of these variant types.
- VariantTypesVariantFilter(Set<VariantContext.Type>) - Constructor for class org.broadinstitute.hellbender.engine.filters.VariantTypesVariantFilter
- VariantTypesVariantFilter(Set<VariantContext.Type>, boolean) - Constructor for class org.broadinstitute.hellbender.engine.filters.VariantTypesVariantFilter
- VariantWalker - Class in org.broadinstitute.hellbender.engine
-
A VariantWalker is a tool that processes a variant at a time from a source of variants, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features.
- VariantWalker() - Constructor for class org.broadinstitute.hellbender.engine.VariantWalker
- VariantWalkerBase - Class in org.broadinstitute.hellbender.engine
-
Base class for variant walkers, which process variants from one or more sources of variants, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features.
- VariantWalkerBase() - Constructor for class org.broadinstitute.hellbender.engine.VariantWalkerBase
- VariantWalkerContext - Class in org.broadinstitute.hellbender.engine.spark
-
Encapsulates a
VariantContextwith the reads that overlap it (theReadsContextand itsReferenceContextandFeatureContext. - VariantWalkerContext(VariantContext, ReadsContext, ReferenceContext, FeatureContext) - Constructor for class org.broadinstitute.hellbender.engine.spark.VariantWalkerContext
- VariantWalkerSpark - Class in org.broadinstitute.hellbender.engine.spark
-
A Spark version of
VariantWalker. - VariantWalkerSpark() - Constructor for class org.broadinstitute.hellbender.engine.spark.VariantWalkerSpark
- variantWasSingleton(VariantContext) - Static method in class org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
-
Returns true if the variant in vc was a singleton in the original input evaluation set, regardless of variant context subsetting that has occurred.
- VAULTRNA - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.KnownGeneBiotype
- VC_FILTERED - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- VC_FILTERED - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- VC_FILTERED_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- vcf() - Method in class picard.vcf.processor.VcfFileSegment
-
Deprecated.
- vcf() - Method in class picard.vcf.processor.VcfPathSegment
- VCF - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.DataSourceType
-
This value indicates a Variant Context File (VCF)
- VCF - Enum constant in enum class org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.OutputFormatType
- VCF - Enum constant in enum class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetFormat
- VCF - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- VCF - Variable in class picard.arrays.VcfToAdpc
- VCF - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- VCF_BUFFER_SIZE_ARG_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- VCF_DIR - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- VCF_FILE_EXTENSION - Static variable in class org.broadinstitute.hellbender.utils.variant.VcfUtils
- VCF_INITIALIZER_THREADS_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- VcfFileSegment - Class in picard.vcf.processor
-
Deprecated.from 2022-03-17, Use VcfPathSegment
- VcfFileSegment() - Constructor for class picard.vcf.processor.VcfFileSegment
-
Deprecated.
- VcfFileSegmentGenerator - Class in picard.vcf.processor
-
Deprecated.from 2022-03-17, Use
VcfPathSegmentGenerator - VcfFileSegmentGenerator() - Constructor for class picard.vcf.processor.VcfFileSegmentGenerator
-
Deprecated.
- VcfFormatConverter - Class in picard.vcf
-
Converts an ASCII VCF file to a binary BCF or vice versa.
- VcfFormatConverter() - Constructor for class picard.vcf.VcfFormatConverter
- VcfFuncotationFactory - Class in org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf
-
A class to create annotations from VCF feature sources.
- VcfFuncotationFactory(String, String, Path, LinkedHashMap<String, String>, FeatureInput<? extends Feature>) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory
-
Create a
VcfFuncotationFactory. - VcfFuncotationFactory(String, String, Path, LinkedHashMap<String, String>, FeatureInput<? extends Feature>, boolean) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory
-
Create a
VcfFuncotationFactory. - VcfFuncotationFactory(String, String, Path, LinkedHashMap<String, String>, FeatureInput<? extends Feature>, boolean, int) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory
-
Create a
VcfFuncotationFactory. - VcfFuncotationMetadata - Class in org.broadinstitute.hellbender.tools.funcotator.metadata
-
A concrete class for
FuncotationMetadatathat can be easily built from a VCF Header. - vcfOutput - Variable in class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
- VcfOutputRenderer - Class in org.broadinstitute.hellbender.tools.funcotator.vcfOutput
-
A Funcotator output renderer for writing to VCF files.
- VcfOutputRenderer(VariantContextWriter, List<DataSourceFuncotationFactory>, VCFHeader, LinkedHashMap<String, String>, LinkedHashMap<String, String>, Set<VCFHeaderLine>, Set<String>, String) - Constructor for class org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer
-
Create a
VcfOutputRenderer. - vcfPath - Variable in class org.broadinstitute.hellbender.tools.reference.CheckReferenceCompatibility
- VcfPathSegment - Class in picard.vcf.processor
-
Describes a segment of a particular VCF file.
- VcfPathSegment() - Constructor for class picard.vcf.processor.VcfPathSegment
- VcfPathSegmentGenerator - Class in picard.vcf.processor
-
Describes a mechanism for producing
VcfPathSegments from a VCF file path. - VcfPathSegmentGenerator() - Constructor for class picard.vcf.processor.VcfPathSegmentGenerator
- VcfToAdpc - Class in picard.arrays
-
A simple program to convert a Genotyping Arrays VCF to an ADPC file (Illumina intensity data file).
- VcfToAdpc() - Constructor for class picard.arrays.VcfToAdpc
- VcfToIntervalList - Class in picard.vcf
-
Converts a VCF or BCF file to a Picard Interval List.
- VcfToIntervalList() - Constructor for class picard.vcf.VcfToIntervalList
- VcfToIntervalList.VARIANT_ID_TYPES - Enum Class in picard.vcf
- VcfUtils - Class in org.broadinstitute.hellbender.utils.variant
-
Utils for dealing with VCF files.
- VcfUtils - Class in picard.vcf
-
Created by farjoun on 4/1/17.
- VcfUtils() - Constructor for class picard.vcf.VcfUtils
- vectorDiff(int[], int[]) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
-
Compute Z=X-Y for two numeric vectors X and Y
- VectorLoglessPairHMM - Class in org.broadinstitute.hellbender.utils.pairhmm
-
Class for performing the pair HMM for global alignment using AVX instructions contained in a native shared library.
- VectorLoglessPairHMM(VectorLoglessPairHMM.Implementation, PairHMMNativeArguments) - Constructor for class org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM
-
Create a VectorLoglessPairHMM
- VectorLoglessPairHMM.Implementation - Enum Class in org.broadinstitute.hellbender.utils.pairhmm
-
Type for implementation of VectorLoglessPairHMM
- VERBOSE - Enum constant in enum class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter.Verbosity
-
Output verbose progress information during the copy.
- VERBOSE - Enum constant in enum class picard.sam.ValidateSamFile.Mode
- verbosity - Variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- VERBOSITY - Variable in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
- VERBOSITY - Variable in class picard.cmdline.CommandLineProgram
- VERBOSITY_DEFAULT - Static variable in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- VERBOSITY_NAME - Static variable in class org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- VERIFIED - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.LocusLevel
-
Verified locus
- verify(List<Integer>) - Method in class picard.illumina.parser.TileIndex
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileBclFileUtil
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileFileUtil
-
expectedCycles are not checked in this implementation.
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Given the expected tiles/expected cycles for this file type, return a list of error messages describing any missing/or malformed files
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileFileUtil
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
- verifyData(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileParser
- verifyData(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileBclParser
- verifyData(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileParser
- VerifyIDIntensityContaminationMetrics - Class in picard.arrays
- VerifyIDIntensityContaminationMetrics() - Constructor for class picard.arrays.VerifyIDIntensityContaminationMetrics
- version - Variable in class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
-
Version number of this
DataSourceFuncotationFactory. - version - Variable in class picard.illumina.parser.readers.FilterFileReader
-
Version number found in the FilterFile, this should equal 3
- version - Variable in enum class picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
- VERSION - Static variable in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRenderer
-
Version of the MAF standard that this
MafOutputRendererwrites. - VERSION_STRING - Static variable in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.Serializer
-
Serialization version.
- ViewSam - Class in picard.sam
-
Prints a SAM or BAM file to the screen.
- ViewSam() - Constructor for class picard.sam.ViewSam
- ViewSam.AlignmentStatus - Enum Class in picard.sam
- ViewSam.PfStatus - Enum Class in picard.sam
- visitNum - Variable in class org.broadinstitute.hellbender.tools.LocalAssembler.WalkData
- VQS_LOD_KEY - Static variable in class org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- VQSLOD_CUTOFF - Variable in class org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSR
- VQSLODTranche - Class in org.broadinstitute.hellbender.tools.walkers.vqsr
- VQSLODTranche(double, long, double, long, double, int, int, VariantRecalibratorArgumentCollection.Mode, String) - Constructor for class org.broadinstitute.hellbender.tools.walkers.vqsr.VQSLODTranche
- VQSRNegativeModelFailure(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.VQSRNegativeModelFailure
- VQSRPositiveModelFailure(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.VQSRPositiveModelFailure
W
- W - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- waitForAck() - Method in class org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor
-
Wait for an acknowledgement (which must have been previously requested).
- waitForAck() - Method in class org.broadinstitute.hellbender.utils.runtime.StreamingProcessController
-
Wait for a previously requested acknowledgement to be received.
- waitForPreviousBatchCompletion() - Method in class org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor
-
Waits for a batch that was previously initiated via
StreamingPythonScriptExecutor.startBatchWrite(String, List)} to complete, flushes the target stream and returns the corresponding completed Future. - waitForPreviousBatchCompletion() - Method in class org.broadinstitute.hellbender.utils.runtime.AsynchronousStreamWriter
-
Waits for a batch that was previously initiated via
AsynchronousStreamWriter.startBatchWrite(List)} to complete, flushes the target stream and returns the corresponding completed Future. - WalkDataFactory() - Constructor for class org.broadinstitute.hellbender.tools.LocalAssembler.WalkDataFactory
- WalkerBase - Class in org.broadinstitute.hellbender.engine
-
Base class for pre-packaged walker traversals in the GATK engine.
- WalkerBase() - Constructor for class org.broadinstitute.hellbender.engine.WalkerBase
- warn(String) - Method in class org.broadinstitute.hellbender.utils.logging.OneShotLogger
- warn(Supplier<?>) - Method in class org.broadinstitute.hellbender.utils.logging.OneShotLogger
- WARN_ON_MISSING_CONTIG - Variable in class picard.vcf.LiftoverVcf
- WarnableAnnotationFailure(String) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.WarnableAnnotationFailure
- warnBigDifferences - Variable in class org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance
- warning - Variable in class org.broadinstitute.hellbender.engine.filters.IntervalOverlapReadFilter
- warning - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.OriginalAlignment
- warning - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.PossibleDeNovo
- warning - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.ReferenceBases
- warnOnNonIlluminaReadGroups(SAMFileHeader, Logger) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Checks if the read header contains any reads groups from non-Illumina and issue a warning of that's the case.
- warnOnToolStatus() - Method in class org.broadinstitute.hellbender.cmdline.CommandLineProgram
-
If a tool is either Experimental or Beta, log a warning against use in production a environment.
- warnUser(String) - Static method in class org.broadinstitute.hellbender.utils.Utils
- warnUser(Logger, String) - Static method in class org.broadinstitute.hellbender.utils.Utils
- warnUserLines(String) - Static method in class org.broadinstitute.hellbender.utils.Utils
- wasClipped() - Method in class org.broadinstitute.hellbender.utils.clipping.ReadClipper
-
Check whether or not this read has been clipped.
- wasLastEdgeFollowedBasedOnJTEvidence() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JTBestHaplotype
- wasValidationRequested() - Method in class org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeterResults
-
Get whether a user requested that a checksum be calculated on the downloaded file.
- WEAK - Static variable in enum class org.broadinstitute.hellbender.utils.Nucleotide
- weightDecay - Variable in class org.broadinstitute.hellbender.tools.walkers.annotator.AllelePseudoDepth
- weightedAverageOfTumorAFs(VariantContext) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- weightedMedianPosteriorProbability(List<ImmutablePair<Integer, Double>>) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2Filter
- wellFormedDouble(double) - Static method in class org.broadinstitute.hellbender.utils.MathUtils
- WellformedFlowBasedReadFilter - Class in org.broadinstitute.hellbender.engine.filters.flow
-
Tests whether a flow based read is "well-formed" -- that is, is free of major internal inconsistencies and issues that could lead to errors downstream.
- WellformedFlowBasedReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.flow.WellformedFlowBasedReadFilter
- WellformedReadFilter - Class in org.broadinstitute.hellbender.engine.filters
-
Tests whether a read is "well-formed" -- that is, is free of major internal inconsistencies and issues that could lead to errors downstream.
- WellformedReadFilter() - Constructor for class org.broadinstitute.hellbender.engine.filters.WellformedReadFilter
- WellformedReadFilter(SAMFileHeader) - Constructor for class org.broadinstitute.hellbender.engine.filters.WellformedReadFilter
- WgsMetrics - Class in picard.analysis
-
Metrics for evaluating the performance of whole genome sequencing experiments.
- WgsMetrics() - Constructor for class picard.analysis.WgsMetrics
-
Create an instance of this metric that is not mergeable.
- WgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Constructor for class picard.analysis.WgsMetrics
-
Create an instance of this metric that is mergeable.
- WgsMetricsCollector(CollectWgsMetrics, int, IntervalList) - Constructor for class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
- WgsMetricsProcessor - Interface in picard.analysis
-
Interface for processing data and generate result for CollectWgsMetrics
- WgsMetricsProcessorImpl<T extends htsjdk.samtools.util.AbstractRecordAndOffset> - Class in picard.analysis
-
Implementation of
WgsMetricsProcessorthat gets input data from a given iterator and processes it with a help of collector - WgsMetricsProcessorImpl(AbstractLocusIterator<T, AbstractLocusInfo<T>>, ReferenceSequenceFileWalker, AbstractWgsMetricsCollector<T>, ProgressLogger) - Constructor for class picard.analysis.WgsMetricsProcessorImpl
- WgsMetricsWithNonZeroCoverage() - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
- WgsMetricsWithNonZeroCoverage(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
- WgsMetricsWithNonZeroCoverageCollector(CollectWgsMetricsWithNonZeroCoverage, int, IntervalList) - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
- which(String) - Static method in class org.broadinstitute.hellbender.utils.runtime.RuntimeUtils
-
Returns the path to an executable or null if it doesn't exist.
- WHOLE_GENOME - Enum constant in enum class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
- WHOLE_GENOME - Static variable in class org.broadinstitute.hellbender.utils.GenomeLoc
- width() - Method in interface org.broadinstitute.hellbender.utils.IntervalPileup
- WIDTH_OF_10_PERCENT - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 10% of all read pairs.
- WIDTH_OF_10_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 10% of all read pairs.
- WIDTH_OF_20_PERCENT - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 20% of all read pairs.
- WIDTH_OF_20_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 20% of all read pairs.
- WIDTH_OF_30_PERCENT - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 30% of all read pairs.
- WIDTH_OF_30_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 30% of all read pairs.
- WIDTH_OF_40_PERCENT - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 40% of all read pairs.
- WIDTH_OF_40_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 40% of all read pairs.
- WIDTH_OF_50_PERCENT - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 50% of all read pairs.
- WIDTH_OF_50_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 50% of all read pairs.
- WIDTH_OF_60_PERCENT - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 60% of all read pairs.
- WIDTH_OF_60_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 60% of all read pairs.
- WIDTH_OF_70_PERCENT - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 70% of all read pairs.
- WIDTH_OF_70_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 70% of all read pairs.
- WIDTH_OF_80_PERCENT - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 80% of all read pairs.
- WIDTH_OF_80_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 80% of all read pairs.
- WIDTH_OF_90_PERCENT - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 90% of all read pairs.
- WIDTH_OF_90_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 90% of all read pairs.
- WIDTH_OF_95_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 95% of all read pairs.
- WIDTH_OF_99_PERCENT - Variable in class org.broadinstitute.hellbender.metrics.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 100% of all read pairs.
- WIDTH_OF_99_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 100% of all read pairs.
- WINDOW_SIZE - Variable in class picard.analysis.GcBiasSummaryMetrics
-
The window size on the genome used to calculate the GC of the sequence.
- WINDOW_SIZE_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- WINDOWS - Variable in class picard.analysis.GcBiasDetailMetrics
-
The number of windows on the reference genome that have this G+C content.
- windowSizes - Variable in class org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
- withApplyEamssFiltering(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures whether or not the converter will apply EAMSS filtering.
- withAsyncWriterPool(AsyncWriterPool) - Method in class picard.illumina.BasecallsConverterBuilder
- withBarcodeExtractor(BarcodeExtractor) - Method in class picard.illumina.BasecallsConverterBuilder
- withBarcodesDir(File) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configure the director used to find barcode files created by ExtractIlluminaBarcodes.
- withBclQualityEvaluationStrategy(BclQualityEvaluationStrategy) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures the bcl quality evaluation strategy that the converter will apply.
- withDataClass(HtsgetClass) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- withDemultiplex(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures whether or not the converter will demultiplex reads by barcode.
- withField(HtsgetRequestField) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- withFields(Collection<HtsgetRequestField>) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- withFormat(HtsgetFormat) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- withIgnoreUnexpectedBarcodes(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures whether or not the converter will ignore unexpected barcodes or throw an exception if one is found.
- withinBounds(int) - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
-
Is the GQ value within the bounds of this GQ (GQ >= minGQ && GQ < maxGQ)
- withIncludeNonPfReads(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures whether or not the converter will ignore non-PF reads.
- withInput(File...) - Method in class picard.vcf.processor.VariantProcessor.Builder
- withInput(PicardHtsPath...) - Method in class picard.vcf.processor.VariantProcessor.Builder
- withInterval(SimpleInterval) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- withMaxRecordsInRam(int) - Method in class picard.illumina.BasecallsConverterBuilder
-
Specify the max number of records in RAM.
- withMolecularIndexQualityTag(String) - Method in class picard.illumina.ClusterDataToSamConverter
-
Sets the SAM tag to use to store the molecular index base qualities.
- withMolecularIndexTag(String) - Method in class picard.illumina.ClusterDataToSamConverter
-
Sets the SAM tag to use to store the molecular index bases.
- withNotag(String) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- withNotags(Collection<String>) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- withoutChromosomes(Set<String>) - Method in class picard.fingerprint.HaplotypeMap
-
Returns a copy of this haplotype map that excludes haplotypes on the chromosomes provided.
- withoutPrefixAndSuffix(byte[], byte[]) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqVertex
-
Return a new SeqVertex derived from this one but not including prefix or suffix bases
- withoutSuffix(byte[]) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqVertex
-
Return a new SeqVertex derived from this one but not including the suffix bases
- withSorting(Comparator<CLUSTER_OUTPUT_RECORD>, SortingCollection.Codec<CLUSTER_OUTPUT_RECORD>, Class<CLUSTER_OUTPUT_RECORD>, List<File>) - Method in class picard.illumina.BasecallsConverterBuilder
-
Builds a new sorting basecalls converter.
- withTag(String) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- withTagPerMolecularIndex(List<String>) - Method in class picard.illumina.ClusterDataToSamConverter
-
Sets the SAM tags to use to store the bases each molecular index.
- withTags(Collection<String>) - Method in class org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- WORKSPACE_ARG_LONG_NAME - Static variable in class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport
- WORST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
- WORST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
- WORST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The Q-score for the worst context.
- WORST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The Q-score for the worst context.
- WORST_POST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
- WORST_POST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
- WORST_POST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The Q-score for the worst post-context.
- WORST_POST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The Q-score for the worst post-context.
- WORST_PRE_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
- WORST_PRE_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
- WORST_PRE_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The Q-score for the worst pre-context.
- WORST_PRE_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The Q-score for the worst pre-context.
- write() - Method in class org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter.LineBuilder
-
Constructs the line and writes it out to the output
- write(byte[]) - Method in class org.broadinstitute.hellbender.utils.io.HardThresholdingOutputStream
- write(byte[], int, int) - Method in class org.broadinstitute.hellbender.utils.io.HardThresholdingOutputStream
- write(byte[], int, int) - Method in class picard.util.CircularByteBuffer
-
Write bytes into the buffer from the supplied array.
- write(Kryo, Output, SAMRecord) - Method in class org.broadinstitute.hellbender.engine.spark.SAMRecordSerializer
- write(Kryo, Output, PSKmerBloomFilter) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerBloomFilter.Serializer
- write(Kryo, Output, PSKmerSet) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet.Serializer
- write(Kryo, Output, PSTaxonomyDatabase) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTaxonomyDatabase.Serializer
- write(Kryo, Output, PSTree) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTree.Serializer
- write(Kryo, Output, PSTreeNode) - Method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode.Serializer
- write(Kryo, Output, AlignedAssembly) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedAssembly.Serializer
- write(Kryo, Output, AlignedContig) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig.Serializer
- write(Kryo, Output, AlignmentInterval) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval.Serializer
- write(Kryo, Output, AssemblyContigWithFineTunedAlignments) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments.Serializer
- write(Kryo, Output, BreakpointComplications.IntraChrStrandSwitchBreakpointComplications) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.IntraChrStrandSwitchBreakpointComplications.Serializer
- write(Kryo, Output, BreakpointComplications.InvertedDuplicationBreakpointComplications) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.InvertedDuplicationBreakpointComplications.Serializer
- write(Kryo, Output, BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications.Serializer
- write(Kryo, Output, BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications.Serializer
- write(Kryo, Output, BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications.Serializer
- write(Kryo, Output, CpxVariantCanonicalRepresentation) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantCanonicalRepresentation.Serializer
- write(Kryo, Output, CpxVariantInducingAssemblyContig) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInducingAssemblyContig.Serializer
- write(Kryo, Output, NovelAdjacencyAndAltHaplotype) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype.Serializer
- write(Kryo, Output, SimpleChimera) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera.Serializer
- write(Kryo, Output, SimpleNovelAdjacencyAndChimericAlignmentEvidence) - Method in class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence.Serializer
- write(Kryo, Output, AlignedAssemblyOrExcuse) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse.Serializer
- write(Kryo, Output, BreakpointEvidence) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.Serializer
- write(Kryo, Output, BreakpointEvidence.ExternalEvidence) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ExternalEvidence.Serializer
- write(Kryo, Output, BreakpointEvidence.InterContigPair) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.InterContigPair.Serializer
- write(Kryo, Output, BreakpointEvidence.LargeIndel) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.LargeIndel.Serializer
- write(Kryo, Output, BreakpointEvidence.MateUnmapped) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.MateUnmapped.Serializer
- write(Kryo, Output, BreakpointEvidence.OutiesPair) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.OutiesPair.Serializer
- write(Kryo, Output, BreakpointEvidence.ReadEvidence) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence.Serializer
- write(Kryo, Output, BreakpointEvidence.SameStrandPair) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SameStrandPair.Serializer
- write(Kryo, Output, BreakpointEvidence.SplitRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SplitRead.Serializer
- write(Kryo, Output, BreakpointEvidence.TemplateSizeAnomaly) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.TemplateSizeAnomaly.Serializer
- write(Kryo, Output, BreakpointEvidence.WeirdTemplateSize) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.WeirdTemplateSize.Serializer
- write(Kryo, Output, EvidenceTargetLink) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink.Serializer
- write(Kryo, Output, KmerAndInterval) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerAndInterval.Serializer
- write(Kryo, Output, LibraryStatistics) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics.Serializer
- write(Kryo, Output, QNameAndInterval) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval.Serializer
- write(Kryo, Output, ReadMetadata) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.Serializer
- write(Kryo, Output, ReadMetadata.LibraryRawStatistics) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.LibraryRawStatistics.Serializer
- write(Kryo, Output, ReadMetadata.PartitionBounds) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionBounds.Serializer
- write(Kryo, Output, ReadMetadata.PartitionStatistics) - Method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionStatistics.Serializer
- write(Kryo, Output, KmerAndCount) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.KmerAndCount.Serializer
- write(Kryo, Output, PairedStrandedIntervalTree<T>) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.Serializer
- write(Kryo, Output, Strand) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.Strand.Serializer
- write(Kryo, Output, StrandedInterval) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval.Serializer
- write(Kryo, Output, SVFastqUtils.FastqRead) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead.Serializer
- write(Kryo, Output, SVKmerLong) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong.Serializer
- write(Kryo, Output, SVKmerShort) - Method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort.Serializer
- write(Kryo, Output, HopscotchCollectionSpark<T>) - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchCollectionSpark.Serializer
- write(Kryo, Output, HopscotchMapSpark) - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMapSpark.Serializer
- write(Kryo, Output, HopscotchMultiMapSpark) - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchMultiMapSpark.Serializer
- write(Kryo, Output, HopscotchSetSpark) - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchSetSpark.Serializer
- write(Kryo, Output, HopscotchUniqueMultiMapSpark) - Method in class org.broadinstitute.hellbender.tools.spark.utils.HopscotchUniqueMultiMapSpark.Serializer
- write(Kryo, Output, IntHistogram) - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.Serializer
- write(Kryo, Output, IntHistogram.CDF) - Method in class org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.CDF.Serializer
- write(Kryo, Output, LargeLongHopscotchSet) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet.Serializer
- write(Kryo, Output, LongBloomFilter) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter.Serializer
- write(Kryo, Output, LongHopscotchSet) - Method in class org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet.Serializer
- write(Kryo, Output, Pair) - Method in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair.Serializer
- write(Kryo, Output, SAMRecordToGATKReadAdapter) - Method in class org.broadinstitute.hellbender.engine.spark.SAMRecordToGATKReadAdapterSerializer
- write(Kryo, Output, SVInterval) - Method in class org.broadinstitute.hellbender.utils.SVInterval.Serializer
- write(Kryo, Output, SVIntervalTree<T>) - Method in class org.broadinstitute.hellbender.utils.SVIntervalTree.Serializer
- write(F) - Method in class org.broadinstitute.hellbender.tools.sv.AbstractEvidenceSortMerger
- write(F) - Method in interface org.broadinstitute.hellbender.utils.codecs.FeatureSink
- write(F) - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Writer
- write(F) - Method in class org.broadinstitute.hellbender.utils.io.FeatureOutputStream
-
Adds new feature and writes to file
- write(F, BlockCompressedIntervalStream.Writer<F>) - Method in interface org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.WriteFunc
- write(VariantContext, FuncotationMap) - Method in class org.broadinstitute.hellbender.tools.funcotator.compositeoutput.CompositeOutputRenderer
-
Write the given
variantandtxToFuncotationMapto the output file. - write(VariantContext, FuncotationMap) - Method in class org.broadinstitute.hellbender.tools.funcotator.genelistoutput.GeneListOutputRenderer
-
Since this output renderer needs to see all of the input before it can render properly, it will not actually write anything during this call.
- write(VariantContext, FuncotationMap) - Method in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRenderer
- write(VariantContext, FuncotationMap) - Method in class org.broadinstitute.hellbender.tools.funcotator.OutputRenderer
-
Write the given
variantandtxToFuncotationMapto the output file. - write(VariantContext, FuncotationMap) - Method in class org.broadinstitute.hellbender.tools.funcotator.simpletsvoutput.SimpleTsvOutputRenderer
- write(VariantContext, FuncotationMap) - Method in class org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer
- write(DataOutputStream) - Method in class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.IndexEntry
- write(DataOutputStream) - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter.Record
- write(File) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractRecordCollection
-
Writes the records to file.
- write(File) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.CalledLegacySegmentCollection
- write(File) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.LegacySegmentCollection
- write(File) - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection
-
Write this collection to a file Dev note: This method will force the default xsv config file on the output.
- write(File) - Method in class picard.pedigree.PedFile
-
Writes a set of pedigrees out to disk.
- write(File, File) - Method in class org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisedCopyRatioResult
- write(Iterable<IlluminaAdpcFileWriter.Record>) - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter
- write(List<BasicValidationResult>, GATKPath) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
- write(DragstrLocus, DataOutput) - Method in interface org.broadinstitute.hellbender.tools.dragstr.DragstrLocus.WriteAction
- write(DepthEvidence) - Method in class org.broadinstitute.hellbender.tools.sv.DepthEvidenceSortMerger
- write(OUTPUT_RECORD) - Method in interface picard.illumina.BasecallsConverter.ConvertedClusterDataWriter
-
Write out a single record of type OUTPUT_RECORD.
- write(IlluminaAdpcFileWriter.Record) - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter
- write(R) - Method in class org.broadinstitute.hellbender.utils.BinaryTableWriter
- WRITE_NS - Enum constant in enum class org.broadinstitute.hellbender.utils.clipping.ClippingRepresentation
-
Clipped bases are changed to Ns
- WRITE_NS_Q0S - Enum constant in enum class org.broadinstitute.hellbender.utils.clipping.ClippingRepresentation
-
Clipped bases are change to have both an N base and a Q0 quality score
- WRITE_ORIGINAL_ALLELES - Variable in class picard.vcf.LiftoverVcf
- WRITE_ORIGINAL_POSITION - Variable in class picard.vcf.LiftoverVcf
- WRITE_Q0S - Enum constant in enum class org.broadinstitute.hellbender.utils.clipping.ClippingRepresentation
-
Clipped bases are changed to have Q0 quality score
- WRITE_READS_FILES - Variable in class picard.sam.FilterSamReads
- writeAlignment(SAMRecord) - Method in class picard.sam.FixMateInformation
- writeAll(Iterable<? extends R>) - Method in class org.broadinstitute.hellbender.utils.BinaryTableWriter
- writeAll(List<DATA>) - Method in class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVVariantComposer
- writeAlleleLikelihoods(AlleleLikelihoods<GATKRead, Haplotype>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleLikelihoodWriter
-
Add a likelihood matrix to the output.
- writeAllRecords(Iterable<R>) - Method in class org.broadinstitute.hellbender.utils.tsv.TableWriter
-
Write all the records in a
Iterable. - writeArtifactPriors(File) - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPriorCollection
- writeAsVcf(File, File) - Method in class picard.fingerprint.HaplotypeMap
- writeBfqFiles() - Method in class picard.fastq.SamToBfqWriter
-
Writes the binary fastq file(s) to the output directory
- writeByteArrayToFile(byte[], File) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Writes the given array of bytes to a file
- writeByteArrayToStream(byte[], OutputStream) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Writes the given array of bytes to a stream
- writeChunkedDoubleMatrix(HDF5File, String, double[][], int) - Static method in class org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils
-
Given a large matrix, chunks the matrix into equally sized subsets of rows (plus a subset containing the remainder, if necessary) and writes these submatrices to indexed sub-paths to avoid a hard limit in Java HDF5 on the number of elements in a matrix given by
MAX_NUMBER_OF_VALUES_PER_HDF5_MATRIX. - writeComment(String) - Method in class org.broadinstitute.hellbender.utils.tsv.TableWriter
-
Writes a comment into the output.
- writeCoverageOutputHeaders(Map<DoCOutputType.Partition, List<String>>) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter
-
Initialize and write the output headers for the output streams that need to be continuously updated during traversal.
- writeCumulativeOutputSummaryFiles(DepthOfCoveragePartitionedDataStore, DoCOutputType.Partition, List<String>) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter
-
Write output summary histogram based metrics.
- writeExtraOutputs(File) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- writeFastqFile(String, Iterator<SVFastqUtils.FastqRead>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils
-
Write a list of FASTQ records into a file.
- writeFastqStream(OutputStream, Iterator<SVFastqUtils.FastqRead>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils
- writeFilteringGraphs - Variable in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- writeFilteringStats(Path) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
-
Write statistics collected in the final pass of
FilterMutectCalls - writeFilteringStats(Path, double, List<Pair<String, String>>) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteringOutputStats
- writeFingerPrint(Fingerprint, File, File, String, String) - Static method in class picard.fingerprint.FingerprintUtils
-
A function that takes a Fingerprint and writes it as a VCF to a file
- writeGFAs - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- writeHDF5(File) - Method in class org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection
- writeHDF5(File, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
-
Writes a representation of the collection to an HDF5 file with the following directory structure:
- writeHeader(VariantContextWriter, SAMSequenceDictionary, Set<VCFHeaderLine>) - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
-
Writes an appropriate VCF header, given our arguments, to the provided writer
- writeHeader(VariantContextWriter, Set<VCFHeaderLine>) - Method in class org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
- writeHeader(VCFHeader) - Method in class org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter
-
Write the VCF header Adds standard GVCF fields to the header
- writeHeader(VCFHeader) - Method in class org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter
-
Defines header for the writer that will be written to all shards.
- writeHeader(String) - Method in class org.broadinstitute.hellbender.utils.io.FeatureOutputStream
-
Writes header to file.
- writeHeader(List<String>) - Method in class org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRenderer
-
Write the header to the output file.
- writeHeader(AnnotatedIntervalHeader) - Method in interface org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalWriter
-
Write only the header (and any SAMFileHeader or comments)
- writeHeader(AnnotatedIntervalHeader) - Method in class org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.SimpleAnnotatedIntervalWriter
- writeHeaderIfApplies() - Method in class org.broadinstitute.hellbender.utils.tsv.TableWriter
-
Writes the header if it has not been written already.
- writeHistograms() - Method in class org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2CountsCollector
- writeIntervalFile(String, SAMFileHeader, List<SVInterval>, List<AlignedAssemblyOrExcuse>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse
-
write a file describing each interval
- writeIntervals(HDF5File, String, List<T>) - Static method in class org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils
-
Given an HDF5 file and an HDF5 path, writes a list of intervals to hard-coded sub-paths.
- writeIntervalsFile(String, Collection<SVInterval>, List<String>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFileUtils
-
Write intervals to a file.
- writeKey(FileWriter) - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
- writeKmerBloomFilter(String, PSKmerBloomFilter) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerUtils
- writeKmerSet(String, PSKmerSet) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerUtils
- writeKmersFile(String, int, Collection<KType>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFileUtils
-
Write kmers to file.
- writeKryoObject(Object, String) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerUtils
-
Writes an object to a URI using Kryo serialization.
- writeLibraryToTempFile(File) - Method in enum class org.broadinstitute.hellbender.utils.R.RScriptLibrary
-
Retrieve the resource for this library and write it to a temp File in
targetDir. - writeM2FilterSummary(Collection<FilterStats>, Path, List<Pair<String, String>>, double, double, double, double, double) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterStats
- writeMatrix(OutputStreamWriter) - Method in class org.broadinstitute.hellbender.utils.read.FlowBasedRead
-
Flow matrix logger This is used exclusively for testing
- writeMetadata(String, String) - Method in class org.broadinstitute.hellbender.utils.tsv.TableWriter
- writeMetadata(ReadMetadata, String) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- writeMissingReferenceAccessions(String, SAMFileHeader, PSTaxonomyDatabase, Logger) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScorer
-
Writes accessions contained in a SAM header that do not exist in the taxonomy database
- writeMixingFractions(List<MixingFraction>, File) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.MixingFraction
- writeModelParameterFiles(File, File) - Method in class org.broadinstitute.hellbender.tools.copynumber.models.MultidimensionalModeller
-
Writes posterior summaries for the global model parameters to a file.
- writeModelReport(GaussianMixtureModel, GaussianMixtureModel, List<String>) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator
- writeOutputGeneStatistics(int[][], int[]) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter
-
Write out the gene statistics.
- writeOutputIntervalStatistics(DoCOutputType.Partition, int[][], int[]) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter
-
Write out the interval summary statistics.
- writeOutRecalibrationTable(VariantContextWriter, SAMSequenceDictionary) - Method in class org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- writePerGeneDepthInformation(RefSeqFeature, DepthOfCoverageStats, List<String>) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter
-
Write summary information for a gene.
- writePerIntervalDepthInformation(DoCOutputType.Partition, SimpleInterval, DepthOfCoverageStats, List<String>) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter
-
Method that should be called once per-partition at the end of each coverage interval.
- writePerLocusCumulativeCoverageMetrics(DepthOfCoveragePartitionedDataStore, DoCOutputType.Partition, List<String>) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter
-
Write per-locus cumulative coverage metrics.
- writePerLocusDepthSummary(SimpleInterval, Map<DoCOutputType.Partition, Map<String, int[]>>, Map<DoCOutputType.Partition, List<String>>, boolean) - Method in class org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter
-
Writes a summary of the given per-locus data out to the main output track.
- writeProcessInput(String) - Method in class org.broadinstitute.hellbender.utils.runtime.StreamingProcessController
-
Write some input to the remote process, without waiting for output.
- writeQNames(String, Iterable<QNameAndInterval>) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval
-
write template names and interval IDs to a file.
- writer - Variable in class org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker
- writer(Writer, TableColumnCollection, BiConsumer<R, DataLine>) - Static method in class org.broadinstitute.hellbender.utils.tsv.TableUtils
-
Creates a new table writer given the destination writer, columns and the data-line composer.
- writer(Path, TableColumnCollection, BiConsumer<R, DataLine>) - Static method in class org.broadinstitute.hellbender.utils.tsv.TableUtils
-
Creates a new table writer given the destination file, columns and the data-line composer.
- Writer(String, OutputStream, SVFeaturesHeader, BlockCompressedIntervalStream.WriteFunc<F>) - Constructor for class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Writer
- Writer(GATKPath, SVFeaturesHeader, BlockCompressedIntervalStream.WriteFunc<F>) - Constructor for class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Writer
- Writer(GATKPath, SVFeaturesHeader, BlockCompressedIntervalStream.WriteFunc<F>, int) - Constructor for class org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Writer
- writeReads(JavaSparkContext, String, JavaRDD<GATKRead>) - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Writes the reads from a
JavaRDDto an output file. - writeReads(JavaSparkContext, String, JavaRDD<GATKRead>, SAMFileHeader, boolean) - Method in class org.broadinstitute.hellbender.engine.spark.GATKSparkTool
-
Writes the reads from a
JavaRDDto an output file. - writeReads(JavaSparkContext, String, GATKPath, JavaRDD<GATKRead>, SAMFileHeader, ReadsWriteFormat) - Static method in class org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink
-
writeReads writes rddReads to outputFile with header as the file header.
- writeReads(JavaSparkContext, String, GATKPath, JavaRDD<GATKRead>, SAMFileHeader, ReadsWriteFormat, int, String, boolean, boolean, boolean, long) - Static method in class org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink
-
writeReads writes rddReads to outputFile with header as the file header.
- writeReads(JavaSparkContext, String, GATKPath, JavaRDD<GATKRead>, SAMFileHeader, ReadsWriteFormat, int, String, boolean, long) - Static method in class org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink
-
writeReads writes rddReads to outputFile with header as the file header.
- writeReadsAlignedToHaplotypes(Collection<Haplotype>, Locatable, Collection<Haplotype>, Set<Haplotype>, AlleleLikelihoods<GATKRead, Haplotype>) - Method in class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter
- writeReadsAlignedToHaplotypes(Collection<Haplotype>, Locatable, Collection<Haplotype>, Set<Haplotype>, AlleleLikelihoods<GATKRead, Haplotype>, Locatable) - Method in class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter
-
Write out a BAM representing for the haplotype caller at this site writerType (ALL_POSSIBLE_HAPLOTYPES or CALLED_HAPLOTYPES) determines inputs to writeHaplotypesAsReads Write out a BAM representing the haplotypes at this site, based on the value for writerType used when the writer was constructed (ALL_POSSIBLE_HAPLOTYPES or CALLED_HAPLOTYPES).
- writeRecord(R) - Method in class org.broadinstitute.hellbender.utils.tsv.TableWriter
-
Writes a new record.
- writeRecord(R, DataOutput) - Method in class org.broadinstitute.hellbender.utils.BinaryTableWriter
- writeReport(File) - Method in class picard.sam.util.SamComparison
- writeReport(File, List<Header>) - Method in class picard.sam.util.SamComparison
- writeReport(PrintStream, StratificationManager<VariantStratifier, EvaluationContext>, Collection<VariantStratifier>, Collection<VariantEvaluator>) - Static method in class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalReportWriter
-
The business end of the class.
- writeResource(Resource, File) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Writes the an embedded resource to a file.
- writerPool - Variable in class picard.illumina.BasecallsConverter
- writeSAMFile(String, Iterator<SAMRecord>, SAMFileHeader, boolean) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVFileUtils
-
Write SAM records to designated
outputName. - writeScores(File, double[]) - Static method in interface org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsScorer
-
Writes a double array of scores to "/data/scores" in an HDF5 file.
- writeScoresFile(Map<Integer, PSPathogenTaxonScore>, PSTree, String) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSScorer
-
Output a tab-delimited table of taxonomic scores
- writeStandalone(ReadMetadata, String) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.Serializer
-
Serializes a read-metadata by itself into a file.
- writeStringListToFile(Iterable<String>, File) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Writes a list of strings to the given filename.
- writeTableBySequenceName(ReferenceSequenceTable) - Method in class org.broadinstitute.hellbender.tools.reference.CompareReferences
-
Given a table, write table by sequence name to standard output
- writeTarGz(String, File...) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
- writeTaxonomyDatabase(String, PSTaxonomyDatabase) - Static method in class org.broadinstitute.hellbender.tools.spark.pathseq.PSBuildReferenceTaxonomyUtils
-
Writes objects using Kryo to specified local file path.
- writeTemp() - Method in enum class org.broadinstitute.hellbender.utils.R.RScriptLibrary
-
Writes the library source code to a temporary tar.gz file and returns the path.
- writeTempFile(String, String, String) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Writes content to a temp file and returns the path to the temporary file.
- writeTempFile(String, String, String, File) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Writes content to a temp file and returns the path to the temporary file.
- writeTempFile(List<String>, String, String) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Writes multiple lines of content to a temp file and returns the temporary file.
- writeTempResource(Resource) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Writes an embedded resource to a temporary file.
- writeTempResourceFromPath(String, Class<?>) - Static method in class org.broadinstitute.hellbender.utils.io.IOUtils
-
Create a resource from a path and a relative class, and write it to a temporary file.
- writeToFile(File) - Method in class picard.fingerprint.HaplotypeMap
-
Writes out a HaplotypeMap file with the contents of this map.
- writeToFile(String, List<MinorAlleleFractionRecord>, File) - Static method in class org.broadinstitute.hellbender.tools.walkers.contamination.MinorAlleleFractionRecord
- writeToFile(String, List<PileupSummary>, File) - Static method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- writeToFile(Collection<FilterAnalysisRecord>, GATKPath) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
- writeToFile(List<File>, File) - Static method in class org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
- writeToFile(List<ContaminationRecord>, File) - Static method in class org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationRecord
- writeToFile(List<MutectStats>, File) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.MutectStats
- writeToFile(List<NormalArtifactRecord>, File) - Static method in class org.broadinstitute.hellbender.tools.walkers.mutect.NormalArtifactRecord
- writeToPath(Collection<FilterAnalysisRecord>, Path) - Static method in class org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
- writeToResultsFileIfApplicable(byte[], byte[], byte[], byte[], byte[], byte[], double) - Method in class org.broadinstitute.hellbender.utils.pairhmm.PairHMM
-
Method to be invoked by implementing HMM engines to output the various hmm inputs/outputs with uniform formatting.
- writeValuesToFile(double[], File) - Static method in class org.broadinstitute.hellbender.utils.param.ParamUtils
-
Writes a double array to the given filename.
- writeVariants(JavaSparkContext, String, JavaRDD<VariantContext>, VCFHeader) - Static method in class org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSink
-
Write variants to the given output file in VCF format with the given header.
- writeVariants(JavaSparkContext, String, JavaRDD<VariantContext>, VCFHeader, boolean) - Static method in class org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSink
-
Write variants to the given output file in VCF format with the given header.
- writeVariants(JavaSparkContext, String, JavaRDD<VariantContext>, VCFHeader, boolean, boolean) - Static method in class org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSink
-
Write variants to the given output file in VCF format with the given header.
- writeVariants(JavaSparkContext, String, JavaRDD<VariantContext>, VCFHeader, boolean, List<Number>, int) - Static method in class org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSink
-
Write variants to the given output file in VCF format with the given header.
- writeVariants(JavaSparkContext, String, JavaRDD<VariantContext>, VCFHeader, boolean, List<Number>, int, int, boolean, boolean) - Static method in class org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSink
-
Write variants to the given output file in VCF format with the given header.
- writeVCF(List<VariantContext>, String, SAMSequenceDictionary, Set<VCFHeaderLine>, Logger) - Static method in class org.broadinstitute.hellbender.tools.spark.sv.utils.SVVCFWriter
-
referenceSequenceDictionaryis required because 2bit Broadcast references currently order their sequence dictionaries in a scrambled order, see https://github.com/broadinstitute/gatk/issues/2037. - WrongFeatureType(File, Class<? extends Feature>) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.WrongFeatureType
- WrongFeatureType(Path, Class<? extends Feature>, List<String>) - Constructor for exception org.broadinstitute.hellbender.exceptions.UserException.WrongFeatureType
X
- x - Variable in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- x - Variable in class picard.sam.util.PhysicalLocationInt
- X - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- X - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
The X coordinate of the read within the tile
- xIsSet() - Method in class picard.illumina.parser.ClusterData
- xor(boolean, boolean) - Static method in class org.broadinstitute.hellbender.utils.Utils
-
Boolean xor operation.
- xPos - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
-
The x-position as it occurs in the file being read
- xQseqCoord - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
-
The QSeq style x-coordinat, an integer = Math.round(xPos*10 + 1000)
- XReadLines - Class in org.broadinstitute.hellbender.utils.text
-
Support for Python-like xreadlines() function as a class.
- XReadLines(File) - Constructor for class org.broadinstitute.hellbender.utils.text.XReadLines
-
Opens the given file for reading lines.
- XReadLines(Reader, boolean, String) - Constructor for class org.broadinstitute.hellbender.utils.text.XReadLines
-
Creates a new xReadLines object to read lines from an bufferedReader
- XReadLines(Path) - Constructor for class org.broadinstitute.hellbender.utils.text.XReadLines
-
Opens the given file for reading lines.
- XReadLines(Path, boolean) - Constructor for class org.broadinstitute.hellbender.utils.text.XReadLines
-
Opens the given file for reading lines and optionally trim whitespaces.
- XReadLines(Path, boolean, String) - Constructor for class org.broadinstitute.hellbender.utils.text.XReadLines
-
Opens the given file for reading lines and optionally trim whitespaces.
- XsvLocatableTableCodec - Class in org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable
-
Codec class to read from XSV (e.g.
- XsvLocatableTableCodec() - Constructor for class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
- XsvLocatableTableCodec(Path) - Constructor for class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec
-
Constructor for when a configuration file is specified.
- XsvTableFeature - Class in org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable
-
A feature to represent a line in an arbitrarily delimited (XSV) file (i.e.
- XsvTableFeature(int, int, int, List<String>, List<String>, String) - Constructor for class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
-
Create an
XsvTableFeature.
Y
- y - Variable in class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
- y - Variable in class picard.sam.util.PhysicalLocationInt
- Y - Enum constant in enum class org.broadinstitute.hellbender.utils.Nucleotide
- Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- Y - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
The Y coordinate of the read within the tile
- yIsSet() - Method in class picard.illumina.parser.ClusterData
- yPos - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
-
The y-position as it occurs in the file being read
- yQseqCoord - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
-
The QSeq style y-coordinates, an integer = Math.round(yPos*10 + 1000)
Z
- ZCALL_THRESHOLDS - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ZCALL_THRESHOLDS_FILE - Variable in class picard.arrays.MergePedIntoVcf
- ZCALL_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The version of ZCall used for calling this sample
- ZCALL_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ZCALL_VERSION - Variable in class picard.arrays.MergePedIntoVcf
- zDropoff - Variable in class org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
- ZERO - Enum constant in enum class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.GenomicPhase
- ZERO_CVG_TARGETS_PCT - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of targets that did not reach coverage=1 over any base.
- ZeroAndOneSegmentCpxVariantExtractor() - Constructor for class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor.ZeroAndOneSegmentCpxVariantExtractor
- ZEROED_OUT_ASSAY - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- zip(File, GATKPath, String...) - Static method in class org.broadinstitute.hellbender.utils.ZipUtils
-
Creates a zip file give a source file/directory to zip and the final destination zip file path.\
- zipLinearChains() - Method in class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqGraph
-
Zip up all of the simple linear chains present in this graph.
- ZipUtils - Class in org.broadinstitute.hellbender.utils
-
Utility class to zip and unzip files.
- ZipUtils() - Constructor for class org.broadinstitute.hellbender.utils.ZipUtils
- ZTHRESH_X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ZTHRESH_Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields
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