A_FOLLOWED_BY_INSERTION_BASE PileupElement
AB_FILTER AlleleBalanceFilter
The filter string used for sites that fail the allele balance filter.
AbstractAlignmentMerger 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(File, File, File, boolean, boolean, boolean, SAMProgramRecord, List<String>, List<String>, Integer, Integer, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean) AbstractAlignmentMerger
Constructor
AbstractAlignmentMerger 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, boolean) 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) AbstractAlignmentMerger
Constructor
AbstractAlignmentMerger.UnmappingReadStrategy picard.sam
AbstractConcordanceWalker 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() AbstractConcordanceWalker
AbstractConcordanceWalker.TruthVersusEval 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.
AbstractIlluminaPositionFileReader 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) AbstractIlluminaPositionFileReader
AbstractIlluminaPositionFileReader(File, int, int) AbstractIlluminaPositionFileReader
Use this ctor if lane and tile are not discernible from file name.
AbstractIlluminaPositionFileReader.PositionInfo picard.illumina.parser.readers
AbstractInputParser picard.util
Class for parsing text files where each line consists of fields separated by whitespace.
AbstractInputParser() 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 a
TableColumnCollection,
and lambdas for reading and writing records.
AbstractMarkDuplicatesCommandLineProgram org.broadinstitute.hellbender.utils.read.markduplicates
Abstract class that holds parameters and methods common to classes that perform duplicate
detection and/or marking within SAM/BAM/CRAM files.
AbstractMarkDuplicatesCommandLineProgram() AbstractMarkDuplicatesCommandLineProgram
AbstractMarkDuplicatesCommandLineProgram picard.sam.markduplicates.util
Abstract class that holds parameters and methods common to classes that perform duplicate
detection and/or marking within SAM/BAM files.
AbstractMarkDuplicatesCommandLineProgram() AbstractMarkDuplicatesCommandLineProgram
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator org.broadinstitute.hellbender.utils.read.markduplicates
Little class used to package up a header and an iterable/iterator.
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator picard.sam.markduplicates.util
Little class used to package up a header and an iterable/iterator.
AbstractOpticalDuplicateFinderCommandLineProgram org.broadinstitute.hellbender.utils.read.markduplicates
Abstract class that holds parameters and methods common to classes that optical duplicate detection.
AbstractOpticalDuplicateFinderCommandLineProgram() AbstractOpticalDuplicateFinderCommandLineProgram
AbstractOpticalDuplicateFinderCommandLineProgram picard.sam.markduplicates.util
Abstract class that holds parameters and methods common to classes that optical duplicate detection.
AbstractOpticalDuplicateFinderCommandLineProgram() AbstractOpticalDuplicateFinderCommandLineProgram
AbstractRecordCollection METADATA extends Metadata ,RECORD > - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
Represents
METADATA (which can be represented as a
SAMFileHeader),
an immutable collection of records,
a set of mandatory column headers given by a
TableColumnCollection,
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 a
TableColumnCollection,
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.
accept(int, int) IntBiConsumer
acceptRead(SAMRecord, ReferenceSequence) CollectSequencingArtifactMetrics
acceptRead(SAMRecord, ReferenceSequence) CollectAlignmentSummaryMetrics
acceptRead(SAMRecord, ReferenceSequence) CollectBaseDistributionByCycle
acceptRead(SAMRecord, ReferenceSequence) CollectGcBiasMetrics
acceptRead(SAMRecord, ReferenceSequence) CollectInsertSizeMetrics
acceptRead(SAMRecord, ReferenceSequence) CollectQualityYieldMetrics
acceptRead(SAMRecord, ReferenceSequence) CollectRnaSeqMetrics
acceptRead(SAMRecord, ReferenceSequence) MeanQualityByCycle
acceptRead(SAMRecord, ReferenceSequence) QualityScoreDistribution
acceptRead(SAMRecord, ReferenceSequence) SinglePassSamProgram
Should be implemented by subclasses to accept SAMRecords one at a time.
acceptRecord(SAMRecord, ReferenceSequence) 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) 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(InsertSizeMetricsCollectorArgs) PerUnitInsertSizeMetricsCollector
acceptRecord(ARGTYPE) PerUnitMetricCollector
Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
acceptRecord(PerUnitExampleMultiMetricsCollectorArgs) PerUnitExampleMultiMetricsCollector
acceptRecord(SAMRecord, ReferenceSequence) AlignmentSummaryMetricsCollector
acceptRecord(SAMRecord, ReferenceSequence) CollectQualityYieldMetrics.QualityYieldMetricsCollector
acceptRecord(SAMRecord, ReferenceSequence) InsertSizeMetricsCollector
acceptRecord(InsertSizeCollectorArgs) InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
acceptRecord(SAMRecord) RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
acceptRecord(SAMRecord) TargetMetricsCollector.PerUnitTargetMetricCollector
Adds information about an individual SAMRecord to the statistics.
acceptRecord(GcBiasCollectorArgs) GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
acceptRecord(SAMRecord, ReferenceSequence) 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(ARGTYPE) PerUnitMetricCollector
Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
accessibleTruthSites Tranche
accessionToTaxId PSTaxonomyDatabase
accumulate(VariantContext) CallingMetricAccumulator
Incorporates the provided variant's data into the metric analysis.
accumulate(VariantContext) GvcfMetricAccumulator
accumulate(VariantContext) VariantProcessor.Accumulator
AccumulateVariantCallingMetrics picard.vcf
Combines multiple Variant Calling Metrics files into a single file.
AccumulateVariantCallingMetrics() AccumulateVariantCallingMetrics
ACCUMULATION_LEVEL GcBiasDetailMetrics
ACCUMULATION_LEVEL GcBiasSummaryMetrics
accumulationLevels MetricAccumulationLevelArgumentCollection
accumulators() VariantAccumulatorExecutor
accumulators() VariantAccumulatorExecutor.MultiThreadedChunkBased
ACCURACY DownsampleSam
ACTION IntervalListTools
activateWriting() OverhangFixingManager
Activates output writing for the Overhang Fixing Manager.
ACTIVE_CLASS_PADDING_HYBRID_MODE_LONG_NAME GermlineDenoisingModelArgumentCollection
activeProbThreshold AssemblyRegionWalker
activeProbThreshold AssemblyRegionWalkerSpark
activeProbThreshold HaplotypeCallerSpark.ShardingArgumentCollection
activeProbThreshold ActivityProfile
ActivityProfile org.broadinstitute.hellbender.utils.activityprofile
Class holding information about per-base activity scores for
assembly region traversal
ActivityProfile(int, double, SAMFileHeader) ActivityProfile
Create a new empty ActivityProfile
ActivityProfile(int, double, Set<SimpleInterval>, SAMFileHeader) ActivityProfile
Create a empty ActivityProfile, restricting output to profiles overlapping intervals, if not null
activityProfileOut AssemblyRegionWalker
If provided, this walker will write out its activity profile (per bp probabilities of being active)
to this file in the IGV formatted TAB deliminated output:
http://www.broadinstitute.org/software/igv/IGV
Intended to make debugging the activity profile calculations easier
ActivityProfileState 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) ActivityProfileState
Create a new ActivityProfileState at loc with probability of being active of activeProb
ActivityProfileState(SimpleInterval, double, ActivityProfileState.Type, Number) 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 org.broadinstitute.hellbender.utils.activityprofile
ADAMAX_BETA_1_LONG_NAME HybridADVIArgumentCollection
ADAMAX_BETA_2_LONG_NAME HybridADVIArgumentCollection
ADAPTER_SEQUENCE CollectAlignmentSummaryMetrics
ADAPTER_TRUNCATION_LENGTH MarkIlluminaAdapters
AdapterMarker picard.util
Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords.
AdapterMarker(AdapterPair...) AdapterMarker
Truncates adapters to DEFAULT_ADAPTER_LENGTH
AdapterMarker(int, AdapterPair...) AdapterMarker
AdapterPair org.broadinstitute.hellbender.utils.illumina
AdapterPair picard.util
ADAPTERS MarkIlluminaAdapters
ADAPTERS_TO_CHECK IlluminaBasecallsToFastq
Deprecated.
ADAPTERS_TO_CHECK IlluminaBasecallsToSam
adapterSequence StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord) AdapterMarker
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, int, double) AdapterMarker
Overrides defaults for minMatchBases and maxErrorRate
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair) ClippingUtility
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair, int, double) ClippingUtility
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair...) ClippingUtility
Invokes adapterTrimIlluminaPairedReads with default less stringent parameters for a pair of reads.
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, int, double, AdapterPair...) ClippingUtility
Invokes adapterTrimIlluminaRead with explicit parameters for a pair of reads.
adapterTrimIlluminaSingleRead(SAMRecord) AdapterMarker
adapterTrimIlluminaSingleRead(SAMRecord, int, double) AdapterMarker
Overrides defaults for minMatchBases and maxErrorRate
adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair) ClippingUtility
adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair, int, double) ClippingUtility
adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair...) ClippingUtility
Invokes adapterTrimIlluminRead with default parameters for a single read.
adapterTrimIlluminaSingleRead(SAMRecord, int, double, AdapterPair...) ClippingUtility
Invokes adapterTrimIlluminRead with explicit matching thresholds for a single read.
AdapterTrimTransformer org.broadinstitute.hellbender.transformers
Trims (hard clips) adapter sequences from read ends.
AdapterTrimTransformer(int, int, List<String>) AdapterTrimTransformer
AdapterUtility picard.analysis
A utility class for matching reads to adapters.
AdapterUtility(List<String>) AdapterUtility
AdaptiveMetropolisSampler 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, double, double) AdaptiveMetropolisSampler
AdaptiveMetropolisSampler(double, double, double, double) AdaptiveMetropolisSampler
add(GATKRead) AssemblyRegion
Add read to this region
Read must have alignment start >= than the last read currently in this active region.
add(JavaSparkContext, JavaRDD<GATKRead>, ReferenceMultiSource, JavaRDD<GATKVariant>, List<String>, JoinStrategy, SAMSequenceDictionary, int, int) AddContextDataToReadSpark
add(JavaSparkContext, List<SimpleInterval>, String, List<GATKVariant>, ReadFilter, ReferenceMultiSource) AddContextDataToReadSparkOptimized
Create shards with reads, variants, and reference bases, using default values for shard sizes and margin.
add(AnnotatedInterval) AnnotatedIntervalWriter
Write one region to the file.
add(AnnotatedInterval) SimpleAnnotatedIntervalWriter
Write one region to the file.
add(GATKRead) FlagStat.FlagStatus
add(PSPathogenTaxonScore) PSPathogenTaxonScore
add(T) HopscotchCollection
add(long) LargeLongHopscotchSet
add(long) LongBloomFilter
add(long) LongHopscotchSet
add(long, int) LongHopscotchSet
add(byte[], byte[]) CompareMatrix
add(CompareMatrix) CompareMatrix
add(Haplotype) AssemblyResultSet
Adds a haplotype to the result set without indicating a generating assembly result.
add(Haplotype, AssemblyResult) AssemblyResultSet
Adds simultaneously a haplotype and the generating assembly-result.
add(BaseEdge) 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(int, byte) ReadErrorCorrector.CorrectionSet
Add a base to this correction set at a particular offset, measured from the start of the read
add(ActivityProfileState) ActivityProfile
Add the next ActivityProfileState to this profile.
add(int) CountSet
Add an integer value to the set.
add(Integer) CountSet
add(E) IndexedSet
Adds a new element to the set.
add(T) CompressedDataList
add(T, int) CompressedDataList
add(CompressedDataList<T>) CompressedDataList
add(GenomeLoc) GenomeLocSortedSet
Adds a GenomeLoc to the collection, inserting at the correct sorted position into the set.
add(GenomeLoc, boolean) GenomeLocSortedSet
Adds a GenomeLoc to the collection, inserting at the correct sorted position into the set.
add(GATKRead) HaplotypeBAMDestination
Write a read to the output specified by this destination.
add(GATKRead) SAMFileDestination
Write a read to the output file specified by this destination.
add(Double) Histogram
Add a value to be stored in the histogram
add(Double, int) Histogram
Add multiple copies of the same value into the histogram to be stored in the histogram
add(Histogram) Histogram
Combine two histogram objects that have the same bin by adding the values to each bin
add(double) MathUtils.RunningAverage
add(Nucleotide) Nucleotide.Counter
Increases by 1 the count for a nucleotide.
add(byte) Nucleotide.Counter
Increases the nucleotide that corresponds to the input base own count by 1.
add(int, double, double, double, double, double, double, int) SynchronizedUnivariateSolver
Add a solver jobDescription
add(int, double, double, double, double, double, int) SynchronizedUnivariateSolver
add(String) ArgumentsBuilder
Add a string to the arguments list
Strings are processed specially, they are reformatted to match the new unix style arguments
add(Object) ArgumentsBuilder
Add any object's string representation to the arguments list
add(VariantContext) GVCFWriter
Add a VariantContext to this writer for emission
Requires that the VC have exactly one genotype
add(HaplotypeProbabilities) Fingerprint
add(PedFile.PedTrio) PedFile
Adds a trio to the PedFile keyed by the individual id.
add(ReadEndsForMateCigar, SamRecordTrackingBuffer, DuplicationMetrics) MarkQueue
Add a record to the mark queue.
add(ReadEndsForMateCigar) PhysicalLocationForMateCigarSet
Adds the end to this set, if not already added based on physical location
ADD_MATE_CIGAR FixMateInformation
ADD_MATE_CIGAR MergeBamAlignment
ADD_OUTPUT_SAM_PROGRAM_RECORD StandardArgumentDefinitions
ADD_OUTPUT_VCF_COMMANDLINE StandardArgumentDefinitions
ADD_PG_TAG_TO_READS PGTagArgumentCollection
addAccession(String, long) PSPathogenReferenceTaxonProperties
addAll(Collection<GATKRead>) AssemblyRegion
Add all readsToAdd to this region
addAll(long[]) LargeLongHopscotchSet
addAll(long[]) LongBloomFilter
addAll(long[]) LongHopscotchSet
addAll(int...) CountSet
Add a arbitrary number of integers to the set.
addAll(Collection<? extends Integer>) CountSet
addAll(int[], int, int) CountSet
Add all values within a range in an integer array.
addAll(CountSet) CountSet
Add all elements present in a int-set.
addAll(Collection<Number>) MathUtils.RunningAverage
addAll(byte[]) Nucleotide.Counter
Increase by one the count for a nucleotide for each
occurrence of such in the input byte array base codes.
addAllLevelsToFile(MetricsFile<METRIC_TYPE, HISTOGRAM_KEY>) 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>) MultiLevelReducibleCollector
Add all metrics to the given file in the following MetricAccumulationLevel order
ALL_READS, SAMPLE, LIBRARY, READ_GROUP.
addAllLevelsToFile(MetricsFile<METRIC_TYPE, Histogram_KEY>) MultiLevelCollector
Add all metrics to the given file in the following MetricAccumulationLevel order
ALL_READS, SAMPLE, LIBRARY, READ_GROUP.
addArg(String) SamFileTester
addArg(String, String) SamFileTester
addArgs(Object...) RScriptExecutor
Adds args to the end of the Rscript command line.
addArgs() SamFileTester
addArgument(String, String) ArgumentsBuilder
add an argument with a given value to this builder
addArgumentWithValueThatIncludesWhitespace(String, String) ArgumentsBuilder
Add an argument with a given value to this builder without splitting the value string into multiple arguments at whitespace.
addBAQTag(GATKRead, byte[]) BAQ
addBase(int) TargetMetricsCollector.Coverage
Adds a single point of depth at the desired offset into the coverage array.
addBase(int, int) TargetMetricsCollector.Coverage
Adds some depth at the desired offset into the coverage array.
addBaseQHistogram(MetricsFile<CollectWgsMetrics.WgsMetrics, Integer>) AbstractWgsMetricsCollector
addBases(ReferenceMultiSource, JavaRDD<GATKRead>) BroadcastJoinReadsWithRefBases
Joins each read of an RDD with that read's corresponding reference sequence.
addBases(ReferenceMultiSource, JavaPairRDD<GATKRead, T>) BroadcastJoinReadsWithRefBases
Joins each read of an RDD with key's corresponding reference sequence.
addBases(ReferenceMultiSource, JavaRDD<GATKRead>) ShuffleJoinReadsWithRefBases
Joins each read of an RDD with that read's corresponding reference sequence.
addBases(ReferenceMultiSource, JavaPairRDD<GATKRead, T>) ShuffleJoinReadsWithRefBases
Joins each read of an RDD with key's corresponding reference sequence.
addBooleanArgument(String, boolean) ArgumentsBuilder
add an argument with a boolean as its parameter
addChild(int) PSTreeNode
addChromosomeCountsToHeader(Set<VCFHeaderLine>) GATKVariantContextUtils
Add chromosome counts (AC, AN and AF) to the VCF header lines
addCigarElements(List<CigarElement>, int, int, int, CigarElement) AlignmentUtils
Helper function for trimCigar that adds cigar elements (of total length X) of elt.op to dest for
X bases that fall between start and end, where the last position of the base is pos.
addColumn(String, String) GATKReportTable
Add a column to the report and the format string used to display the data.
AddCommentsToBam picard.sam
A tool to add comments to a BAM file header.
AddCommentsToBam() AddCommentsToBam
AddContextDataToReadSpark org.broadinstitute.hellbender.engine.spark
AddContextDataToRead pairs reference bases and overlapping variants with each GATKRead in the RDD input.
AddContextDataToReadSpark() AddContextDataToReadSpark
AddContextDataToReadSparkOptimized org.broadinstitute.hellbender.engine.spark
AddContextDataToReadSparkOptimized() AddContextDataToReadSparkOptimized
AddContextDataToReadSparkOptimized.SubdivideAndFillReadsIterator org.broadinstitute.hellbender.engine.spark
addCovariate(int, int, int, int) 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[]) Gene.Transcript
addCustomBindings(DocWorkUnit) GATKHelpDocWorkUnitHandler
Add any custom freemarker bindings discovered via custom javadoc tags.
addData(ClipReads.ClippingData) ClipReads.ClippingData
addData(ClipReads.ClippingData) ClipReads.ReadClipperWithData
addData(ClusterData, PositionalData) BaseIlluminaDataProvider
addData(ClusterData, PfData) BaseIlluminaDataProvider
addData(ClusterData, BarcodeData) BaseIlluminaDataProvider
addDescendentScore(double) PSPathogenTaxonScore
addEdge(Node, Node) GraphUtils.Graph
addEdges(V, V...) BaseGraph
Convenience function to add multiple edges to the graph
addEdges(Supplier<E>, V, V...) BaseGraph
Convenience function to add multiple edges to the graph
addExon(GencodeGtfExonFeature) GencodeGtfTranscriptFeature
addExon(int, int) Gene.Transcript
addExpressions(Set<String>, List<FeatureInput<VariantContext>>, boolean) VariantAnnotatorEngine
addFeatureInputsAfterInitialization(String, String, Class<? extends Feature>, int) GATKTool
A method to allow a user to inject data sources after initialization that were not specified as command-line
arguments.
addFileArgument(String, File) ArgumentsBuilder
add an argument with a file as its parameter
addFilterToGenotype(String, String) OrientationBiasUtils
Create an updated genotype string when trying to add a filter value.
addFirstOfPairOrFragment(SAMRecord) HitsForInsert
addHaplotype(HaplotypeBlock) HaplotypeMap
Adds a HaplotypeBlock to the map and updates all the relevant caches/indices.
addHomRefSite(VariantContext, Genotype) GVCFWriter
Add hom-ref site from vc to this gVCF hom-ref state tracking, emitting any pending states if appropriate
addInfo(AbstractLocusInfo<T>, ReferenceSequence, boolean) AbstractWgsMetricsCollector
Accumulates the data from AbstractLocusInfo in inner structures
addInfo(AbstractLocusInfo<SamLocusIterator.RecordAndOffset>, ReferenceSequence, boolean) CollectWgsMetrics.WgsMetricsCollector
addInfo(AbstractLocusInfo<EdgingRecordAndOffset>, ReferenceSequence, boolean) FastWgsMetricsCollector
addInput(File) ArgumentsBuilder
addKmer(Kmer, int) KMerCounter
Add a kmer that occurred kmerCount times
addLeadingZeros() BarcodeFileFaker
addLeadingZeros() BciFileFaker
addLeadingZeros() BclFileFaker
addLeadingZeros() ClocsFileFaker
addLeadingZeros() FileFaker
addLeadingZeros() FilterFileFaker
addLeadingZeros() LocsFileFaker
addLeadingZeros() MultiTileBclFileFaker
addLeadingZeros() MultiTileLocsFileFaker
addLeadingZeros() PosFileFaker
addLibrary(RScriptLibrary) RScriptExecutor
addLocationInformation(String, PhysicalLocation) ReadNameParser
Method used to extract tile/x/y from the read name and add it to the PhysicalLocationShort so that it
can be used later to determine optical duplication
addMappedFragment(int, int, boolean, int) SamFileTester
addMappedFragment(int, int, boolean, int, boolean) SamFileTester
addMappedFragment(int, int, boolean, String, int) SamFileTester
addMappedFragment(int, int, boolean, String, String, int) SamFileTester
addMappedFragment(String, int, int, boolean, String, String, boolean, boolean, int) SamFileTester
addMappedPair(int, int, int, boolean, boolean, int) SamFileTester
addMappedPair(int, int, int, boolean, boolean, String, String, boolean, int) SamFileTester
addMappedPair(int, int, int, boolean, boolean, String, String, boolean, boolean, boolean, int) SamFileTester
addMatePair(int, int, int, boolean, boolean, boolean, boolean, String, String, boolean, boolean, boolean, boolean, boolean, int) SamFileTester
addMatePair(String, int, int, int, int, boolean, boolean, boolean, boolean, String, String, boolean, boolean, boolean, boolean, boolean, int, String) SamFileTester
addMatePair(String, int, int, int, boolean, boolean, boolean, boolean, String, String, boolean, boolean, boolean, boolean, boolean, int) SamFileTester
addMetricsByLibrary(String, GATKDuplicationMetrics) LibraryIdGenerator
addMetricsByLibrary(String, DuplicationMetrics) LibraryIdGenerator
addMetricsToFile(MetricsFile<InsertSizeMetrics, Integer>) PerUnitInsertSizeMetricsCollector
addMetricsToFile(MetricsFile<BEAN, HKEY>) PerUnitMetricCollector
Any metrics collected will be added to the metric file provided.
addMetricsToFile(MetricsFile<ExampleMultiMetrics, Integer>) PerUnitExampleMultiMetricsCollector
addMetricsToFile(MetricsFile<CollectQualityYieldMetrics.QualityYieldMetrics, Integer>) CollectQualityYieldMetrics.QualityYieldMetricsCollector
addMetricsToFile(MetricsFile<InsertSizeMetrics, Integer>) InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
addMetricsToFile(MetricsFile<RnaSeqMetrics, Integer>) RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
addMetricsToFile(MetricsFile<METRIC_TYPE, Integer>) TargetMetricsCollector.PerUnitTargetMetricCollector
addMetricsToFile(MetricsFile<GcBiasMetrics, Integer>) GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
addMetricsToFile(MetricsFile<BEAN, HKEY>) PerUnitMetricCollector
Any metrics collected will be added to the metric file provided.
addMissingAlleles(Collection<A>, double) ReadLikelihoods
Add alleles that are missing in the read-likelihoods collection giving all reads a default
likelihood value.
addMissingTruthAndMissingCallStates(double, long, GenotypeConcordanceCounts) 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) PSTree
Adds a node to the tree.
addNode(Node) GraphUtils.Graph
addNonReferenceAllele(A) ReadLikelihoods
Adds the non-reference allele to the read-likelihood collection setting each read likelihood to the second
best found (or best one if only one allele has likelihood).
addObservation(GATKRead) KSWindowFinder
addObservation(int) IntHistogram
addObservations(int, long) IntHistogram
addObservations(IntHistogram) IntHistogram
addOp(ClippingOp) ReadClipper
Add clipping operation to the read.
AddOrReplaceReadGroups picard.sam
Assigns all the reads in a file to a single new read-group.
AddOrReplaceReadGroups() AddOrReplaceReadGroups
addOrUpdateEdge(V, V, E) BaseGraph
Add edge between source -> target if none exists, or add e to an already existing one if present
addOutput(File) ArgumentsBuilder
addOutputSAMProgramRecord GATKTool
addOutputVCFCommandLine GATKTool
addParameterSampler(V2, ParameterSampler<U, V2, S2, T2>, Class<U>) ParameterizedModel.GibbsBuilder
addPileup(ReadPileup) AllelePileupCounter
addPositionalArgument(String) ArgumentsBuilder
add a positional argument to this builder
addPrefetcher(int, SeekableByteChannel) SeekableByteChannelPrefetcher
Wraps the provided SeekableByteChannel within a SeekableByteChannelPrefetcher, using the provided buffer size
addRange(int, int) CountSet
Adds a range of integer values to the collection.
addRaw(String) ArgumentsBuilder
Add a string to the arguments list without processing the string itself.
addRead(GATKRead) QualityYieldMetrics
addRead(GATKRead) ExampleMultiMetrics
Process a single read
addRead(GATKRead) ExampleSingleMetrics
addRead(int, int, int, boolean) ReadMetadata.LibraryRawStatistics
addRead(String) 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) GATKReadWriter
addRead(GATKRead) SAMFileGATKReadWriter
addReadData(ClusterData, int, BaseData) BaseIlluminaDataProvider
addReadData(ClusterData, int, QualityData) BaseIlluminaDataProvider
addReadData(ClusterData, int, CbclData) BaseIlluminaDataProvider
addReadGroup(List<GATKRead>) OverhangFixingManager
Add a family of split reads to the manager
addReadKmers(GATKRead) ReadErrorCorrector
Main entry routine to add all kmers in a read to the read map counter
addReads(Map<String, List<GATKRead>>, double) ReadLikelihoods
Add more reads to the collection.
addReads(Map<String, List<GATKRead>>, double) UnfilledReadsLikelihoods
addReadsToKmers(Collection<GATKRead>) ReadErrorCorrector
Top-level entry point that adds a collection of reads to our kmer list.
addRecord(SAMRecord) SamFileTester
addReference(File) ArgumentsBuilder
addRegion(GenomeLoc) GenomeLocSortedSet
Adds a GenomeLoc to the collection, merging it if it overlaps another region.
addResults(MatchResults) FingerprintResults
addRow(Object...) GATKReport
This method provides an efficient way to populate a simplified GATK report.
addRow(GenotypeConcordanceStates.CallState, GenotypeConcordanceStates.ContingencyState[]...) GenotypeConcordanceScheme
Adds a row to the scheme
addRowID(String, boolean) GATKReportTable
Add a mapping from ID to the index of a new row added to the table.
addRowIDMapping(String, int) GATKReportTable
Add a mapping from ID to row index.
addRowIDMapping(Object, int, boolean) GATKReportTable
Add a mapping from ID to row index.
addSample(Sample) SampleDB
Protected function to add a single sample to the database
addSamplesFromPedigreeFiles(List<File>) SampleDBBuilder
addSamplesFromPedigreeStrings(List<String>) SampleDBBuilder
addScoreNormalized(double) PSPathogenTaxonScore
addScript(Resource) RScriptExecutor
addScript(File) RScriptExecutor
addSecondOfPair(SAMRecord) HitsForInsert
addSelenocysteine(GencodeGtfSelenocysteineFeature) GencodeGtfTranscriptFeature
addSelfScore(double) PSPathogenTaxonScore
addSequence(String, byte[], boolean) ReadThreadingGraph
Add all bases in sequence to this graph
addSequence(String, byte[], int, boolean) ReadThreadingGraph
Add all bases in sequence to this graph
addSnp(Snp) HaplotypeBlock
Adds a SNP to the haplotype.
addSplicePosition(String, int, int) OverhangFixingManager
Add a new observed split to the list to use
addSupplementalFirstOfPairOrFragment(SAMRecord) HitsForInsert
addSupplementalSecondOfPair(SAMRecord) HitsForInsert
addTable(String, String, int) GATKReport
Add a new, empty table to the report
addTable(String, String, int, GATKReportTable.Sorting) GATKReport
Add a new, empty table to the report
addTable(GATKReportTable) GATKReport
Adds a table, empty or populated, to the report
addTables(List<GATKReportTable>) GATKReport
addTag(SATagBuilder) 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.
addTag(GATKRead) SATagBuilder
Add a read to the SATag for the encapsulated read.
addToArrayInPlace(double[], double[]) MathUtils
addToIntervalStrings(String) IntervalArgumentCollection
Add an extra interval string to the intervals to include.
addToIntervalStrings(String) OptionalIntervalArgumentCollection
addToIntervalStrings(String) RequiredIntervalArgumentCollection
addToLogLikelihoods(Snp, List<Allele>, double[]) 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<CollectWgsMetrics.WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingPairedFilter) AbstractWgsMetricsCollector
Adds collected metrics and depth histogram to file
addToMetricsFile(MetricsFile<CollectWgsMetrics.WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingPairedFilter) CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
addToMetricsFile(MetricsFile<CollectWgsMetrics.WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingPairedFilter) WgsMetricsProcessor
Adds result metric's data to input file
addToMetricsFile(MetricsFile<CollectWgsMetrics.WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingPairedFilter) WgsMetricsProcessorImpl
Adds result metric's data to input file
addToProbs(Snp, byte, byte) 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) 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.
addTotalReads(int) PSPathogenTaxonScore
addTrainingSet(TrainingSet) VariantDataManager
addTranscript(GencodeGtfTranscriptFeature) GencodeGtfGeneFeature
addTranscript(String, int, int, int, int, int) Gene
addUmiObservation(String, String) UmiMetrics
Add an observation of a UMI to the metrics
addUmiObservationN() UmiMetrics
Add an observation of a UMI containing at least one N to the metrics
addUnambiguousReads(int) PSPathogenTaxonScore
addUnmappedFragment(int, int) SamFileTester
addUnmappedFragment(int, String) SamFileTester
addUnmappedPair(int, int) SamFileTester
addUtr(GencodeGtfUTRFeature) GencodeGtfTranscriptFeature
addVC(VariantContext) EventMap
Add VariantContext vc to this map, merging events with the same start sites if necessary
addVC(VariantContext, boolean) EventMap
Add VariantContext vc to this map
addVCF(File) ArgumentsBuilder
addVertices(V...) BaseGraph
Convenience function to add multiple vertices to the graph at once
addVertices(Collection<V>) BaseGraph
Convenience function to add multiple vertices to the graph at once
adjustQualsOfOverlappingPairedFragments(GATKRead, GATKRead) FragmentUtils
Fix two overlapping reads from the same fragment by adjusting base qualities, if possible
firstRead and secondRead must be part of the same fragment (though this isn't checked).
adjustQualsOfOverlappingPairedFragments(List<GATKRead>) FragmentUtils
advance() AbstractInputParser
advanceBlock(GATKRead) KSWindowFinder
advanceFile() BasicInputParser
advanceToLocus(int, boolean) 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 ExomeStandardArgumentDefinitions
AF_PARAMETER_FILE_SHORT_NAME ExomeStandardArgumentDefinitions
AFCalculationResult 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[], double[], Map<Allele, Double>) AFCalculationResult
Create a results object capability of storing results for calls with up to maxAltAlleles
AFCalculator org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
Generic interface for calculating the probability of alleles segregating given priors and genotype likelihoods
AFCalculator() AFCalculator
AFCalculatorImplementation org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
Enumeration of usable AF calculation, their constraints (i.e.
AFCalculatorProvider org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
Instantiates Exact AF calculators given the required ploidy specs.
AFCalculatorProvider() AFCalculatorProvider
afCalculatorProvider GenotypingEngine
Affection 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)
afOfAllelesNotInGermlineResource M2ArgumentCollection
Population allele fraction assigned to alleles not found in germline resource.
AFPriorProvider org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
Class that produces allele-frequency priors.
AFPriorProvider() AFPriorProvider
afterExecute(Runnable, Throwable) ThreadPoolExecutorWithExceptions
afterFile AnalyzeCovariates
File containing the recalibration tables from the second pass.
afterFirstPass() TwoPassReadWalker
afterFirstPass() TwoPassVariantWalker
Process the data collected during the first pass.
afterFirstPass() ExampleTwoPassVariantWalker
afterFirstPass() SplitNCigarReads
afterPipeline(JavaSparkContext) SparkCommandLineProgram
Extend this method to run code after the pipeline returns.
aggregate(List<Integer>) BaseQuality
aggregate(List<Integer>) FragmentLength
aggregate(List<Integer>) MappingQuality
aggregate(List<Integer>) PerAlleleAnnotation
aggregate(List<Integer>) ReadPosition
AggregatedSubHaplotypeFinder F extends org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestSubHaplotypeFinder> - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
K-best sub-haplotype finder that selects the best solutions out of a collection of sub-haplotype finders.
AggregatedSubHaplotypeFinder(Collection<F>) AggregatedSubHaplotypeFinder
Creates a new aggregated sub-haplotype finder given its sub-finders.
align(JavaRDD<GATKRead>, boolean) BwaSparkEngine
Performs read alignment on a RDD.
align(Iterable<? extends T>) SingleSequenceReferenceAligner
align(List<? extends T>) 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>) SingleSequenceReferenceAligner
Composes a map of the aligned sequences.
align(byte[], byte[], SWParameters, SWOverhangStrategy) SmithWatermanAligner
perform a Smith-Waterman alignment of alt against ref
align(byte[], byte[], SWParameters, SWOverhangStrategy) SmithWatermanIntelAligner
Aligns the alternate sequence to the reference sequence
align(byte[], byte[], SWParameters, SWOverhangStrategy) SmithWatermanJavaAligner
Aligns the alternate sequence to the reference sequence
align(byte[], byte[], SWParameters, SWOverhangStrategy) SWNativeAlignerWrapper
ALIGN_LENGTHS GATKSVVCFConstants
ALIGNED_BAM MergeBamAlignment
ALIGNED_READS GcBiasSummaryMetrics
The total number of aligned reads used to compute the gc bias metrics.
ALIGNED_READS_ONLY CollectBaseDistributionByCycle
ALIGNED_READS_ONLY MeanQualityByCycle
ALIGNED_READS_ONLY QualityScoreDistribution
ALIGNED_READS_ONLY MergeBamAlignment
AlignedAssembly org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
Holding necessary information about a local assembly for use in SV discovery.
AlignedAssembly(int, List<AlignedContig>) AlignedAssembly
AlignedAssembly.Serializer org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
AlignedAssemblyOrExcuse 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) AlignedAssemblyOrExcuse
AlignedAssemblyOrExcuse(int, FermiLiteAssembly, int, List<List<BwaMemAlignment>>) AlignedAssemblyOrExcuse
AlignedAssemblyOrExcuse.Serializer org.broadinstitute.hellbender.tools.spark.sv.evidence
AlignedContig 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>) AlignedContig
AlignedContig.Serializer org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
AlignedContigGenerator org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
Loads various upstream assembly and alignment formats and turn into custom
AlignedContig format in the discovery stage.
AlignedContigGenerator() AlignedContigGenerator
alignedContigs AlignedAssembly
alignedInput PSFilterArgumentCollection
PathSeq will rapidly filter the reads if they are aligned to a host reference, thus reducing run time.
alignedReadsOnly CollectBaseDistributionByCycleSpark
alignedReadsOnly MeanQualityByCycleSpark
alignedReadsOnly QualityScoreDistributionSpark
ALIGNER_PROPER_PAIR_FLAGS MergeBamAlignment
alignerIndexImageFile StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
ALIGNMENT_ARTIFACT_FILTER_NAME GATKVCFConstants
ALIGNMENT_LOW_READ_UNIQUENESS_THRESHOLD AssemblyContigAlignmentsConfigPicker
ALIGNMENT_LOW_REF_UNIQUENESS_THRESHOLD AssemblyContigAlignmentsConfigPicker
ALIGNMENT_STATUS ViewSam
alignmentAgreesWithHeader(SAMFileHeader, GATKRead) ReadUtils
Check to ensure that the alignment makes sense based on the contents of the header.
AlignmentAgreesWithHeaderReadFilter org.broadinstitute.hellbender.engine.filters
Filter out reads where the alignment does not match the contents of the header.
AlignmentAgreesWithHeaderReadFilter() AlignmentAgreesWithHeaderReadFilter
AlignmentAgreesWithHeaderReadFilter(SAMFileHeader) AlignmentAgreesWithHeaderReadFilter
AlignmentContext org.broadinstitute.hellbender.engine
Bundles together a pileup and a location.
AlignmentContext(Locatable, ReadPileup) AlignmentContext
AlignmentContext(Locatable, ReadPileup, boolean) AlignmentContext
AlignmentContext.ReadOrientation org.broadinstitute.hellbender.engine
AlignmentContextIteratorBuilder org.broadinstitute.hellbender.utils.locusiterator
Create an iterator for traversing alignment contexts in a specified manner.
AlignmentContextIteratorBuilder() AlignmentContextIteratorBuilder
AlignmentInterval 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(String) AlignmentInterval
Compose an alignment interval instance from a SAM supplementary alignment formatted string.
AlignmentInterval(SAMRecord) AlignmentInterval
AlignmentInterval(GATKRead) AlignmentInterval
Constructs an alignment interval that reflects on the mapping properties of a
GATKRead instance.
AlignmentInterval(BwaMemAlignment, List<String>, int) AlignmentInterval
AlignmentInterval(SimpleInterval, int, int, Cigar, boolean, int, int, int, ContigAlignmentsModifier.AlnModType) AlignmentInterval
AlignmentInterval.Serializer org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
AlignmentStateMachine 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) AlignmentStateMachine
AlignmentSummaryMetrics 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() AlignmentSummaryMetrics
AlignmentSummaryMetrics.Category picard.analysis
AlignmentSummaryMetricsCollector picard.analysis
AlignmentSummaryMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, boolean, List<String>, int, Set<SamPairUtil.PairOrientation>, boolean) AlignmentSummaryMetricsCollector
AlignmentUtils org.broadinstitute.hellbender.utils.read
AlignmentUtils.MismatchCount org.broadinstitute.hellbender.utils.read
alignPaired(JavaRDD<GATKRead>) BwaSparkEngine
Performs pair-end alignment on a RDD.
alignUnpaired(JavaRDD<GATKRead>) BwaSparkEngine
Performs single-end alignment on a RDD.
ALL_COVARIATES_REPORT_TABLE_TITLE RecalUtils
ALL_GTS_FILTERED FilterApplyingVariantIterator
Filter string that is used to filter a Variant when all variant genotypes are filtered out.
ALL_SITES_LONG_NAME GenotypeGVCFs
allAlleles GenotypeConcordance.Alleles
allele ReadLikelihoods.BestAllele
Null if there is no possible match (no allele?).
ALLELE_BALANCE_HET_KEY GATKVCFConstants
ALLELE_BALANCE_HOM_KEY GATKVCFConstants
ALLELE_BALANCE_KEY GATKVCFConstants
ALLELE_EXTENSION AssemblyBasedCallerGenotypingEngine
ALLELE_FRACTION_KEY GATKVCFConstants
ALLELE_FRACTION_MODEL_PARAMETER_FILE_SUFFIX ModelSegments
ALLELE_SPECIFIC_PREFIX GATKVCFConstants
AlleleBalanceFilter picard.vcf.filter
Filters out a record if the allele balance for heterozygotes is out of a defined range across all samples.
AlleleBalanceFilter(double) AlleleBalanceFilter
AlleleBiasedDownsamplingUtils org.broadinstitute.hellbender.utils.downsampling
The purpose of this set of utilities is to downsample a set of reads to remove contamination.
alleleCount() GenotypeLikelihoodCalculator
Returns the total number of alleles for this genotype calculator.
alleleCountAt(int) GenotypeAlleleCounts
Returns the count of an allele in the genotype given is rank in the genotype (not the allele index itself).
alleleCountFor(int) GenotypeAlleleCounts
Returns the count of an allele in the genotype given it index.
alleleCountsByIndex(int) GenotypeAlleleCounts
Returns the allele counts for each allele index to maximum.
alleleCountsToIndex(int...) GenotypeLikelihoodCalculator
Returns the likelihood index given the allele counts.
AlleleFractionKernelSegmenter org.broadinstitute.hellbender.tools.copynumber.segmentation
Segments alternate-allele-fraction data using kernel segmentation.
AlleleFractionKernelSegmenter(AllelicCountCollection) AlleleFractionKernelSegmenter
AlleleFractionModeller 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 org.broadinstitute.hellbender.tools.copynumber.models
Enumerates the parameters for AlleleFractionState.
AlleleFractionPrior org.broadinstitute.hellbender.tools.copynumber.models
Represents priors for the allele-fraction model.
AlleleFractionPrior(double) AlleleFractionPrior
AlleleFractionSegment org.broadinstitute.hellbender.tools.copynumber.formats.records
AlleleFractionSegment(SimpleInterval, int) AlleleFractionSegment
AlleleFractionSegment(SimpleInterval, List<AllelicCount>) AlleleFractionSegment
AlleleFractionSegmentCollection org.broadinstitute.hellbender.tools.copynumber.formats.collections
Represents an allele-fraction segmentation.
AlleleFractionSegmentCollection(File) AlleleFractionSegmentCollection
AlleleFractionSegmentCollection(SampleLocatableMetadata, List<AlleleFractionSegment>) AlleleFractionSegmentCollection
alleleFractionsPosterior(RealMatrix, double[]) SomaticLikelihoodsEngine
Given a likelihoods matrix, calculate the parameters of the Dirichlet posterior distribution on their allele
fractions, which define a discrete distribution.
alleleFractionsPosterior(RealMatrix) SomaticLikelihoodsEngine
AlleleFrequencyCalculator org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
AlleleFrequencyCalculator(double, double, double, int) AlleleFrequencyCalculator
alleleIndexAt(int) GenotypeAlleleCounts
Returns the index of the allele from its rank in the genotype.
AlleleLikelihoodMatrixMapper A extends htsjdk.variant.variantcontext.Allele> - Interface in org.broadinstitute.hellbender.tools.walkers.genotyper
Creates
LikelihoodMatrix mappers to be used when working with a subset of the original alleles.
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) GATKVariantContextUtils.AlleleMapper
AlleleMapper(Map<Allele, Allele>) GATKVariantContextUtils.AlleleMapper
AllelePileupCounter 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) AllelePileupCounter
AllelePileupCounter(Allele, List<Allele>, int, ReadPileup) AllelePileupCounter
alleleRankFor(int) GenotypeAlleleCounts
Returns the rank of an allele in the genotype by its index.
alleles StandardCallerArgumentCollection
When the caller is put into GENOTYPE_GIVEN_ALLELES mode it will genotype the samples using only the alleles provide in this rod binding
alleles() SubsettedLikelihoodMatrix
alleles() LikelihoodMatrix
List of alleles in the matrix sorted by their index in the collection.
alleles ReadLikelihoods
Allele list
alleles() ReadLikelihoods
Returns the samples in this read-likelihood collection.
Alleles(OrderedSet<String>, String, String, String, String) GenotypeConcordance.Alleles
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) AlleleSpecificAnnotationData
alleleSpecificAnnotationEquals(VariantContext, VariantContext, String) VariantContextTestUtils
allelesToIndex(int...) GenotypeLikelihoodCalculator
Give a list of alleles, returns the likelihood array index.
AlleleSubsettingUtils org.broadinstitute.hellbender.tools.walkers.genotyper
Utilities class containing methods for restricting VariantContext and GenotypesContext objects 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 picard.util
Utilities class containing methods for restricting VariantContext and GenotypesContext objects 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() AlleleSubsettingUtils
ALLELIC_COUNTS_FILE_LONG_NAME ExomeStandardArgumentDefinitions
ALLELIC_COUNTS_FILE_LONG_NAME CopyNumberStandardArgument
ALLELIC_COUNTS_FILE_SHORT_NAME ExomeStandardArgumentDefinitions
ALLELIC_PON_FILE_LONG_NAME ExomeStandardArgumentDefinitions
ALLELIC_PON_FILE_SHORT_NAME ExomeStandardArgumentDefinitions
AllelicCount org.broadinstitute.hellbender.tools.copynumber.formats.records
Reference and alternate allele counts at a site specified by an interval.
AllelicCount(SimpleInterval, int, int, Nucleotide, Nucleotide) AllelicCount
Construct the allelic count object.
AllelicCount(SimpleInterval, int, int) AllelicCount
AllelicCountCollection org.broadinstitute.hellbender.tools.copynumber.formats.collections
Simple data structure to pass and read/write a List of
AllelicCount objects.
AllelicCountCollection(File) AllelicCountCollection
AllelicCountCollection(SampleLocatableMetadata, List<AllelicCount>) AllelicCountCollection
AllelicCountCollector org.broadinstitute.hellbender.tools.copynumber.datacollection
Collects reference/alternate allele counts at specified sites.
AllelicCountCollector(SampleLocatableMetadata) AllelicCountCollector
AllLocusIterator org.broadinstitute.hellbender.utils.iterators
A super-simplified/stripped-down/faster version of
IntervalAlignmentContextIterator that takes a locus iterator and
a *single* interval, and returns an AlignmentContext for every locus in the interval.
AllLocusIterator(SimpleInterval, Iterator<AlignmentContext>) AllLocusIterator
allMatch(double[], DoublePredicate) MathUtils
Test whether all elements of a double[] array satisfy a double -> boolean predicate
allMatch(int[], IntPredicate) MathUtils
Test whether all elements of an int[] array satisfy an int -> boolean predicate
ALLOSOMAL_CONTIG_LONG_NAME PostprocessGermlineCNVCalls
ALLOW_ALL_READS ReadFilterLibrary
Static, stateless read filter instances
ALLOW_ALL_VARIANTS VariantFilterLibrary
ALLOW_AND_IGNORE_EMPTY_LINES FastqToSam
ALLOW_CONTIG_LENGTH_DISCORDANCE ReorderSam
ALLOW_DUPLICATE_READS CrosscheckFingerprints
ALLOW_HG19_GENCODE_B37_CONTIG_MATCHING_LONG_NAME FuncotatorArgumentDefinitions
ALLOW_INCOMPLETE_DICT_CONCORDANCE ReorderSam
ALLOW_MISSING_FIELDS_IN_HEADER LiftoverVcf
ALLOW_MISSING_UMIS UmiAwareMarkDuplicatesWithMateCigar
ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS PositionBasedDownsampleSam
AllowAllReadsReadFilter() ReadFilterLibrary.AllowAllReadsReadFilter
allowedShortFragmentOverhang StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
allowHg19ContigNamesWithB37 Funcotator
allowNonUniqueKmersInRef ReadThreadingAssemblerArgumentCollection
By default, the program does not allow processing of reference sections that contain non-unique kmers.
alnModType AlignmentInterval
when
alnModType is not
ContigAlignmentsModifier.AlnModType.NONE, fields "mapQual", "mismatches", "alnScore" should be
viewed with care as they were either simply copied from the original alignment (e.g.
alnScore AlignmentInterval
ALSO_IGNORE_DUPLICATES CollectGcBiasMetrics
ALT ValidateBasicSomaticShortMutations
ALT_BASE ErrorSummaryMetrics
The alternative base (or it's complement).
ALT_BASE SequencingArtifactMetrics.BaitBiasDetailMetrics
The (upper-case) alternative base that is called as a result of DNA damage.
ALT_BASE SequencingArtifactMetrics.BaitBiasSummaryMetrics
The (upper-case) alternative base that is called as a result of DNA damage.
ALT_BASE SequencingArtifactMetrics.PreAdapterDetailMetrics
The (upper-case) alternative base that is called as a result of DNA damage.
ALT_BASE SequencingArtifactMetrics.PreAdapterSummaryMetrics
The (upper-case) alternative base that is called as a result of DNA damage.
ALT_COUNT ErrorSummaryMetrics
The number of alt bases observed.
ALT_NONOXO_BASES 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_OXO_BASES 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.
altAllele SvType
altValues() Transition
Like values(), but ignores the ref:ref "transitions".
altValues() Transition
Like values(), but ignores the ref:ref "transitions".
AMBIGUOUS_FILTER_BASES_NAME ReadFilterArgumentDefinitions
AMBIGUOUS_FILTER_FRACTION_NAME ReadFilterArgumentDefinitions
AmbiguousBaseReadFilter org.broadinstitute.hellbender.engine.filters
Filters out reads that have greater than the threshold number for unknown (N) bases.
AmbiguousBaseReadFilter() AmbiguousBaseReadFilter
AmbiguousBaseReadFilter(int) AmbiguousBaseReadFilter
AminoAcid org.broadinstitute.hellbender.tools.funcotator
AMPLICON_INTERVALS CollectTargetedPcrMetrics
AMPLICON_TERRITORY TargetedPcrMetrics
The number of unique bases covered by the intervals of all amplicons in the amplicon set
ANALYSIS_DIR BamToBfq
AnalyzeCovariates org.broadinstitute.hellbender.tools.walkers.bqsr
Evaluate and compare base quality score recalibration tables
AnalyzeCovariates() AnalyzeCovariates
and(CountingReadFilter) CountingReadFilter
Specialization of Predicate.and(Predicate) so that CountingReadFilter and'ed with other CountingReadFilter produce a CountingReadFilter
and(CountingVariantFilter) CountingVariantFilter
Specialization of Predicate.and(Predicate) so that CountingVariantFilter and'ed with other CountingVariantFilter produce a CountingVariantFilter
and(ReadFilter) ReadFilter
Specialization of Predicate.and(Predicate) so that ReadFilters anded with other ReadFilters produce a ReadFilter
and(VariantFilter) VariantFilter
andThen(ReadTransformer) ReadTransformer
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) AS_InbreedingCoeff
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) AS_QualByDepth
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) AS_RankSumTest
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) AS_RMSMappingQuality
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) ChromosomeCounts
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) Coverage
annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, ReadLikelihoods<Allele>) DepthPerAlleleBySample
annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, ReadLikelihoods<Allele>) DepthPerSampleHC
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) ExcessHet
annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, ReadLikelihoods<Allele>) GenotypeAnnotation
Computes the annotation for the given genotype and the likelihoods per read.
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) GenotypeSummaries
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) InbreedingCoeff
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) InfoFieldAnnotation
Computes the annotation for the given variant and the likelihoods per read.
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) MappingQualityZero
annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, ReadLikelihoods<Allele>) OxoGReadCounts
annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, ReadLikelihoods<Allele>) 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, ReadLikelihoods<Allele>) PossibleDeNovo
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) QualByDepth
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) RankSumTest
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) ReferenceBases
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) RMSMappingQuality
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) SampleList
annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, ReadLikelihoods<Allele>) StrandArtifact
annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, ReadLikelihoods<Allele>) StrandBiasBySample
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) StrandBiasTest
annotate(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) TandemRepeat
annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, ReadLikelihoods<Allele>) UniqueAltReadCount
ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED 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 StandardCallerArgumentCollection
Advanced, experimental argument: if SNP likelihood model is specified, and if EMIT_ALL_SITES output mode is set, when we set this argument then we will also emit PLs at all sites.
annotateBreakpointBasedCallsWithImpreciseEvidenceLinks(List<VariantContext>, PairedStrandedIntervalTree<EvidenceTargetLink>, ReadMetadata, ReferenceMultiSource, StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection, Logger) AnnotatedVariantProducer
annotateContext(VariantContext, FeatureContext, ReferenceContext, ReadLikelihoods<Allele>, Predicate<VariantAnnotation>) VariantAnnotatorEngine
Annotates the given variant context - adds all annotations that satisfy the predicate.
ANNOTATED_INTERVAL_DEFAULT_CONFIG_RESOURCE AnnotatedIntervalCollection
ANNOTATED_INTERVALS_FILE_LONG_NAME CopyNumberStandardArgument
AnnotatedInterval org.broadinstitute.hellbender.tools.copynumber.formats.records
Represents an interval with a set of annotations.
AnnotatedInterval(SimpleInterval, AnnotationSet) AnnotatedInterval
AnnotatedInterval org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
Simple class that just has an interval and sorted name-value pairs.
AnnotatedInterval(SimpleInterval, SortedMap<String, String>) AnnotatedInterval
AnnotatedIntervalCodec org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
AnnotatedIntervalCodec() AnnotatedIntervalCodec
AnnotatedIntervalCodec(Path) AnnotatedIntervalCodec
AnnotatedIntervalCollection org.broadinstitute.hellbender.tools.copynumber.formats.collections
AnnotatedIntervalCollection(File) AnnotatedIntervalCollection
AnnotatedIntervalCollection(LocatableMetadata, List<AnnotatedInterval>) AnnotatedIntervalCollection
AnnotatedIntervalCollection org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
Represents a collection of annotated intervals.
AnnotatedIntervalHeader org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
AnnotatedIntervalHeader(String, String, String, List<String>, SAMFileHeader) AnnotatedIntervalHeader
AnnotatedIntervalUtils org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
AnnotatedIntervalWriter org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
AnnotatedVariantProducer org.broadinstitute.hellbender.tools.spark.sv.discovery
Given identified pair of breakpoints for a simple SV and its supportive evidence, i.e.
AnnotatedVariantProducer() AnnotatedVariantProducer
AnnotateIntervals org.broadinstitute.hellbender.tools.copynumber
Annotates intervals with GC content.
AnnotateIntervals() AnnotateIntervals
annotateOverlap(List<VariantContext>, String, VariantContext) 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) VariantOverlapAnnotator
Add overlap attributes to vcToAnnotate against all overlaps in featureContext
AnnotatePairOrientation org.broadinstitute.hellbender.tools
AnnotatePairOrientation() AnnotatePairOrientation
annotateRawData(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) AS_QualByDepth
Note: There is no raw annotation for AS_QualByDepth and thus this method does nothing.
annotateRawData(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) 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, ReadLikelihoods<Allele>) AS_RMSMappingQuality
annotateRawData(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) AS_StrandBiasTest
Uses the ReadLikelihoods 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, ReadLikelihoods<Allele>) ReducibleAnnotation
Generate the raw data necessary to calculate the annotation.
annotateRawData(ReferenceContext, VariantContext, ReadLikelihoods<Allele>) RMSMappingQuality
Generate the raw data necessary to calculate the annotation.
annotateRsID(FeatureContext, VariantContext) VariantOverlapAnnotator
Update rsID in vcToAnnotate with rsIDs from dbSNP fetched from featureContext
annotateRsID(List<VariantContext>, VariantContext) VariantOverlapAnnotator
Update rsID of vcToAnnotate with rsID match found in vcsAtLoc, if one exists
annotateSingleVariant(VariantContext, GenotypeBuilder, ReadPileup, int) OxoGReadCounts
Annotate the given variant context with the OxoG read count attributes, directly from the read pileup.
annotateVariantContextsWithFilterResults(double, SortedSet<Transition>, List<VariantContext>, Map<Transition, Double>) OrientationBiasFilterer
Filter genotypes with orientation bias filter while trying to keep the false discovery rate for the sample below the threshold specified.
annotateVariantContextWithPreprocessingValues(VariantContext, SortedSet<Transition>, Map<Transition, Double>) OrientationBiasFilterer
Adds the annotations that can be created for individual variants.
AnnotateVcfWithBamDepth org.broadinstitute.hellbender.tools.walkers.validation
Annotate every variant in a VCF with the depth at that locus in a bam.
AnnotateVcfWithBamDepth() AnnotateVcfWithBamDepth
AnnotateVcfWithExpectedAlleleFraction 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() AnnotateVcfWithExpectedAlleleFraction
Annotation 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_DEFAULT_VALUE FuncotatorArgumentDefinitions
ANNOTATION_DEFAULTS_LONG_NAME FuncotatorArgumentDefinitions
ANNOTATION_GROUP_LONG_NAME StandardArgumentDefinitions
ANNOTATION_GROUP_SHORT_NAME StandardArgumentDefinitions
ANNOTATION_LONG_NAME StandardArgumentDefinitions
ANNOTATION_OVERRIDES_DEFAULT_VALUE FuncotatorArgumentDefinitions
ANNOTATION_OVERRIDES_LONG_NAME FuncotatorArgumentDefinitions
ANNOTATION_SHORT_NAME StandardArgumentDefinitions
annotationDefaults Funcotator
annotationEngine GenotypingEngine
AnnotationException picard.annotation
Exception thrown when loading gene annotations.
AnnotationException(String) AnnotationException
AnnotationException(String, Throwable) AnnotationException
annotationKeys VariantDataManager
annotationOverrideMap DataSourceFuncotationFactory
Map of ANNOTATION_NAME -> OVERRIDE_VALUE.
annotationOverrides Funcotator
ANNOTATIONS_TO_EXCLUDE_LONG_NAME StandardArgumentDefinitions
ANNOTATIONS_TO_EXCLUDE_SHORT_NAME StandardArgumentDefinitions
AnnotationSet org.broadinstitute.hellbender.tools.copynumber.formats.records
Represents a set of annotations for an interval.
AnnotationSet(double) AnnotationSet
annotationSource GencodeGtfFeatureBaseData
Keyword identifying the source of this feature.
AnnotationUtils org.broadinstitute.hellbender.tools.walkers.annotator
annotatorEngine ReferenceConfidenceVariantContextMerger
anonymousOptionalFields GencodeGtfFeatureBaseData
Additional optional GTF fields.
ApacheSingularValueDecomposer org.broadinstitute.hellbender.utils.svd
Perform singular value decomposition (and pseudoinverse calculation) in pure Java, Commons Math.
ApacheSingularValueDecomposer() ApacheSingularValueDecomposer
append(String) DataLine
Sets the next string value in the data-line that correspond to a column.
append(int) DataLine
Sets the next int value in the data-line that correspond to a column.
append(long) DataLine
Sets the next long value in the data-line that correspond to a column.
append(long...) DataLine
Sets the next long values in the data-line that correspond to next few columns.
append(double) DataLine
Sets the next double value in the data-line that correspond to a column.
append(int...) DataLine
Sets the next int values in the data-line that correspond to next few columns.
append(String...) DataLine
Sets the next string values in the data-line that correspond to next few columns.
append(double...) DataLine
Sets the next double values in the data-line that correspond to next few columns.
append(List<T>, T...) Utils
Create a new list that contains the elements of left along with elements elts
appendBases(byte[]) FastaReferenceWriter
Adds bases to current sequence from a byte array.
appendBases(byte[], int, int) FastaReferenceWriter
Adds bases to current sequence from a range in a byte array.
appendSATagString(StringBuilder) AlignmentInterval
Appends the SA string representation of this interval into a builder.
appendSequence(String, byte[]) FastaReferenceWriter
Appends a new sequence to the output.
appendSequence(String, String, byte[]) FastaReferenceWriter
Appends a new sequence to the output with or without a description.
appendSequence(String, String, int, byte[]) FastaReferenceWriter
Appends a new sequence to the output with or without a description and an alternative number of bases-per-line.
apply(AbstractConcordanceWalker.TruthVersusEval, ReadsContext, ReferenceContext) AbstractConcordanceWalker
apply(AssemblyRegion, ReferenceContext, FeatureContext) AssemblyRegionWalker
Process an individual AssemblyRegion.
apply(GATKRead) ReferenceWindowFunctions.FixedWindowFunction
apply(F, ReadsContext, ReferenceContext, FeatureContext) FeatureWalker
Process an individual feature.
apply(SimpleInterval, ReadsContext, ReferenceContext, FeatureContext) IntervalWalker
Process an individual interval.
apply(AlignmentContext, ReferenceContext, FeatureContext) LocusWalker
Process an individual AlignmentContext (with optional contextual information).
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) 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(List<VariantContext>, ReferenceContext) MultiVariantWalkerGroupedOnStart
This method must be implemented by tool authors.
apply(GATKRead, ReferenceContext, FeatureContext) ReadWalker
Process an individual read (with optional contextual information).
apply(GATKRead, ReferenceContext, FeatureContext) TwoPassReadWalker
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) TwoPassVariantWalker
Make final to hide it from subclasses
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) VariantWalkerBase
Process an individual variant.
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) AnnotatePairOrientation
apply(GATKRead, ReferenceContext, FeatureContext) ClipReads
apply(AlignmentContext, ReferenceContext, FeatureContext) CollectAllelicCounts
apply(GATKRead, ReferenceContext, FeatureContext) CollectReadCounts
apply(GATKRead, ReferenceContext, FeatureContext) CountBases
apply(GATKRead, ReferenceContext, FeatureContext) CountReads
apply(AssemblyRegion, ReferenceContext, FeatureContext) ExampleAssemblyRegionWalker
apply(BEDFeature, ReadsContext, ReferenceContext, FeatureContext) ExampleFeatureWalker
apply(SimpleInterval, ReadsContext, ReferenceContext, FeatureContext) ExampleIntervalWalker
apply(AlignmentContext, ReferenceContext, FeatureContext) ExampleLocusWalker
apply(GATKRead, ReferenceContext, FeatureContext) ExamplePostTraversalPythonExecutor
apply(GATKRead, ReferenceContext, FeatureContext) ExampleReadWalkerWithReference
apply(GATKRead, ReferenceContext, FeatureContext) ExampleReadWalkerWithVariants
apply(GATKRead, ReferenceContext, FeatureContext) ExampleStreamingPythonExecutor
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) ExampleVariantWalker
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) FilterByOrientationBias
Just adds the Pre Adapter Q annotation to the variant and creates a new variant.
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) FixCallSetSampleOrdering
apply(GATKRead, ReferenceContext, FeatureContext) FixMisencodedBaseQualityReads
apply(GATKRead, ReferenceContext, FeatureContext) FlagStat
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) Funcotator
apply(GATKRead, ReferenceContext, FeatureContext) LeftAlignIndels
apply(GATKRead, ReferenceContext, FeatureContext) PrintReads
apply(Iterator<GATKRead>, SAMFileHeader) PSBwaAligner
apply(Iterator<GATKRead>) PSBwaFilter
apply(BreakpointEvidence) BreakpointEvidenceClusterer
apply(Tuple2<Integer, List<SVFastqUtils.FastqRead>>) 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(Iterator<GATKRead>) KmerCounter
apply(GATKRead) QNameFinder
apply(GATKRead) QNameIntervalFinder
apply(GATKRead) QNameKmerizer
apply(GATKRead) QNamesForKmersFinder
apply(GATKRead) ReadClassifier
apply(T, U, V) SingleSequenceReferenceAligner.TriFunction
apply(JavaRDD<GATKRead>, Broadcast<RecalibrationReport>, SAMFileHeader, ApplyBQSRArgumentCollection) ApplyBQSRSparkFn
apply(JavaPairRDD<GATKRead, ReadContextData>, SAMFileHeader, SAMSequenceDictionary, RecalibrationArgumentCollection) BaseRecalibratorSparkFn
apply(Iterator<ContextShard>) BaseRecalibratorEngineSparkWrapper
apply(GATKRead, ReferenceContext, FeatureContext) SplitReads
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) VariantAnnotator
For each site of interest, annotate based on the requested annotation types
apply(GATKRead, ReferenceContext, FeatureContext) ApplyBQSR
apply(GATKRead, ReferenceContext, FeatureContext) 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(List<VariantContext>, ReferenceContext) CombineGVCFs
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) GetPileupSummaries
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) CountVariants
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) VariantFiltration
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) GenotypeGVCFs
apply(AssemblyRegion, ReferenceContext, FeatureContext) HaplotypeCaller
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) FilterMutectCalls
apply(AssemblyRegion, ReferenceContext, FeatureContext) Mutect2
apply(AlignmentContext, ReferenceContext, FeatureContext) CheckPileup
apply(AlignmentContext, ReferenceContext, FeatureContext) Pileup
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) FilterAlignmentArtifacts
apply(GATKRead, ReferenceContext, FeatureContext) RevertBaseQualityScores
apply(AlignmentContext, ReferenceContext, FeatureContext) ASEReadCounter
apply(GATKRead, ReferenceContext, FeatureContext) UnmarkDuplicates
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) AnnotateVcfWithBamDepth
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) AnnotateVcfWithExpectedAlleleFraction
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) ValidateBasicSomaticShortMutations
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) CalculateMixingFractions
apply(AbstractConcordanceWalker.TruthVersusEval, ReadsContext, ReferenceContext) Concordance
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) CountFalsePositives
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) RemoveNearbyIndels
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) CalculateGenotypePosteriors
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) SelectVariants
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) UpdateVCFSequenceDictionary
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) ValidateVariants
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) VariantsToTable
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) ApplyVQSR
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) CNNScoreVariants
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) VariantRecalibrator
apply(GATKRead) AdapterTrimTransformer
apply(GATKRead) BaseQualityClipReadTransformer
Clip bases on the right end of the read from
argmax_x{ \sum{i = x + 1}^l (qTrimmingThreshold - qual).
apply(GATKRead) BaseQualityReadTransformer
apply(GATKRead) BQSRReadTransformer
Recalibrates the base qualities of a read
apply(GATKRead) DUSTReadTransformer
apply(GATKRead) MappingQualityReadTransformer
apply(GATKRead) MisencodedBaseQualityReadTransformer
apply(GATKRead) NDNCigarReadTransformer
apply(GATKRead) SimpleRepeatMaskTransformer
apply(GATKRead) StripMateNumberTransformer
apply(ClippingRepresentation, GATKRead) ClippingOp
Clips the bases in read according to this operation's start and stop.
apply(int, int) IntToDoubleBiFunction
apply(List<D>, List<T>, HMM<D, T, S>) ForwardBackwardAlgorithm
Runs the forward-backward algorithm on a data-positions list pair given a type-compatible model.
apply(List<D>, List<T>, HMM<D, T, S>) ViterbiAlgorithm
Calculates the most likely the hidden state sequence that explains the observed data
given the corresponding sequence of observation positions.
apply(int) MathUtils.IntToDoubleArrayFunction
apply(GATKRead) BaseRecalibrationEngine.BQSRReferenceWindowFunction
apply(T) SerializableFunction
APPLY_EAMSS_FILTER IlluminaBasecallsToFastq
APPLY_EAMSS_FILTER IlluminaBasecallsToSam
applyAlignment(String, byte[], byte[], String, BwaMemAlignment, List<String>, SAMFileHeader, boolean, boolean) BwaMemAlignmentUtils
Builds a SAMRecord from unaligned read data and an alignment.
ApplyBQSR org.broadinstitute.hellbender.tools.walkers.bqsr
Apply base quality score recalibration
ApplyBQSR() ApplyBQSR
applyBqsrArgs BQSRPipelineSpark
command-line arguments to fine tune the apply BQSR step.
applyBqsrArgs ReadsPipelineSpark
command-line arguments to fine tune the apply BQSR step.
ApplyBQSRArgumentCollection org.broadinstitute.hellbender.tools
The collection of all arguments needed for ApplyBQSR.
ApplyBQSRArgumentCollection() ApplyBQSRArgumentCollection
ApplyBQSRSpark org.broadinstitute.hellbender.tools.spark
Apply base quality score recalibration with Spark.
ApplyBQSRSpark() ApplyBQSRSpark
ApplyBQSRSparkFn org.broadinstitute.hellbender.tools.spark.transforms
ApplyBQSRSparkFn() ApplyBQSRSparkFn
ApplyBQSRUniqueArgumentCollection org.broadinstitute.hellbender.tools
The collection of those arguments for ApplyBQSR that are not already defined in RecalibrationArgumentCollection.
ApplyBQSRUniqueArgumentCollection() ApplyBQSRUniqueArgumentCollection
applyCigarToCigar(Cigar, Cigar) 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>) SVReadFilter
applyFilters(M2FiltersArgumentCollection, VariantContext, VariantContextBuilder) Mutect2FilteringEngine
applyMapFunc(Function<I, Iterator<O>>, Iterator<? extends I>) FlatMapGluer
applyMapFunc(Function<I, Iterator<O>>, Iterator<? extends I>, I) FlatMapGluer
applyToArray(double[], DoubleUnaryOperator) 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) 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) 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.
ApplyVQSR org.broadinstitute.hellbender.tools.walkers.vqsr
Apply a score cutoff to filter variants based on a recalibration table
ApplyVQSR() ApplyVQSR
approximateLog10SumLog10(double[]) MathUtils
approximateLog10SumLog10(double[], int) MathUtils
approximateLog10SumLog10(double, double, double) MathUtils
approximateLog10SumLog10(double, double) MathUtils
approximateLog10SumLog10(double[], int, int) MathUtils
Calculate the approximate log10 sum of an array range.
areAlignmentsEqual() SamComparison
Returns true if the alignments are equal, false otherwise.
areEqual() SamComparison
areEqual() CompareSAMs
areHeadersEqual() SamComparison
Returns true if the headers are equal, false otherwise.
areHistogramsEmpty() CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
areVariantsAtSameLocusConcordant(VariantContext, VariantContext) AbstractConcordanceWalker
areVariantsAtSameLocusConcordant(VariantContext, VariantContext) Concordance
argmax(Function<Double, Double>, double, double, double) OptimizationUtils
argmax(Function<Double, Double>, double, double, double, double, double, int) OptimizationUtils
args SamFileTester
ARGUMENT_COLUMN_NAME RecalUtils
ARGUMENT_REPORT_TABLE_TITLE RecalUtils
ARGUMENT_VALUE_COLUMN_NAME RecalUtils
ArgumentsBuilder org.broadinstitute.hellbender.utils.test
Builder for command line argument lists
It will convert old style "Argument=Value" into new style "--Argument value" strings
Use this only in test code.
ArgumentsBuilder() ArgumentsBuilder
ArgumentsBuilder(Object[]) ArgumentsBuilder
ARRAY_DIM StrandBiasTest
ARRAY_SIZE StrandBiasTest
arrayListCollector(int) SVUtils
Provides a stream collector that will collect items into an array list with a given initial capacity.
arrayMax(double[]) MathUtils
arrayMin(int[]) MathUtils
ARTIFACT_IN_NORMAL_FILTER_NAME GATKVCFConstants
ARTIFACT_MODES_FULL_NAME FilterByOrientationBias
ARTIFACT_MODES_SHORT_NAME FilterByOrientationBias
ARTIFACT_NAME SequencingArtifactMetrics.BaitBiasSummaryMetrics
A "nickname" of this artifact, if it is a known error mode.
ARTIFACT_NAME SequencingArtifactMetrics.PreAdapterSummaryMetrics
A "nickname" of this artifact, if it is a known error mode.
ArtifactStatisticsScorer org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter
ArtifactStatisticsScorer() ArtifactStatisticsScorer
ArtificialBAMBuilder 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) ArtificialBAMBuilder
ArtificialBAMBuilder(SAMSequenceDictionary, int, int) ArtificialBAMBuilder
ArtificialReadIterator org.broadinstitute.hellbender.utils.read
this fake iterator allows us to look at how specific piles of reads are handled
ArtificialReadQueryIterator org.broadinstitute.hellbender.utils.read
ArtificialReadUtils org.broadinstitute.hellbender.utils.read
ArtificialReadUtils() ArtificialReadUtils
AS_BASE_QUAL_RANK_SUM_KEY GATKVCFConstants
AS_BaseQualityRankSumTest org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
Allele-specific rank Sum Test of REF versus ALT base quality scores
AS_BaseQualityRankSumTest() AS_BaseQualityRankSumTest
AS_CULPRIT_KEY GATKVCFConstants
AS_FILTER_STATUS_KEY GATKVCFConstants
AS_FISHER_STRAND_KEY GATKVCFConstants
AS_FisherStrand org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
Allele-specific strand bias estimated using Fisher's Exact Test
*
AS_FisherStrand() AS_FisherStrand
AS_HETEROZYGOSITY_KEY GATKVCFConstants
AS_INBREEDING_COEFFICIENT_KEY GATKVCFConstants
AS_InbreedingCoeff org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
Allele-specific likelihood-based test for the inbreeding among samples
AS_InbreedingCoeff() AS_InbreedingCoeff
AS_InbreedingCoeff(Set<String>) AS_InbreedingCoeff
AS_MAP_QUAL_RANK_SUM_KEY GATKVCFConstants
AS_MappingQualityRankSumTest org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
Allele specific Rank Sum Test for mapping qualities of REF versus ALT reads
AS_MappingQualityRankSumTest() AS_MappingQualityRankSumTest
AS_QUAL_BY_DEPTH_KEY GATKVCFConstants
AS_QUAL_KEY GATKVCFConstants
AS_QualByDepth org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
Allele-specific call confidence normalized by depth of sample reads supporting the allele
AS_QualByDepth() AS_QualByDepth
AS_RankSumTest org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
Allele-specific implementation of rank sum test annotations
AS_RankSumTest() AS_RankSumTest
AS_RAW_BASE_QUAL_RANK_SUM_KEY GATKVCFConstants
AS_RAW_MAP_QUAL_RANK_SUM_KEY GATKVCFConstants
AS_RAW_READ_POS_RANK_SUM_KEY GATKVCFConstants
AS_RAW_RMS_MAPPING_QUALITY_KEY GATKVCFConstants
AS_READ_POS_RANK_SUM_KEY GATKVCFConstants
AS_ReadPosRankSumTest org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
Allele-specific Rank Sum Test for relative positioning of REF versus ALT allele within reads
AS_ReadPosRankSumTest() AS_ReadPosRankSumTest
AS_RMS_MAPPING_QUALITY_KEY GATKVCFConstants
AS_RMSMappingQuality org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
Allele-specific Root Mean Square of the mapping quality of reads across all samples.
AS_RMSMappingQuality() AS_RMSMappingQuality
AS_SB_TABLE_KEY GATKVCFConstants
AS_StandardAnnotation 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 GATKVCFConstants
AS_StrandBiasTest org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
Allele-specific implementation of strand bias annotations
AS_StrandBiasTest() AS_StrandBiasTest
AS_StrandOddsRatio org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
Allele-specific strand bias estimated by the Symmetric Odds Ratio test
AS_StrandOddsRatio() AS_StrandOddsRatio
AS_VQS_LOD_KEY GATKVCFConstants
asAlleleList(List<T>) GenotypeAlleleCounts
Composes a list with the alleles, possibly containing repeats i.e.
asDoubleArray(Collection<Allele>) PerAlleleCollection
ASEReadCounter org.broadinstitute.hellbender.tools.walkers.rnaseq
Calculate read counts per allele for allele-specific expression analysis of RNAseq data
ASEReadCounter() ASEReadCounter
ASEReadCounter.CountPileupType org.broadinstitute.hellbender.tools.walkers.rnaseq
ASEReadCounter.OUTPUT_FORMAT org.broadinstitute.hellbender.tools.walkers.rnaseq
asList() IndexedSet
Returns a list view of the elements in the set.
asList(int...) Utils
Returns a List<Integer> representation of an primitive int array.
asList(double...) Utils
Returns a List<Double> representation of an primitive double array.
asList() GenotypeConcordance.Alleles
asListOfAlleles() AlleleList
Returns a List unmodifiable view of this allele-list
asListOfSamples() SampleList
Returns a List unmodifiable view of a sample-list
AssembledEvidenceResults(ReadMetadata, List<SVInterval>, List<AlignedAssemblyOrExcuse>, List<EvidenceTargetLink>) FindBreakpointEvidenceSpark.AssembledEvidenceResults
assemblerArgs AssemblyBasedCallerArgumentCollection
assembleReads(AssemblyRegion, List<VariantContext>, AssemblyBasedCallerArgumentCollection, SAMFileHeader, SampleList, Logger, ReferenceSequenceFile, ReadThreadingAssembler, SmithWatermanAligner) 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
assembliesSortOrder StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
ASSEMBLY_NAME_KEY GATKVCFConstants
ASSEMBLY_PADDING_LONG_NAME AssemblyRegionWalker
ASSEMBLY_REGION_OUT_LONG_NAME AssemblyRegionWalker
AssemblyBasedCallerArgumentCollection org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Set of arguments for Assembly Based Callers
AssemblyBasedCallerArgumentCollection() AssemblyBasedCallerArgumentCollection
AssemblyBasedCallerGenotypingEngine org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Created by davidben on 12/21/16.
AssemblyBasedCallerGenotypingEngine(AssemblyBasedCallerArgumentCollection, SampleList, AFCalculatorProvider, boolean) AssemblyBasedCallerGenotypingEngine AssemblyBasedCallerGenotypingEngine.CalledHaplotypes org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Carries the result of a call to #assignGenotypeLikelihoods
AssemblyBasedCallerUtils org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Created by davidben on 9/8/16.
AssemblyBasedCallerUtils() AssemblyBasedCallerUtils
AssemblyContigAlignmentsConfigPicker 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.
AssemblyContigAlignmentsConfigPicker() AssemblyContigAlignmentsConfigPicker
AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings 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()
Note that a special case needs attention:
if
AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings.getMayBeNullGoodMappingToNonCanonicalChromosome() returns non-null result,
it is indicating an equally good--or better--non-chimeric mapping to a non-canonical chromosome exists,
but to preserve the SV signal, we keep the chimeric alignments to canonical chromosomes and
signal the situation to downstream units.
AssemblyContigWithFineTunedAlignments org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
AssemblyContigWithFineTunedAlignments(AlignedContig) AssemblyContigWithFineTunedAlignments
AssemblyContigWithFineTunedAlignments(AlignedContig, List<String>, boolean, AlignmentInterval) AssemblyContigWithFineTunedAlignments
AssemblyContigWithFineTunedAlignments(AlignedContig, List<String>, boolean, String) AssemblyContigWithFineTunedAlignments
AssemblyContigWithFineTunedAlignments.AlignmentSignatureBasicType org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
AssemblyContigWithFineTunedAlignments.ReasonForAlignmentClassificationFailure org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
AssemblyContigWithFineTunedAlignments.Serializer org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
assemblyId AlignedAssembly
assemblyImpreciseEvidenceOverlapUncertainty StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection
AssemblyRegion org.broadinstitute.hellbender.engine
Region of the genome that gets assembled by the local assembly engine.
AssemblyRegion(SimpleInterval, List<ActivityProfileState>, boolean, int, SAMFileHeader) AssemblyRegion
Create a new AssemblyRegion containing no reads
AssemblyRegion(SimpleInterval, int, SAMFileHeader) AssemblyRegion
Simple interface to create an assembly region that isActive without any profile state
AssemblyRegionEvaluator 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).
assemblyRegionEvaluator() AssemblyRegionWalker
assemblyRegionEvaluator() AssemblyRegionWalkerSpark
assemblyRegionEvaluator() ExampleAssemblyRegionWalker
assemblyRegionEvaluator() ExampleAssemblyRegionWalkerSpark
assemblyRegionEvaluator() HaplotypeCaller
assemblyRegionEvaluator() Mutect2
AssemblyRegionIterator org.broadinstitute.hellbender.engine
AssemblyRegionIterator(MultiIntervalShard<GATKRead>, SAMFileHeader, ReferenceDataSource, FeatureManager, AssemblyRegionEvaluator, int, int, int, double, int, boolean) AssemblyRegionIterator
Constructs an AssemblyRegionIterator over a provided read shard
assemblyRegionOut 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 AssemblyRegionWalker
assemblyRegionPadding AssemblyRegionWalkerSpark
assemblyRegionPadding HaplotypeCallerSpark.ShardingArgumentCollection
AssemblyRegionTrimmer org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Helper component to manage active region trimming
It receives the user arguments that controls trimming and also performs the trimming region calculation.
AssemblyRegionTrimmer() AssemblyRegionTrimmer
AssemblyRegionTrimmer.Result org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Holds the result of trimming.
assemblyRegionTrimmerArgs AssemblyBasedCallerArgumentCollection
AssemblyRegionTrimmerArgumentCollection org.broadinstitute.hellbender.tools.walkers.haplotypecaller
AssemblyRegionTrimmerArgumentCollection() AssemblyRegionTrimmerArgumentCollection
AssemblyRegionWalker 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() AssemblyRegionWalker
AssemblyRegionWalkerContext org.broadinstitute.hellbender.engine.spark
AssemblyRegionWalkerContext(AssemblyRegion, ReferenceContext, FeatureContext) AssemblyRegionWalkerContext
AssemblyRegionWalkerSpark org.broadinstitute.hellbender.engine.spark
AssemblyRegionWalkerSpark() AssemblyRegionWalkerSpark
assemblyRegionWithWellMappedReads(AssemblyRegion, int, SAMFileHeader) AssemblyBasedCallerUtils
AssemblyResult org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Result of assembling, with the resulting graph and status
AssemblyResult(AssemblyResult.Status, SeqGraph, ReadThreadingGraph) AssemblyResult
Create a new assembly result
AssemblyResult.Status org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Status of the assembly result
AssemblyResultSet org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Collection of read assembly using several kmerSizes.
AssemblyResultSet() AssemblyResultSet
Constructs a new empty assembly result set.
assemblyToMappedSizeRatioGuess StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
assertAttributeNameIsLegal(String) 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) DataSourceUtils
Asserts that the given field is contained in the given props and is a boolean value.
assertCondition(Iterable<T>, Iterable<T>, BiConsumer<T, T>) BaseTest
assertConfigFilePropertiesAreValid(Properties, Path) FuncotatorArgumentDefinitions.DataSourceType
assertConfigPropertiesContainsKey(String, Properties, Path) DataSourceUtils
Asserts that the given key is contained in the given configProperties.
assertContains(String, String) BaseTest
assertCRAMContents(Path) SamAssertionUtils
Unconditionally validate/assert that the contents are CRAM
assertCRAMContentsIfCRAM(File) SamAssertionUtils
Validate/assert that the contents are CRAM if the extension is .cram
assertCRAMContentsIfCRAM(Path) SamAssertionUtils
Validate/assert that the contents are CRAM if the extension is .cram
assertEqualBamFiles(File, File, boolean, ValidationStringency) SamAssertionUtils
Compares the two given bam files, optionally sorting them before comparison.
assertEqualBamFiles(File, File, File, boolean, ValidationStringency) SamAssertionUtils
Compares the two given bam files, optionally sorting them before comparison.
assertEqualsDoubleArray(double[], double[], double) BaseTest
Checks whether two double array contain the same values or not.
assertEqualsDoubleSmart(Object, Double, double) BaseTest
assertEqualsDoubleSmart(double, double) BaseTest
assertEqualsDoubleSmart(double, double, double) BaseTest
assertEqualsDoubleSmart(double, double, double, String) BaseTest
assertEqualsLongArray(long[], long[]) BaseTest
Checks whether two long arrays contain the same values or not.
assertEqualsSet(Set<T>, Set<T>, String) BaseTest
assertEqualTextFiles(File, File) IntegrationTestSpec
assertEqualTextFiles(File, File, String) IntegrationTestSpec
Compares two text files and ignores all lines that start with the comment prefix.
assertEqualVariants(List<VariantContext>, List<VariantContext>) VariantContextTestUtils
Validates that the given lists have variant
context that correspond to the same variants in the same order.
assertFileIsReadable(Path) IOUtils
assertGenotypePosteriorsAttributeWasRemoved(VariantContext, VariantContext) VariantContextTestUtils
assertGenotypesAreEqual(Genotype, Genotype) VariantContextTestUtils
assertIntegerPropertiesField(Properties, String, Path) DataSourceUtils
Asserts that the given field is contained in the given props and is an integer value.
assertMatchingFiles(List<File>, List<String>, boolean, ValidationStringency) IntegrationTestSpec
assertMinimumQualities() BclQualityEvaluationStrategy
Reviews the qualities observed thus far and throws an exception if any are below the minimum quality threshold.
assertPairedMates(SAMRecord, SAMRecord) SamToFastq
assertPathFilePropertiesField(Properties, String, Path) DataSourceUtils
Asserts that the given field is contained in the given props and is a file path.
assertProperFileStructure(File) BclReader
assertSamsEqual(File, File, ValidationStringency, File) SamAssertionUtils
causes an exception if the given sam files aren't equal
assertSamsEqual(Path, Path, ValidationStringency, Path) SamAssertionUtils
assertSamsEqual(File, File, ValidationStringency) SamAssertionUtils
causes an exception if the given sam files aren't equal
assertSamsEqual(File, File, File) SamAssertionUtils
causes an exception if the given sam files aren't equal
assertSamsEqual(Path, Path, Path) SamAssertionUtils
assertSamsEqual(File, File) SamAssertionUtils
causes an exception if the given sam files aren't equal
assertSamValid(File, ValidationStringency, File) SamAssertionUtils
causes an exception if the given sam isn't valid
assertSamValid(File, ValidationStringency) SamAssertionUtils
causes an exception if the given sam isn't valid
assertSamValid(File, File) SamAssertionUtils
causes an exception if the given sam isn't valid
assertSamValid(File) SamAssertionUtils
causes an exception if the given sam isn't valid
the default ValidationStringency value for this method is LENIENT
assertSorted(Iterable<T>, Comparator<T>) BaseTest
assert that the iterable is sorted according to the comparator
assertSorted(Iterator<T>, Comparator<T>) BaseTest
assert that the iterator is sorted according to the comparator
assertSorted(SAMFileHeader.SortOrder) MarkDuplicatesWithMateCigarIterator
Establishes that records returned by this iterator are expected to
be in the specified sort order.
assertValidStrand(Strand) FuncotatorUtils
Asserts that the given strand is non-null and is not equal to Strand.NONE.
assertVariantContextsAreEqual(VariantContext, VariantContext, List<String>) VariantContextTestUtils
assertVariantContextsAreEqualAlleleOrderIndependent(VariantContext, VariantContext, List<String>, VCFHeader) VariantContextTestUtils
Method which compares two variant contexts for equality regardless of different allele ordering.
assertVariantContextsHaveSameGenotypes(VariantContext, VariantContext) VariantContextTestUtils
asSetOfSamples() SampleList
Returns a Set unmodifiable view of the sample-list
ASSIGNED_UMI_TAG UmiAwareMarkDuplicatesWithMateCigar
assignGenotypeLikelihoods(List<Haplotype>, ReadLikelihoods<Haplotype>, Map<String, List<GATKRead>>, byte[], SimpleInterval, SimpleInterval, FeatureContext, List<VariantContext>, boolean, int, SAMFileHeader) 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[]) Gene.Transcript
Write into locusFunctions the function of each position from start to start + locusFunctions.length
relative to this transcript.
ASSUME_SORT_ORDER AbstractMarkDuplicatesCommandLineProgram
ASSUME_SORT_ORDER_SHORT_NAME StandardOptionDefinitions
ASSUME_SORTED CollectMultipleMetricsSpark
ASSUME_SORTED AbstractMarkDuplicatesCommandLineProgram
ASSUME_SORTED CollectMultipleMetrics
ASSUME_SORTED CollectRrbsMetrics
ASSUME_SORTED SinglePassSamProgram
ASSUME_SORTED FixMateInformation
ASSUME_SORTED AbstractMarkDuplicatesCommandLineProgram
Deprecated.
ASSUME_SORTED MergeSamFiles
ASSUME_SORTED_LONG_NAME StandardArgumentDefinitions
ASSUME_SORTED_SHORT_NAME StandardArgumentDefinitions
ASSUME_SORTED_SHORT_NAME StandardOptionDefinitions
asTag(BwaMemAlignment, List<String>) BwaMemAlignmentUtils
Describes an alignment as a string for use in an SA tag, for example.
asVcf(ReferenceSequenceFile) HaplotypeMap
AsynchronousStreamWriterService 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.
AsynchronousStreamWriterService(ExecutorService, OutputStream, Function<T, ByteArrayOutputStream>) AsynchronousStreamWriterService
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) AsyncIterator
AT_DROPOUT HsMetrics
A measure of how undercovered <= 50% GC regions are relative to the mean.
AT_DROPOUT TargetedPcrMetrics
A measure of how regions with low GC content (<= 50%), are undercovered relative to mean coverage.
AT_DROPOUT TargetMetrics
A measure of how undercovered <= 50% GC regions are relative to the mean.
AT_DROPOUT GcBiasSummaryMetrics
Illumina-style AT dropout metric.
atEndOfCurrentCigar() 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.
AtomicIterator T > - Interface in picard.util
Describes
atomicIteratorOf(Iterable<E>) Iterators
atomicIteratorOf(Iterator<E>) Iterators
atStartOfCurrentCigar() 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_LOCUS 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 RevertSam
attributeMap ReducibleAnnotationData
ATTRIBUTES_TO_REMOVE MergeBamAlignment
ATTRIBUTES_TO_RETAIN MergeBamAlignment
ATTRIBUTES_TO_REVERSE MergeBamAlignment
ATTRIBUTES_TO_REVERSE_COMPLEMENT MergeBamAlignment
AUTOSOMAL_REF_COPY_NUMBER_LONG_NAME PostprocessGermlineCNVCalls
AVG_INTERVAL_DP_BY_SAMPLE_KEY GATKVCFConstants
AVG_INTERVAL_DP_KEY GATKVCFConstants
awaitCompletion() VariantAccumulatorExecutor
Blocks until the work is complete.
awaitCompletion() VariantAccumulatorExecutor.MultiThreadedChunkBased
C_FOLLOWED_BY_INSERTION_BASE PileupElement
C_QUALITY_THRESHOLD CollectRrbsMetrics
C_REF_ALT_BASES CollectOxoGMetrics.CpcgMetrics
The number of alt (A/T) basecalls observed at sites where the genome reference == C.
C_REF_OXO_ERROR_RATE 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 CollectOxoGMetrics.CpcgMetrics
C_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
C_REF_REF_BASES CollectOxoGMetrics.CpcgMetrics
The number of ref basecalls observed at sites where the genome reference == C.
CACHE_LOOKAHEAD AbstractConcordanceWalker
CachingIndexedFastaSequenceFile org.broadinstitute.hellbender.utils.fasta
A caching version of the IndexedFastaSequenceFile that avoids going to disk as often as the raw indexer.
CachingIndexedFastaSequenceFile(Path, FastaSequenceIndex, long, boolean, boolean) CachingIndexedFastaSequenceFile
Same as general constructor but allows one to override the default cacheSize
CachingIndexedFastaSequenceFile(Path, long, boolean, boolean) CachingIndexedFastaSequenceFile
Open the given indexed fasta sequence file.
CachingIndexedFastaSequenceFile(Path, FastaSequenceIndex, long) CachingIndexedFastaSequenceFile
Same as general constructor but allows one to override the default cacheSize
By default, this CachingIndexedFastaReader converts all incoming bases to upper case
CachingIndexedFastaSequenceFile(Path) CachingIndexedFastaSequenceFile
Open the given indexed fasta sequence file.
CachingIndexedFastaSequenceFile(Path, boolean) CachingIndexedFastaSequenceFile
Open the given indexed fasta sequence file.
CachingIndexedFastaSequenceFile(Path, long) CachingIndexedFastaSequenceFile
Open the given indexed fasta sequence file.
calcAlignmentByteArrayOffset(Cigar, PileupElement, int, int) AlignmentUtils
calcAlignmentByteArrayOffset(Cigar, int, boolean, int, int) AlignmentUtils
Calculate the index into the read's bases of the beginning of the encompassing cigar element for a given cigar and offset
calcBAQFromHMM(GATKRead, ReferenceDataSource) BAQ
calcBAQFromHMM(byte[], byte[], byte[], int, int) BAQ
calcBAQFromHMM(GATKRead, byte[], int) BAQ
calcBAQFromTag(GATKRead, boolean, boolean) BAQ
Returns a new qual array for read that includes the BAQ adjustment.
calcBAQFromTag(GATKRead, int, boolean) BAQ
Returns the BAQ adjusted quality score for this read at this offset.
calcEfficiency() CachingIndexedFastaSequenceFile
Returns the efficiency (% of hits of all queries) of this object
calcEpsilon(byte, byte, byte) BAQ
calcFirstBaseMatchingReferenceInCigar(Cigar, int) AlignmentUtils
Get the offset (base 0) of the first reference aligned base in Cigar that occurs after readStartByBaseOfCigar base of the cigar
The main purpose of this routine is to find a good start position for a read given it's cigar.
calcGenotypeLikelihoodsOfRefVsAny(int, ReadPileup, byte, byte, MathUtils.RunningAverage) ReferenceConfidenceModel
Calculate the genotype likelihoods for the sample in pileup for being hom-ref contrasted with being ref vs.
calcMD5(String) Utils
calcMD5(byte[]) Utils
Calculate the md5 for bytes, and return the result as a 32 character string
CalcMetadataSpark org.broadinstitute.hellbender.tools.spark.sv.evidence
(Internal) Collects read metrics relevant to structural variant discovery
CalcMetadataSpark() CalcMetadataSpark
calcNumDifferentBases(Cigar, byte[], byte[]) AlignmentUtils
Get the number of bases at which refSeq and readSeq differ, given their alignment
calcNumHighQualitySoftClips(GATKRead, byte) 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
CALCULATE_TUMOR_AWARE_RESULTS CrosscheckFingerprints
calculateAllGcs(byte[], int, int) GcBiasUtils
calculateAnnotationFromGTfield(GenotypesContext) AS_StrandBiasTest
calculateAnnotationFromGTfield(GenotypesContext) FisherStrand
calculateAnnotationFromGTfield(GenotypesContext) StrandBiasTest
calculateAnnotationFromGTfield(GenotypesContext) StrandOddsRatio
calculateAnnotationFromLikelihoods(ReadLikelihoods<Allele>, VariantContext) AS_FisherStrand
calculateAnnotationFromLikelihoods(ReadLikelihoods<Allele>, VariantContext) AS_StrandOddsRatio
calculateAnnotationFromLikelihoods(ReadLikelihoods<Allele>, VariantContext) FisherStrand
calculateAnnotationFromLikelihoods(ReadLikelihoods<Allele>, VariantContext) StrandBiasTest
calculateAnnotationFromLikelihoods(ReadLikelihoods<Allele>, VariantContext) StrandOddsRatio
calculateAnnotationFromStratifiedContexts(Map<String, List<PileupElement>>, VariantContext) AS_StrandBiasTest
calculateAnnotationFromStratifiedContexts(Map<String, List<PileupElement>>, VariantContext) FisherStrand
calculateAnnotationFromStratifiedContexts(Map<String, List<PileupElement>>, VariantContext) StrandBiasTest
calculateAnnotationFromStratifiedContexts(Map<String, List<PileupElement>>, VariantContext) StrandOddsRatio
calculateArtifactPValue(int, int, double) ArtifactStatisticsScorer
p-value for being an artifact
calculateBaseDistributionByCycle(JavaRDD<GATKRead>) CollectBaseDistributionByCycleSpark
Computes the MeanQualityByCycle.
calculateBasicValidationResult(Genotype, Allele, ReadPileup, int, int, int, SimpleInterval, String) BasicSomaticShortMutationValidator
Perform basic somatic pileup validation and return a result instance.
calculateCigar(byte[], SmithWatermanAligner) Path
Calculate the cigar elements for this path against the reference sequence
calculateCigar(byte[], byte[], SmithWatermanAligner) CigarUtils
Calculate the cigar elements for this path against the reference sequence
CalculateContamination org.broadinstitute.hellbender.tools.walkers.contamination
Calculates the fraction of reads coming from cross-sample contamination, given results from
GetPileupSummaries.
CalculateContamination() CalculateContamination
calculateDerivedFields() ErrorSummaryMetrics
calculateDerivedFields() CollectWgsMetrics.WgsMetrics
calculateDerivedFields() MergeableMetricBase
placeholder method that will calculate the derived fields from the other ones.
calculateDerivedFields() IndependentReplicateMetric
calculateDerivedFields() CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
calculateDerivedFields() DuplicationMetrics
Fills in the ESTIMATED_LIBRARY_SIZE based on the paired read data examined where
possible and the PERCENT_DUPLICATION.
calculateDerivedFields() UmiMetrics
calculateDerivedFields() CollectVariantCallingMetrics.VariantCallingDetailMetrics
calculateDerivedFields() CollectVariantCallingMetrics.VariantCallingSummaryMetrics
calculateDerivedFields() MendelianViolationMetrics
calculateDerivedMetrics() DuplicationMetrics
Deprecated.
calculateDerivedStatistics() SequencingArtifactMetrics.BaitBiasDetailMetrics
Calculate the error rate given the raw counts.
calculateDerivedStatistics() SequencingArtifactMetrics.PreAdapterDetailMetrics
Calculate the error rate given the raw counts.
calculateFileMD5(File) Utils
Calculates the MD5 for the specified file and returns it as a String
Warning: this loads the whole file into memory, so it's not suitable
for large files.
calculateFractionalErrorArray(int[], byte[]) BaseRecalibrationEngine
calculateFromDerivedFields() CollectVariantCallingMetrics.VariantCallingDetailMetrics
calculateFromDerivedFields(long) CollectVariantCallingMetrics.VariantCallingSummaryMetrics
calculateGc(byte[], int, int, GcBiasUtils.CalculateGcState) GcBiasUtils
calculateGcContent(Allele, Allele, ReferenceContext, int) GencodeFuncotationFactory
Calculates the fraction of Guanine and Cytosine bases in a window of a given size around a variant.
calculateGenotypeConcordance(GenotypeConcordanceScheme, boolean) 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 org.broadinstitute.hellbender.tools.walkers.variantutils
Calculate genotype posterior probabilities given family and/or known population genotypes
CalculateGenotypePosteriors() CalculateGenotypePosteriors
calculateGenotypeQualityFromPLs(Genotype) GATKProtectedVariantContextUtils
Instead of using the GQ value, it re-calculates the quality from the PL so that it does not need
to be bounded by an artificial maximum such as the standard GQ = 99.
calculateGenotypes(VariantContext, GenotypeLikelihoodsCalculationModel, SAMFileHeader) GenotypingEngine
Completes a variant context with genotype calls and associated annotations given the genotype likelihoods and
the model that need to be applied.
calculateGenotypes(FeatureContext, ReferenceContext, AlignmentContext, Map<String, AlignmentContext>, VariantContext, GenotypeLikelihoodsCalculationModel, boolean, ReadLikelihoods<Allele>, SAMFileHeader) GenotypingEngine
Main entry function to calculate genotypes of a given VC with corresponding GL's that is shared across genotypers (namely UG and HC).
calculateGermlineProbabilities(double[], double[], double[], Optional<double[]>, double) GermlineProbabilityCalculator
calculateGLsForThisEvent(ReadLikelihoods<Allele>, VariantContext, List<Allele>) 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[]) GATKVariantContextUtils
Calculate the Genotype Quality (GQ) by subtracting the smallest Phred-scaled likelihoods (PL) from the second smallest.
calculateHighestPosteriorDensityAndDecilesSummary(List<Double>, double, JavaSparkContext) PosteriorSummaryUtils
Given a list of posterior samples, returns a PosteriorSummary with central tendency given by the posterior mode
(which is estimated using mllib kernel density estimation in
KernelDensity,
see
PosteriorSummaryUtils.calculatePosteriorMode(List, JavaSparkContext)), lower/upper credible-interval
bounds given by the (1-
alpha) highest-posterior-density interval (i.e., the narrowest interval
that contains (1-
alpha) of the samples), and deciles.
calculateHighestPosteriorDensitySummary(List<Double>, double, JavaSparkContext) PosteriorSummaryUtils
Given a list of posterior samples, returns a PosteriorSummary with central tendency given by the posterior mode
(which is estimated using mllib kernel density estimation in
KernelDensity,
see
PosteriorSummaryUtils.calculatePosteriorMode(List, JavaSparkContext)) and lower/upper credible-interval
bounds given by the (1-
alpha) highest-posterior-density interval (i.e., the narrowest interval
that contains (1-
alpha) of the samples).
calculateIC(VariantContext, Allele) AS_InbreedingCoeff
calculateIsSNPOrIndel(GATKRead, ReferenceDataSource, int[], int[], int[]) 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>) BaseRecalibrationEngine
calculateLikelihoods(AlleleList<A>, GenotypingData<A>) IndependentSampleGenotypesModel
calculateLogChainPriorProbability(List<T>) HMM
Calculates the expected log probability of the HMM chain with respect to prior state probabilities:
\log(\pi_i) \pi_i + \sum_{t=1}^{T-1} \log(T_{t, t+1}^{i, j}) \pi_i \pi_j
where \pi_i is the prior probability of state i, and T_{t, t+1}^{i, j} is the transition matrix from
position and state (t, i) to (t+1, j).
calculateMatchResults(Fingerprint, Fingerprint, double, double) FingerprintChecker
calculateMatchResults(Fingerprint, Fingerprint, double, double, boolean, boolean) 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) 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) PowerCalculationUtils
Calculate the fraction of non-ref reads in the given pileup.
calculateMeanQualityByCycle(JavaRDD<GATKRead>) MeanQualityByCycleSpark
Computes the MeanQualityByCycle.
calculateMinCountForSignal(int, double) PowerCalculationUtils
CalculateMixingFractions 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() CalculateMixingFractions
calculateMostLikelyAlleles(VariantContext, int, int) 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) 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.
calculateOneSidedU(double[], double[], MannWhitneyU.TestType) 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) Utils
Calculates the MD5 for the specified file and returns it as a String
Warning: this loads the whole file into memory, so it's not suitable
for large files.
calculatePosteriorGLs(VariantContext) FamilyLikelihoods
Computes phred-scaled genotype posteriors given the data in the given variant context and family priors given by this object.
calculatePosteriorMode(List<Double>, JavaSparkContext) PosteriorSummaryUtils
Given a list of posterior samples, returns an estimate of the posterior mode (using
mllib kernel density estimation in KernelDensity and BrentOptimizer).
calculatePosteriorProbs(VariantContext, List<VariantContext>, int, PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions) PosteriorProbabilitiesUtils
Calculates phred-scaled posterior probabilities for genotypes given the data and allele frequency priors.
calculatePosteriorProbs(List<double[]>, double[], int, boolean) PosteriorProbabilitiesUtils
Given genotype likelihoods and known allele counts, calculate the posterior probabilities
over the genotype states
calculatePower(int, int, int, int) PowerCalculationUtils
Calculate the power to validate the mutation with given alt and total counts.
calculateRank(double[], double[]) MannWhitneyU
calculateRankSum(Map<Allele, CompressedDataList<Integer>>, Allele) AS_RankSumTest
calculateRawData(VariantContext, ReadLikelihoods<Allele>, ReducibleAnnotationData) AS_RMSMappingQuality
calculateRawData(VariantContext, ReadLikelihoods<Allele>, ReducibleAnnotationData) RMSMappingQuality
CalculateReadGroupChecksum picard.sam
CalculateReadGroupChecksum() CalculateReadGroupChecksum
calculateReducedData(AlleleSpecificAnnotationData<List<Integer>>) AS_FisherStrand
calculateReducedData(Map<Allele, Histogram>, Allele) AS_RankSumTest
calculateReducedData(AlleleSpecificAnnotationData<List<Integer>>) 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>>) AS_StrandOddsRatio
calculateRefConfidence(Haplotype, Collection<Haplotype>, SimpleInterval, AssemblyRegion, ReadLikelihoods<Haplotype>, PloidyModel, List<VariantContext>) ReferenceConfidenceModel
calculateRefConfidence(Haplotype, Collection<Haplotype>, SimpleInterval, AssemblyRegion, ReadLikelihoods<Haplotype>, PloidyModel, List<VariantContext>, boolean, List<VariantContext>) 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) GcBiasUtils
calculateRoiHistogram() DuplicationMetrics
Calculates a histogram using the estimateRoi method to estimate the effective yield
doing x sequencing for x=1..10.
calculateRunningMetric(List<VariantDatum>) TrancheManager.SelectionMetric
calculateRunningMetric(List<VariantDatum>) TrancheManager.TruthSensitivityMetric
calculateSingleSampleRefVsAnyActiveStateProfileValue(double[]) GenotypingEngine
Calculates the active state profile value for a single sample.
calculateSOR(int[][]) StrandOddsRatio
Computes the SOR value of a table after augmentation.
calculateSortOrder(double[]) VariantDataManager
Get a list of indices which give the ascending sort order of the data array
calculateSuppressionFactorFromPreAdapterQ(double, double, double) ArtifactStatisticsScorer
Reduces the number of artifacts to cut based on the preAdapterQ score.
calculateSuppressionFactorFromPreAdapterQ(double) ArtifactStatisticsScorer
calculateTwoSidedU(double[], double[]) MannWhitneyU
Calculates the two-sided rank-sum test statisic U (sometimes W) from two sets of input data.
calculateU1andU2(double[], double[]) MannWhitneyU
Rank both groups together and return a TestStatistic object that includes U1, U2 and number of ties for sigma
calculateUnfilteredNonRefGenotypeCount(List<VariantContext>, String) OrientationBiasUtils
calculateVCDepth(VariantContext) ReferenceConfidenceVariantContextMerger
lookup the depth from the VC DP field or calculate by summing the depths of the genotypes
calculateWordCount(byte[]) AbstractInputParser
Calculates the number of delimiter-separated "words" in a line and sets the value of wordCount
calculateWorstPerformingAnnotation(List<VariantDatum>, GaussianMixtureModel, GaussianMixtureModel) VariantRecalibratorEngine
calculateZ(double, int, int, double, MannWhitneyU.TestType) MannWhitneyU
Calculates the Z score (i.e.
call(GATKRead) ContainsKmerReadFilterSpark
call(GATKRead) ReadFilterSparkifier
call(GATKRead) ReadTransformerSparkifier
call() Transition
call() ProcessControllerBase.OutputCapture
Runs the capture.
call() Transition
Gets the call for the transition.
CALL_SAMPLE GenotypeConcordance
CALL_SAMPLE GenotypeConcordanceContingencyMetrics
The name of the 'call' sample
CALL_SAMPLE GenotypeConcordanceDetailMetrics
The name of the 'call' sample
CALL_SAMPLE GenotypeConcordanceSummaryMetrics
The name of the 'call' sample
CALL_STATE GenotypeConcordanceDetailMetrics
The state of the 'call' sample (i.e.
CALL_VCF GenotypeConcordance
callableEvents AssemblyRegionTrimmer.Result
Holds the collection of callable events within the variant trimming region.
callableRegion AssemblyRegionTrimmer.Result
Holds variant-containing callable region.
callableSpan AssemblyRegionTrimmer.Result
Holds the smaller range that contain all relevant callable variants in the
input active region (not considering the extension).
callAllele1 GenotypeConcordance.Alleles
callAllele2 GenotypeConcordance.Alleles
callAlleles() GenotypeConcordance.Alleles
CallCopyRatioSegments org.broadinstitute.hellbender.tools.copynumber
Calls copy-ratio segments as amplified, deleted, or copy-number neutral.
CallCopyRatioSegments() CallCopyRatioSegments
CalledCopyRatioSegment org.broadinstitute.hellbender.tools.copynumber.formats.records
CalledCopyRatioSegment(CopyRatioSegment, CalledCopyRatioSegment.Call) CalledCopyRatioSegment
CalledCopyRatioSegment.Call org.broadinstitute.hellbender.tools.copynumber.formats.records
CalledCopyRatioSegmentCollection org.broadinstitute.hellbender.tools.copynumber.formats.collections
CalledCopyRatioSegmentCollection(File) CalledCopyRatioSegmentCollection
CalledCopyRatioSegmentCollection(SampleLocatableMetadata, List<CalledCopyRatioSegment>) CalledCopyRatioSegmentCollection
CalledHaplotypes(List<VariantContext>, Set<Haplotype>) AssemblyBasedCallerGenotypingEngine.CalledHaplotypes
CALLER_EXTERNAL_ADMIXING_RATE_LONG_NAME HybridADVIArgumentCollection
CALLER_INTERNAL_ADMIXING_RATE_LONG_NAME HybridADVIArgumentCollection
CALLER_UPDATE_CONVERGENCE_THRESHOLD_LONG_NAME HybridADVIArgumentCollection
callImpreciseDeletionFromEvidenceLinks(PairedStrandedIntervalTree<EvidenceTargetLink>, ReadMetadata, ReferenceMultiSource, int, int, Logger) ImpreciseVariantDetector
CALLING_COPY_RATIO_Z_SCORE_THRESHOLD_LONG_NAME CallCopyRatioSegments
CallingMetricAccumulator picard.vcf
Collects variants and generates metrics about them.
CallingMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets) CallingMetricAccumulator
CallingMetricAccumulator.Result picard.vcf
callMutations(ReadLikelihoods<Haplotype>, AssemblyResultSet, ReferenceContext, SimpleInterval, FeatureContext, List<VariantContext>, SAMFileHeader) 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(AssemblyRegion, FeatureContext) HaplotypeCallerEngine
Generate variant calls for an assembly region
callRegion(AssemblyRegion, ReferenceContext, FeatureContext) Mutect2Engine
CALLS_PATH_SUFFIX DetermineGermlineContigPloidy
CALLS_PATH_SUFFIX GermlineCNVCaller
CALLS_SHARD_PATH_LONG_NAME PostprocessGermlineCNVCalls
callsAtTruthSites Tranche
callSourceString() GenotypingEngine
What string to use as source of variant-context generated by this genotyper-engine.
callSourceString() MinimalGenotypingEngine
callSourceString() HaplotypeCallerGenotypingEngine
callSourceString() SomaticGenotypingEngine
callState GenotypeConcordanceStates.TruthAndCallStates
callVariantsWithHaplotypeCaller(JavaSparkContext, JavaRDD<GATKRead>, SAMFileHeader, ReferenceMultiSource, List<SimpleInterval>, HaplotypeCallerArgumentCollection, HaplotypeCallerSpark.ShardingArgumentCollection, VariantAnnotatorEngine) HaplotypeCallerSpark
Call Variants using HaplotypeCaller on Spark and return an RDD of VariantContext
This may be called from any spark pipeline in order to call variants from an RDD of GATKRead
callVariantsWithHaplotypeCallerAndWriteOutput(JavaSparkContext, JavaRDD<GATKRead>, SAMFileHeader, ReferenceMultiSource, List<SimpleInterval>, HaplotypeCallerArgumentCollection, HaplotypeCallerSpark.ShardingArgumentCollection, int, String, Collection<Annotation>) HaplotypeCallerSpark
Call Variants using HaplotypeCaller on Spark and write out a VCF file.
canDecode(String) AnnotatedIntervalCodec
canDecode(String) GencodeGtfCodec
canDecode(String) ProgressReportingDelegatingCodec
canDecode(String) SAMPileupCodec
canDecode(String) TableCodec
canDecode(String) XsvLocatableTableCodec
canDecodeMinusExtensionChecks(String) XsvLocatableTableCodec
Minus checking the file extension, can this class decode the given path.
canMakeInstances(Class<?>) ClassUtils
Returns true iff we can make instances of this class.
canMerge(MergeableMetricBase) 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 ReadUtils
CannotExecuteScript(String, String) UserException.CannotExecuteScript
CannotHandleGzippedRef() UserException.CannotHandleGzippedRef
canonical(int) SVKmer
canonical(int) SVKmerLong
Returns a SVKmerLong that is a canonical representation of this one.
canonical(int) SVKmerShort
Returns a SVKmerShort that is a canonical representation of this one.
canonicalizeAndMask(SVKmerShort, int, SVKmerShort) PSKmerCollection
Definition for the order of canonicalization and masking
canonicalStream(CharSequence, int, int, SVKmer) SVDUSTFilteredKmerizer
canonicalStream(byte[], int, int, SVKmer) SVDUSTFilteredKmerizer
canonicalStream(byte[], int, SVKmer) SVKmerizer
canReadFile(File...) IOUtils
Checks that one or more user provided files are in fact regular (i.e.
canSkip() RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
canSkipSAMFile(File, int, boolean, File) RevertOriginalBaseQualitiesAndAddMateCigar
Checks if we can skip the SAM/BAM file when reverting origin base qualities and adding mate cigars.
capacity() HopscotchCollection
maximum number of elements that can be held without resizing.
capacity() LargeLongHopscotchSet
capacity() LongHopscotchSet
maximum number of elements that can be held without resizing.
capBaseByBAQ(byte, byte, int, int) BAQ
CAPTURE_ASSEMBLY_FAILURE_BAM_LONG_NAME AssemblyBasedCallerArgumentCollection
captureAssemblyFailureBAM AssemblyBasedCallerArgumentCollection
CapturedStreamOutput org.broadinstitute.hellbender.utils.runtime
Stream output captured from a stream.
CapturedStreamOutput(OutputStreamSettings, InputStream, PrintStream) CapturedStreamOutput
CapturedStreamOutputSnapshot org.broadinstitute.hellbender.utils.runtime
Stream output captured from a streaming stream.
CapturedStreamOutputSnapshot(OutputStreamSettings, InputStream, PrintStream) CapturedStreamOutputSnapshot
captureStderr(Runnable) BaseTest
captures System.err while runnable is executing
captureStdout(Runnable) BaseTest
captures System.out while runnable is executing
Casava18ReadNameEncoder picard.fastq
A read name encoder conforming to the standard described by Illumina Casava 1.8.
Casava18ReadNameEncoder(String, String, String) Casava18ReadNameEncoder
CASE_SAMPLE_CALLING_PYTHON_SCRIPT GermlineCNVCaller
CATEGORY 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 CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
One of either WHOLE_GENOME or NON_ZERO_REGIONS
CbclData picard.illumina.parser
This class provides that data structure for cbcls.
CbclData(int[], int) CbclData
CbclReader 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[], boolean) CbclReader
cd BAQ
CDF(IntHistogram) IntHistogram.CDF
CHAIN LiftOverIntervalList
CHAIN LiftoverVcf
changeReads(Map<GATKRead, GATKRead>) ReadLikelihoods
changeReads(Map<GATKRead, GATKRead>) UnfilledReadsLikelihoods
ChannelAsSeekableStream org.broadinstitute.hellbender.utils.nio
A SeekableByteChannel in SeekableStream clothes.
ChannelAsSeekableStream(SeekableByteChannel) ChannelAsSeekableStream
ChannelAsSeekableStream(SeekableByteChannel, String) ChannelAsSeekableStream
charAt(int) SVKmerizer.ASCIICharSequence
CHART_OUTPUT CollectBaseDistributionByCycle
CHART_OUTPUT CollectGcBiasMetrics
CHART_OUTPUT CollectRnaSeqMetrics
CHART_OUTPUT CollectWgsMetricsWithNonZeroCoverage
CHART_OUTPUT MeanQualityByCycle
CHART_OUTPUT QualityScoreDistribution
chartOutput CollectBaseDistributionByCycleSpark
chartOutput MeanQualityByCycleSpark
chartOutput QualityScoreDistributionSpark
CHECK_FIRST_N_RECORDS FixVcfHeader
checkAndClearHeaderSequences(SAMFileHeader, PSFilterArgumentCollection, Logger) PSUtils
Returns a deep copy of the input header with an empty sequence dictionary, and logs warnings if the input may
be aligned but --isHostAligned was not set to true (or vice versa).
checkAndCreate(Path) CachingIndexedFastaSequenceFile
Create reference data source from fasta file, after performing several preliminary checks on the file.
checkAndCreate(Path, boolean) CachingIndexedFastaSequenceFile
Create reference data source from fasta file, after performing several preliminary checks on the file.
checkCigarAndConvertTerminalInsertionToSoftClip(Cigar) SvCigarUtils
Checks the input CIGAR for assumption that operator 'D' is not immediately adjacent to clipping operators.
checkCommand(String[]) ProcessSettings
checkError() GVCFWriter
CheckFingerprint 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() CheckFingerprint
checkFingerprints(List<Path>, List<Path>, String, boolean) 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) 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) Utils
Checks that the collection does not contain a duplicate value (throws an IllegalArgumentException if it does).
checkHasTrainingSet() VariantDataManager
checkHasTruthSet() VariantDataManager
checkHistograms(List<BreakpointEvidence>) KSWindowFinder
Used in production to gather evidence derived from K-S calculation on windows.
CheckIlluminaDirectory picard.illumina
Program to check a lane of an Illumina output directory.
CheckIlluminaDirectory() CheckIlluminaDirectory
checkIndexVersionAndModificationTime(File, File, Index) IndexUtils
checkMandatoryColumns(TableColumnCollection, TableColumnCollection, Function<String, RuntimeException>) TableUtils
checkNames(Object[], Function<String, RuntimeException>) TableColumnCollection
Checks that a column name, as objects, array is valid.
checkNames(String[], Function<String, RuntimeException>) TableColumnCollection
Checks that a column name array is valid.
checkOutOfBounds(int) 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.
checkOutputSpecs(JobContext) ReadsSparkSink.SparkBAMOutputFormat
checkOutputSpecs(JobContext) ReadsSparkSink.SparkCRAMOutputFormat
checkOutputSpecs(JobContext) ReadsSparkSink.SparkSAMOutputFormat
checkOutputSpecs(JobContext) VariantsSparkSink.SparkVCFOutputFormat
CheckPileup org.broadinstitute.hellbender.tools.walkers.qc
Compare GATK's internal pileup to a reference Samtools pileup
CheckPileup() CheckPileup
checkPythonEnvironmentForPackage(String) PythonScriptExecutor
checkSettings(InputStreamSettings) ProcessSettings
checkSettings(OutputStreamSettings) ProcessSettings
checkStructure() PSTree
Because of the piecemeal way we allow the tree to be constructed, we can end up with invalid tree structures.
CheckTerminatorBlock picard.sam
Simple class to check the terminator block of a SAM file.
CheckTerminatorBlock() CheckTerminatorBlock
checkTileCount() ParameterizedFileUtil
checkTileCount() PerTileOrPerRunFileUtil
checkVariationClass(VariantContext, VariantContext) VariantDataManager
checkVariationClass(VariantContext, VariantRecalibratorArgumentCollection.Mode) VariantDataManager
checkVariationClass(VariantContext, Allele, VariantRecalibratorArgumentCollection.Mode) VariantDataManager
CHIMERA_KB_MIN CollectJumpingLibraryMetrics
ChimeraUtil picard.analysis
ChimeraUtil() ChimeraUtil
CHIMERIC_ALIGNMENTS_HIGHMQ_THRESHOLD StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection
CHIMERIC_PAIRS 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.
chooseAlleleForRead(PileupElement, Allele, List<Allele>, int) GATKProtectedVariantContextUtils
Given a set of alleles (reference and alternate), choose the allele that is the best match for the given read (and offset)
CHR10_B36 SequenceDictionaryUtils
CHR10_B37 SequenceDictionaryUtils
CHR10_HG18 SequenceDictionaryUtils
CHR10_HG19 SequenceDictionaryUtils
CHR1_B36 SequenceDictionaryUtils
CHR1_B37 SequenceDictionaryUtils
CHR1_HG18 SequenceDictionaryUtils
CHR1_HG19 SequenceDictionaryUtils
CHR2_B36 SequenceDictionaryUtils
CHR2_B37 SequenceDictionaryUtils
CHR2_HG18 SequenceDictionaryUtils
CHR2_HG19 SequenceDictionaryUtils
CHROM FingerprintingDetailMetrics
The chromosome on which the SNP resides.
ChromosomeCounts org.broadinstitute.hellbender.tools.walkers.annotator
Counts and frequency of alleles in called genotypes
ChromosomeCounts() ChromosomeCounts
CHUNK_INDEX_PATH_SUFFIX HDF5Utils
CIEND GATKSVVCFConstants
CIGAR_CONTAINS_NO_N_OPERATOR ReadFilterLibrary
cigarAlong5to3DirectionOfContig AlignmentInterval
cigarAlongReference() AlignmentInterval
Returns the cigar of this alignment interval along the reference.
CigarContainsNoNOperator() ReadFilterLibrary.CigarContainsNoNOperator
cigarHasZeroSizeElement(Cigar) AlignmentUtils
Does one of the elements in cigar have a 0 length?
CigarUtils org.broadinstitute.hellbender.utils.read
CIPOS GATKSVVCFConstants
CircularByteBuffer 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) CircularByteBuffer
Constructs a buffer capable of holding the given number of bytes.
CLASS_COHERENCE_LENGTH_LONG_NAME GermlineCallingArgumentCollection
ClassFinder picard.cmdline
Utility class that can scan for classes in the classpath and find all the ones
annotated with a particular annotation.
ClassFinder() ClassFinder
ClassFinder(ClassLoader) ClassFinder
ClassFinder(File) ClassFinder
CLASSIFICATION 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) GenotypeConcordance
classifyVariants(Optional<VariantContext>, String, Optional<VariantContext>, String, Optional<GenotypeConcordanceCounts>, Optional<GenotypeConcordanceCounts>, int, int, boolean) 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 org.broadinstitute.hellbender.utils
Utilities for dealing with reflection.
cleanerMaxCopyNumber StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
cleanerMaxIntervals StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
cleanerMinKmerCount StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
cleanNonRefPaths() 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
CleanSam picard.sam
CleanSam() CleanSam
CleanSamTester org.broadinstitute.hellbender.utils.test.testers
This class is the extension of the SamFileTester to test CleanSam with SAM files generated on the fly.
CleanSamTester(String, int, int) CleanSamTester
cleanUpCigar(Cigar) AlignmentUtils
Clean up the incoming cigar
Removes elements with zero size
Clips away beginning deletion operators
cleanUpSymbolicUnassembledEvents(List<Haplotype>) HaplotypeCallerGenotypingEngine
Removes symbolic events from list of haplotypes
clear() SVIntervalTree
Remove all entries.
clear() HopscotchCollection
clear() IntHistogram
clear() LongBloomFilter
clear() LongHopscotchSet
clear() KMerCounter
Remove all current counts, resetting the counter to an empty state
clear() CountSet
clear() IndexedSet
Removes all elements in the set.
clear() Nucleotide.Counter
Reset all the counts to 0.
clear() SATagBuilder
Clears all SA tag units from the SATagBuilder as they exist.
clear() CounterManager
Clears all inner Counter arrays
clear() CbclReader
CLEAR_DT MarkDuplicates
clearAttribute(String) GATKRead
Clear an individual attribute on the read.
clearAttribute(String) SAMRecordToGATKReadAdapter
clearAttributes() GATKRead
Clear all attributes on the read.
clearAttributes() SAMRecordToGATKReadAdapter
clearItems() Downsampler
Empty the downsampler of all finalized/pending items
clearItems() FractionalDownsampler
clearItems() LevelingDownsampler
clearItems() MutectDownsampler
clearItems() PassThroughDownsampler
clearItems() PositionalDownsampler
clearItems() ReservoirDownsampler
Clear the data structures used to hold information
clearReads() AssemblyRegion
Clear all of the reads currently in this region
CLIP_ADAPTERS BamToBfq
CLIP_ADAPTERS MergeBamAlignment
CLIP_OVERLAPPING_READS CollectTargetedMetrics
CLIP_OVERLAPPING_READS MergeBamAlignment
CLIP_REPRESENTATION_LONG_NAME ClipReads
CLIP_REPRESENTATION_SHORT_NAME ClipReads
CLIP_SEQUENCE_LONG_NAME ClipReads
CLIP_SEQUENCE_SHORT_NAME ClipReads
CLIP_SEQUENCES_FILE_LONG_NAME ClipReads
CLIP_SEQUENCES_FILE_SHORT_NAME ClipReads
clipAlignmentInterval(AlignmentInterval, int, boolean) ContigAlignmentsModifier
Given
clipLengthOnRead to be clipped from an aligned contig's
AlignmentIntervalinput,
return a modified
AlignmentInterval with the requested number of bases clipped away and ref span recomputed.
clipByReferenceCoordinates(int, int, ClippingRepresentation, boolean) ReadClipper
Generic functionality to clip a read, used internally by hardClipByReferenceCoordinatesLeftTail
and hardClipByReferenceCoordinatesRightTail.
clipForOverlappingReads(SAMRecord, SAMRecord) AbstractAlignmentMerger
Checks to see whether the ends of the reads overlap and soft clips reads
them if necessary.
clipForOverlappingReads(SAMRecord, SAMRecord) AbstractAlignmentMerger
Checks to see whether the ends of the reads overlap and soft clips reads
them if necessary.
clipLowQualEnds(GATKRead, byte, ClippingRepresentation) ReadClipper
CLIPPING_ACTION SamToFastq
CLIPPING_ATTRIBUTE SamToFastq
CLIPPING_GOAL_NOT_REACHED ReadUtils
CLIPPING_MIN_LENGTH SamToFastq
CLIPPING_RANK_SUM_KEY GATKVCFConstants
ClippingData(List<ClipReads.SeqToClip>) ClipReads.ClippingData
ClippingOp org.broadinstitute.hellbender.utils.clipping
Represents a clip on a read.
ClippingOp(int, int) ClippingOp
ClippingRankSumTest org.broadinstitute.hellbender.tools.walkers.annotator
Rank Sum Test for hard-clipped bases on REF versus ALT reads
ClippingRankSumTest() ClippingRankSumTest
ClippingRepresentation org.broadinstitute.hellbender.utils.clipping
How should we represent a clipped bases in a read?
ClippingUtility picard.util
Utilities to clip the adapter sequence from a SAMRecord read
ClippingUtility() ClippingUtility
clipRead(ClippingRepresentation) ReadClipper
Clips a read according to ops and the chosen algorithm.
ClipReads org.broadinstitute.hellbender.tools
Read clipping based on quality, position or sequence matching.
ClipReads() ClipReads
ClipReads.ClippingData org.broadinstitute.hellbender.tools
ClipReads.ReadClipperWithData org.broadinstitute.hellbender.tools
ClocsFileFaker picard.illumina.parser.fakers
ClocsFileFaker() ClocsFileFaker
ClocsFileReader 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) ClocsFileReader
clone() SAMRecordSparkCodec
clone() BaseGraph
clone() SeqGraph
clone() ReadThreadingGraph
clone() TestingReadThreadingGraph
clone() MathUtils.RunningAverage
clone() ReadEndsForMarkDuplicatesCodec
For an explanation of why codecs must implement clone(),
see the HTSJDK documentation for SortingCollection.Codec.
clone() ReadEndsForMarkDuplicates
clone() ReadEndsForMarkDuplicatesCodec
clone() ReadEndsForMarkDuplicatesWithBarcodes
clone() ReadEndsForMarkDuplicatesWithBarcodesCodec
clone() RepresentativeReadIndexerCodec
cloneSAMFileHeader(SAMFileHeader) ReadUtils
HACK: This is used to make a copy of a header.
cloneSAMRecord(SAMRecord) ReadUtils
HACK: This is used to make a copy of a read.
close() FeatureDataSource
Permanently close this data source, invalidating any open iteration over it, and making it invalid for future
iterations and queries.
close() FeatureManager
Permanently closes this manager by closing all backing data sources
close() MultiVariantDataSource
Permanently close this data source, invalidating any open iteration over it, and making it invalid for future
iterations and queries.
close() ReadsDataSource
Shut down this data source permanently, closing all iterations and readers.
close() ReferenceDataSource
Permanently close this data source.
close() ReferenceFileSource
Permanently close this data source
close() ReferenceMemorySource
no-op (nothing's open)
close() AnnotatedIntervalWriter
attempt to close the file
close() SimpleAnnotatedIntervalWriter
attempt to close the file
close() DataSourceFuncotationFactory
close() CosmicFuncotationFactory
close() GencodeFuncotationFactory
close() MafOutputRenderer
close() OutputRenderer
close() VcfOutputRenderer
close() HaplotypeCallerSpark.ReferenceMultiSourceAdapter
close() BwaSparkEngine
close() PSFilterEmptyLogger
close() PSFilterFileLogger
close() PSFilterLogger
close() PSScoreFileLogger
close() PSScoreLogger
close() PSBwaAlignerSpark
close() PSFilter
After doFilter(), this should be run after a Spark action (e.g.
close() PSPairedUnpairedSplitterSpark
Call only after Spark is done with all closures involving the paired/unpaired RDDs,
i.e.
close() SingleSequenceReferenceAligner
close() PairHMMLikelihoodCalculationEngine
close() RandomLikelihoodCalculationEngine
close() ReadLikelihoodCalculationEngine
This method must be called when the client is done with likelihood calculations.
close(LineIterator) GencodeGtfCodec
close() LineIteratorReader
close(B) ProgressReportingDelegatingCodec
close() HaplotypeBAMWriter
Close any output resource associated with this writer.
close() SamReaderQueryingIterator
close() ChannelAsSeekableStream
close() PathLineIterator
close() SeekableByteChannelPrefetcher
Closes this channel.
close() PairHMM
Called at the end of the program to close files, print profiling information etc
close() VectorLoglessPairHMM
close() ArtificialReadIterator
close() AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
close() AbstractAlignmentMerger
close() MultiHitAlignedReadIterator
close() SAMFileGATKReadWriter
close() FastaReferenceWriter
Closes this writer flushing all remaining writing operation input the output resources.
close() SmithWatermanAligner
Implementations may optionally implement close in order to release any resources that they are holding.
close() SmithWatermanIntelAligner
Close the aligner
close() SmithWatermanJavaAligner
close() SWNativeAlignerWrapper
Report total compute time and close aligner
close() XorWrapper
close() XReadLines
close() TableReader
close() TableWriter
close() GVCFWriter
Close this GVCF writer.
close() BaseIlluminaDataProvider
close() IlluminaDataProvider
close() MultiTileFilterParser
close() MultiTileLocsParser
close() NewIlluminaDataProvider
close() PerTileParser
close() BarcodeFileReader
close() BclReader
close() CbclReader
close() ClocsFileReader
close() LocsFileReader
close() PosFileReader
close() AbstractAlignmentMerger
close() MarkDuplicatesWithMateCigarIterator
close() AbstractInputParser
Closes this stream and releases any system resources associated with it.
close() AsyncIterator
Stops the thread and then calls synchronouslyClose() to allow implementation to do any one time clean up.
close() BasicInputParser
Closes the underlying stream
close() CircularByteBuffer
Signals that the buffer is closed and no further writes will occur.
close() DelimitedTextFileWithHeaderIterator
close() TabbedTextFileWithHeaderParser
Release all resources associated with the parser.
close() FilterApplyingVariantIterator
close() PredicateFilterDecoratingClosableIterator
close() VariantIteratorProducer
closeAllDistributedInstances(JavaSparkContext) ContainsKmerReadFilterSpark
Closes kmer library on all executors
closeAllDistributedInstances(JavaSparkContext) BwaMemIndexCache
Closes all instances in all the VMs involved in the spark context provided.
closeInstance(String) BwaMemIndexCache
Closes an index instance in the cache given its index file name.
closeInstance(BwaMemIndex) BwaMemIndexCache
Closes an index instance.
closeInstances() BwaMemIndexCache
Closes all instances in the VM.
closeKmerLib() ContainsKmerReadFilter
closeTool() GATKTool
This method is called by the GATK framework at the end of the
GATKTool.doWork() template method.
closeTool() AnnotatePairOrientation
closeTool() ClipReads
closeTool() ExampleAssemblyRegionWalker
closeTool() ExampleFeatureWalker
closeTool() ExampleIntervalWalker
closeTool() ExampleLocusWalker
closeTool() ExamplePostTraversalPythonExecutor
closeTool() ExampleReadWalkerWithReference
closeTool() ExampleReadWalkerWithVariants
closeTool() ExampleStreamingPythonExecutor
closeTool() ExampleTwoPassVariantWalker
closeTool() ExampleVariantWalker
closeTool() FilterByOrientationBias
closeTool() FixCallSetSampleOrdering
closeTool() FixMisencodedBaseQualityReads
closeTool() Funcotator
closeTool() LeftAlignIndels
closeTool() PrintReads
closeTool() SplitReads
closeTool() VariantAnnotator
Make sure that the writer is closed upon completing the tool.
closeTool() ApplyBQSR
closeTool() CombineGVCFs
closeTool() VariantFiltration
closeTool() GenotypeGVCFs
closeTool() HaplotypeCaller
closeTool() FilterMutectCalls
closeTool() Mutect2
closeTool() CheckPileup
closeTool() Pileup
closeTool() FilterAlignmentArtifacts
closeTool() RevertBaseQualityScores
closeTool() ASEReadCounter
closeTool() SplitNCigarReads
closeTool() UnmarkDuplicates
closeTool() AnnotateVcfWithBamDepth
closeTool() AnnotateVcfWithExpectedAlleleFraction
closeTool() RemoveNearbyIndels
closeTool() CalculateGenotypePosteriors
closeTool() SelectVariants
Close out the new variants file.
closeTool() UpdateVCFSequenceDictionary
Close out the new variants file.
closeTool() ApplyVQSR
closeTool() VariantRecalibrator
closeWriter() FixMateInformation
CLOUD_INDEX_PREFETCH_BUFFER_LONG_NAME StandardArgumentDefinitions
CLOUD_INDEX_PREFETCH_BUFFER_SHORT_NAME StandardArgumentDefinitions
CLOUD_PREFETCH_BUFFER_LONG_NAME StandardArgumentDefinitions
CLOUD_PREFETCH_BUFFER_SHORT_NAME StandardArgumentDefinitions
cloudIndexPrefetchBuffer GATKTool
cloudIndexPrefetchBuffer() GATKConfig
cloudPrefetchBuffer GATKTool
cloudPrefetchBuffer GatherVcfsCloud
cloudPrefetchBuffer() GATKConfig
cluster(Iterator<BreakpointEvidence>) EvidenceTargetLinkClusterer
CLUSTER ClusteredCrosscheckMetric
cluster() GraphUtils.Graph
returns the cluster map of connected components
CLUSTER_DENSITY IlluminaLaneMetrics
The number of clusters per unit area on the this lane expressed in units of [cluster / mm^2].
CLUSTER_SIZE ClusteredCrosscheckMetric
The number of different groups that are assigned to this cluster.
CLUSTER_SIZE_LONG_NAME VariantFiltration
CLUSTER_WINDOW_SIZE_LONG_NAME VariantFiltration
ClusterCrosscheckMetrics picard.fingerprint
Summary
ClusterCrosscheckMetrics() ClusterCrosscheckMetrics
ClusterData picard.illumina.parser
Store the information from Illumina files for a single cluster with one or more reads.
ClusterData(ReadData...) ClusterData
Used for testing, reads is set directly with no copying to the input array
ClusterData(ReadType[]) ClusterData
Creates a ClusterData with one read for each type provided
ClusterDataToSamConverter picard.illumina
Takes ClusterData provided by an IlluminaDataProvider into one or two SAMRecords,
as appropriate, and optionally marking adapter sequence.
ClusterDataToSamConverter(String, String, ReadStructure, List<AdapterPair>) ClusterDataToSamConverter
Constructor
CLUSTERED_EVENTS_FILTER_NAME GATKVCFConstants
CLUSTERED_SNP_FILTER_NAME VariantFiltration
ClusteredCrosscheckMetric picard.fingerprint
ClusteredCrosscheckMetric() ClusteredCrosscheckMetric
ClusteredCrosscheckMetric(CrosscheckMetric) ClusteredCrosscheckMetric
clusterSize VariantFiltration
Works together with the --cluster-window-size argument.
clusterWindow VariantFiltration
Works together with the --cluster-size argument.
CNN_1D_KEY GATKVCFConstants
CNN_2D_KEY GATKVCFConstants
CNNScoreVariants org.broadinstitute.hellbender.tools.walkers.vqsr
Annotate a VCF with scores from a Convolutional Neural Network (CNN).
CNNScoreVariants() CNNScoreVariants
CNNVariantTrain org.broadinstitute.hellbender.tools.walkers.vqsr
Train a Convolutional Neural Network (CNN) for filtering variants.
CNNVariantTrain() CNNVariantTrain
CNNVariantWriteTensors org.broadinstitute.hellbender.tools.walkers.vqsr
Write variant tensors for training a Convolutional Neural Network (CNN) for filtering variants.
CNNVariantWriteTensors() CNNVariantWriteTensors
CNV_COHERENCE_LENGTH_LONG_NAME GermlineCallingArgumentCollection
cnvCallsFile StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection
CNVInputReader org.broadinstitute.hellbender.tools.spark.sv.utils
CNVInputReader() CNVInputReader
code() MarkDuplicates.DuplicateType
codec_packages() GATKConfig
CODING_BASES RnaSeqMetrics
Number of bases in primary alignments that align to a non-UTR coding base for some gene, and not ribosomal sequence.
codingEnd Gene.Transcript
codingStart Gene.Transcript
COHORT_DENOISING_CALLING_PYTHON_SCRIPT GermlineCNVCaller
CollectAlignmentRefArgCollection() CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
CollectAlignmentSummaryMetrics picard.analysis
A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment.
CollectAlignmentSummaryMetrics() CollectAlignmentSummaryMetrics
CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection picard.analysis
CollectAllelicCounts org.broadinstitute.hellbender.tools.copynumber
Collects reference and alternate allele counts at specified sites.
CollectAllelicCounts() CollectAllelicCounts
collectAtLocus(Nucleotide, ReadPileup, Locatable, int) AllelicCountCollector
Add counts to this class for a specific locus.
CollectBaseDistributionByCycle picard.analysis
CollectBaseDistributionByCycle() CollectBaseDistributionByCycle
CollectBaseDistributionByCycleSpark org.broadinstitute.hellbender.tools.spark.pipelines.metrics
Collects base distribution per cycle in SAM/BAM/CRAM file(s).
CollectBaseDistributionByCycleSpark() CollectBaseDistributionByCycleSpark
CollectGcBiasMetrics picard.analysis
Tool to collect information about GC bias in the reads in a given BAM file.
CollectGcBiasMetrics() CollectGcBiasMetrics
CollectHiSeqXPfFailMetrics picard.illumina.quality
Collect metrics regarding the reason for reads (sequenced by HiSeqX) not passing the Illumina PF Filter.
CollectHiSeqXPfFailMetrics() CollectHiSeqXPfFailMetrics
CollectHiSeqXPfFailMetrics.PFFailDetailedMetric picard.illumina.quality
a metric class for describing FP failing reads from an Illumina HiSeqX lane *
CollectHiSeqXPfFailMetrics.PFFailSummaryMetric picard.illumina.quality
Metrics produced by the GetHiSeqXPFFailMetrics program.
CollectHiSeqXPfFailMetrics.ReadClassifier picard.illumina.quality
CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason picard.illumina.quality
CollectHsMetrics 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() CollectHsMetrics
CollectIlluminaBasecallingMetrics 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() CollectIlluminaBasecallingMetrics
CollectIlluminaLaneMetrics picard.illumina
CollectIlluminaLaneMetrics() CollectIlluminaLaneMetrics
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector picard.illumina
Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
CollectIndependentReplicateMetrics 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() CollectIndependentReplicateMetrics
CollectInsertSizeMetrics picard.analysis
Command line program to read non-duplicate insert sizes, create a Histogram
and report distribution statistics.
CollectInsertSizeMetrics() CollectInsertSizeMetrics
CollectInsertSizeMetricsSpark org.broadinstitute.hellbender.tools.spark.pipelines.metrics
Collects insert size distribution information in alignment data.
CollectInsertSizeMetricsSpark() CollectInsertSizeMetricsSpark
CollectJumpingLibraryMetrics picard.analysis
Command-line program to compute metrics about outward-facing pairs, inward-facing
pairs, and chimeras in a jumping library.
CollectJumpingLibraryMetrics() CollectJumpingLibraryMetrics
collectLaneMetrics(File, File, String, MetricsFile<MetricBase, Comparable<?>>, MetricsFile<MetricBase, Comparable<?>>, ReadStructure, String, ValidationStringency, boolean) CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files
collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) ExampleCollectMultiMetricsSpark
Execute the actual metrics collection.
collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) ExampleMultiMetricsCollectorSpark
Do he actual Metrics collection.
collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) ExampleCollectSingleMetricsSpark
Execute the actual metrics collection.
collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) ExampleSingleMetricsCollectorSpark
Do the actual metrics collection on the provided RDD.
collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) CollectInsertSizeMetricsSpark
collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) CollectQualityYieldMetricsSpark
collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) InsertSizeMetricsCollectorSpark
collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) MetricsCollectorSpark
Do the actual metrics collection on the provided RDD.
collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) MetricsCollectorSparkTool
collectMetrics(JavaRDD<GATKRead>, SAMFileHeader) QualityYieldMetricsCollectorSpark
Do the actual metrics collection on the provided RDD.
CollectMultipleMetrics 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() CollectMultipleMetrics
CollectMultipleMetrics.Program picard.analysis
CollectMultipleMetrics.ProgramInterface picard.analysis
CollectMultipleMetricsSpark org.broadinstitute.hellbender.tools.spark.pipelines.metrics
Runs multiple metrics collection modules for a given alignment file.
CollectMultipleMetricsSpark() CollectMultipleMetricsSpark
CollectMultipleMetricsSpark.SparkCollectorProvider org.broadinstitute.hellbender.tools.spark.pipelines.metrics
CollectMultipleMetricsSpark.SparkCollectors org.broadinstitute.hellbender.tools.spark.pipelines.metrics
CollectOxoGMetrics picard.analysis
Class for trying to quantify the CpCG->CpCA error rate.
CollectOxoGMetrics() CollectOxoGMetrics
CollectOxoGMetrics.CpcgMetrics picard.analysis
Metrics class for outputs.
CollectQualityYieldMetrics picard.analysis
Command line program to calibrate quality yield metrics
CollectQualityYieldMetrics() CollectQualityYieldMetrics
CollectQualityYieldMetrics.QualityYieldMetrics picard.analysis
A set of metrics used to describe the general quality of a BAM file
CollectQualityYieldMetrics.QualityYieldMetricsCollector picard.analysis
CollectQualityYieldMetricsSpark org.broadinstitute.hellbender.tools.spark.pipelines.metrics
Collects quality yield metrics in SAM/BAM/CRAM file(s).
CollectQualityYieldMetricsSpark() CollectQualityYieldMetricsSpark
CollectRawWgsMetrics 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() CollectRawWgsMetrics
CollectRawWgsMetrics.RawWgsMetrics picard.analysis
CollectReadCounts org.broadinstitute.hellbender.tools.copynumber
Collects read counts at specified intervals.
CollectReadCounts() CollectReadCounts
CollectRnaSeqMetrics picard.analysis
CollectRnaSeqMetrics() CollectRnaSeqMetrics
CollectRrbsMetrics 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() CollectRrbsMetrics
CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection picard.analysis
CollectRrbsMetricsReferenceArgumentCollection() CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
CollectSequencingArtifactMetrics picard.analysis.artifacts
Quantify substitution errors caused by mismatched base pairings during various
stages of sample / library prep.
CollectSequencingArtifactMetrics() CollectSequencingArtifactMetrics
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() CollectTargetedMetrics
CollectTargetedPcrMetrics picard.analysis.directed
This tool calculates a set of PCR-related metrics from an aligned SAM or
BAM file containing targeted sequencing data.
CollectTargetedPcrMetrics() CollectTargetedPcrMetrics
CollectVariantCallingMetrics picard.vcf
Collects summary and per-sample metrics about variant calls in a VCF file.
CollectVariantCallingMetrics() CollectVariantCallingMetrics
CollectVariantCallingMetrics.VariantCallingDetailMetrics picard.vcf
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
CollectVariantCallingMetrics.VariantCallingSummaryMetrics picard.vcf
A collection of metrics relating to snps and indels within a variant-calling file (VCF).
CollectWgsMetrics picard.analysis
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
CollectWgsMetrics() CollectWgsMetrics
CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection picard.analysis
CollectWgsMetrics.WgsMetrics picard.analysis
Metrics for evaluating the performance of whole genome sequencing experiments.
CollectWgsMetrics.WgsMetricsCollector picard.analysis
CollectWgsMetricsIntervalArgumentCollection() CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
CollectWgsMetricsWithNonZeroCoverage picard.analysis
CollectWgsMetricsWithNonZeroCoverage() CollectWgsMetricsWithNonZeroCoverage
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage picard.analysis
Metrics for evaluating the performance of whole genome sequencing experiments.
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category picard.analysis
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector picard.analysis
COLOR_STATUS CommandLineDefaults
Implementation note, this is duplicate code stolen from HTSJDK's Default.java
/**
Decides if we want to write colors to the terminal.
COLUMN_SEPARATOR TableUtils
Column separator .
COLUMN_SEPARATOR_STRING TableUtils
Column separator as an string.
columnCount() TableFeature
Gets the number of columns in the feature.
columnCount() TableColumnCollection
Returns the number of columns.
columnLabels() DelimitedTextFileWithHeaderIterator
columnLabels() TabbedTextFileWithHeaderParser
columnLabelsList() TabbedTextFileWithHeaderParser
columnMeans(RealMatrix) MathUtils
Calculates the mean per column from a matrix.
COLUMNS OrientationBiasFilterSummaryTableColumn
COLUMNS ParameterTableColumn
columns() DataLine
Returns the column collection for this data-line instance.
columns() TableReader
Returns the column collection for this reader.
COLUMNS_OF_INTEREST_LONG_NAME CombineSegmentBreakpoints
columnStdDevs(RealMatrix) MathUtils
Calculates the standard deviation per column from a matrix.
columnSums(RealMatrix) MathUtils
Return an array with column sums in each entry
combine(InsertSizeMetricsCollector, InsertSizeMetricsCollector) InsertSizeMetricsCollector
Combine two InsertSizeMetricsCollector objects and return a single InsertSizeMetricsCollector
object representing the combined results.
combine(MultiLevelReducibleCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE, UNIT_COLLECTOR>) MultiLevelReducibleCollector
Combine a source MultiLevelReducibleCollector object into this MultiLevelReducibleCollector.
combine(PerUnitInsertSizeMetricsCollector) PerUnitInsertSizeMetricsCollector
Combine this PerUnitInsertSizeMetricsCollector with sourceCollector and return a combined
PerUnitInsertSizeMetricsCollector.
combine(QualityYieldMetrics) QualityYieldMetrics
combine(ExampleMultiMetrics) ExampleMultiMetrics
Combines two ExampleMultiMetrics objects
combine(ExampleMultiMetricsCollector, ExampleMultiMetricsCollector) ExampleMultiMetricsCollector
Combine two ExampleMultiMetricsCollector objects and return a single ExampleMultiMetricsCollector
object representing the combined results.
combine(PerUnitExampleMultiMetricsCollector) PerUnitExampleMultiMetricsCollector
Combine this PerUnitExampleMultiMetricsCollector with sourceCollector and return a combined
PerUnitExampleMultiMetricsCollector.
combine(ExampleSingleMetrics) ExampleSingleMetrics
combine(RecalDatum) 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) 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) RecalibrationTables
Merge all of the tables from toMerge into into this set of tables
combineAdjacentCigarElements(Cigar) CigarUtils
Combines equal adjacent elements of a Cigar object
combineAndSortBreakpoints(List<T>, List<T>, SAMSequenceDictionary) IntervalUtils
Combine the breakpoints of multiple intervals and return a list of locatables based on the updated breakpoints.
combineAnnotations(List<Allele>, Map<String, List<?>>) VariantAnnotatorEngine
Combine (raw) data for reducible annotations (those that use raw data in gVCFs)
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<Histogram>, ReducibleAnnotationData<Histogram>) AS_RankSumTest
combineAttributeMap(ReducibleAnnotationData<Double>, ReducibleAnnotationData<Double>) AS_RMSMappingQuality
combineAttributeMap(ReducibleAnnotationData<List<Integer>>, ReducibleAnnotationData<List<Integer>>) AS_StrandBiasTest
combineAttributeMap(ReducibleAnnotationData<Double>, ReducibleAnnotationData<Double>) RMSMappingQuality
CombineGVCFs org.broadinstitute.hellbender.tools.walkers
Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file
CombineGVCFs() CombineGVCFs
combineRawData(List<Allele>, List<ReducibleAnnotationData<?>>) AS_QualByDepth
Note there is no raw annotation data for AS_QualByDepth and thus data cannot be combined
combineRawData(List<Allele>, List<ReducibleAnnotationData<?>>) 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<?>>) 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<?>>) 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<?>>) 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<?>>) RMSMappingQuality
CombineSegmentBreakpoints org.broadinstitute.hellbender.tools.copynumber.utils
CombineSegmentBreakpoints() CombineSegmentBreakpoints
combineTables(NestedIntegerArray<RecalDatum>, NestedIntegerArray<RecalDatum>) RecalUtils
Combines the recalibration data for table1 and table2 into table1
Note that table1 is the destination, so it is modified
combineUnit(PerUnitInsertSizeMetricsCollector, PerUnitInsertSizeMetricsCollector) InsertSizeMetricsCollector
Combine two PerUnitInsertSizeMetricsCollector objects and return a single PerUnitInsertSizeMetricsCollector
object representing the combined results.
combineUnit(UNIT_COLLECTOR, UNIT_COLLECTOR) MultiLevelReducibleCollector
Combined two UNIT_COLLECTOR objects into a single object representing the combined collectors.
combineUnit(PerUnitExampleMultiMetricsCollector, PerUnitExampleMultiMetricsCollector) ExampleMultiMetricsCollector
Combine two PerUnitExampleMultiMetricsCollector objects and return a single PerUnitExampleMultiMetricsCollector
object representing the combined results.
combiningResultsBy(VariantProcessor.ResultMerger<R>) VariantProcessor.Builder
CommandLineDefaults picard.cmdline
Embodies defaults for global values that affect how the Picard Command Line operates.
CommandLineDefaults() CommandLineDefaults
CommandLineProgram org.broadinstitute.hellbender.cmdline
Abstract class to facilitate writing command-line programs.
CommandLineProgram() CommandLineProgram
CommandLineProgram picard.cmdline
Abstract class to facilitate writing command-line programs.
CommandLineProgram() CommandLineProgram
CommandLineProgramTester org.broadinstitute.hellbender.utils.test
Utility interface for CommandLine Program testing.
CommandLineSyntaxTranslater 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() CommandLineSyntaxTranslater
COMMENT AbstractMarkDuplicatesCommandLineProgram
COMMENT AddCommentsToBam
COMMENT FastqToSam
COMMENT AbstractMarkDuplicatesCommandLineProgram
COMMENT MergeSamFiles
COMMENT IntervalListTools
COMMENT_DELIMITER TableCodec
COMMENT_PREFIX TableUtils
Comment line prefix string "#".
COMMENT_START ReadGroupBlackListReadFilter
COMMENT_STRING Tranche
commonMaximumPrefixLength(List<byte[]>) GraphUtils
Compute the maximum shared prefix length of list of bytes.
commonMaximumSuffixLength(List<byte[]>, int) GraphUtils
Compute the maximum shared suffix length of list of bytes.
CommonSuffixSplitter 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() GATKRead
A human-digestable representation of the read.
compactifyNeighboringSoftClippings(List<CigarElement>) SvCigarUtils
Compactify two neighboring soft clippings, one of which was converted from an insertion operation.
compare(PairedEnds, PairedEnds) MarkDuplicatesSparkUtils.PairedEndsCoordinateComparator
compare(T, T) Tranche.TrancheComparator
compare(TruthSensitivityTranche, TruthSensitivityTranche) Tranche.TrancheTruthSensitivityComparator
compare(SAMRecord, SAMRecord) HeaderlessSAMRecordCoordinateComparator
compare(GATKRead, GATKRead) ReadCoordinateComparator
compare(GATKRead, GATKRead) ReadQueryNameComparator
compare(int, int) MathUtil
COMPARE_STRINGS_NULLS_FIRST Utils
Comparator for strings that sorts null first;
CompareBaseQualities org.broadinstitute.hellbender.tools.validation
Compares the base qualities of two SAM/BAM/CRAM files.
CompareBaseQualities() CompareBaseQualities
compareContigs(GenomeLoc) GenomeLoc
conpare this genomeLoc's contig to another genome loc
compareContigs(Locatable, Locatable, SAMSequenceDictionary) IntervalUtils
Determines the relative contig ordering of first and second using the provided sequence dictionary
compareCoordinates(PairedEnds, PairedEnds) MarkDuplicatesSparkUtils.PairedEndsCoordinateComparator
compareCoordinates(GATKRead, GATKRead, SAMFileHeader) ReadCoordinateComparator
compareDictionaries(SAMSequenceDictionary, SAMSequenceDictionary, boolean) SequenceDictionaryUtils
Workhorse routine that takes two dictionaries and returns their compatibility.
compareDoubles(double, double) MathUtils
Compares double values for equality (within 1e-6), or inequality.
compareDoubles(double, double, double) MathUtils
Compares double values for equality (within epsilon), or inequality.
CompareDuplicatesSpark org.broadinstitute.hellbender.tools.spark.validation
Determine if two potentially identical BAMs have the same duplicate reads.
CompareDuplicatesSpark() CompareDuplicatesSpark
compareLocatables(Locatable, Locatable, SAMSequenceDictionary) IntervalUtils
Compare two locations using a SAMSequenceDictionary sequence ordering
CompareMatrix org.broadinstitute.hellbender.tools.validation
CompareMatrix contains a square matrix of linear dimension QualityUtils.MAX_SAM_QUAL_SCORE.
CompareMatrix(byte[]) CompareMatrix
CompareMetrics picard.analysis
Compare two metrics files.
CompareMetrics() CompareMetrics
compareReadNames(GATKRead, GATKRead) ReadQueryNameComparator
compare read names lexicographically without any additional tie breakers
compareReportArguments(RecalibrationArgumentCollection, String, String) RecalibrationArgumentCollection
CompareSAMs picard.sam
Rudimentary SAM comparer.
CompareSAMs() CompareSAMs
compareTo(IntegerCopyNumberState) IntegerCopyNumberState
compareTo(SVInterval) SVInterval
compareTo(SVKmerLong) SVKmerLong
SVKmerLong comparison is consistent with equals.
compareTo(SVKmerShort) SVKmerShort
SVKmerShort comparison is consistent with equals.
compareTo(SVLocation) SVLocation
compareTo(GenotypeAlleleCounts) GenotypeAlleleCounts
Compares to genotypes.
compareTo(KBestHaplotype) KBestHaplotype
Compares k-best haplotypes based on the score where the one with larger score comes first (descending orther).
compareTo(VQSLODTranche) VQSLODTranche
compareTo(GencodeGtfFeature) GencodeGtfFeature
compareTo(GenomeLoc) GenomeLoc
compareTo(DocWorkUnit) GATKDocWorkUnit
Sort in order of the name of this WorkUnit
compareTo(PrimaryAlignmentKey) PrimaryAlignmentKey
compareTo(QualQuantizer.QualInterval) QualQuantizer.QualInterval
compareTo(Sample) Sample
compareTo(SequencingArtifactMetrics.BaitBiasDetailMetrics) SequencingArtifactMetrics.BaitBiasDetailMetrics
compareTo(SequencingArtifactMetrics.PreAdapterDetailMetrics) SequencingArtifactMetrics.PreAdapterDetailMetrics
compareTo(Gene) Gene
compareTo(HaplotypeBlock) HaplotypeBlock
compareTo(MatchResults) MatchResults
Provides a natural sort so that better matches (by LOD) sort earlier.
compareTo(Snp) Snp
compareTo(GenotypeConcordanceStates.TruthAndCallStates) GenotypeConcordanceStates.TruthAndCallStates
complement() Transition
Return the complementary transition.
complement() Transition
Return the complementary transition.
ComplexityPartitioner org.broadinstitute.hellbender.tools.spark.sv.utils
A Spark Partitioner that puts tasks with greater complexities into earlier partitions.
ComplexityPartitioner(int[]) ComplexityPartitioner
compose(ReadTransformer) ReadTransformer
composeAlleleFrequencyPriorProvider(int, double, List<Double>) GenotypingEngine
Function that fills vector with allele frequency priors.
composeCallAttributes(boolean, VariantContext, AlignmentContext, Map<String, AlignmentContext>, FeatureContext, ReferenceContext, List<Integer>, boolean, AFCalculationResult, List<Allele>, GenotypesContext, GenotypeLikelihoodsCalculationModel, ReadLikelihoods<Allele>) GenotypingEngine
composeGivenAllelesVariantContextFromRod(FeatureContext, Locatable, boolean, boolean, Logger, FeatureInput<VariantContext>) GenotypingGivenAllelesUtils
Composes the given allele variant-context providing information about the rods and reference location.
composeGivenHaplotypes(Haplotype, List<VariantContext>, GenomeLoc) GenotypingGivenAllelesUtils
Create the list of artificial GGA-mode haplotypes by injecting each of the provided alternate alleles into the reference haplotype
composeHaplotypeBasedOnReference(int, int, ReferenceMultiSource) SVContext
Composes the haplotype that corresponds to an allele based on the reference sequence.
composeLine(ConcordanceSummaryRecord, DataLine) ConcordanceSummaryRecord.Writer
composeLine(Map.Entry<T, PosteriorSummary>, DataLine) ParameterWriter
composeLine(R, DataLine) TableWriter
Composes the data-line to write into the output to represent a given record
composeVariantContextHeader(Set<VCFHeaderLine>) GermlineCNVIntervalVariantComposer
composeVariantContextHeader(Set<VCFHeaderLine>) GermlineCNVSegmentVariantComposer
COMPRESS_OUTPUTS ExtractIlluminaBarcodes
COMPRESS_OUTPUTS IlluminaBasecallsToFastq
COMPRESS_OUTPUTS_PER_RG SamToFastq
COMPRESS_OUTPUTS_PER_TAG_GROUP SamToFastqWithTags
CompressedDataList T > - Class in org.broadinstitute.hellbender.utils
A class to represent data as a list of pairs.
CompressedDataList() CompressedDataList
COMPRESSION_LEVEL PicardCommandLineProgram
COMPRESSION_LEVEL CommandLineProgram
comps 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 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.
COMPUTE_SLOD UnifiedArgumentCollection
Note that calculating the SLOD increases the runtime by an appreciable amount.
computeAlleleFrequencyPriors(int, double[], double, List<Double>) GenotypingEngine
Function that fills vector with allele frequency priors.
computeAssociatedDistOnRead(Cigar, int, int, boolean) SvCigarUtils
Computes the corresponding distance needs to be walked on the read, given the Cigar and distance walked on the reference.
computeAssociatedDistOnRef(Cigar, int, int) SvCigarUtils
Computes the corresponding distance needs to be walked on the reference, given the Cigar and distance walked on the read.
computeCovariates(GATKRead, SAMFileHeader, StandardCovariateList, boolean, CovariateKeyCache) RecalUtils
Computes all requested covariates for every offset in the given read
by calling covariate.getValues(..).
computeCovariates(GATKRead, SAMFileHeader, StandardCovariateList, ReadCovariates, boolean) RecalUtils
Computes all requested covariates for every offset in the given read
by calling covariate.getValues(..).
computeDerivedMetrics() PSFilterMetrics
Computes number of reads filtered at each step and total final reads.
computeDiploidGenotypeCounts(VariantContext, GenotypesContext, boolean) GenotypeUtils
Returns a triple of ref/het/hom genotype "counts".
computeForwardClipping(List<Allele>) GATKVariantContextUtils
Clip out any unnecessary bases off the front of the alleles
The VCF spec represents alleles as block substitutions, replacing AC with A for a
1 bp deletion of the C.
computeIndelBQSRTables RecalibrationArgumentCollection
computeLog10Likelihoods(LikelihoodMatrix<Haplotype>, List<GATKRead>, Map<GATKRead, byte[]>) 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<Haplotype>, List<GATKRead>, Map<GATKRead, byte[]>) 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.
computeLog10PNonRef(VariantContext, int, double[], StateTracker) AFCalculator
Actually carry out the log10PNonRef calculation on vc, storing results in results
computeLog10PNonRef(VariantContext, int, double[], StateTracker) AlleleFrequencyCalculator
computeLog10PNonRef(VariantContext, int, double[], StateTracker) GeneralPloidyExactAFCalculator
computeLog10PNonRef(VariantContext, int, double[], StateTracker) IndependentAllelesDiploidExactAFCalculator
computeLog10PNonRef(VariantContext, int, double[], StateTracker) ReferenceDiploidExactAFCalculator
computeMaxAcceptableAlleleCount(int, int) GenotypeLikelihoodCalculators
Compute the maximally acceptable allele count (ref allele included) given the maximally acceptable genotype count.
computeReadLikelihoods(AssemblyResultSet, SampleList, Map<String, List<GATKRead>>) PairHMMLikelihoodCalculationEngine
computeReadLikelihoods(AssemblyResultSet, SampleList, Map<String, List<GATKRead>>) RandomLikelihoodCalculationEngine
computeReadLikelihoods(AssemblyResultSet, SampleList, Map<String, List<GATKRead>>) ReadLikelihoodCalculationEngine
Calculates the likelihood of reads across many samples evaluated against haplotypes resulting from the
active region assembly process.
computeReverseClipping(List<Allele>, byte[]) GATKVariantContextUtils
computeTaxScores(Iterator<PSPathogenAlignmentHit>, PSTaxonomyDatabase, boolean) PSScorer
Computes abundance scores and returns key-values of taxonomic id and scores
CON_ALT_BASES 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 SequencingArtifactMetrics.PreAdapterDetailMetrics
The number of REF_BASE:REF_BASE alignments having a read number and orientation that refutes the presence of this artifact.
concat(GATKReport) GATKReport
This is the main function is charge of gathering the reports.
concat(GATKReportTable) GATKReportTable
Concatenates the rows from the table to this one
concat(byte[]...) Utils
Concatenates byte arrays
concatenateLists(List<T>, List<T>) SVUtils
Concatenate two lists.
concatIterators(Iterator<Iterator<T>>) FlatMapGluer
concatIterators(Iterator<? extends Iterable<T>>) Utils
Concatenates a series of Iterators (all of the same type) into a single Iterator.
Concordance org.broadinstitute.hellbender.tools.walkers.validation
Evaluate site-level concordance of an input VCF against a truth VCF.
Concordance() Concordance
ConcordanceState org.broadinstitute.hellbender.tools.walkers.validation
Created by davidben on 3/2/17.
ConcordanceSummaryRecord org.broadinstitute.hellbender.tools.walkers.validation
Created by tsato on 2/8/17.
ConcordanceSummaryRecord(VariantContext.Type, long, long, long) ConcordanceSummaryRecord
ConcordanceSummaryRecord.Reader org.broadinstitute.hellbender.tools.walkers.validation
ConcordanceSummaryRecord.Writer org.broadinstitute.hellbender.tools.walkers.validation
CONCRETE_TYPES ValidateVariants.ValidationType
Unmodifiable set of concrete validation types.
ConcurrentAFCalculatorProvider org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
Produces independent AF calculators per thread.
ConcurrentAFCalculatorProvider() ConcurrentAFCalculatorProvider
Create a new concurrent af-calculator provider instance.
confidence ReadLikelihoods.BestAllele
Confidence that the read actually was generated under that likelihood.
CONFIDENCE_REGION_LONG_NAME AbstractConcordanceWalker
CONFIDENCE_REGION_SHORT_NAME AbstractConcordanceWalker
confidentlyCalled(double, double) GenotypingEngine
Checks whether a variant site seems confidently called base on user threshold that the score provided
by the exact model.
CONFIG_FILE_CONTIG_COLUMN_KEY XsvLocatableTableCodec
CONFIG_FILE_DATA_SOURCE_NAME_KEY XsvLocatableTableCodec
CONFIG_FILE_DELIMITER_KEY XsvLocatableTableCodec
CONFIG_FILE_END_COLUMN_KEY XsvLocatableTableCodec
CONFIG_FILE_FIELD_NAME_CONTIG_COLUMN DataSourceUtils
CONFIG_FILE_FIELD_NAME_END_COLUMN DataSourceUtils
CONFIG_FILE_FIELD_NAME_GENCODE_FASTA_PATH DataSourceUtils
CONFIG_FILE_FIELD_NAME_NAME DataSourceUtils
CONFIG_FILE_FIELD_NAME_ORIGIN_LOCATION DataSourceUtils
CONFIG_FILE_FIELD_NAME_PREPROCESSING_SCRIPT DataSourceUtils
CONFIG_FILE_FIELD_NAME_SRC_FILE DataSourceUtils
CONFIG_FILE_FIELD_NAME_START_COLUMN DataSourceUtils
CONFIG_FILE_FIELD_NAME_TYPE DataSourceUtils
CONFIG_FILE_FIELD_NAME_VERSION DataSourceUtils
CONFIG_FILE_FIELD_NAME_XSV_DELIMITER DataSourceUtils
CONFIG_FILE_FIELD_NAME_XSV_KEY DataSourceUtils
CONFIG_FILE_FIELD_NAME_XSV_KEY_COLUMN DataSourceUtils
CONFIG_FILE_FIELD_NAME_XSV_PERMISSIVE_COLS DataSourceUtils
CONFIG_FILE_START_COLUMN_KEY XsvLocatableTableCodec
CONFIG_FILE_VARIABLE_CLASS_PATH GATKConfig
Name of the configuration file variable to be used in the
Config.Sources annotation for
GATKConfig
as a place to find the configuration file corresponding to this interface.
CONFIG_FILE_VARIABLE_FILE_NAME GATKConfig
Name of the configuration file variable to be used in the
Config.Sources annotation for
GATKConfig
as a place to find the configuration file corresponding to this interface.
ConfigFactory org.broadinstitute.hellbender.utils.config
A singleton class to act as a user interface for loading configuration files from org.aeonbits.owner.
configuration GenotypingEngine
cons(T, List<T>) Utils
consensusMode ReadThreadingAssemblerArgumentCollection
This argument is specifically intended for 1000G consensus analysis mode.
CONSOLIDATE_ARG_NAME GenomicsDBImport
consolidateCigar(Cigar) AlignmentUtils
Need a well-formed, consolidated Cigar string so that the left aligning code works properly.
constantsAreInitialized PairHMM
constructHaplotypeMapping(List<VariantContext>, Set<Haplotype>) AssemblyBasedCallerGenotypingEngine
Construct the mapping from alternate allele to the set of haplotypes that contain that allele
constructPhaseGroups(List<VariantContext>, Map<VariantContext, Pair<Integer, String>>, int) AssemblyBasedCallerGenotypingEngine
Assemble the phase groups together and update the original calls accordingly
constructPhaseSetMapping(List<VariantContext>, Map<VariantContext, Set<Haplotype>>, int, Map<VariantContext, Pair<Integer, String>>) AssemblyBasedCallerGenotypingEngine
Construct the mapping from call (variant context) to phase set ID
constructStaticQuantizedMapping(List<Integer>, boolean) BQSRReadTransformer
Constructs an array that maps particular quantized values to a rounded value in staticQuantizedQuals
Rounding is done in probability space.
consumeCachedReads() ReadCachingIterator
consumeFinalizedItems() Downsampler
Return (and *remove*) all items that have survived downsampling and are waiting to be retrieved.
consumeFinalizedItems() FractionalDownsampler
consumeFinalizedItems() LevelingDownsampler
consumeFinalizedItems() MutectDownsampler
consumeFinalizedItems() PassThroughDownsampler
Note that this list is a linked list and so doesn't support fast random access
consumeFinalizedItems() PositionalDownsampler
consumeFinalizedItems() ReservoirDownsampler
containedInRegionToIgnore(SVInterval, SVIntervalTree<SVInterval>) SVReadFilter
contains(SVKmerShort) PSKmerBloomFilter
Input should not be canonicalized/masked
contains(SVKmerShort) PSKmerSet
Input should not be canonicalized/masked
contains(PairedStrandedIntervals) PairedStrandedIntervalTree
contains(Object) HopscotchCollection
contains(long) LargeLongHopscotchSet
contains(long) LongBloomFilter
contains(long) LongHopscotchSet
contains(long, int) LongHopscotchSet
contains(Locatable) GencodeGtfFeature
contains(int) CountSet
Checks whether a integer value is included in the set.
contains(Object) CountSet
contains(Object) IndexedSet
contains(Locatable) SimpleInterval
Determines whether this interval contains the entire region represented by other
(in other words, whether it covers it).
contains(String) TableColumnCollection
Check whether there is such a column by name.
contains(Snp) HaplotypeBlock
Returns true if the SNP is contained within the haplotype block, false otherwise.
containsAll(long[]) LargeLongHopscotchSet
containsAll(long[]) LongBloomFilter
containsAll(long[]) LongHopscotchSet
containsAll(Collection<?>) CountSet
containsAll(String...) TableColumnCollection
Checks whether columns contain all the names in an array.
containsAll(Iterable<String>) TableColumnCollection
Checks whether columns contain all the names in an array.
containsAllele(int) GenotypeAlleleCounts
Checks whether this genotype contain at least one call on a particular allele index.
containsAllele(A) AlleleList
Returns true if this AlleleList contains the specified allele
and false otherwise.
containsAllVertices(Collection<? extends V>) BaseGraph
Checks whether the graph contains all the vertices in a collection.
containsExactly(String...) TableColumnCollection
Checks whether columns contain all the names in an array and no other.
containsGapOfEqualOrLargerSize(int) AlignmentInterval
containsIndelLargerOrSmallerThan(VariantContext, int, int) SelectVariants
ContainsKmerReadFilter org.broadinstitute.hellbender.tools.spark.pathseq
Keep reads that do NOT contain one or more kmers from a set of SVKmerShorts
ContainsKmerReadFilter(String, int) ContainsKmerReadFilter
ContainsKmerReadFilterSpark org.broadinstitute.hellbender.tools.spark.pathseq
Wrapper for ContainsKmerReadFilter to avoid serializing the kmer filter in Spark
ContainsKmerReadFilterSpark(String, int) ContainsKmerReadFilterSpark
containsNoNull(Collection<?>, String) Utils
Checks that the collection does not contain a null value (throws an IllegalArgumentException if it does).
containsNOperator(Cigar) CigarUtils
Returns whether the cigar has any N operators.
containsNOperator(List<CigarElement>) CigarUtils
Returns whether the list has any N operators.
containsOnRead(AlignmentInterval) AlignmentInterval
containsOnRef(AlignmentInterval) AlignmentInterval
containsP(GenomeLoc) GenomeLoc
containsVertex(T) Path
Does this path contain the given vertex?
contamination HaplotypeProbabilitiesFromContaminatorSequence
CONTAMINATION IdentifyContaminant
CONTAMINATION_FILTER_NAME GATKVCFConstants
CONTAMINATION_FRACTION 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 StandardCallerArgumentCollection
This argument specifies a file with two columns "sample" and "contamination" specifying the contamination level for those samples.
CONTAMINATION_TABLE_LONG_NAME M2FiltersArgumentCollection
contaminationDownsampling(Map<String, Double>) ReadLikelihoods
Downsamples reads based on contamination fractions making sure that all alleles are affected proportionally.
contaminationDownsampling(Map<String, Double>) UnfilledReadsLikelihoods
ContaminationRecord org.broadinstitute.hellbender.tools.walkers.contamination
Created by David Benjamin on 2/13/17.
ContaminationRecord(String, double, double) ContaminationRecord
ContaminationRecord.Level org.broadinstitute.hellbender.tools.walkers.contamination
contaminationTable M2FiltersArgumentCollection
CONTEXT SequencingArtifactMetrics.BaitBiasDetailMetrics
The sequence context to which the analysis is constrained.
CONTEXT SequencingArtifactMetrics.PreAdapterDetailMetrics
The sequence context to which the analysis is constrained.
CONTEXT CollectOxoGMetrics.CpcgMetrics
The sequence context being reported on.
CONTEXT_SIZE CollectSequencingArtifactMetrics
CONTEXT_SIZE CollectOxoGMetrics
ContextCovariate org.broadinstitute.hellbender.utils.recalibration.covariates
ContextCovariate(RecalibrationArgumentCollection) ContextCovariate
contextFromKey(int) ContextCovariate
Converts a key into the dna string representation.
contextMatchesLoc(VariantContext, Locatable) GATKVariantContextUtils
CONTEXTS CollectOxoGMetrics
CONTEXTS_TO_PRINT CollectSequencingArtifactMetrics
ContextShard org.broadinstitute.hellbender.engine
Immutable storage class.
ContextShard(SimpleInterval) ContextShard
CONTIG ValidateBasicSomaticShortMutations
contig() VcfFileSegment
CONTIG_COL_COMMENT AnnotatedIntervalCodec
CONTIG_ID_KEY GATKVCFConstants
CONTIG_LENGTH_KEY GATKVCFConstants
CONTIG_NAMES GATKSVVCFConstants
CONTIG_PLOIDY_CALLS_DIRECTORY_LONG_NAME GermlineCNVCaller
CONTIG_PLOIDY_CALLS_LONG_NAME PostprocessGermlineCNVCalls
CONTIG_PLOIDY_PRIORS_FILE_LONG_NAME DetermineGermlineContigPloidy
CONTIG_SEPARATOR SimpleInterval
ContigAlignmentsModifier org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
ContigAlignmentsModifier() ContigAlignmentsModifier
ContigAlignmentsModifier.AlnModType org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
ContigAlignmentsModifier.AlnModType.ModTypeString org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
contigIndex GenomeLoc
the basic components of a genome loc, its contig index,
start and stop position, and (optionally) the contig name
contigIndex ArtificialReadQueryIterator
contigIsInDictionary(String) GenomeLocParser
Determines whether the given contig is valid with respect to the sequence dictionary
already installed in the GenomeLoc.
contigLength ActivityProfile
A cached value of the regionStartLoc contig length, to make calls to
getCurrentContigLength efficient
contigName GenomeLoc
contigsAligner(String, byte[], Function<? super T, String>, Function<? super T, byte[]>) SingleSequenceReferenceAligner
Composes a contig aligner from an arbitrary input type given contig name and base sequence generation functions.
contiguousP(GenomeLoc) GenomeLoc
CONTINGENCY_METRICS_FILE_EXTENSION GenotypeConcordance
CONTINGENCY_STATE_HEADER_LINE GenotypeConcordance
CONTINGENCY_STATE_TAG GenotypeConcordance
CONTINGENCY_VALUES GenotypeConcordanceDetailMetrics
The list of contingency table values (TP, TN, FP, FN) that are deduced from the truth/call state comparison, given the reference.
continueAfterAnError CheckPileup
By default the program will quit if it encounters an error (such as missing truth data for a given position).
controllerId ProcessControllerBase
CONVERGENCE_SNR_AVERAGING_WINDOW_LONG_NAME HybridADVIArgumentCollection
CONVERGENCE_SNR_COUNTDOWN_WINDOW_LONG_NAME HybridADVIArgumentCollection
CONVERGENCE_SNR_TRIGGER_THRESHOLD_LONG_NAME HybridADVIArgumentCollection
CONVERGENCE_THRESHOLD SomaticLikelihoodsEngine
convert(Method, String) CustomBooleanConverter
convert(GATKRead, SAMFileHeader) GATKReadToBDGAlignmentRecordConverter
convert(GATKRead, SAMFileHeader, SequenceDictionary, RecordGroupDictionary) GATKReadToBDGAlignmentRecordConverter
convert(SAMRecord, SequenceDictionary, RecordGroupDictionary) GATKReadToBDGAlignmentRecordConverter
convertB37ContigToHg19Contig(String) FuncotatorUtils
Converts a given B37 style contig name to the equivalent in hg19.
convertClusterToOutputRecord(ClusterData) ClusterDataToSamConverter
Creates the SAMRecord for each read in the cluster
CONVERTED_SITES RrbsCpgDetailMetrics
Number of times this CpG site was converted (TG for + strand, CA for - strand)
convertGenomeLocsToSimpleIntervals(List<GenomeLoc>) IntervalUtils
Convert a List of intervals in GenomeLoc format into a List of intervals in SimpleInterval format.
ConvertHeaderlessHadoopBamShardToBam 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() ConvertHeaderlessHadoopBamShardToBam
convertHeaderlessHadoopBamShardToBam(File, SAMFileHeader, File) SparkUtils
Converts a headerless Hadoop bam shard (eg., a part0000, part0001, etc.
convertInsToSoftClipFromOneEnd(List<CigarElement>, boolean) SvCigarUtils
Actually convert terminal 'I' to 'S' and in case there's an 'S' comes before 'I', compactify the two neighboring 'S' operations into one.
convertIUPACtoN(byte[], boolean, boolean) BaseUtils
convertMetric(TargetMetrics) HsMetricCollector
convertMetric(TargetMetrics) TargetedPcrMetricsCollector
convertMetric(TargetMetrics) TargetMetricsCollector
convertRealMatrixToSparkRowMatrix(JavaSparkContext, RealMatrix, int) SparkConverter
Create a distributed matrix given an Apache Commons RealMatrix.
ConvertSequencingArtifactToOxoG picard.analysis.artifacts
ConvertSequencingArtifactToOxoG() ConvertSequencingArtifactToOxoG
convertSimpleIntervalToQueryInterval(SimpleInterval, SAMSequenceDictionary) IntervalUtils
Converts an interval in SimpleInterval format into an htsjdk QueryInterval.
convertSolexaQualityAscii_1_1_ToPhredBinary(byte[]) IlluminaUtil
Converts from Solexa ASCII to Phred binary in place.
convertSparkMatrixToRealMatrix(Matrix) SparkConverter
Convert a local (not distributed) Spark Matrix to an Apache Commons matrix.
convertSparkRowMatrixToRealMatrix(RowMatrix, int) SparkConverter
Create an Apache Commons RealMatrix from a Spark RowMatrix.
convertToBDGAlignmentRecord() BDGAlignmentRecordToGATKReadAdapter
convertToSAMRecord(SAMFileHeader) GATKRead
Convert this read into a SAMRecord.
convertToSAMRecord(SAMFileHeader) SAMRecordToGATKReadAdapter
coordinateByHitIndex() HitsForInsert
Some alignment strategies expect to receive alignments for ends that are coordinated by
hit index (HI) tag.
copy() PSTreeNode
copy() BaseEdge
Create a new copy of this BaseEdge
copy() MultiSampleEdge
copy() ParameterizedState
copy() GATKRead
Return a copy of this read.
copy() GATKDuplicationMetrics
copy() SAMRecordToGATKReadAdapter
copy(ExtractIlluminaBarcodes.BarcodeMetric) ExtractIlluminaBarcodes.BarcodeMetric
Creates a copy of metric initialized with only non-accumulated and non-calculated values set
COPY_NUMBER_FORMAT GATKSVVCFConstants
COPY_NUMBER_POSTERIOR_EXPECTATION_MODE_LONG_NAME GermlineDenoisingModelArgumentCollection
COPY_NUMBER_POSTERIOR_FILE_NAME GermlineCNVNamingConstants
COPY_NUMBER_QUALITY_FORMAT GATKSVVCFConstants
COPY_NUMBER_SEGMENTS_FILE_NAME GermlineCNVNamingConstants
COPY_NUMBER_TABLE_COLUMN_PREFIX GermlineCNVNamingConstants
COPY_OF_QD_KEY_NAME ExampleTwoPassVariantWalker
COPY_RATIO_MODEL_PARAMETER_FILE_SUFFIX ModelSegments
COPY_RATIO_SEGMENTS_FOR_CALLER_FILE_SUFFIX ModelSegments
copyAlleleCounts(int[], int) GenotypeAlleleCounts
Copies the sorted allele counts into an array.
copyAlleleLikelihoods(int, double[], int) SubsettedLikelihoodMatrix
copyAlleleLikelihoods(int, double[], int) LikelihoodMatrix
Copies the likelihood of all the reads for a given allele into an array from a particular offset.
copyFile(String, String) BucketUtils
Copies a file.
copyFromBaseClass(T, S) ReflectionUtil
CopyNumberArgumentValidationUtils org.broadinstitute.hellbender.tools.copynumber.arguments
CopyNumberFormatsUtils org.broadinstitute.hellbender.tools.copynumber.formats
CopyNumberPosteriorDistribution org.broadinstitute.hellbender.tools.copynumber.formats.records
A record containing the integer copy-number posterior distribution for a single interval.
CopyNumberPosteriorDistribution(Map<IntegerCopyNumberState, Double>) CopyNumberPosteriorDistribution
Constructor for storing copy number posterior distribution given a mapping between copy number states
and their respective probabilities in log scale
CopyNumberPosteriorDistributionCollection org.broadinstitute.hellbender.tools.copynumber.formats.collections
Collection of integer copy-number posteriors.
CopyNumberPosteriorDistributionCollection(File) CopyNumberPosteriorDistributionCollection
CopyNumberProgramGroup org.broadinstitute.hellbender.cmdline.programgroups
Tools that analyze read coverage to detect copy number variants
CopyNumberProgramGroup() CopyNumberProgramGroup
CopyNumberStandardArgument org.broadinstitute.hellbender.tools.copynumber.arguments
CopyNumberStandardArgument() CopyNumberStandardArgument
CopyRatio org.broadinstitute.hellbender.tools.copynumber.formats.records
CopyRatio(SimpleInterval, double) CopyRatio
CopyRatioCollection org.broadinstitute.hellbender.tools.copynumber.formats.collections
CopyRatioCollection(File) CopyRatioCollection
CopyRatioCollection(SampleLocatableMetadata, List<CopyRatio>) CopyRatioCollection
CopyRatioKernelSegmenter org.broadinstitute.hellbender.tools.copynumber.segmentation
Segments copy-ratio data using kernel segmentation.
CopyRatioKernelSegmenter(CopyRatioCollection) CopyRatioKernelSegmenter
CopyRatioModeller org.broadinstitute.hellbender.tools.copynumber.models
Represents a segmented model for copy ratio fit to denoised log2 copy-ratio data.
CopyRatioParameter org.broadinstitute.hellbender.tools.copynumber.models
Enumerates the parameters for CopyRatioState.
CopyRatioSegment org.broadinstitute.hellbender.tools.copynumber.formats.records
CopyRatioSegment(SimpleInterval, int, double) CopyRatioSegment
CopyRatioSegment(SimpleInterval, List<CopyRatio>) CopyRatioSegment
CopyRatioSegmentCollection org.broadinstitute.hellbender.tools.copynumber.formats.collections
CopyRatioSegmentCollection(File) CopyRatioSegmentCollection
CopyRatioSegmentCollection(SampleLocatableMetadata, List<CopyRatioSegment>) CopyRatioSegmentCollection
copyStandardCallerArgsFrom(StandardCallerArgumentCollection) StandardCallerArgumentCollection
Copies the values from other into this StandardCallerArgumentCollection
copyTo(int[], int) CountSet
Copy the content of the set into an array.
copyTo(int[]) CountSet
Copy the content of the set into an array.
copyWithNewPriors(double[]) AFCalculationResult
Return a new AFCalcResult with a new prior probability
CORRECT_STRAND_READS RnaSeqMetrics
Number of aligned reads that are mapped to the correct strand.
correctGCBias(RealMatrix, double[]) GCBiasCorrector
Corrects GC bias of read counts in place.
CorrectionSet(int) ReadErrorCorrector.CorrectionSet
Main class constructor.
correctReads(Collection<GATKRead>) ReadErrorCorrector
Correct a collection of reads based on stored k-mer counts
correspondingInterval() VcfFileSegment
CosmicFuncotationFactory org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic
Factory for creating
Funcotations by handling a SQLite database containing information from COSMIC.
CosmicFuncotationFactory(Path) CosmicFuncotationFactory
CosmicFuncotationFactory(Path, LinkedHashMap<String, String>, String) CosmicFuncotationFactory
CouldNotCreateOutputFile(File, String, Exception) UserException.CouldNotCreateOutputFile
CouldNotCreateOutputFile(File, String) UserException.CouldNotCreateOutputFile
CouldNotCreateOutputFile(String, String, Exception) UserException.CouldNotCreateOutputFile
CouldNotCreateOutputFile(File, Exception) UserException.CouldNotCreateOutputFile
CouldNotCreateOutputFile(String, Exception) UserException.CouldNotCreateOutputFile
CouldNotIndexFile(File, Exception) UserException.CouldNotIndexFile
CouldNotReadInputFile(String, Exception) UserException.CouldNotReadInputFile
CouldNotReadInputFile(File) UserException.CouldNotReadInputFile
CouldNotReadInputFile(Path) UserException.CouldNotReadInputFile
CouldNotReadInputFile(File, String) UserException.CouldNotReadInputFile
CouldNotReadInputFile(Path, String) UserException.CouldNotReadInputFile
CouldNotReadInputFile(Path, String, Throwable) UserException.CouldNotReadInputFile
CouldNotReadInputFile(String, String) UserException.CouldNotReadInputFile
CouldNotReadInputFile(File, String, Exception) UserException.CouldNotReadInputFile
CouldNotReadInputFile(File, Exception) UserException.CouldNotReadInputFile
CouldNotReadInputFile(Path, Exception) UserException.CouldNotReadInputFile
CouldNotReadInputFile(String) UserException.CouldNotReadInputFile
COUNT GenotypeConcordanceDetailMetrics
The number of events of type TRUTH_STATE and CALL_STATE for the EVENT_TYPE and SAMPLEs
COUNT_PANEL_OF_NORMALS_FILE_LONG_NAME CopyNumberStandardArgument
COUNT_UNPAIRED CollectWgsMetrics
countAlignedBases(Cigar) CigarUtils
CountBases org.broadinstitute.hellbender.tools
Calculate and print to the standard output the overall number of bases in a SAM/BAM/CRAM file
CountBases() CountBases
CountBasesSpark org.broadinstitute.hellbender.tools.spark.pipelines
Calculate the overall number of bases SAM/BAM/CRAM file
CountBasesSpark() CountBasesSpark
countBooleanOccurrences(boolean, boolean[]) Utils
Returns the number of occurrences of a boolean element in a boolean array.
countCallsAtTruth(List<VariantDatum>, double) TrancheManager
Counter() Nucleotide.Counter
Creates a new counter with all counts set to 0.
counter AbstractWgsMetricsCollector
The number of processed genomic bases
CounterManager 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) CounterManager
Constructor creates new CounterManager without any Counters,
counters are added to CounterManager via newCounter() method
CounterManager.Counter 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 org.broadinstitute.hellbender.tools.walkers.validation
Count variants which were not filtered in a VCF.
CountFalsePositives() CountFalsePositives
countFamilyViolations(SampleDB, Set<String>, VariantContext) MendelianViolation
CountingDuplicateFilter picard.filter
Counting filter that discards reads that have been marked as duplicates.
CountingDuplicateFilter() CountingDuplicateFilter
CountingFilter picard.filter
A SamRecordFilter that counts the number of bases in the reads which it filters out.
CountingFilter() CountingFilter
CountingMapQFilter picard.filter
Counting filter that discards reads below a configurable mapping quality threshold.
CountingMapQFilter(int) CountingMapQFilter
CountingPairedFilter picard.filter
Counting filter that discards reads that are unpaired in sequencing and paired reads whose mates are not mapped.
CountingPairedFilter() CountingPairedFilter
CountingReadFilter org.broadinstitute.hellbender.engine.filters
Wrapper/adapter for
ReadFilter that counts the number of
reads filtered, and provides a filter count summary.
CountingReadFilter(ReadFilter) CountingReadFilter
CountingReadFilter.CountingAndReadFilter org.broadinstitute.hellbender.engine.filters
Private class for Counting AND filters
CountingVariantFilter org.broadinstitute.hellbender.engine.filters
Wrapper/adapter for
VariantFilter that counts the number of variants filtered,
and provides a filter count summary.
CountingVariantFilter(VariantFilter) CountingVariantFilter
CountingVariantFilter.CountingAndVariantFilter org.broadinstitute.hellbender.engine.filters
Private class for Counting AND filters
countLeftClippedBases(Cigar) CigarUtils
Total number of bases clipped on the left/head side of the cigar.
countLeftHardClippedBases(Cigar) CigarUtils
Returns the number of based hard-clipped to the left/head of the cigar.
CountReads org.broadinstitute.hellbender.tools
Calculate and print to the standard output the overall number of reads in a SAM/BAM/CRAM file
CountReads() CountReads
CountReadsSpark org.broadinstitute.hellbender.tools.spark.pipelines
Calculate the overall number of reads in a SAM/BAM file
CountReadsSpark() CountReadsSpark
countRefBasesBasedOnCigar(GATKRead, int, int) CigarUtils
Compute the number of reference bases between the start (inclusive) and end (exclusive) cigar elements.
countRightClippedBases(Cigar) CigarUtils
Total number of bases clipped (soft or hard) on the right/tail side of the cigar.
countRightHardClippedBases(Cigar) CigarUtils
Returns the number of based hard-clipped to the right/tail of the cigar.
CountSet org.broadinstitute.hellbender.utils.collections
Efficient implementation for a small set of integer primitive values.
CountSet(int) CountSet
Creates a new set indicating the expected maximum number of elements it will contain.
countType ASEReadCounter
These options modify how the tool deals with overlapping read pairs.
countUnclippedReadBases(Cigar) CigarUtils
Returns the length of the original read considering all clippings based on this cigar.
CountVariants org.broadinstitute.hellbender.tools.walkers
Count variant records in a VCF file, regardless of filter status.
CountVariants() CountVariants
CountVariantsSpark org.broadinstitute.hellbender.tools.spark.pipelines
CountVariantsSpark() CountVariantsSpark
Covariate org.broadinstitute.hellbender.utils.recalibration.covariates
The Covariate interface.
COVARIATE_NAME_COLUMN_NAME RecalUtils
COVARIATE_VALUE_COLUMN_NAME RecalUtils
CovariateKeyCache org.broadinstitute.hellbender.utils.recalibration.covariates
CovariateKeyCache() CovariateKeyCache
covariateNames() StandardCovariateList
Return a human-readable string representing the used covariates
Coverage org.broadinstitute.hellbender.tools.walkers.annotator
Total depth of coverage per sample and over all samples.
Coverage() Coverage
Coverage(Interval, int) TargetMetricsCollector.Coverage
Constructs a new coverage object for the provided mapping with the desired padding either side.
COVERAGE_CAP CollectWgsMetrics
COVERAGE_CAP CollectTargetedMetrics
CoverageAnalysisProgramGroup org.broadinstitute.hellbender.cmdline.programgroups
Tools that count coverage, e.g.
CoverageAnalysisProgramGroup() CoverageAnalysisProgramGroup
coverageCap AbstractWgsMetricsCollector
Positions with coverage exceeding this value are treated as if they had coverage at this value
coverageCap CollectWgsMetrics.WgsMetrics
The maximum depth/coverage to consider.
CoveragePerContig 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>) CoveragePerContig
CoveragePerContigCollection 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>) CoveragePerContigCollection
coveredSize() GenomeLocSortedSet
Return the size, in bp, of the genomic regions by all of the regions in this set
CpcgMetrics() CollectOxoGMetrics.CpcgMetrics
CPG_BASES_CONVERTED RrbsSummaryMetrics
Number of CpG sites that were converted (TG for +, CA for -)
CPG_BASES_SEEN RrbsSummaryMetrics
Number of CpG sites encountered
CPX_EVENT_ALT_ARRANGEMENTS GATKSVVCFConstants
CPX_SV_REF_SEGMENTS GATKSVVCFConstants
CPX_SV_SYB_ALT_ALLELE_STR GATKSVVCFConstants
CpxVariantInterpreter 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() CpxVariantInterpreter
CpxVariantReInterpreterSpark org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
(Internal) Tries to extract simple variants from a provided GATK-SV CPX.vcf
CpxVariantReInterpreterSpark() CpxVariantReInterpreterSpark
create(File, String, SAMSequenceDictionary, RealMatrix, List<String>, List<SimpleInterval>, double[], double, double, double, double, boolean, double, int, int, JavaSparkContext) HDF5SVDReadCountPanelOfNormals
Create the panel of normals and write it to an HDF5 file.
create(List<AnnotatedInterval>, SAMFileHeader, List<String>) AnnotatedIntervalCollection
Create a collection from components.
create(Path, Path, Set<String>) AnnotatedIntervalCollection
Create a collection based on the contents of an input file and a given config file.
create(Path, Set<String>) AnnotatedIntervalCollection
create(String[]) GencodeGtfCDSFeature
create(GencodeGtfFeatureBaseData) GencodeGtfCDSFeature
create(String[]) GencodeGtfExonFeature
create(GencodeGtfFeatureBaseData) GencodeGtfExonFeature
create(GencodeGtfFeatureBaseData) GencodeGtfFeature
create(String) GencodeGtfFeature
create(String[]) GencodeGtfFeature
create(GencodeGtfFeatureBaseData) GencodeGtfFeature.FeatureType
create(String[]) GencodeGtfFeature.FeatureType
create(String[]) GencodeGtfGeneFeature
create(GencodeGtfFeatureBaseData) GencodeGtfGeneFeature
create(String[]) GencodeGtfSelenocysteineFeature
create(GencodeGtfFeatureBaseData) GencodeGtfSelenocysteineFeature
create(String[]) GencodeGtfStartCodonFeature
create(GencodeGtfFeatureBaseData) GencodeGtfStartCodonFeature
create(String[]) GencodeGtfStopCodonFeature
create(GencodeGtfFeatureBaseData) GencodeGtfStopCodonFeature
create(String[]) GencodeGtfTranscriptFeature
create(GencodeGtfFeatureBaseData) GencodeGtfTranscriptFeature
create(String[]) GencodeGtfUTRFeature
create(GencodeGtfFeatureBaseData) GencodeGtfUTRFeature
create(Class<? extends T>, Map<?, ?>...) ConfigFactory
Wrapper around ConfigFactory.create(Class, Map[]) which will ensure that
path variables specified in Config.Sources annotations are resolved prior
to creation.
create(ReadPileup) FragmentCollection
Create a FragmentCollection containing PileupElements from the ReadBackedPileup rbp
create(List<GATKRead>) FragmentCollection
Create a FragmentCollection containing SAMRecords from a list of reads
create(HaplotypeBAMWriter.WriterType, Path, boolean, boolean, SAMFileHeader) HaplotypeBAMWriter
Create a new HaplotypeBAMWriter of type "type" for writing SAMRecords to an output file
create(HaplotypeBAMWriter.WriterType, HaplotypeBAMDestination) HaplotypeBAMWriter
Create a new HaplotypeBAMWriter of type "type" for writing SAMRecords to and output destination
create(HaplotypeBAMDestination) HaplotypeBAMWriter.WriterType
Create an instance of the HaplotypeBAMWriter corresponding to this type.
CREATE_BAI_LONG_NAME CreateHadoopBamSplittingIndex
CREATE_INDEX PicardCommandLineProgram
CREATE_INDEX CommandLineProgram
CREATE_MD5_FILE PicardCommandLineProgram
CREATE_MD5_FILE CommandLineProgram
CREATE_OUTPUT_BAM_INDEX_LONG_NAME StandardArgumentDefinitions
CREATE_OUTPUT_BAM_INDEX_SHORT_NAME StandardArgumentDefinitions
CREATE_OUTPUT_BAM_MD5_LONG_NAME StandardArgumentDefinitions
CREATE_OUTPUT_BAM_MD5_SHORT_NAME StandardArgumentDefinitions
CREATE_OUTPUT_VARIANT_INDEX_LONG_NAME StandardArgumentDefinitions
CREATE_OUTPUT_VARIANT_INDEX_SHORT_NAME StandardArgumentDefinitions
CREATE_OUTPUT_VARIANT_MD5_LONG_NAME StandardArgumentDefinitions
CREATE_OUTPUT_VARIANT_MD5_SHORT_NAME StandardArgumentDefinitions
createAlleleMapper(List<VariantContext>, VariantContext, int, List<Haplotype>) AssemblyBasedCallerGenotypingEngine
createAlleleMapping(Allele, VariantContext, Collection<Allele>) 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.
createAminoAcidSequence(String) FuncotatorUtils
Creates an amino acid sequence from a given coding sequence.
createAminoAcidSequence(String, boolean) FuncotatorUtils
Creates an amino acid sequence from a given coding sequence.
createAndSetHeader(int) ArtificialBAMBuilder
createArtificialRead(SAMFileHeader, String, int, int, int) ArtificialReadUtils
Create an artificial GATKRead based on the parameters.
createArtificialRead(SAMFileHeader, String, int, int, byte[], byte[]) ArtificialReadUtils
Create an artificial GATKRead based on the parameters.
createArtificialRead(SAMFileHeader, String, String, int, byte[], byte[]) ArtificialReadUtils
Create an artificial GATKRead based on the parameters.
createArtificialRead(SAMFileHeader, String, int, int, byte[], byte[], String) ArtificialReadUtils
Create an artificial GATKRead based on the parameters
createArtificialRead(SAMFileHeader, String, String, int, byte[], byte[], String) ArtificialReadUtils
Create an artificial GATKRead based on the parameters
createArtificialRead(SAMFileHeader, byte[], byte[], String) 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(byte[], byte[], String) ArtificialReadUtils
createArtificialRead(SAMFileHeader, String) ArtificialReadUtils
createArtificialRead(SAMFileHeader, Cigar) ArtificialReadUtils
createArtificialRead(Cigar) ArtificialReadUtils
createArtificialRead(Cigar, String) ArtificialReadUtils
createArtificialRead(String) ArtificialReadUtils
createArtificialSamHeader(int, int, int) ArtificialReadUtils
Creates an artificial sam header, matching the parameters, chromosomes which will be labeled chr1, chr2, etc
createArtificialSamHeader() ArtificialReadUtils
Creates an artificial sam header with standard test parameters
createArtificialSamHeader(SAMSequenceDictionary) ArtificialReadUtils
Creates an artificial sam header based on the sequence dictionary dict
createArtificialSamHeaderWithGroups(int, int, int, int) ArtificialReadUtils
Creates an artificial sam header, matching the parameters, chromosomes which will be labeled chr1, chr2, etc
It also adds read groups.
createArtificialSamHeaderWithReadGroup(SAMReadGroupRecord) ArtificialReadUtils
createArtificialSAMRecord(SAMFileHeader, String, int, int, int) ArtificialReadUtils
Create an artificial SAMRecord based on the parameters.
createArtificialSAMRecord(SAMFileHeader, String, int, int, byte[], byte[]) ArtificialReadUtils
Create an artificial SAMRecord based on the parameters.
createArtificialSAMRecord(SAMFileHeader, String, int, int, byte[], byte[], String) ArtificialReadUtils
Create an artificial SAMRecord based on the parameters
createArtificialSAMRecord(SAMFileHeader, byte[], byte[], String) 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(byte[], byte[], String) ArtificialReadUtils
createArtificialSAMRecord(SAMFileHeader, Cigar, String) ArtificialReadUtils
createArtificialSAMRecord(SAMFileHeader, Cigar) ArtificialReadUtils
createArtificialSAMRecord(Cigar) ArtificialReadUtils
createArtificialUnmappedRead(SAMFileHeader, byte[], byte[]) ArtificialReadUtils
createArtificialUnmappedReadWithAssignedPosition(SAMFileHeader, String, int, byte[], byte[]) ArtificialReadUtils
createBai CreateHadoopBamSplittingIndex
createBamWriter(AssemblyBasedCallerArgumentCollection, boolean, boolean, SAMFileHeader) AssemblyBasedCallerUtils
createBracketedSymbAlleleString(String) SimpleSVType
createCollector(String, Set<MetricAccumulationLevel>, List<Header>, SAMFileHeader) 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.
createCommonSAMWriter(File, File, SAMFileHeader, boolean, boolean, boolean) ReadUtils
Create a common SAMFileWriter for use with GATK tools.
createCommonSAMWriter(Path, File, SAMFileHeader, boolean, boolean, boolean) ReadUtils
Create a common SAMFileWriter for use with GATK tools.
createCommonSAMWriterFromFactory(SAMFileWriterFactory, File, File, SAMFileHeader, boolean) ReadUtils
Create a common SAMFileWriter from a factory for use with GATK tools.
createCommonSAMWriterFromFactory(SAMFileWriterFactory, Path, File, SAMFileHeader, boolean, OpenOption...) ReadUtils
Create a common SAMFileWriter from a factory for use with GATK tools.
createCosmicDataSource(Path, Properties, LinkedHashMap<String, String>) DataSourceUtils
createDataSourceFuncotationFactoriesForDataSources(Map<Path, Properties>, LinkedHashMap<String, String>, TranscriptSelectionMode, Set<String>) DataSourceUtils
Create a
List of
DataSourceFuncotationFactory based on meta data on the data sources, overrides, and transcript reporting priority information.
createDefaultFuncotationsOnVariant(VariantContext, ReferenceContext) DataSourceFuncotationFactory
Creates a
List of
Funcotation for the given
variant and
referenceContext.
createDefaultFuncotationsOnVariant(VariantContext, ReferenceContext) CosmicFuncotationFactory
createDefaultFuncotationsOnVariant(VariantContext, ReferenceContext) GencodeFuncotationFactory
createDefaultFuncotationsOnVariant(VariantContext, ReferenceContext) VcfFuncotationFactory
createDefaultFuncotationsOnVariant(VariantContext, ReferenceContext) LocatableXsvFuncotationFactory
createDefaultFuncotationsOnVariant(VariantContext, ReferenceContext) SimpleKeyXsvFuncotationFactory
createDiploidGenotype(byte, byte) DiploidGenotype
create a diploid genotype, given 2 chars which may not necessarily be ordered correctly
createDiploidGenotype(int, int) DiploidGenotype
create a diploid genotype, given 2 base indexes which may not necessarily be ordered correctly
createDirectory(String) IOUtils
Creates a directory, in local FS, HDFS, or Google buckets to write individual files in.
createDownsampler() AssemblyRegionWalker
createDownsampler() Mutect2
createDummyStratifiedReadMap(Haplotype, SampleList, AssemblyRegion) HaplotypeCallerEngine
Create a context that maps each read to the reference haplotype with log10 L of 0
createEmptyHistogram() LibraryStatistics
createEmptyHistogram() IntHistogram.CDF
createEvenlySpacedPoints(double, double, int) MathUtils
Create a set number of points, linearly spaced, between a minimum and maximum.
createFIFO() StreamingProcessController
Create a temporary FIFO suitable for sending output to the remote process.
createFile(String) BucketUtils
Open a binary file for writing regardless of whether it's on GCS, HDFS or local disk.
createFilterListWithAppend(VariantContext, String) GATKVariantContextUtils
Create a string with existing filters plus the one to append
createFuncotations(VariantContext, ReferenceContext, Map<String, List<Feature>>) DataSourceFuncotationFactory
Creates a
List of
Funcotation for the given
variant,
referenceContext, and
featureContext.
createFuncotations(VariantContext, ReferenceContext, Map<String, List<Feature>>, List<GencodeFuncotation>) DataSourceFuncotationFactory
Creates a
List of
Funcotation for the given
variant,
referenceContext,
featureContext, and
gencodeFuncotations.
createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>) DataSourceFuncotationFactory
Creates a
List of
Funcotation for the given
variant,
referenceContext, and
featureContext.
createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>, List<GencodeFuncotation>) DataSourceFuncotationFactory
Creates a
List of
Funcotation for the given
variant,
referenceContext,
featureContext, and
gencodeFuncotations.
createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>) CosmicFuncotationFactory
createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>, List<GencodeFuncotation>) CosmicFuncotationFactory
createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>) GencodeFuncotationFactory
createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>, List<GencodeFuncotation>) GencodeFuncotationFactory
createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>) VcfFuncotationFactory
createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>, List<GencodeFuncotation>) VcfFuncotationFactory
createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>) LocatableXsvFuncotationFactory
createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>, List<GencodeFuncotation>) LocatableXsvFuncotationFactory
createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>) SimpleKeyXsvFuncotationFactory
createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>, List<GencodeFuncotation>) SimpleKeyXsvFuncotationFactory
createGATKReport() RecalibrationReport
Creates the recalibration report.
createGencodeDataSource(Path, Properties, LinkedHashMap<String, String>, TranscriptSelectionMode, Set<String>) DataSourceUtils
createGenomeLoc(String, int, int) GenomeLocParser
createGenomeLoc(String, int, int, boolean) GenomeLocParser
createGenomeLoc(String, int, int, int) GenomeLocParser
createGenomeLoc(String, int, int, int, boolean) GenomeLocParser
Create a GenomeLoc on contig, starting at start and ending (inclusive) at stop.
createGenomeLoc(String, int) GenomeLocParser
Create a new GenomeLoc, on contig, including the single position pos.
createGenomeLoc(GATKRead) GenomeLocParser
createGenomeLoc(Feature) GenomeLocParser
Creates a GenomeLoc from a Tribble feature
createGenomeLoc(Locatable) GenomeLocParser
Creates a GenomeLoc from a Locatable.
createGenomeLocAtStart(GenomeLoc, int) GenomeLocParser
Creates a loc to the left (starting at the loc start + 1) of maxBasePairs size.
createGenomeLocAtStop(GenomeLoc, int) GenomeLocParser
Creates a loc to the right (starting at the loc stop + 1) of maxBasePairs size.
createGenomeLocOnContig(String, int, int) GenomeLocParser
createGenomeLocOnContig(String, int, int, int) 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>>) GATKHelpDoclet
Create a GSONWorkUnit-derived object that holds our custom data.
CreateHadoopBamSplittingIndex org.broadinstitute.hellbender.tools.spark
Create a Hadoop BAM splitting index and optionally a BAM index from a BAM file.
CreateHadoopBamSplittingIndex() CreateHadoopBamSplittingIndex
createHeaderForWriter(Path, List<String>, SAMFileHeader) 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) AnnotatedIntervalCodec
createHeaderlessSamBackedRead(String, String, int, int) ArtificialReadUtils
Creates an artificial GATKRead backed by a SAMRecord with no header.
createHomGenotype(byte) DiploidGenotype
create a diploid genotype, given a character to make into a hom genotype
createIdenticalArtificialReads(int, SAMFileHeader, String, int, int, int) ArtificialReadUtils
Create a collection of identical artificial reads based on the parameters.
createIndex GatherVcfsCloud
createInstanceForPlugin(Class<?>) GATKAnnotationPluginDescriptor
Return an instance of the specified pluggable class.
createInstanceForPlugin(Class<?>) GATKReadFilterPluginDescriptor
createLibraryStatistics(long) ReadMetadata.LibraryRawStatistics
createLikelihoodCalculationEngine(LikelihoodEngineArgumentCollection) AssemblyBasedCallerUtils
Instantiates the appropriate likelihood calculation engine.
createLocatableXsvDataSource(Path, Properties, LinkedHashMap<String, String>) DataSourceUtils
createNewCigarsIfMapsOffEndOfReference(SAMRecord) AbstractAlignmentMerger
Soft-clip an alignment that hangs off the end of its reference sequence.
createNewCigarsIfMapsOffEndOfReference(SAMRecord) AbstractAlignmentMerger
Soft-clip an alignment that hangs off the end of its reference sequence.
createNextRead() ArtificialReadIterator
createNonIndelPileupElement(int, Allele, int) ArtificialReadUtils
createOptimalCoverageAlignmentSetsForContigs(JavaRDD<GATKRead>, SAMFileHeader, Set<String>, Double, Logger) AssemblyContigAlignmentsConfigPicker
createOutputBamIndex GATKTool
createOutputBamIndex() GATKConfig
createOutputBamMD5 GATKTool
createOutputVariantIndex GATKTool
createOutputVariantMD5 GATKTool
createOverEntireContig(String) GenomeLocParser
Creates a GenomeLoc than spans the entire contig.
createOverlapMap(List<T>, List<U>, SAMSequenceDictionary) 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) GenomeLocParser
Creates a loc padded in both directions by maxBasePairs size (if possible).
createPair(SAMFileHeader, String, int, int, int, boolean, boolean) ArtificialReadUtils
createPair(SAMFileHeader, String, int, int, int, int, boolean, boolean) ArtificialReadUtils
createPileupForReadAndGenomeLoc(GATKRead, Locatable) PileupElement
Create a pileup element for read at a particular spot on the genome.
createPileupForReadAndOffset(GATKRead, int) PileupElement
Create a pileup element for read at offset.
createProvider() ConcurrentAFCalculatorProvider
createRandomRead(SAMFileHeader, int) ArtificialReadUtils
createRandomRead(int) ArtificialReadUtils
createRandomRead(SAMFileHeader, int, boolean) ArtificialReadUtils
createRandomRead(int, boolean) ArtificialReadUtils
createRandomReadBases(int, boolean) ArtificialReadUtils
Create random read qualities
createRandomReadQuals(int) ArtificialReadUtils
Create random read qualities
createReadAlignedToRef(GATKRead, Haplotype, Haplotype, int, boolean, SmithWatermanAligner) 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 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() CreateReadCountPanelOfNormals
createReadThreadingAssembler(AssemblyBasedCallerArgumentCollection) AssemblyBasedCallerUtils
createRecalibrationGATKReport(GATKReportTable, QuantizationInfo, RecalibrationTables, StandardCovariateList) RecalUtils
Creates a consolidated GATK report, first generating report tables.
createRecalibrationGATKReport(GATKReportTable, GATKReportTable, List<GATKReportTable>) RecalUtils
Creates a consolidated GATK report from the tables.
createRecalibrationReport(GATKReportTable, GATKReportTable, List<GATKReportTable>) RecalUtils
Creates a consolidated RecalibrationReport report from the tables.
createRecord(DataLine) ConcordanceSummaryRecord.Reader
createRecord(DataLine) ParameterReader
createRecord(DataLine) TableReader
Transforms a data-line column values into a record.
createReferenceHaplotype(AssemblyRegion, SimpleInterval, ReferenceSequenceFile) AssemblyBasedCallerUtils
Helper function to create the reference haplotype out of the active region and a padded loc
createReferenceHaplotype(AssemblyRegion, byte[], SimpleInterval) ReferenceConfidenceModel
Create a reference haplotype for an active region
createReferenceReader(String) AssemblyBasedCallerUtils
createReverseComplementTransitions(Collection<Transition>) OrientationBiasUtils
Create new Transitions that are complements of the given collection.
createSamBackedRead(String, int, int) ArtificialReadUtils
Creates an artificial GATKRead backed by a SAMRecord.
createSamBackedRead(String, String, int, int) ArtificialReadUtils
Creates an artificial GATKRead backed by a SAMRecord.
createSamFileHeader() FastqToSam
Creates a simple header with the values provided on the command line.
createSamFileWriter(SAMFileHeader) FixMateInformation
createSampleToGenotypeVariantContextSortedMap(List<String>, Collection<VariantContext>) OrientationBiasFilterer
Creates a map that includes the artifact mode complements.
createSAMWriter(File, File, SAMFileHeader, boolean) PicardCommandLineProgram
Create a common SAMFileWriter for use with Picard tools.
createSAMWriter(File, boolean) GATKTool
createSAMWriter(Path, boolean) GATKTool
createSATags(List<BwaMemAlignment>, List<String>) BwaMemAlignmentUtils
Produces an SA tag for each primary line and supplemental alignment as a map from alignment to tag value.
CreateSeqDictReferenceArgumentCollection() CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
CreateSequenceDictionary picard.sam
Create a SAM/BAM file from a fasta containing reference sequence.
CreateSequenceDictionary() CreateSequenceDictionary
CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection picard.sam
createSequenceDictionaryFromFeatureIndex(File) 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_LENGTH is used.
createSetFromList(GenomeLocParser, List<GenomeLoc>) GenomeLocSortedSet
Create a sorted genome location set from a list of GenomeLocs.
createSetFromSequenceDictionary(SAMSequenceDictionary) GenomeLocSortedSet
create a list of genomic locations, given a reference sequence
createSimpleXsvDataSource(Path, Properties, LinkedHashMap<String, String>) DataSourceUtils
createSnpAndIndelBitSets(File, SAMSequenceDictionary) DbSnpBitSetUtil
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
createSnpAndIndelBitSets(File, SAMSequenceDictionary, IntervalList) 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>) DbSnpBitSetUtil
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
CreateSomaticPanelOfNormals org.broadinstitute.hellbender.tools.walkers.mutect
Create a panel of normals (PoN) containing germline and artifactual sites for use with Mutect2.
CreateSomaticPanelOfNormals() CreateSomaticPanelOfNormals
CreateSomaticPanelOfNormals.DuplicateSampleStrategy org.broadinstitute.hellbender.tools.walkers.mutect
createSplicedDeletionPileupElement(int, Allele, int) ArtificialReadUtils
createSplicedInsertionPileupElement(int, Allele, int) ArtificialReadUtils
Create a pileupElement with the given insertion added to the bases.
createSpliceSiteCodonChange(int, int, int, int, Strand, int) FuncotatorUtils
Gets a codon change string for a splice site.
createSVD(RealMatrix) ApacheSingularValueDecomposer
Create a SVD instance using Apache Commons Math.
createSVD(RealMatrix) OjAlgoSingularValueDecomposer
Create a SVD instance using ojAlgo.
createSVD(RealMatrix) SingularValueDecomposer
createSVD(RealMatrix) SparkSingularValueDecomposer
Create a SVD of the given matrix using the given Java Spark Context.
createSVD(RealMatrix) SVDFactory
Create a SVD instance using Apache Commons Math.
createSVD(RealMatrix, JavaSparkContext) SVDFactory
Create a SVD instance using a spark context.
createTempDir(String) IOUtils
Creates a temp directory with the given prefix.
createTempDir(String) BaseTest
Creates an empty temp directory which will be deleted on exit after tests are complete
createTempFile(String, String) 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.
createTempFile(String, String) BaseTest
Creates a temp file that will be deleted on exit after tests are complete.
createTempFileInDirectory(String, String, File) 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.
createTempGenomicsDB(File, Locatable) GenomicsDBTestUtils
Create a temporary GenomicsDB containing a single interval of data from a set of gvcfs
this database will be deleted on jvm shutdown automatically
createTempGenomicsDB(List<File>, Locatable) GenomicsDBTestUtils
Create a temporary GenomicsDB containing a single interval of data from a set of gvcfs
this database will be deleted on jvm shutdown automatically
createThreadSafeProvider(StandardCallerArgumentCollection) FixedAFCalculatorProvider
Creates a fixed AF calculator provider that is thread safe.
createTransitionMatrix(int) PairHMMModel
Creates a transition probability matrix large enough to work with sequences of a particular length.
createUniqueArtificialRead(Cigar) ArtificialReadUtils
Makes a new read with a name that is unique (so that it will return false to equals(otherRead)
createUniqueArtificialRead(String) ArtificialReadUtils
Makes a new read with a name that is unique (so that it will return false to equals(otherRead)
createUniqueArtificialSAMRecord(Cigar) ArtificialReadUtils
Makes a new read with a name that is unique (so that it will return false to equals(otherRead)
createVariantContextWriter(Configuration, OutputStream) VariantsSparkSink.GvcfKeyIgnoringVCFRecordWriter
createVcfDataSource(Path, Properties, LinkedHashMap<String, String>, TranscriptSelectionMode, Set<String>) DataSourceUtils
createVCFHeader(VCFHeader, String, List<String>) OrientationBiasFilterer
Ingest the current VCF header and update it with the information necessary for the Orientation Bias filter to run.
createVCFWriter(File) GATKTool
Creates a VariantContextWriter whose outputFile type is determined by
the outFile's extension, using the best available sequence dictionary for
this tool, and default index, leniency and md5 generation settings.
createVCFWriter(File, SAMSequenceDictionary, boolean, Options...) GATKVariantContextUtils
Creates a VariantContextWriter whose outputFile type is based on the extension of the output file name.
createVCSetFromFingerprint(Fingerprint, ReferenceSequenceFile, String) FingerprintUtils
A utility function that takes a fingerprint and returns a VariantContextSet with variants representing the haplotypes in the fingerprint
createWorkUnit(DocumentedFeature, ClassDoc, Class<?>) GATKHelpDoclet
createWorkUnit(DocumentedFeature, ClassDoc, Class<?>) PicardHelpDoclet
CROSSCHECK_BY CrosscheckFingerprints
CROSSCHECK_LIBRARIES CrosscheckReadGroupFingerprints
Deprecated.
CROSSCHECK_MODE CrosscheckFingerprints
CROSSCHECK_SAMPLES CrosscheckReadGroupFingerprints
Deprecated.
CrosscheckFingerprints picard.fingerprint
Checks that all data in the set of input files appear to come from the same
individual.
CrosscheckFingerprints() CrosscheckFingerprints
CrosscheckMetric picard.fingerprint
A class to hold the result of crosschecking fingerprints.
CrosscheckMetric() CrosscheckMetric
CrosscheckMetric.DataType picard.fingerprint
CrosscheckMetric.FingerprintResult picard.fingerprint
CrosscheckReadGroupFingerprints picard.fingerprint
CrosscheckReadGroupFingerprints() CrosscheckReadGroupFingerprints
Deprecated.
crossContigsToIgnoreFile 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.
csvFile AnalyzeCovariates
Output csv file name.
CsvInputParser picard.util
CsvInputParser(boolean, InputStream...) CsvInputParser
Constructor
CsvInputParser(boolean, File...) CsvInputParser
Constructor
csvPrinter(File, StandardCovariateList) RecalUtils
Returns a csv output printer.
CTG_GOOD_NONCANONICAL_MAPPING GATKSVVCFConstants
CULPRIT_KEY GATKVCFConstants
cumulativeProbability(int) BetaBinomialDistribution
curContig KSWindowFinder
curEnd KSWindowFinder
CURRENT_MINIMUM_DATA_SOURCE_VERSION DataSourceUtils
The minimum version of the data sources required for funcotator to run.
currentChromo ArtificialReadIterator
currentInterval IntervalLocusIterator
currentRead ArtificialReadIterator
CUSHION_FOR_INDELS CycleCovariate
CUSTOM_AMPLICON_SET TargetedPcrMetrics
The name of the amplicon set used in this metrics collection run
CUSTOM_AMPLICON_SET_NAME CollectTargetedPcrMetrics
CustomAFPriorProvider org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
Custom priors provided as an array.
CustomAFPriorProvider(List<Double>) CustomAFPriorProvider
CustomBooleanConverter org.broadinstitute.hellbender.utils.config
Converts a given string into a Boolean after trimming whitespace from that string.
CustomBooleanConverter() CustomBooleanConverter
customCommandLineValidation() CommandLineProgram
Put any custom command-line validation in an override of this method.
customCommandLineValidation() CNNScoreVariants
customCommandLineValidation() AbstractOpticalDuplicateFinderCommandLineProgram
customCommandLineValidation() CollectSequencingArtifactMetrics
customCommandLineValidation() CollectInsertSizeMetrics
Put any custom command-line validation in an override of this method.
customCommandLineValidation() CollectMultipleMetrics
customCommandLineValidation() CollectOxoGMetrics
customCommandLineValidation() CollectRnaSeqMetrics
customCommandLineValidation() CollectRrbsMetrics
customCommandLineValidation() CollectTargetedMetrics
customCommandLineValidation() CommandLineProgram
Put any custom command-line validation in an override of this method.
customCommandLineValidation() BamToBfq
customCommandLineValidation() CheckFingerprint
customCommandLineValidation() CrosscheckFingerprints
customCommandLineValidation() CrosscheckReadGroupFingerprints
Deprecated.
customCommandLineValidation() CheckIlluminaDirectory
customCommandLineValidation() ExtractIlluminaBarcodes
Validate that POSITION >= 1, and that all BARCODEs are the same length and unique
customCommandLineValidation() IlluminaBasecallsToFastq
customCommandLineValidation() IlluminaBasecallsToSam
Put any custom command-line validation in an override of this method.
customCommandLineValidation() MarkIlluminaAdapters
customCommandLineValidation() CollectHiSeqXPfFailMetrics
customCommandLineValidation() AddOrReplaceReadGroups
customCommandLineValidation() CreateSequenceDictionary
Use reference filename to create URI to go into header if URI was not passed on cmd line.
customCommandLineValidation() DownsampleSam
customCommandLineValidation() FastqToSam
customCommandLineValidation() FilterSamReads
customCommandLineValidation() EstimateLibraryComplexity
customCommandLineValidation() AbstractOpticalDuplicateFinderCommandLineProgram
customCommandLineValidation() MergeBamAlignment
Put any custom command-line validation in an override of this method.
customCommandLineValidation() MergeSamFiles
customCommandLineValidation() PositionBasedDownsampleSam
customCommandLineValidation() RevertSam
Enforce that output ordering is queryname when sanitization is turned on since it requires a queryname sort.
customCommandLineValidation() SamToFastq
Put any custom command-line validation in an override of this method.
customCommandLineValidation() SamToFastqWithTags
customCommandLineValidation() SplitSamByNumberOfReads
customCommandLineValidation() ValidateSamFile
customCommandLineValidation() ViewSam
customCommandLineValidation() BaitDesigner
customCommandLineValidation() IntervalListTools
customCommandLineValidation() FixVcfHeader
customCommandLineValidation() GenotypeConcordance
customCommandLineValidation() FindMendelianViolations
Validates that the sex chromosomes don't overlap and parses the pseudo-autosomal regions into usable
objects to ensure their parsability
CUTOFF_LONG_NAME AnnotatePairOrientation
CUTOFF_LONG_NAME ValidateBasicSomaticShortMutations
CUTOFF_SHORT_NAME AnnotatePairOrientation
cutToShards(Iterable<SimpleInterval>, int) IntervalUtils
Splits the given input intervals into shards of at most the requested size.
CYCLE BaseDistributionByCycleMetrics
CYCLE BaseDistributionByCycleMetrics
cycle EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
CYCLE_CONTAINING_TILE_METRICS TileMetricsUtil
The cycle directory that contain the tile metrics output.
CYCLE_SUBDIRECTORY_PATTERN IlluminaFileUtil
CycleCovariate org.broadinstitute.hellbender.utils.recalibration.covariates
The Cycle covariate.
CycleCovariate(RecalibrationArgumentCollection) CycleCovariate
cycleFromKey(int) CycleCovariate
Decodes the cycle number from the key.
cycleKey(int, GATKRead, boolean, int) CycleCovariate
Computes the encoded value of CycleCovariate's key for the given position at the read.
CYCLES_TO_TRIM_LONG_NAME ClipReads
CYCLES_TO_TRIM_SHORT_NAME ClipReads
F ReadEnds
F ReadEnds
F1R2_KEY GATKVCFConstants
F2R1_KEY GATKVCFConstants
failMissingValues 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) UserException.FailsStrictValidation
failsVendorQualityCheck() GATKRead
failsVendorQualityCheck() SAMRecordToGATKReadAdapter
FAIR_BINOMIAL_PROB_LOG10_0_5 MathUtils
FAKE_FILES CheckIlluminaDirectory
fakeBciFile(File, List<Integer>) BciFileFaker
fakeFile(ByteBuffer) BarcodeFileFaker
fakeFile(ByteBuffer) BciFileFaker
fakeFile(ByteBuffer) BclFileFaker
fakeFile(ByteBuffer) ClocsFileFaker
fakeFile(ByteBuffer) FileFaker
fakeFile(File, int, int, String) FileFaker
fakeFile(File, List<Integer>, int, String) FileFaker
fakeFile(File, Integer) FileFaker
fakeFile(ByteBuffer) FilterFileFaker
fakeFile(ByteBuffer) LocsFileFaker
fakeFile(ByteBuffer) MultiTileBclFileFaker
fakeFile(ByteBuffer) MultiTileLocsFileFaker
fakeFile(ByteBuffer) PosFileFaker
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) MultiTileBclFileUtil
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) MultiTileFileUtil
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) 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) PerTileFileUtil
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) PerTilePerCycleFileUtil
faker ParameterizedFileUtil
FakeReferenceSource org.broadinstitute.hellbender.utils.test
FakeReferenceSource() FakeReferenceSource
falseNegative(VariantContext) AbstractConcordanceWalker.TruthVersusEval
falsePositive(VariantContext) AbstractConcordanceWalker.TruthVersusEval
FalsePositiveRecord org.broadinstitute.hellbender.tools.walkers.validation
Created by tsato on 2/14/17.
FalsePositiveRecord(String, long, long, long) FalsePositiveRecord
FAMILY_ID MendelianViolationMetrics
The family ID assigned to the trio for which these metrics are calculated.
FamilyLikelihoods org.broadinstitute.hellbender.tools.walkers.variantutils
Utility to compute genotype posteriors given family priors.
FamilyLikelihoods(SampleDB, double, Set<String>, Map<String, Set<Sample>>) FamilyLikelihoods
FastaReferenceWriter org.broadinstitute.hellbender.utils.reference
Writes a FASTA formatted reference file.
FastaReferenceWriter(Path, boolean, boolean) FastaReferenceWriter
Creates a reference FASTA file writer.
FastaReferenceWriter(Path, int, boolean, boolean) FastaReferenceWriter
Creates a reference FASTA file writer.
FastaReferenceWriter(Path, Path, Path) FastaReferenceWriter
Creates a reference FASTA file writer.
FastaReferenceWriter(Path, int, Path, Path) FastaReferenceWriter
Creates a reference FASTA file writer.
FastaReferenceWriter(OutputStream, int, OutputStream, OutputStream) FastaReferenceWriter
Creates a reference FASTA file writer.
FASTQ FastqToSam
FASTQ SamToFastq
FASTQ2 FastqToSam
fastqDir StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
FastqRead(GATKRead) SVFastqUtils.FastqRead
FastqRead(GATKRead, boolean) SVFastqUtils.FastqRead
FastqToSam picard.sam
Converts a FASTQ file to an unaligned BAM or SAM file.
FastqToSam() FastqToSam
fastRound(double) MathUtils
FastWgsMetricsCollector picard.analysis
Class represents fast algorithm for collecting data from AbstractLocusInfo
with a list of aligned EdgingRecordAndOffset objects.
FastWgsMetricsCollector(CollectWgsMetrics, int, IntervalList) FastWgsMetricsCollector
Creates a collector and initializes the inner data structures
FATHER MendelianViolationMetrics
The ID of the father within the trio.
fdrToTiTv(double, double) TrancheManager
FEATURE_ARGUMENT_KEY_VALUE_PAIR_DELIMITER FeatureInput
Delimiter between key-value pairs in the --argument_name logical_name,key1=value1,key2=value2:feature_file syntax.
FEATURE_ARGUMENT_KEY_VALUE_SEPARATOR FeatureInput
Separator between keys and values in the --argument_name logical_name,key1=value1,key2=value2:feature_file syntax.
FEATURE_ARGUMENT_TAG_DELIMITER FeatureInput
Delimiter between the logical name and the file name in the --argument_name logical_name:feature_file syntax
FEATURE_CACHE_LOOKAHEAD 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 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 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_CACHE_LOOKAHEAD VariantWalkerBase
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 StandardArgumentDefinitions
FEATURE_SHORT_NAME StandardArgumentDefinitions
FeatureContext 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() FeatureContext
Creates an empty FeatureContext with no backing data source.
FeatureContext(FeatureManager, SimpleInterval) 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) FeatureDataSource
Creates a FeatureDataSource backed by the provided File.
FeatureDataSource(String) FeatureDataSource
Creates a FeatureDataSource backed by the provided path.
FeatureDataSource(File, String) FeatureDataSource
Creates a FeatureDataSource backed by the provided File and assigns this data source the specified logical
name.
FeatureDataSource(File, String, int) FeatureDataSource
Creates a FeatureDataSource backed by the provided File and assigns this data source the specified logical
name.
FeatureDataSource(String, String, int, Class<? extends Feature>) FeatureDataSource
Creates a FeatureDataSource backed by the resource at the provided path.
FeatureDataSource(FeatureInput<T>, int, Class<? extends Feature>) FeatureDataSource
Creates a FeatureDataSource backed by the provided FeatureInput.
FeatureDataSource(String, String, int, Class<? extends Feature>, int, int) FeatureDataSource
Creates a FeatureDataSource backed by the resource at the provided path.
FeatureDataSource(FeatureInput<T>, int, Class<? extends Feature>, int, int) FeatureDataSource
Creates a FeatureDataSource backed by the provided FeatureInput.
FeatureDataSource(FeatureInput<T>, int, Class<? extends Feature>, int, int, Path) FeatureDataSource
Creates a FeatureDataSource backed by the provided FeatureInput.
featureFile IndexFeatureFile
featureFiles OptionalFeatureInputArgumentCollection
featureFiles RequiredFeatureInputArgumentCollection
featureFileToIntervals(GenomeLocParser, String) 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>) FeatureInput
Construct a FeatureInput from raw components: name, key value pairs and the file.
FeatureManager 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) 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) 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) 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, Path) FeatureManager
Create a FeatureManager given a CommandLineProgram tool instance, discovering all FeatureInput
arguments in the tool and creating query-able FeatureDataSources for them.
featureOrderNumber GencodeGtfFeatureBaseData
The relative order of this Feature.
features GATKSparkTool
featuresFile ExampleFeatureWalker
featureType 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 Feature at a time from a source of Features, with
optional contextual information from a reference, sets of reads, and/or supplementary sources
of Features.
FeatureWalker() FeatureWalker
FEMALE_CHROMS FindMendelianViolations
FermiLiteAssemblyHandler org.broadinstitute.hellbender.tools.spark.sv.evidence
LocalAssemblyHandler that uses FermiLite.
FermiLiteAssemblyHandler(String, int, String, boolean, boolean, boolean, boolean, int) FermiLiteAssemblyHandler
fetch(long) SeekableByteChannelPrefetcher
FF ReadEnds
FF ReadEnds
FIELD_DELIMITER VcfOutputRenderer
The delimiter for each field within the VCF Funcotation field.
FifoBuffer picard.util
Summary
FifoBuffer(InputStream, PrintStream) FifoBuffer
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their
start/end information logged is often undesirable.
FifoBuffer() FifoBuffer
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their
start/end information logged is often undesirable.
FILE_EXTENSION CollectSequencingArtifactMetrics
FILE_EXTENSION CollectMultipleMetrics
FILE_EXTENSION CollectIlluminaLaneMetrics
FILE_PREFIX BucketUtils
fileExists(String) BucketUtils
Returns true if we can read the first byte of the file.
FileFaker picard.illumina.parser.fakers
FileFaker() FileFaker
filesAvailable() MultiTileBclFileUtil
filesAvailable() MultiTileFileUtil
filesAvailable() ParameterizedFileUtil
Determine whether or not files are available
filesAvailable() PerTileFileUtil
filesAvailable() PerTileOrPerRunFileUtil
filesAvailable() PerTilePerCycleFileUtil
fileSize(String) BucketUtils
Returns the file size of a file pointed to by a GCS/HDFS/local path
fileToTile(String) NewIlluminaDataProvider
fileToTile(String) ParameterizedFileUtil
Returns only lane and tile information as PerTileFt's do not have End information.
FILL_POOLS BaitDesigner
fillContext(ReferenceMultiSource, ContextShard) AddContextDataToReadSparkOptimized
Given a shard that has reads and variants, query Google Genomics' Reference server and get reference info
(including an extra margin on either side), and fill that and the correct variants into readContext.
fillIdx KSWindowFinder
fillQualsFromLikelihood(VariantContext, ReadLikelihoods<Allele>, List<Double>, List<Double>, int) RankSumTest
fillVariants(List<SimpleInterval>, List<GATKVariant>, int) AddContextDataToReadSparkOptimized
Given a list of shards and a list of variants,
add each variant to every (shard+margin) that it overlaps.
fillWithRandomBases(byte[], int, int) BaseUtils
Fill an array section with random bases.
filter(IntPredicate) IndexRange
Find the elements of this range for which an int -> boolean predicate is true
FILTER FilterSamReads
filter(VariantContext) AlleleBalanceFilter
filter(VariantContext, Genotype) DepthFilter
filter(VariantContext) FisherStrandFilter
filter(VariantContext, Genotype) GenotypeFilter
Test whether or not the genotype should be filtered out.
filter(VariantContext, Genotype) GenotypeQualityFilter
filter(VariantContext) QdFilter
filter(VariantContext) VariantFilter
Check to see if the VariantContext should have a filter applied to it.
FILTER_ANALYSIS_LONG_NAME Concordance
FILTER_BWA_IMAGE_LONG_NAME PSFilterArgumentCollection
FILTER_BWA_IMAGE_SHORT_NAME PSFilterArgumentCollection
FILTER_BWA_SEED_LENGTH_LONG_NAME PSFilterArgumentCollection
FILTER_BWA_SEED_LENGTH_SHORT_NAME PSFilterArgumentCollection
FILTER_CANNOT_LIFTOVER_INDEL LiftoverVcf
Filter name to use when a target cannot be lifted over.
FILTER_DUPLICATES_LONG_NAME PSFilterArgumentCollection
FILTER_DUPLICATES_SHORT_NAME PSFilterArgumentCollection
FILTER_ENTRY_SEPARATOR ReadGroupBlackListReadFilter
FILTER_EXPRESSION_LONG_NAME VariantFiltration
FILTER_INDEL_STRADDLES_TWO_INTERVALS 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 PSFilterArgumentCollection
FILTER_METRICS_FILE_SHORT_NAME PSFilterArgumentCollection
FILTER_MISMATCHING_REF_ALLELE LiftoverVcf
Filter name to use when a target is lifted over, but the reference allele doesn't match the new reference.
FILTER_NAME QdFilter
FILTER_NAME_LONG_NAME VariantFiltration
FILTER_NO_TARGET LiftoverVcf
Filter name to use when a target cannot be lifted over.
FILTER_NOT_IN_MASK_LONG_NAME VariantFiltration
FILTER_READS_PER_PARTITION_LONG_NAME PSFilterArgumentCollection
FILTER_READS_PER_PARTITION_SHORT_NAME PSFilterArgumentCollection
FILTER_TOO_SHORT_NAME ReadFilterArgumentDefinitions
FilterAlignmentArtifacts org.broadinstitute.hellbender.tools.walkers.realignmentfilter
Filter false positive alignment artifacts from a VCF callset.
FilterAlignmentArtifacts() FilterAlignmentArtifacts
filterAnalysis Concordance
FilterAnalysisRecord org.broadinstitute.hellbender.tools.walkers.validation
FilterAnalysisRecord(String, int, int, int, int) FilterAnalysisRecord
filterAndConvertToAlignedContigDirect(Iterable<AlignedAssemblyOrExcuse>, List<String>, SAMFileHeader) StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser
Filter out "failed" assemblies, unmapped and secondary (i.e.
filterAndConvertToAlignedContigViaSAM(List<AlignedAssemblyOrExcuse>, SAMFileHeader, JavaSparkContext) StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser
Filters out "failed" assemblies, unmapped and secondary (i.e.
FilterApplyingVariantIterator picard.vcf.filter
Iterator that dynamically applies filter strings to VariantContext records supplied by an underlying
iterator.
FilterApplyingVariantIterator(Iterator<VariantContext>, Collection<VariantFilter>, Collection<GenotypeFilter>) FilterApplyingVariantIterator
Constructs an iterator from an underlying iterator and the provided (possibly empty)
collections of variant and genotype filters.
filterArgs PathSeqFilterSpark
filterArgs PathSeqPipelineSpark
FilterByOrientationBias org.broadinstitute.hellbender.tools.exome
Additionally filter Mutect2 somatic variant calls for sequence context-dependent artifacts, e.g.
FilterByOrientationBias() FilterByOrientationBias
filterDuplicates PSFilterArgumentCollection
If true, then for any two reads with identical sequences (or identical to the other's reverse complement), one
will be filtered.
FILTERED_INDELS CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of indels that are filtered
FILTERED_SNPS CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of SNPs that are filtered
FILTERED_TRUE_NEGATIVES_AND_FALSE_NEGATIVES_LONG_NAME Concordance
FILTERED_TRUE_NEGATIVES_AND_FALSE_NEGATIVES_SHORT_NAME Concordance
filteredCount CountingReadFilter
filteredCount CountingVariantFilter
filteredFalseNegative(VariantContext, VariantContext) AbstractConcordanceWalker.TruthVersusEval
filteredTrueNegative(VariantContext) AbstractConcordanceWalker.TruthVersusEval
filteredTrueNegativesAndFalseNegativesVcf Concordance
filterExpressions VariantFiltration
VariantFiltration accepts any number of JEXL expressions (so you can have two named filters by using
--filterName One --filterExpression "X < 1" --filterName Two --filterExpression "X > 2").
FilterFileFaker picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
FilterFileFaker() FilterFileFaker
FilterFileReader 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) FilterFileReader
FILTERING_STATUS_VCF_KEY Mutect2FilteringEngine
filterMetricsFileUri 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 org.broadinstitute.hellbender.tools.walkers.mutect
Filter variants in a Mutect2 VCF callset.
FilterMutectCalls() FilterMutectCalls
filterNames VariantFiltration
This name is put in the FILTER field for variants that get filtered.
filterOut(SAMRecord) CountingFilter
filterOut(SAMRecord, SAMRecord) CountingFilter
filterPoorlyModeledReads(double) ReadLikelihoods
Removes those read that the best possible likelihood given any allele is just too low.
filterPoorlyModeledReads(double) UnfilledReadsLikelihoods
filterReadsPerPartition PSFilterArgumentCollection
This is a parameter for fine-tuning memory performance.
filterRecordsNotInMask VariantFiltration
By default, if the -mask argument is used, any variant falling in a mask will be filtered.
filterReferenceConfidenceAnnotations(Collection<Annotation>) HaplotypeCallerEngine
Common method to use in order to remove unwanted annotations from the list returned by the plugin specifically
for reference confidence mode.
FilterSamReads picard.sam
Summary
FilterSamReads() FilterSamReads
FilterSamReads.Filter picard.sam
filterSuspectSites() 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.
filterToOnlyOverlappingUnclippedReads(SimpleInterval) ReadLikelihoods
Remove those reads that do not overlap certain genomic location.
filterToOnlyOverlappingUnclippedReads(SimpleInterval) UnfilledReadsLikelihoods
FilterVariantTranches org.broadinstitute.hellbender.tools.walkers.vqsr
Apply tranche filtering to VCF based on scores from the INFO field.
FilterVariantTranches() FilterVariantTranches
FilterVcf picard.vcf.filter
Applies a set of hard filters to Variants and to Genotypes within a VCF.
FilterVcf() FilterVcf
Constructor to default to having index creation on.
FINAL_FIT_FILE_TAG ModelSegments
FINAL_PAIRED_READS PSFilterMetrics
The number of non-host reads that have mates
FINAL_TOTAL_READS PSFilterMetrics
The number of non-host reads in total
FINAL_UNPAIRED_READS PSFilterMetrics
The number of non-host unpaired reads
finalize() ProcessControllerBase
finalizeAndWriteMetrics(LibraryIdGenerator) AbstractMarkDuplicatesCommandLineProgram
Writes the metrics given by the libraryIdGenerator to the METRICS_FILE.
finalizeAndWriteMetrics(LibraryIdGenerator) AbstractMarkDuplicatesCommandLineProgram
Writes the metrics given by the libraryIdGenerator to the METRICS_FILE.
finalizeAnnotations(VariantContext, VariantContext) VariantAnnotatorEngine
Finalize reducible annotations (those that use raw data in gVCFs)
finalizeData() BaseRecalibrationEngine
Finalize, if appropriate, all derived data in recalibrationTables.
finalizeMetrics(Map<String, ExtractIlluminaBarcodes.BarcodeMetric>, ExtractIlluminaBarcodes.BarcodeMetric) ExtractIlluminaBarcodes
finalizeRawData(VariantContext, VariantContext) 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) 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) 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) 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) ReducibleAnnotation
Calculate the final annotation value from the raw data which was generated by either annotateRawData or calculateRawData
finalizeRawData(VariantContext, VariantContext) RMSMappingQuality
finalizeRawMQ(VariantContext) RMSMappingQuality
finalizeRecalibrationTables(RecalibrationTables) BaseRecalibrationEngine
Finalize, if appropriate, all derived data in recalibrationTables.
finalizeRegion(AssemblyRegion, boolean, boolean, byte, SAMFileHeader, SampleList) AssemblyBasedCallerUtils
finalPos ArtificialReadQueryIterator
find(SVInterval) SVIntervalTree
Find an interval.
find(Object) HopscotchCollection
find an entry equivalent to the key, or return null
find(String, Class<?>) ClassFinder
Scans the classpath for classes within the specified package and sub-packages that
extend the parentType.
findAndProcessHeaderLine() TableReader
Process the first lines of the input source until the header line.
FindBadGenomicKmersSpark org.broadinstitute.hellbender.tools.spark.sv.evidence
Identifies sequences that occur at high frequency in a reference
FindBadGenomicKmersSpark() FindBadGenomicKmersSpark
findBestBarcodeAndUpdateMetrics(byte[][], byte[][], boolean, Map<String, ExtractIlluminaBarcodes.BarcodeMetric>, ExtractIlluminaBarcodes.BarcodeMetric, int, int, int, int) ExtractIlluminaBarcodes.PerTileBarcodeExtractor
Find the best barcode match for the given read sequence, and accumulate metrics
FindBreakpointEvidenceSpark org.broadinstitute.hellbender.tools.spark.sv.evidence
(Internal) Produces local assemblies of genomic regions that may harbor structural variants
FindBreakpointEvidenceSpark() FindBreakpointEvidenceSpark
FindBreakpointEvidenceSpark.AssembledEvidenceResults org.broadinstitute.hellbender.tools.spark.sv.evidence
FindBreakpointEvidenceSpark.IntPair org.broadinstitute.hellbender.tools.spark.sv.evidence
FindBreakpointEvidenceSparkArgumentCollection() StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
findByIndex(int) SVIntervalTree
Find the nth interval in the tree.
findChangepoints(int, BiFunction<DATA, DATA, Double>, int, List<Integer>, double, double, KernelSegmenter.ChangepointSortOrder) 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.
findEach(Object) HopscotchCollection
get an iterator over each of the elements equivalent to the key
findFirstPositionWhereHaplotypesDiffer(byte[], byte[]) 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.
findIndexOfClipSequence(byte[], byte[], int, double) 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.
findIndexOfFirstNonClippingOperation(List<CigarElement>, boolean) SvCigarUtils
Returns the index of the first non-clipping operation into the input cigarElements.
findKmer(Kmer) KmerSearchableGraph
Returns the vertex that represents or contains the last base of a given kmer.
findKmer(Kmer) ReadThreadingGraph
FindMendelianViolations picard.vcf.MendelianViolations
Summary
FindMendelianViolations() FindMendelianViolations
findNumberOfRepetitions(byte[], byte[], boolean) GATKVariantContextUtils
Finds number of repetitions a string consists of.
findNumberOfRepetitions(byte[], int, int, byte[], int, int, boolean) GATKVariantContextUtils
Finds number of repetitions a string consists of.
findOpticalDuplicates(List<? extends PhysicalLocation>, PhysicalLocation) OpticalDuplicateFinder
Finds which reads within the list of duplicates that are likely to be optical/co-localized duplicates of
one another.
findPlausiblePairs(List<BwaMemAlignment>, List<BwaMemAlignment>, int) RealignmentEngine
findPreferredFormat(IlluminaDataType, IlluminaFileUtil) IlluminaDataProviderFactory
Given a data type find the most preferred file format even if files are not available
findRepeatedSubstring(byte[]) GATKVariantContextUtils
Find out if a string can be represented as a tandem number of substrings.
findSegmentation(int, double, int, List<Integer>, double, double) AlleleFractionKernelSegmenter
findSegmentation(int, double, int, List<Integer>, double, double) CopyRatioKernelSegmenter
findSegmentation(int, double, double, double, int, List<Integer>, double, double) MultidimensionalKernelSegmenter
findTile(int) TileIndex
findTranche(List<VariantDatum>, TrancheManager.SelectionMetric, double, VariantRecalibratorArgumentCollection.Mode) TrancheManager
findTranches(List<VariantDatum>, List<Double>, TrancheManager.SelectionMetric, VariantRecalibratorArgumentCollection.Mode) TrancheManager
findTranches(List<VariantDatum>, List<Double>, TrancheManager.SelectionMetric, VariantRecalibratorArgumentCollection.Mode, File) TrancheManager
findUnmatchedTypes(Set<IlluminaDataType>, Map<IlluminaFileUtil.SupportedIlluminaFormat, Set<IlluminaDataType>>) 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) TrancheManager
findVQSLODTranches(List<VariantDatum>, List<Double>, TrancheManager.SelectionMetric, VariantRecalibratorArgumentCollection.Mode) TrancheManager
Fingerprint picard.fingerprint
Small 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) Fingerprint
FINGERPRINT_DETAIL_FILE_SUFFIX CheckFingerprint
FINGERPRINT_SUMMARY_FILE_SUFFIX CheckFingerprint
FingerprintChecker 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) FingerprintChecker
Creates a fingerprint checker that will work with the set of haplotypes stored in
the supplied file.
FingerprintChecker(HaplotypeMap) FingerprintChecker
Creates a fingerprint checker that will work with the set of haplotyped provided.
fingerprintFiles(Collection<Path>, int, int, TimeUnit) FingerprintChecker
Fingerprints one or more SAM/BAM/VCF files at all available loci within the haplotype map, using multiple threads
to speed up the processing.
FingerprintIdDetails picard.fingerprint
class to hold the details of a element of fingerprinting PU tag
FingerprintIdDetails() FingerprintIdDetails
FingerprintIdDetails(String, String) FingerprintIdDetails
FingerprintIdDetails(SAMReadGroupRecord, String) FingerprintIdDetails
FingerprintingDetailMetrics picard.analysis
Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.
FingerprintingDetailMetrics() FingerprintingDetailMetrics
FingerprintingSummaryMetrics 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() FingerprintingSummaryMetrics
FingerprintResults 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) FingerprintResults
fingerprintSamFile(Path, IntervalList) FingerprintChecker
Generates a Fingerprint per read group in the supplied SAM file using the loci provided in
the interval list.
FingerprintUtils picard.fingerprint
A set of utilities used in the fingerprinting environment
FingerprintUtils() FingerprintUtils
FingerprintUtils.VariantContextSet picard.fingerprint
A class that holds VariantContexts sorted by genomic position
fingerprintVcf(Path) FingerprintChecker
finish(MetricsFile<InsertSizeMetrics, Integer>, String) InsertSizeMetricsCollector
Finish the metrics collection by saving any results to a metrics file.
finish() MultiLevelCollector
Call finish on all PerUnitMetricCollectors
finish() MultiLevelReducibleCollector
Call finish on all PerUnitMetricCollectors
finish() PerUnitInsertSizeMetricsCollector
finish() PerUnitMetricCollector
When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
finish() QualityYieldMetrics
finish() ExampleMultiMetrics
Complete any calculations/processing.
finish() PerUnitExampleMultiMetricsCollector
finish() ExampleSingleMetrics
finish() CollectSequencingArtifactMetrics
finish() CollectAlignmentSummaryMetrics
finish() CollectBaseDistributionByCycle
finish() CollectGcBiasMetrics
finish() CollectInsertSizeMetrics
finish() CollectQualityYieldMetrics
finish() CollectQualityYieldMetrics.QualityYieldMetricsCollector
finish() CollectRnaSeqMetrics
finish() InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
finish() RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
finish() TargetMetricsCollector.PerUnitTargetMetricCollector
finish() GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
finish() MeanQualityByCycle
finish() QualityScoreDistribution
finish() SinglePassSamProgram
Should be implemented by subclasses to do one-time finalization work.
finish() MultiLevelCollector
Call finish on all PerUnitMetricCollectors
finish() PerUnitMetricCollector
When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
first(int) GenotypeAlleleCounts
Instantiates the first genotype possible provided a total ploidy.
FIRST_OF_PAIR ReadFilterLibrary
FIRST_TILE IlluminaBasecallsToFastq
FIRST_TILE IlluminaBasecallsToSam
firstBase(int) SVKmer
firstBase(int) SVKmerLong
firstBase(int) SVKmerShort
FirstOfPairReadFilter() ReadFilterLibrary.FirstOfPairReadFilter
firstPassApply(GATKRead, ReferenceContext, FeatureContext) TwoPassReadWalker
Process an individual read (with optional contextual information) on the first pass through the reads.
firstPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) TwoPassVariantWalker
First pass through the variants.
firstPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) ExampleTwoPassVariantWalker
firstPassApply(GATKRead, ReferenceContext, FeatureContext) SplitNCigarReads
firstTrimer(int) SVKmer
firstTrimer(int) SVKmerLong
firstTrimer(int) SVKmerShort
FISHER_STRAND_KEY GATKVCFConstants
FisherExactTest org.broadinstitute.hellbender.utils
Implements the Fisher's exact test for 2x2 tables
assuming the null hypothesis of odd ratio of 1.
FisherExactTest() FisherExactTest
FisherStrand org.broadinstitute.hellbender.tools.walkers.annotator
Strand bias estimated using Fisher's Exact Test
FisherStrand() FisherStrand
FisherStrandFilter picard.vcf.filter
Filters records based on the phred scaled p-value from the Fisher Strand test stored in
the FS attribute.
FisherStrandFilter(double) FisherStrandFilter
FIVE_PRIME_ADAPTER IlluminaBasecallsToSam
FIVE_PRIME_ADAPTER MarkIlluminaAdapters
FixCallSetSampleOrdering org.broadinstitute.hellbender.tools
FixCallSetSampleOrdering() FixCallSetSampleOrdering
FixedAFCalculatorProvider org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
A single fixed instance AF calculator provider.
FixedAFCalculatorProvider(StandardCallerArgumentCollection, boolean) FixedAFCalculatorProvider
Constructs a fixed AF Calculator provider.
FixedAFCalculatorProvider(GenotypeCalculationArgumentCollection, boolean) FixedAFCalculatorProvider
Constructs a fixed AF Calculator provider.
FixedAFCalculatorProvider(AFCalculatorImplementation, GenotypeCalculationArgumentCollection, boolean) FixedAFCalculatorProvider
Constructs a fixed AF Calculator provider.
FixedWindowFunction(int, int) ReferenceWindowFunctions.FixedWindowFunction
fixGenotypes(GenotypesContext, List<Allele>, List<Allele>) LiftoverUtils
FixMateInformation picard.sam
Summary
FixMateInformation() FixMateInformation
FixMisencodedBaseQualityReads org.broadinstitute.hellbender.tools
FixMisencodedBaseQualityReads() FixMisencodedBaseQualityReads
fixNmMdAndUq(SAMRecord, ReferenceSequenceFileWalker, boolean) AbstractAlignmentMerger
Calculates and sets the NM, MD, and and UQ tags from the record and the reference
fixOverlaps() ReadPileup
Fixes the quality of all the elements that come from an overlapping pair in the same way as
samtools does
function in
samtools .
fixTooHighQD(double) QualByDepth
The haplotype caller generates very high quality scores when multiple events are on the
same haplotype.
fixUq(SAMRecord, ReferenceSequenceFileWalker, boolean) AbstractAlignmentMerger
Calculates and sets UQ tag from the record and the reference
FixVcfHeader picard.vcf
Tool for replacing or fixing up a VCF header.
FixVcfHeader() FixVcfHeader
FlagStat org.broadinstitute.hellbender.tools
Accumulate flag statistics given a BAM file, e.g.
FlagStat() FlagStat
FlagStat.FlagStatus org.broadinstitute.hellbender.tools
FlagStatSpark org.broadinstitute.hellbender.tools.spark.pipelines
Spark tool to accumulate flag statistics given a BAM file, e.g.
FlagStatSpark() FlagStatSpark
FlagStatus() FlagStat.FlagStatus
flatBAQArray(GATKRead) BaseRecalibrationEngine
Create a BAQ style array that indicates no alignment uncertainty
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>) FlatMapGluer
FlatMapGluer(Function<I, Iterator<O>>, Iterator<? extends I>, I) FlatMapGluer
flattenSplitIntervals(List<List<GenomeLoc>>) IntervalUtils
flip() Snp
Returns a new SNP object with the alleles swapped and MAF corrected.
FLOWCELL_BARCODE BamToBfq
FLOWCELL_BARCODE IlluminaBasecallsToFastq
flush() OverhangFixingManager
Close out the manager stream by clearing the read cache
flushSingleSampleMultiplicity() 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_COUNT GenotypeConcordanceContingencyMetrics
The FN (false negative) count across all variants
FN_ONLY GenotypeConcordanceScheme
fnvByteArray64(byte[]) SVUtils
64-bit FNV-1a hash for byte arrays
fnvByteArray64(long, byte[]) SVUtils
fnvLong64(long) SVUtils
64-bit FNV-1a hash for long's
fnvLong64(long, long) SVUtils
FOB OrientationBiasFilterConstants
FOLD_80_BASE_PENALTY HsMetrics
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 TargetedPcrMetrics
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 TargetMetrics
The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to
the mean coverage level in those targets.
FOLD_ENRICHMENT HsMetrics
The fold by which the baited region has been amplified above genomic background.
FOLD_ENRICHMENT TargetedPcrMetrics
The fold by which the amplicon region has been amplified above genomic background.
FOLD_ENRICHMENT 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(T, Collection<T>) CollectVariantCallingMetrics.VariantCallingSummaryMetrics
FORCE_GC IlluminaBasecallsToFastq
FORCE_GC IlluminaBasecallsToSam
FORCE_PLATFORM RecalibrationArgumentCollection
forceJVMLocaleToUSEnglish() Utils
Set the Locale to US English so that numbers will always be formatted in the US style.
forceKeepAllele(Allele) GenotypingEngine
Checks whether even if the allele is not well supported by the data, we should keep it for genotyping.
forceKeepAllele(Allele) MinimalGenotypingEngine
forceKeepAllele(Allele) HaplotypeCallerGenotypingEngine
forceKeepAllele(Allele) SomaticGenotypingEngine
forceSiteEmission() GenotypingEngine
Indicates whether we have to emit any site no matter what.
forceSiteEmission() MinimalGenotypingEngine
forceSiteEmission() AssemblyBasedCallerGenotypingEngine
forEach(IntConsumer) IndexRange
Iterate through all indexes in the range in ascending order to be processed by the
provided integer consumer lambda function.
forEach(Consumer<? super String>) PathLineIterator
forEachAlleleIndexAndCount(IntBiConsumer) GenotypeAlleleCounts
forKey(byte) XorWrapper
FORMAT_LONG_NAME CollectReadCounts
formatAssemblyID(int) AlignedAssemblyOrExcuse
formatContigInfo(Tuple2<String, List<String>>) AlignedContig
Format provided tigNameAndMappings for debugging.
formatContigName(int, int) AlignedAssemblyOrExcuse
formatDouble(double) CopyNumberFormatsUtils
formatException(String) TableReader
Composes the exception to be thrown due to a formatting error.
formatExceptionWithoutLocation(String) TableReader
Composes the exception to be thrown due to a formatting error.
formatKey(int) ContextCovariate
formatKey(int) Covariate
Converts the internal representation of the key to String format for file output.
formatKey(int) CycleCovariate
formatKey(int) QualityScoreCovariate
formatKey(int) ReadGroupCovariate
formattedValue(double) StrandOddsRatio
formatToDataTypes IlluminaDataProviderFactory
A Map of file formats to the dataTypes they will provide for this run.
forRead(GATKRead) TemplateFragmentOrdinal
forTotalPloidy(int) AFPriorProvider
Returns the priors given a total-ploidy (the total number of genome copies across all samples).
forumPost(String) HelpConstants
forVcf(File) VcfFileSegmentGenerator
FORWARD AS_StrandBiasTest
ForwardBackwardAlgorithm org.broadinstitute.hellbender.utils.hmm
Performs the Forward-backward algorithm for
HMM
on a sequence of data points and positions.
ForwardBackwardAlgorithm() ForwardBackwardAlgorithm
ForwardBackwardAlgorithm.Result D ,T ,S > - Interface in org.broadinstitute.hellbender.utils.hmm
The forward-backward algorithm result query interface.
forwardStrand AlignmentInterval
FourChannelIntensityData picard.illumina.parser
Holds a 4 short values for each cycle of a read.
FourChannelIntensityData(int) FourChannelIntensityData
FP_COUNT GenotypeConcordanceContingencyMetrics
The FP (false positive) count across all variants
FP_FN GenotypeConcordanceScheme
FP_ONLY GenotypeConcordanceScheme
FP_TN GenotypeConcordanceScheme
FP_TN_FN GenotypeConcordanceScheme
FR ReadEnds
FR ReadEnds
FRACTION PositionBasedDownsampleSam
FractionalDownsampler org.broadinstitute.hellbender.utils.downsampling
Fractional Downsampler: selects a specified fraction of the reads for inclusion.
FractionalDownsampler(double) FractionalDownsampler
Construct a FractionalDownsampler
Fragment org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
Class representing a single read fragment at a particular start location without a mapped mate.
Fragment(GATKRead, SAMFileHeader, int, MarkDuplicatesScoringStrategy) Fragment
FRAGMENT_NUMBER_SEPARATOR_CHR SVFastqUtils
FRAGMENT_SIZE_LONG_NAME FilterAlignmentArtifacts
FragmentCollection T > - Class in org.broadinstitute.hellbender.utils.fragments
Represents the results of the reads -> fragment calculation.
FragmentLength org.broadinstitute.hellbender.tools.walkers.annotator
Median fragment length of reads supporting each allele.
FragmentLength() FragmentLength
FragmentLengthReadFilter org.broadinstitute.hellbender.engine.filters
Keep only read pairs (0x1) with absolute insert length less than or equal to the given value.
FragmentLengthReadFilter() FragmentLengthReadFilter
FRAGMENTS JumpingLibraryMetrics
The number of fragments in the SAM file
FragmentUtils org.broadinstitute.hellbender.utils.fragments
from IndexRange
First index in the range.
fromBases(byte[]) DiploidGenotype
Converts a pair of bases into a DiploidGenotype regardless of base order or case
fromBases(byte, byte) DiploidGenotype
Converts a pair of bases into a DiploidGenotype regardless of base order or case
fromCalculatorClass(Class<? extends AFCalculator>) AFCalculatorImplementation
Returns the value that corresponds to a given implementation calculator class.
fromCode(int) Sex
Decodes the Sex from a numeric code.
fromFile(File, boolean) PedFile
Attempts to read a pedigree file into memory.
fromFormatString(String) GATKReportDataType
Returns a GATK report data type from the format string specified.
fromHeader(SAMFileHeader, Metadata.Type) MetadataUtils
fromHeader(String) GATKReportVersion
Returns the GATK Report Version from the file header.
fromIndex(int) Permutation
Given an index on the resulting list, it gives you the index of that element on the original list.
fromIndex(int) AlleleList.ActualPermutation
fromIndex(int) AlleleList.NonPermutation
fromList(List<ReadFilter>, SAMFileHeader) CountingReadFilter
Return a composite (and)
CountingReadFilter constructed from a list of
ReadFilter.
fromList(List<VariantFilter>) CountingVariantFilter
Return a composite (and)
CountingVariantFilter constructed from a list of
VariantFilter.
fromList(List<ReadFilter>, SAMFileHeader) ReadFilter
Return a composite (and) ReadFilter constructed from a list of ReadFilter.
fromList() Permutation
Returns an unmodifiable view to the original element list.
fromList() AlleleList.ActualPermutation
fromList() AlleleList.NonPermutation
fromObject(Object) GATKReportDataType
Returns a GATK report data type from the Object specified.
fromRead(GATKRead, SAMFileHeader) NGSPlatform
Convenience get -- get the NGSPlatform from a Read.
fromReadGroupPL(String) NGSPlatform
Returns the NGSPlatform corresponding to the PL tag in the read group
fromSexMap(Map<String, Sex>) PedFile
Function that accepts a map from sample-name to its sex and creates a PEDFile documenting the sexes.
fromSize() Permutation
Length of the original element list.
fromSize() AlleleList.ActualPermutation
fromSize() AlleleList.NonPermutation
Funcotation org.broadinstitute.hellbender.tools.funcotator
Abstract class representing a
Funcotator annotation.
Funcotator 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() Funcotator
FUNCOTATOR_VCF_FIELD_NAME VcfOutputRenderer
The name of the field inside the VCF INFO field in which to put
Funcotator results.
FuncotatorArgumentDefinitions org.broadinstitute.hellbender.tools.funcotator
Class to store argument definitions specific to
Funcotator.
FuncotatorArgumentDefinitions() FuncotatorArgumentDefinitions
FuncotatorArgumentDefinitions.DataSourceType org.broadinstitute.hellbender.tools.funcotator
An enum to handle the different types of input files for data sources.
FuncotatorArgumentDefinitions.OutputFormatType org.broadinstitute.hellbender.tools.funcotator
The file format of the output file.
FuncotatorUtils org.broadinstitute.hellbender.tools.funcotator
FuncotatorUtils.TranscriptCodingSequenceException org.broadinstitute.hellbender.tools.funcotator
Class representing exceptions that arise when trying to create a coding sequence for a variant:
FWD_CXT_ALT_BASES SequencingArtifactMetrics.BaitBiasDetailMetrics
The number of REF_BASE:ALT_BASE alignments at sites with the given reference context.
FWD_CXT_REF_BASES SequencingArtifactMetrics.BaitBiasDetailMetrics
The number of REF_BASE:REF_BASE alignments at sites with the given reference context.
FWD_ERROR_RATE 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>) SVIntervalTree.FwdIterator
G_FOLLOWED_BY_INSERTION_BASE PileupElement
G_REF_ALT_BASES CollectOxoGMetrics.CpcgMetrics
The number of alt (A/T) basecalls observed at sites where the genome reference == G.
G_REF_OXO_ERROR_RATE 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 CollectOxoGMetrics.CpcgMetrics
G_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
G_REF_REF_BASES CollectOxoGMetrics.CpcgMetrics
The number of ref basecalls observed at sites where the genome reference == G.
GA4GH_CLIENT_SECRETS CommandLineProgram
GA4GHScheme picard.vcf
The scheme is defined in the constructor.
GA4GHScheme() GA4GHScheme
GA4GHSchemeWithMissingAsHomRef picard.vcf
The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme.
GA4GHSchemeWithMissingAsHomRef() GA4GHSchemeWithMissingAsHomRef
gapLen(SVInterval) SVInterval
GAPPED_ALIGNMENT_BREAK_DEFAULT_SENSITIVITY StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection
GATHER_TYPE_LONG_NAME GatherVcfsCloud
GatherBamFiles picard.sam
Concatenate efficiently BAM files that resulted from a scattered parallel analysis.
GatherBamFiles() GatherBamFiles
GatherBQSRReports org.broadinstitute.hellbender.tools.walkers.bqsr
GatherBQSRReports() GatherBQSRReports
gatherEvidenceAndWriteContigSamFile(JavaSparkContext, StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection, SAMFileHeader, JavaRDD<GATKRead>, String, Logger) FindBreakpointEvidenceSpark
Gathers evidence reads and outputs them in a directory where reads are written out as interleaved FASTQ's.
gatherReports(List<File>) RecalibrationReport
gatherReportsIntoOneFile(List<File>, File) RecalibrationReport
GatherTranches org.broadinstitute.hellbender.tools.walkers.vqsr
GatherTranches() GatherTranches
gatherType GatherVcfsCloud
GatherVcfs picard.vcf
Simple little class that combines multiple VCFs that have exactly the same set of samples
and totally discrete sets of loci.
GatherVcfs() GatherVcfs
GatherVcfsCloud org.broadinstitute.hellbender.tools
This tool combines together rows of variant calls from multiple VCFs, e.g.
GatherVcfsCloud() GatherVcfsCloud
GatherVcfsCloud.GatherType org.broadinstitute.hellbender.tools
GATK_CONFIG_FILE CommandLineProgram
GATK_CONFIG_FILE_OPTION StandardArgumentDefinitions
The option specifying a main configuration file.
GATK_FORUM_URL HelpConstants
GATK_MAIN_SITE HelpConstants
gatk_stacktrace_on_user_exception() GATKConfig
GATKAnnotationArgumentCollection 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() GATKAnnotationArgumentCollection
GATKAnnotationPluginDescriptor org.broadinstitute.hellbender.cmdline.GATKPlugin
A plugin descriptor for managing the dynamic discovery of both
InfoFieldAnnotation and
GenotypeAnnotation objects
within the packages defined by the method getPackageNames() (default
org.broadinstitute.hellbender.tools.walkers.annotator).
GATKAnnotationPluginDescriptor(GATKAnnotationArgumentCollection, List<Annotation>, List<Class<? extends Annotation>>) 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(List<Annotation>, List<Class<? extends Annotation>>) 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.
GATKConfig 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 org.broadinstitute.hellbender.utils.help
Custom DocWorkUnit used for generating GATK help/documentation.
GATKDocWorkUnit(DocWorkUnitHandler, DocumentedFeature, ClassDoc, Class<?>) GATKDocWorkUnit
GATKDuplicationMetrics org.broadinstitute.hellbender.utils.read.markduplicates
Metrics that are calculated during the process of marking duplicates
within a stream of SAMRecords.
GATKDuplicationMetrics() GATKDuplicationMetrics
GATKException org.broadinstitute.hellbender.exceptions
GATKException(String) GATKException
GATKException(String, Throwable) GATKException
GATKException.MissingReadField org.broadinstitute.hellbender.exceptions
GATKException.ReadAttributeTypeMismatch org.broadinstitute.hellbender.exceptions
GATKException.ShouldNeverReachHereException org.broadinstitute.hellbender.exceptions
For wrapping errors that are believed to never be reachable
GATKGSONWorkUnit org.broadinstitute.hellbender.utils.help
Class representing a GSONWorkUnit for GATK work units.
GATKGSONWorkUnit() GATKGSONWorkUnit
GATKHelpDoclet org.broadinstitute.hellbender.utils.help
Custom Barclay-based Javadoc Doclet used for generating GATK help/documentation.
GATKHelpDoclet() GATKHelpDoclet
GATKHelpDocWorkUnitHandler org.broadinstitute.hellbender.utils.help
The GATK Documentation work unit handler class that is the companion to GATKHelpDoclet.
GATKHelpDocWorkUnitHandler(HelpDoclet) GATKHelpDocWorkUnitHandler
GATKProtectedVariantContextUtils org.broadinstitute.hellbender.utils
Miscellaneous utilities to work with Variant data structures.
GATKProtectedVariantContextUtils() GATKProtectedVariantContextUtils
GATKRead org.broadinstitute.hellbender.utils.read
Unified read interface for use throughout the GATK.
GATKReadFilterArgumentCollection 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() GATKReadFilterArgumentCollection
GATKReadFilterPluginDescriptor org.broadinstitute.hellbender.cmdline.GATKPlugin
A CommandLinePluginDescriptor for ReadFilter plugins
GATKReadFilterPluginDescriptor(GATKReadFilterArgumentCollection, List<ReadFilter>) GATKReadFilterPluginDescriptor
GATKReadFilterPluginDescriptor(List<ReadFilter>) GATKReadFilterPluginDescriptor
GATKReadToBDGAlignmentRecordConverter org.broadinstitute.hellbender.utils.read
Converts a GATKRead to a BDG AlignmentRecord
GATKReadToBDGAlignmentRecordConverter(SAMFileHeader) GATKReadToBDGAlignmentRecordConverter
GATKReadWriter org.broadinstitute.hellbender.utils.read
Interface for classes that are able to write GATKReads to some output destination.
GATKRegistrator org.broadinstitute.hellbender.engine.spark
GATKRegistrator registers Serializers for our project.
GATKRegistrator() GATKRegistrator
GATKReport org.broadinstitute.hellbender.utils.report
Container class for GATK report tables
GATKReport() GATKReport
Create a new, empty GATKReport.
GATKReport(String) GATKReport
Create a new GATKReport with the contents of a GATKReport on disk.
GATKReport(File) GATKReport
Create a new GATKReport with the contents of a GATKReport on disk.
GATKReport(InputStream) GATKReport
GATKReport(GATKReportTable...) GATKReport
Create a new GATK report from GATK report tables
GATKREPORT_HEADER_PREFIX GATKReport
GATKReportColumn org.broadinstitute.hellbender.utils.report
column information within a GATK report table
GATKReportColumn(String, String) GATKReportColumn
Construct the column object, specifying the column name, default value, whether or not the column should be
displayed, and the format string.
GATKReportColumnFormat org.broadinstitute.hellbender.utils.report
Column width and left/right alignment.
GATKReportColumnFormat(int, GATKReportColumnFormat.Alignment) GATKReportColumnFormat
GATKReportColumnFormat.Alignment org.broadinstitute.hellbender.utils.report
GATKReportDataType org.broadinstitute.hellbender.utils.report
The gatherable data types acceptable in a GATK report column.
GATKReportTable org.broadinstitute.hellbender.utils.report
GATKReportTable(BufferedReader, GATKReportVersion) 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) GATKReportTable
GATKReportTable(String, String, int, GATKReportTable.Sorting) GATKReportTable
Construct a new GATK report table with the specified name and description and whether to sort rows by the row ID.
GATKReportTable.Sorting org.broadinstitute.hellbender.utils.report
GATKReportTable.TableDataHeaderFields org.broadinstitute.hellbender.utils.report
GATKReportTable.TableNameHeaderFields org.broadinstitute.hellbender.utils.report
GATKReportVersion org.broadinstitute.hellbender.utils.report
GATKSparkTool org.broadinstitute.hellbender.engine.spark
Base class for GATK spark tools that accept standard kinds of inputs (reads, reference, and/or intervals).
GATKSparkTool() GATKSparkTool
GATKSV_CONTIG_ALIGNMENTS_READ_GROUP_ID SVUtils
GATKSVVCFConstants org.broadinstitute.hellbender.tools.spark.sv.utils
GATKSVVCFConstants() GATKSVVCFConstants
GATKSVVCFHeaderLines org.broadinstitute.hellbender.tools.spark.sv.utils
GATKSVVCFHeaderLines() GATKSVVCFHeaderLines
GATKTool org.broadinstitute.hellbender.engine
Base class for all GATK tools.
GATKTool() GATKTool
GATKVariant org.broadinstitute.hellbender.utils.variant
Variant is (currently) a minimal variant interface needed by the Hellbender pipeline.
GATKVariantContextUtils org.broadinstitute.hellbender.utils.variant
GATKVariantContextUtils() GATKVariantContextUtils
GATKVariantContextUtils.AlleleMapper org.broadinstitute.hellbender.utils.variant
GATKVariantContextUtils.FilteredRecordMergeType org.broadinstitute.hellbender.utils.variant
GATKVariantContextUtils.GenotypeMergeType org.broadinstitute.hellbender.utils.variant
GATKVCFConstants org.broadinstitute.hellbender.utils.variant
This class contains any constants (primarily FORMAT/INFO keys) in VCF files used by the GATK.
GATKVCFConstants() GATKVCFConstants
GATKVCFHeaderLines org.broadinstitute.hellbender.utils.variant
This class contains the
VCFHeaderLine definitions for the annotation keys in
GATKVCFConstants.
GATKVCFHeaderLines() GATKVCFHeaderLines
GATKVCFIndexType org.broadinstitute.hellbender.utils.variant
Choose the Tribble indexing strategy
GC GcBiasDetailMetrics
The G+C content of the reference sequence represented by this bin.
GC_CONTENT_KEY GATKVCFConstants
GC_CURVE_STANDARD_DEVIATION_LONG_NAME GermlineDenoisingModelArgumentCollection
GC_DROPOUT HsMetrics
A measure of how undercovered >= 50% GC regions are relative to the mean.
GC_DROPOUT TargetedPcrMetrics
A measure of how regions of high GC content (>= 50% GC) are undercovered relative to the mean coverage
value.
GC_DROPOUT TargetMetrics
A measure of how undercovered >= 50% GC regions are relative to the mean.
GC_DROPOUT GcBiasSummaryMetrics
Illumina-style GC dropout metric.
GC_NC_0_19 GcBiasSummaryMetrics
Normalized coverage over quintile of GC content ranging from 0 - 19.
GC_NC_20_39 GcBiasSummaryMetrics
Normalized coverage over each quintile of GC content ranging from 20 - 39.
GC_NC_40_59 GcBiasSummaryMetrics
Normalized coverage over each quintile of GC content ranging from 40 - 59.
GC_NC_60_79 GcBiasSummaryMetrics
Normalized coverage over each quintile of GC content ranging from 60 - 79.
GC_NC_80_100 GcBiasSummaryMetrics
Normalized coverage over each quintile of GC content ranging from 80 - 100.
GCBiasCorrector org.broadinstitute.hellbender.tools.copynumber.denoising
Learn multiplicative correction factors as a function of GC content using a simple regression.
GcBiasDetailMetrics picard.analysis
Class that holds detailed metrics about reads that fall within windows of a certain
GC bin on the reference genome.
GcBiasDetailMetrics() GcBiasDetailMetrics
GcBiasMetrics picard.metrics
GcBiasMetrics() GcBiasMetrics
GcBiasMetricsCollector picard.analysis
Calculates GC Bias Metrics on multiple levels
Created by kbergin on 3/23/15.
GcBiasMetricsCollector(Set<MetricAccumulationLevel>, int[], List<SAMReadGroupRecord>, int, boolean) GcBiasMetricsCollector
GcBiasMetricsCollector(Set<MetricAccumulationLevel>, int[], List<SAMReadGroupRecord>, int, boolean, boolean) GcBiasMetricsCollector
GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector picard.analysis
GcBiasSummaryMetrics picard.analysis
High level metrics that capture how biased the coverage in a certain lane is.
GcBiasSummaryMetrics() GcBiasSummaryMetrics
GcBiasUtils picard.analysis
Utilities to calculate GC Bias
Created by kbergin on 9/23/15.
GcBiasUtils() GcBiasUtils
gcpHMM LikelihoodEngineArgumentCollection
GCS_PREFIX BucketUtils
gcsMaxRetries() GATKConfig
GENBANK_CATALOG_LONG_NAME PathSeqBuildReferenceTaxonomy
GENBANK_CATALOG_SHORT_NAME PathSeqBuildReferenceTaxonomy
genbankCatalogPath 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.
GENCODE_GTF_FILE_EXTENSION GencodeGtfCodec
GENCODE_GTF_FILE_PREFIX GencodeGtfCodec
GENCODE_GTF_MAX_VERSION_NUM_INCLUSIVE GencodeGtfCodec
Maximum version of gencode that will not generate a warning.
GENCODE_GTF_MIN_VERSION_NUM_INCLUSIVE GencodeGtfCodec
GencodeFuncotation org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode
A class to represent a Functional Annotation from the Gencode data source.
GencodeFuncotation() GencodeFuncotation
GencodeFuncotation(GencodeFuncotation) GencodeFuncotation
GencodeFuncotation.VariantClassification org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode
Represents the type and severity of a variant.
GencodeFuncotation.VariantType org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode
GencodeFuncotationBuilder org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode
GencodeFuncotationBuilder() GencodeFuncotationBuilder
GencodeFuncotationFactory org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode
GencodeFuncotationFactory(Path, String, String, TranscriptSelectionMode, Set<String>, LinkedHashMap<String, String>) GencodeFuncotationFactory
GencodeGtfCDSFeature org.broadinstitute.hellbender.utils.codecs.gencode
A Gencode GTF Feature representing a CDS.
GencodeGtfCodec org.broadinstitute.hellbender.utils.codecs.gencode
Tribble Codec to read data from a GENCODE GTF file.
GencodeGtfCodec() GencodeGtfCodec
GencodeGtfExonFeature org.broadinstitute.hellbender.utils.codecs.gencode
A Gencode GTF Feature representing an exon.
GencodeGtfFeature org.broadinstitute.hellbender.utils.codecs.gencode
GencodeGtfFeature(String[]) GencodeGtfFeature
Populate this GencodeGtfFeature with the given data.
GencodeGtfFeature(GencodeGtfFeatureBaseData) GencodeGtfFeature
Populate this GencodeGtfFeature with the given data.
GencodeGtfFeature.AnnotationSource org.broadinstitute.hellbender.utils.codecs.gencode
Keyword identifying the source of the feature, like a program
(e.g.
GencodeGtfFeature.FeatureTag org.broadinstitute.hellbender.utils.codecs.gencode
Additional relevant information appended to a feature.
GencodeGtfFeature.FeatureType org.broadinstitute.hellbender.utils.codecs.gencode
Type of the feature represented in a single line of a GENCODE GTF File.
GencodeGtfFeature.GeneTranscriptStatus org.broadinstitute.hellbender.utils.codecs.gencode
Indication of whether a feature is new, tenatative, or already known.
GencodeGtfFeature.GeneTranscriptType org.broadinstitute.hellbender.utils.codecs.gencode
Biotype / transcript type for the transcript or gene represented in a feature.
GencodeGtfFeature.GenomicPhase org.broadinstitute.hellbender.utils.codecs.gencode
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.LocusLevel org.broadinstitute.hellbender.utils.codecs.gencode
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.gencode
GencodeGtfFeature.RemapStatus org.broadinstitute.hellbender.utils.codecs.gencode
Attribute that indicates the status of the mapping.
GencodeGtfFeature.RemapTargetStatus org.broadinstitute.hellbender.utils.codecs.gencode
Attribute that compares the mapping to the existing target annotations.
GencodeGtfFeature.TranscriptSupportLevel org.broadinstitute.hellbender.utils.codecs.gencode
Transcript score according to how well mRNA and EST alignments match over its full length.
GencodeGtfFeatureBaseData org.broadinstitute.hellbender.utils.codecs.gencode
Struct-like container class for the fields in a
GencodeGtfFeature
This is designed to be a basic dummy class to make feature instantiation easier.
GencodeGtfFeatureBaseData() GencodeGtfFeatureBaseData
GencodeGtfFeatureBaseData(int, String, GencodeGtfFeature.AnnotationSource, GencodeGtfFeature.FeatureType, int, int, Strand, GencodeGtfFeature.GenomicPhase, String, String, GencodeGtfFeature.GeneTranscriptType, GencodeGtfFeature.GeneTranscriptStatus, String, GencodeGtfFeature.GeneTranscriptType, GencodeGtfFeature.GeneTranscriptStatus, String, int, String, GencodeGtfFeature.LocusLevel, List<GencodeGtfFeature.OptionalField<?>>, String) GencodeGtfFeatureBaseData
GencodeGtfGeneFeature org.broadinstitute.hellbender.utils.codecs.gencode
A Gencode GTF Feature representing a gene.
GencodeGtfSelenocysteineFeature org.broadinstitute.hellbender.utils.codecs.gencode
A Gencode GTF Feature representing a selenocysteine.
GencodeGtfStartCodonFeature org.broadinstitute.hellbender.utils.codecs.gencode
A Gencode GTF Feature representing a start codon.
GencodeGtfStopCodonFeature org.broadinstitute.hellbender.utils.codecs.gencode
A Gencode GTF Feature representing a stop codon.
GencodeGtfTranscriptFeature org.broadinstitute.hellbender.utils.codecs.gencode
A Gencode GTF Feature representing a transcript.
GencodeGtfUTRFeature org.broadinstitute.hellbender.utils.codecs.gencode
A Gencode GTF Feature representing an untranslated region.
Gene picard.annotation
Holds annotation of a gene for storage in an OverlapDetector.
Gene(String, int, int, boolean, String) Gene
Gene.Transcript picard.annotation
A single transcript of a gene.
Gene.Transcript.Exon picard.annotation
1-based, inclusive representation of an exon.
GeneAnnotationReader picard.annotation
Load gene annotations into an OverlapDetector of Gene objects.
GeneAnnotationReader() GeneAnnotationReader
geneId GencodeGtfFeatureBaseData
geneName GencodeGtfFeatureBaseData
GeneralPloidyExactAFCalculator org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
GeneralPloidyExactAFCalculator() GeneralPloidyExactAFCalculator
GeneralPloidyFailOverAFCalculatorProvider org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
Provider that defaults to the general ploidy implementation when the preferred one does not handle the required
ploidy.
GeneralPloidyFailOverAFCalculatorProvider(GenotypeCalculationArgumentCollection) GeneralPloidyFailOverAFCalculatorProvider
Creates a new AF calculator provider given the genotyping arguments and logger reference.
generateAdditionalWriters(List<SAMReadGroupRecord>, FastqWriterFactory) SamToFastq
generateAdditionalWriters(List<SAMReadGroupRecord>, FastqWriterFactory) SamToFastqWithTags
generateCigarList(int) ReadClipperTestUtils
This function generates every valid permutation of cigar strings (with a given set of cigarElement) with a given length.
generateCigarList(int, CigarElement[]) ReadClipperTestUtils
This function generates every valid permutation of cigar strings (with a given set of cigarElement) with a given length.
generateCsv(File, Map<String, RecalibrationReport>) 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).
generateFilterString(double) ApplyVQSR
Generate the VCF filter string for this record based on the provided lod score
generateFilterStringFromAlleles(VariantContext, double) ApplyVQSR
Generate the VCF filter string for this record based on the ApplyRecalibration modes run so far
generateHiddenStateChain(List<T>) HMM
generateModel(List<VariantDatum>, int) VariantRecalibratorEngine
generatePlots(File, File, File) RecalUtils
s
Write recalibration plots into a file
generatePythonArguments(GermlineCNVCaller.RunMode) GermlineCallingArgumentCollection
generatePythonArguments(DetermineGermlineContigPloidy.RunMode) GermlineContigPloidyModelArgumentCollection
generatePythonArguments(GermlineCNVCaller.RunMode) GermlineDenoisingModelArgumentCollection
Generates arguments for the python CLI tool.
generatePythonArguments() HybridADVIArgumentCollection
generateReadName(ClusterData, Integer) Casava18ReadNameEncoder
generateReadName(ClusterData, Integer) IlluminaReadNameEncoder
generateReadName(ClusterData, Integer) ReadNameEncoder
Generates a read name string for the provided cluster.
generateReportTable() QuantizationInfo
generateReportTable(String) RecalibrationArgumentCollection
generateReportTables(RecalibrationTables, StandardCovariateList) RecalUtils
generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, int, Histogram<Integer>, int) CollectRawWgsMetrics
generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, int, Histogram<Integer>, int) CollectWgsMetrics
generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, int, Histogram<Integer>, int) CollectWgsMetricsWithNonZeroCoverage
generatingAccumulatorsBy(VariantProcessor.AccumulatorGenerator<A, R>) VariantProcessor.Builder
geneStatus GencodeGtfFeatureBaseData
geneType GencodeGtfFeatureBaseData
GENOME_ASSEMBLY CreateSequenceDictionary
GENOME_SIZE HsMetrics
The number of bases in the reference genome used for alignment.
GENOME_SIZE TargetedPcrMetrics
The number of bases in the reference genome used for alignment
GENOME_SIZE TargetMetrics
The number of bases in the reference genome used for alignment.
GENOME_TERRITORY CollectWgsMetrics.WgsMetrics
The number of non-N bases in the genome reference over which coverage will be evaluated.
GenomeLoc org.broadinstitute.hellbender.utils
Genome location representation.
GenomeLoc(String, int, int, int) GenomeLoc
GenomeLocParser org.broadinstitute.hellbender.utils
Factory class for creating GenomeLocs
GenomeLocParser(ReferenceSequenceFile) GenomeLocParser
set our internal reference contig order
GenomeLocParser(SAMSequenceDictionary) GenomeLocParser
Create a new GenomeLocParser based on seqDictionary with the standard validation level
GenomeLocParser(SAMSequenceDictionary, GenomeLocParser.ValidationLevel) GenomeLocParser
Create a genome loc parser based on seqDict with the specified level of validation
GenomeLocParser.ValidationLevel org.broadinstitute.hellbender.utils
How much validation should we do at runtime with this parser?
genomeLocsFromLocatables(GenomeLocParser, Collection<? extends Locatable>) IntervalUtils
Generates a list of
GenomeLoc instances given the appropriate
GenomeLocParser factory
and a collection of
Locatable instances.
GenomeLocSortedSet org.broadinstitute.hellbender.utils
Class GenomeLocCollection
a set of genome locations.
GenomeLocSortedSet(GenomeLocParser) GenomeLocSortedSet
Create a new, empty GenomeLocSortedSet
GenomeLocSortedSet(GenomeLocParser, GenomeLoc) GenomeLocSortedSet
Create a new GenomeLocSortedSet containing location e
GenomeLocSortedSet(GenomeLocParser, Collection<GenomeLoc>) GenomeLocSortedSet
Create a new GenomeLocSortedSet containing locations l
The elements in l can be in any order, and can be overlapping.
GENOMIC_DB_URI_SCHEME FeatureDataSource
identifies a path as a GenomicsDB URI
genomicPhase GencodeGtfFeatureBaseData
Frame/phase of this feature.
genomicPosition GencodeGtfFeatureBaseData
Location of this feature on the genome.
GenomicsDBConstants org.broadinstitute.hellbender.tools.genomicsdb
Constants related to GenomicsDB
GenomicsDBImport org.broadinstitute.hellbender.tools.genomicsdb
Import single-sample GVCFs into GenomicsDB before joint genotyping.
GenomicsDBImport() GenomicsDBImport
GenomicsDBTestUtils org.broadinstitute.hellbender.utils.test
genomicStrand GencodeGtfFeatureBaseData
Which strand this feature is on.
GENOTYPE_AND_VALIDATE_STATUS_KEY GATKVCFConstants
GENOTYPE_CONCORDANCE GenotypeConcordanceSummaryMetrics
The genotype concordance for all possible states.
GENOTYPE_FILTER_EXPRESSION_LONG_NAME VariantFiltration
GENOTYPE_FILTER_NAME_LONG_NAME VariantFiltration
GENOTYPE_GERMLINE_SITES_LONG_NAME M2ArgumentCollection
GENOTYPE_LOD_THRESHOLD CheckFingerprint
GENOTYPE_PON_SITES_LONG_NAME M2ArgumentCollection
GENOTYPE_PRIOR_KEY GATKVCFConstants
GenotypeAlleleCounts org.broadinstitute.hellbender.tools.walkers.genotyper
Collection of allele counts for a genotype.
genotypeAlleleCountsAt(int) GenotypeLikelihoodCalculator
Returns the genotype associated to a particular likelihood index.
GenotypeAnnotation org.broadinstitute.hellbender.tools.walkers.annotator
Represents an annotation that is computed for a single genotype.
GenotypeAnnotation() GenotypeAnnotation
genotypeArgs StandardCallerArgumentCollection
GenotypeAssignmentMethod org.broadinstitute.hellbender.tools.walkers.genotyper
Created by davidben on 6/10/16.
GenotypeCalculationArgumentCollection org.broadinstitute.hellbender.tools.walkers.genotyper
GenotypeCalculationArgumentCollection() GenotypeCalculationArgumentCollection
Creates a GenotypeCalculationArgumentCollection with default values.
GenotypeCalculationArgumentCollection(GenotypeCalculationArgumentCollection) GenotypeCalculationArgumentCollection
Creates a GenotypeCalculationArgumentCollection with the values from other
GenotypeConcordance picard.vcf
Summary
GenotypeConcordance() GenotypeConcordance
GenotypeConcordance.Alleles picard.vcf
A simple structure to return the results of getAlleles.
GenotypeConcordanceContingencyMetrics picard.vcf
Class that holds metrics about the Genotype Concordance contingency tables.
GenotypeConcordanceContingencyMetrics() GenotypeConcordanceContingencyMetrics
Empty constructor - needed for unit tests
GenotypeConcordanceContingencyMetrics(VariantContext.Type, GenotypeConcordanceCounts, String, String, boolean) GenotypeConcordanceContingencyMetrics
GenotypeConcordanceCounts picard.vcf
A class to store the counts for various truth and call state classifications relative to a reference.
GenotypeConcordanceCounts() GenotypeConcordanceCounts
GenotypeConcordanceDetailMetrics picard.vcf
Class that holds detail metrics about Genotype Concordance
GenotypeConcordanceDetailMetrics() GenotypeConcordanceDetailMetrics
GenotypeConcordanceScheme 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() GenotypeConcordanceScheme
GenotypeConcordanceSchemeFactory picard.vcf
Created by kbergin on 6/19/15.
GenotypeConcordanceSchemeFactory() GenotypeConcordanceSchemeFactory
GenotypeConcordanceStateCodes picard.vcf
Created by kbergin on 7/30/15.
GenotypeConcordanceStates picard.vcf
A class to store the various classifications for:
1.
GenotypeConcordanceStates() GenotypeConcordanceStates
GenotypeConcordanceStates.CallState picard.vcf
These states represent the relationship between the call genotype and the truth genotype relative to
a reference sequence.
GenotypeConcordanceStates.ContingencyState picard.vcf
A specific state for a 2x2 contingency table.
GenotypeConcordanceStates.TruthAndCallStates picard.vcf
A minute class to store the truth and call state respectively.
GenotypeConcordanceStates.TruthState picard.vcf
These states represent the relationship between a truth genotype and the reference sequence.
GenotypeConcordanceSummaryMetrics picard.vcf
Class that holds summary metrics about Genotype Concordance
GenotypeConcordanceSummaryMetrics() GenotypeConcordanceSummaryMetrics
Empty constructor - needed for unit tests
GenotypeConcordanceSummaryMetrics(VariantContext.Type, GenotypeConcordanceCounts, String, String, boolean) GenotypeConcordanceSummaryMetrics
genotypeCount() GenotypeLikelihoodCalculator
Returns the number of possible genotypes given ploidy and the maximum allele index.
genotypeCount(int, int) GenotypeLikelihoodCalculators
Returns the number of possible genotypes given the ploidy and number of different alleles.
GenotypeCounts org.broadinstitute.hellbender.utils
GenotypeCounts(double, double, double) GenotypeCounts
GenotypeFilter picard.vcf.filter
An interface for classes that perform Genotype filtration.
genotypeFilteredAlleles StandardCallerArgumentCollection
When set to true an when in GENOTYPE_GIVEN_ALLELES mode all given alleles, even filtered ones, are genotyped
genotypeFilterExpressions VariantFiltration
Similar to the INFO field based expressions, but used on the FORMAT (genotype) fields instead.
genotypeFilterNames VariantFiltration
Similar to the INFO field based expressions, but used on the FORMAT (genotype) fields instead.
genotypeGermlineSites M2ArgumentCollection
Usually we exclude sites in the panel of normals from active region determination, which saves time.
GenotypeGVCFs org.broadinstitute.hellbender.tools.walkers
Perform joint genotyping on one or more samples pre-called with HaplotypeCaller
GenotypeGVCFs() GenotypeGVCFs
genotypeIndexMap(int[], GenotypeLikelihoodCalculators) GenotypeLikelihoodCalculator
Composes a genotype index map given a allele index recoding.
GenotypeLikelihoodCalculator org.broadinstitute.hellbender.tools.walkers.genotyper
Helper to calculate genotype likelihoods given a ploidy and an allele count (number of possible distinct alleles).
GenotypeLikelihoodCalculator(int, int, int[][], GenotypeAlleleCounts[][]) GenotypeLikelihoodCalculator
Creates a new calculator providing its ploidy and number of genotyping alleles.
GenotypeLikelihoodCalculators org.broadinstitute.hellbender.tools.walkers.genotyper
Genotype likelihood calculator utility.
GenotypeLikelihoodCalculators() GenotypeLikelihoodCalculators
genotypeLikelihoods(LikelihoodMatrix<A>) GenotypeLikelihoodCalculator
Calculate the likelihoods given the list of alleles and the likelihood map.
GenotypeLikelihoodsCalculationModel org.broadinstitute.hellbender.tools.walkers.genotyper
The model representing how we calculate genotype likelihoods
genotypePonSites M2ArgumentCollection
Usually we exclude sites in the panel of normals from active region determination, which saves time.
GenotypeQualityFilter picard.vcf.filter
Genotype filter that filters out genotypes below a given quality threshold.
GenotypeQualityFilter(int) GenotypeQualityFilter
GENOTYPES CheckFingerprint
GenotypeSummaries org.broadinstitute.hellbender.tools.walkers.annotator
Summarize genotype statistics from all samples at the site level
GenotypeSummaries() GenotypeSummaries
GenotypeUtils org.broadinstitute.hellbender.utils
GENOTYPING_BASE_ERROR_RATE_LONG_NAME ModelSegments
GENOTYPING_ERROR_RATE CrosscheckFingerprints
GENOTYPING_HOMOZYGOUS_LOG_RATIO_THRESHOLD_LONG_NAME ModelSegments
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, ReadLikelihoods<A>) GenotypingData
Constructs a new genotyping-data collection providing the ploidy model to apply to the input model
and the read-likelihoods collection.
GenotypingEngine Config extends StandardCallerArgumentCollection > - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
Base class for genotyper engines.
GenotypingEngine(Config, SampleList, AFCalculatorProvider, boolean) GenotypingEngine
Construct a new genotyper engine, on a specific subset of samples.
GenotypingGivenAllelesUtils org.broadinstitute.hellbender.tools.walkers.genotyper
Compendium of utils to work in GENOTYPE_GIVEN_ALLELES mode.
GenotypingGivenAllelesUtils() GenotypingGivenAllelesUtils
GenotypingLikelihoods A extends htsjdk.variant.variantcontext.Allele> - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
Genotyping Likelihoods collection.
GenotypingOutputMode org.broadinstitute.hellbender.tools.walkers.genotyper
Enumeration of possible genotyping modes.
genotypingOutputMode StandardCallerArgumentCollection
GERMLINE_POSTERIORS_VCF_ATTRIBUTE GATKVCFConstants
GERMLINE_RESOURCE_LONG_NAME M2ArgumentCollection
GERMLINE_RISK_FILTER_NAME GATKVCFConstants
GERMLINE_TAG_HEADER TagGermlineEvents
GermlineCallingArgumentCollection org.broadinstitute.hellbender.tools.copynumber.arguments
GermlineCallingArgumentCollection() GermlineCallingArgumentCollection
GermlineCNVCaller org.broadinstitute.hellbender.tools.copynumber
GermlineCNVCaller() GermlineCNVCaller
GermlineCNVCaller.RunMode org.broadinstitute.hellbender.tools.copynumber
GermlineCNVHybridADVIArgumentCollection org.broadinstitute.hellbender.tools.copynumber.arguments
GermlineCNVHybridADVIArgumentCollection() GermlineCNVHybridADVIArgumentCollection
GermlineCNVIntervalVariantComposer org.broadinstitute.hellbender.tools.copynumber.gcnv
GermlineCNVIntervalVariantComposer(VariantContextWriter, String, IntegerCopyNumberState, Set<String>) GermlineCNVIntervalVariantComposer
GermlineCNVNamingConstants org.broadinstitute.hellbender.tools.copynumber.gcnv
GermlineCNVNamingConstants() GermlineCNVNamingConstants
GermlineCNVSegmentVariantComposer org.broadinstitute.hellbender.tools.copynumber.gcnv
GermlineCNVSegmentVariantComposer(VariantContextWriter, String, IntegerCopyNumberState, Set<String>) GermlineCNVSegmentVariantComposer
Constructor.
GermlineCNVVariantComposer DATA extends htsjdk.samtools.util.Locatable> - Class in org.broadinstitute.hellbender.tools.copynumber.gcnv
GermlineContigPloidyHybridADVIArgumentCollection org.broadinstitute.hellbender.tools.copynumber.arguments
GermlineContigPloidyHybridADVIArgumentCollection() GermlineContigPloidyHybridADVIArgumentCollection
GermlineContigPloidyModelArgumentCollection org.broadinstitute.hellbender.tools.copynumber.arguments
GermlineContigPloidyModelArgumentCollection() GermlineContigPloidyModelArgumentCollection
GermlineDenoisingModelArgumentCollection org.broadinstitute.hellbender.tools.copynumber.arguments
GermlineDenoisingModelArgumentCollection() GermlineDenoisingModelArgumentCollection
GermlineDenoisingModelArgumentCollection.CopyNumberPosteriorExpectationMode org.broadinstitute.hellbender.tools.copynumber.arguments
GermlineProbabilityCalculator org.broadinstitute.hellbender.tools.walkers.mutect
Created by David Benjamin on 5/4/17.
GermlineProbabilityCalculator() GermlineProbabilityCalculator
germlineResource M2ArgumentCollection
A resource, such as gnomAD, containing population allele frequencies of common and rare variants.
get(String) TableFuncotation
get(int) KBestHaplotypeFinder
get(int) ReadErrorCorrector.CorrectionSet
Get list of corrections for a particular offset
get(Allele) PerAlleleCollection
Get the value for an allele, REF or ALT
get(int, int) SubsettedLikelihoodMatrix
get(String) TableFeature
Gets the value associated with the key.
get(String) XsvTableFeature
get(int) XsvTableFeature
get(int) ExpandingArrayList
Returns the element at the specified position in this list.
get(int) IndexedSet
Returns the element given its index within the set.
get(int...) NestedIntegerArray
get(Object) ConfigFactory
Wrapper around ConfigCache.get(Object).
get(int, int) LikelihoodMatrix
Returns the likelihood of a read given a haplotype.
get(Double) Histogram
Return the count of items in the bin corresponding to the provided value
get(Decile) DecileCollection
Gets the specified decile.
get(T, Class<U>) ParameterizedState
get(Nucleotide) Nucleotide.Counter
Returns the current count for a given nucleotide.
get(int) CovariateKeyCache
Get the cached value for the given readlength or null is no value is cached.
get(int) StandardCovariateList
Get the covariate by the index.
get(Object, String) GATKReportTable
Get a value from the given position in the table
get(int, String) GATKReportTable
Get a value from the given position in the table
get(int, int) GATKReportTable
Get a value from the given position in the table
get(int) DataLine
Returns the string value in a column by its index.
get(String) DataLine
Returns the string value in a column by its index.
get(String, String) DataLine
Returns the string value in a column by its index.
get(Enum<?>) DataLine
Returns the string value of a column by its name.
get(int) CounterManager.Counter
get(int) BclIndexReader
get(int) ReadStructure.Substructure
get1Key(int) NestedIntegerArray
Specialized version of get for 1 parameter.
get2Keys(int, int) NestedIntegerArray
Specialized version of get for 2 parameters.
get3Keys(int, int, int) NestedIntegerArray
Specialized version of get for 3 parameters.
get3PrimeAdapter() AdapterPair
get3PrimeAdapter() IlluminaAdapterPair
get3PrimeAdapter() AdapterPair
get3PrimeAdapter() IlluminaUtil.IlluminaAdapterPair
get3PrimeAdapterBytes() AdapterPair
get3PrimeAdapterBytes() IlluminaUtil.IlluminaAdapterPair
get3PrimeAdapterBytesInReadOrder() AdapterPair
get3PrimeAdapterBytesInReadOrder() IlluminaUtil.IlluminaAdapterPair
get3PrimeAdapterInReadOrder() AdapterPair
get3PrimeAdapterInReadOrder() IlluminaUtil.IlluminaAdapterPair
get4Keys(int, int, int, int) NestedIntegerArray
Specialized version of get for 4 parameters.
get5PrimeAdapter() AdapterPair
get5PrimeAdapter() IlluminaAdapterPair
get5PrimeAdapter() AdapterPair
get5PrimeAdapter() IlluminaUtil.IlluminaAdapterPair
get5PrimeAdapterBytes() AdapterPair
get5PrimeAdapterBytes() IlluminaUtil.IlluminaAdapterPair
get5PrimeAdapterBytesInReadOrder() AdapterPair
get5PrimeAdapterBytesInReadOrder() IlluminaUtil.IlluminaAdapterPair
get5PrimeAdapterInReadOrder() AdapterPair
get5PrimeAdapterInReadOrder() IlluminaUtil.IlluminaAdapterPair
getA() FourChannelIntensityData
getAbbreviation() ConcordanceState
getAbsoluteAccuracy() UnivariateSolverSpecifications
getAccessionLength(String) PSPathogenReferenceTaxonProperties
getAccessions() PSPathogenReferenceTaxonProperties
getACcounts() ExactACset
getAccumulatedOutput() StreamingPythonScriptExecutor
getAccurateKmerCoverage(int) ReadMetadata
getACsum() ExactACset
sum of all the non-reference alleles
getActualTiles(List<IlluminaFileUtil.SupportedIlluminaFormat>) 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(String, TraversalParameters, SAMFileHeader) ReadsSparkSource
Loads ADAM reads stored as Parquet.
getAdaptorBoundary() GATKRead
Finds the adaptor boundary around the read and returns the first base inside the adaptor that is closest to
the read boundary.
getAdaptorBoundary(GATKRead) ReadUtils
Finds the adaptor boundary around the read and returns the first base inside the adaptor that is closest to
the read boundary.
getAdaptorBoundary() SAMRecordToGATKReadAdapter
getAdditionalCovariates() StandardCovariateList
returns an unmodifiable view of the additional covariates stored in this list.
getAdditionalInfo() BaseVertex
getAdditionalInfo() MultiDeBruijnVertex
getAdditionalSequence(V) BaseGraph
Pull out the additional sequence implied by traversing this node in the graph
getAdditionalSequence(boolean) 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) 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).
getAdditionalTables() RecalibrationTables
getAffection() Sample
getAfterLastAlignedBaseOffset(GATKRead) ReadUtils
Returns the offset (0-based) after the last base in the record that is aligned against the reference.
getAlignedAlternateAllele() SequenceComparison
getAlignedAlternateAlleleStop() SequenceComparison
getAlignedAssemblyOrExcuseList() FindBreakpointEvidenceSpark.AssembledEvidenceResults
getAlignedCodingSequenceAllele(String, Integer, Integer, Allele, Integer, Strand) FuncotatorUtils
Gets the coding sequence for the allele with given start and stop positions, codon-aligned to the start of the reference sequence.
getAlignedCodingSequenceAlleleStart() SequenceComparison
getAlignedCodingSequenceAlternateAllele() SequenceComparison
getAlignedCodingSequenceReferenceAllele() SequenceComparison
getAlignedContigs() AlignedContigGenerator
getAlignedContigs() SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SAMFormattedContigAlignmentParser
getAlignedContigs() StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser
getAlignedContigsInOneAssembly(AlignedAssemblyOrExcuse, List<String>, SAMFileHeader) StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser
Work on "successful" assembly and turn its contigs' alignments to custom
AlignmentInterval format.
getAlignedEndPosition(int) FuncotatorUtils
Get the sequence-aligned end position for the given allele end position.
getAlignedPosition(int) FuncotatorUtils
Gets the sequence aligned position (1-based, inclusive) for the given coding sequence position.
getAlignedRefAllele(String, int, Allele, int, int) FuncotatorUtils
Get the aligned coding sequence for the given reference allele.
getAlignedReferenceAllele() SequenceComparison
getAlignedReferenceAlleleStop() SequenceComparison
getAligner() SingleSequenceReferenceAligner
Gives access to the underlying aligner so that you can modify its options.
getAligner(SmithWatermanAligner.Implementation) SmithWatermanAligner
Factory method to get an instance of an aligner corresponding to the given implementation
getAlignment() GATKReportColumnFormat
getAlignmentContext() LocusWalkerContext
getAlignmentEnd() ArtificialBAMBuilder
getAlignmentEvidence() SimpleNovelAdjacencyAndChimericAlignmentEvidence
getAlignmentOffset() SmithWatermanAlignment
getAlignments(JavaSparkContext) LocusWalkerSpark
Loads alignments and the corresponding reference and features into a JavaRDD for the intervals specified.
getAlignments() AlignedContig
getAlignments() AssemblyContigWithFineTunedAlignments
getAlignmentSignatureBasicType() AssemblyContigWithFineTunedAlignments
getAlignmentStart() ArtificialBAMBuilder
getAlignmentStartHapwrtRef() Haplotype
getAll() DecileCollection
Gets a list of all deciles.
getAllAnnotations() VariantContextTestUtils
Uses the AnnotationsPlugin interface to instantiate and return a list of every annotation currently visible to the gatk
getAllele(int) GenotypingData
getAllele(int) GenotypingLikelihoods
getAllele(int) SubsettedLikelihoodMatrix
getAllele(int) AlleleList.ActualPermutation
getAllele(int) AlleleList
Returns the allele at the given index in this AlleleList.
getAllele(int) AlleleList.NonPermutation
getAllele(int) IndexedAlleleList
getAllele(int) LikelihoodMatrix
Returns the allele given its index.
getAllele(int) ReadLikelihoods
Returns the allele given its index.
getAllele1() DiploidGenotype
getAllele1() Snp
getAllele2() DiploidGenotype
getAllele2() Snp
getAlleleCount(Allele) HeterozygosityCalculator
getAlleleCountAtMLE(Allele) AFCalculationResult
Returns the AC of allele a la #getAlleleCountsOfMLE
getAlleleCountsOfMLE() 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).
getAlleleFrequency() PileupSummary
getAlleleFrequencyPriors(VariantContext, int, GenotypeLikelihoodsCalculationModel) GenotypingEngine
Returns the log10 prior probability for all possible allele counts from 0 to N where N is the total number of
genomes (total-ploidy).
getAlleles() AlleleSpecificAnnotationData
getAlleles() ReducibleAnnotationData
Note: parent class ReducibleAnnotationData is non-allele specific and stores all values with the no-call allele
getAlleleStart() SequenceComparison
getAlleleString() Snp
getAllelesUsedInGenotyping() AFCalculationResult
Get the list of alleles actually used in genotyping.
getAllelicCounts() AllelicCountCollector
Get the allelic counts gathered so far.
getAllFeatures() GencodeGtfExonFeature
getAllFeatures() GencodeGtfGeneFeature
getAllFeatures() GencodeGtfTranscriptFeature
getAllFilterLines() GATKVCFHeaderLines
getAllFormatLines() GATKVCFHeaderLines
getAllInfoLines() GATKVCFHeaderLines
getAllIntervals() SVFastqUtils.Mapping
getAllIntervals() ReadsPreprocessingPipelineTestData
getAllIntervalsForReference(SAMSequenceDictionary) IntervalUtils
Builds a list of intervals that cover the whole given sequence.
getAllLeaves() NestedIntegerArray
getAllLibraryStatistics() ReadMetadata
getAllowedShortFragmentOverhang() SVReadFilter
getAllowedValuesForDescriptorHelp(String) GATKAnnotationPluginDescriptor
Return the allowed values for annotationNames/disableAnnotations/annotationGroups for use by the help system.
getAllowedValuesForDescriptorHelp(String) GATKReadFilterPluginDescriptor
Return the allowed values for read-filter/disable-read-filter names for use by the help system.
getAllReadsCollector() MultiLevelCollector
Get the PerUnitMetricCollector that collects reads for all levels
getAllReadsCollector() MultiLevelReducibleCollector
Get the PerUnitMetricCollector that collects reads for all levels
getAllReadsCollector() MultiLevelCollector
Get the PerUnitMetricCollector that collects reads for all levels
getAllReferenceBases() ReferenceFileSource
getAllSequenceDictionaries() FeatureManager
Returns the sequence dictionaries associated with all feature sources.
getAllSnps() HaplotypeMap
Returns an unmodifiable collection of all SNPs in all Haplotype blocks.
getAllTiles() CbclReader
getAllValues() TableFeature
Gets all the values in order.
getAllValues() NestedIntegerArray
getAllVariantContexts(List<Haplotype>) EventMap
Get all of the VariantContexts in the event maps for all haplotypes, sorted by their start position
getAllVariantHeaders() FeatureManager
This method finds and returns all of the variant headers from the feature sources.
getAlt(Allele) PerAlleleCollection
getAltAllele() GencodeFuncotation
getAltAllele() TableFuncotation
getAltAllele() Funcotation
getAltAllele() SvType
getAltAlleles() PerAlleleCollection
getAltCount() PileupSummary
getAlternate() BasicValidationResult
getAlternateAllele() SequenceComparison
getAlternateAlleleFraction() AllelicCount
getAlternateAminoAcidSequence() SequenceComparison
getAlternateSequence(String, int, Allele, Allele) FuncotatorUtils
Get the full alternate sequence given a reference coding sequence, and two alleles.
getAltFraction() PileupSummary
getAltHaplotypeSequence() NovelAdjacencyAndAltHaplotype
getAltHaplotypeSequence() SimpleNovelAdjacencyAndChimericAlignmentEvidence
getAltNucleotide() AllelicCount
getAltReadCount() AllelicCount
getAminoAcidByLetter(String) FuncotatorUtils
Returns the
AminoAcid corresponding to the given single-letter abbreviation.
getAminoAcidByLetter(char) FuncotatorUtils
Returns the
AminoAcid corresponding to the given single-letter abbreviation.
getAminoAcidCodes() FuncotatorUtils
getAminoAcidNames() FuncotatorUtils
getAndValidateConfigFileContents(Path) XsvLocatableTableCodec
Get the properties from the given configFilePath, validate that all required properties are present,
and return the property map.
getAndValidateDataSourcesFromPaths(String, List<String>) DataSourceUtils
getAnnotationFeatureClass() DataSourceFuncotationFactory
getAnnotationFeatureClass() CosmicFuncotationFactory
getAnnotationFeatureClass() GencodeFuncotationFactory
getAnnotationFeatureClass() VcfFuncotationFactory
getAnnotationFeatureClass() LocatableXsvFuncotationFactory
getAnnotationFeatureClass() SimpleKeyXsvFuncotationFactory
getAnnotationKeys() VariantDataManager
getAnnotations() AnnotatedInterval
Returns a copy of the annotations as a map.
getAnnotations() AnnotatedIntervalCollection
getAnnotations() AnnotatedIntervalHeader
getAnnotationSet() AnnotatedInterval
getAnnotationSource() GencodeGtfFeature
getAnnotationTranscript() GencodeFuncotation
getAnnotationValue(String) AnnotatedInterval
getAnnotationValueOrDefault(String, String) AnnotatedInterval
getAnonymousOptionalFields() GencodeGtfFeature
getApprisRank() GencodeFuncotation
getAppropriateVCFInfoHeaders() GenotypingEngine
getApproximateCommandLine() PythonExecutorBase
Return a (not necessarily executable) string representing the current command line for this executor
for error reporting purposes.
getApproximateCommandLine() PythonScriptExecutor
Return a (not necessarily executable) string representing the current command line for this executor
for error reporting purposes.
getApproximateCommandLine() StreamingPythonScriptExecutor
Return a (not necessarily executable) string representing the current command line for this executor
for error reporting purposes.
getApproximateCommandLine() RScriptExecutor
getApproximateCommandLine() ScriptExecutor
Return a (not necessarily executable) string representing the command line for this executor for error
reporting purposes.
getArgs() IntegrationTestSpec
getArgs() SamFileTester
getArgsArray() ArgumentsBuilder
getArgsList() ArgumentsBuilder
getArtifactMode() OrientationSampleTransitionSummary
getArtifactModeComplement() OrientationSampleTransitionSummary
getArtificialReadsBasedOnSATag(SAMFileHeader) SATagBuilder
Returns a list of artificial GATKReads corresponding to the reads described by the SA tag in read.
getAsRealMatrix(LikelihoodMatrix<Allele>) SomaticGenotypingEngine
getAssembledIntervals() SvDiscoveryInputMetaData.SampleSpecificData
getAssembledIntervals() FindBreakpointEvidenceSpark.AssembledEvidenceResults
getAssembly() AlignedAssemblyOrExcuse
getAssemblyId() AlignedAssemblyOrExcuse
getAssemblyRegion() AssemblyRegionWalkerContext
getAssemblyRegionReference(ReferenceSequenceFile) AssemblyRegion
getAssemblyRegionReference(ReferenceSequenceFile, int) AssemblyRegion
Get the reference bases from referenceReader spanned by the extended location of this active region,
including additional padding bp on either side.
getAssemblyRegions(JavaSparkContext) AssemblyRegionWalkerSpark
Loads assembly regions and the corresponding reference and features into a JavaRDD for the intervals specified.
getAssignedContig() GATKRead
getAssignedContig() SAMRecordToGATKReadAdapter
getAssignedReferenceIndex(GATKRead, SAMFileHeader) ReadUtils
Returns the reference index in the given header of the read's assigned contig.
getAssignedStart() GATKRead
getAssignedStart() SAMRecordToGATKReadAdapter
getAsynchronousStreamWriterService(OutputStream, Function<T, ByteArrayOutputStream>) StreamingPythonScriptExecutor
getAsynchronousStreamWriterService(OutputStream, Function<T, ByteArrayOutputStream>) StreamingProcessController
getAttribute(String) FeatureInput
Gets the value for the given key associated with this Feature source or null
if no value is associated with a given key.
getAttribute(Allele) ReducibleAnnotationData
getAttributeAsByteArray(String) GATKRead
Retrieve the value of a particular attribute typed as a byte array.
getAttributeAsByteArray(String) SAMRecordToGATKReadAdapter
getAttributeAsDouble(Genotype, String, double) GATKProtectedVariantContextUtils
Returns an attribute as a double.
getAttributeAsDoubleArray(VariantContext, String, Supplier<double[]>, double) GATKProtectedVariantContextUtils
Composes the double array from a genotype annotation.
getAttributeAsDoubleArray(Genotype, String, Supplier<double[]>, double) GATKProtectedVariantContextUtils
Composes the double array from a genotype annotation.
getAttributeAsInt(Genotype, String, int) GATKProtectedVariantContextUtils
Returns an attribute as an integer.
getAttributeAsIntArray(Genotype, String, Supplier<int[]>, int) GATKProtectedVariantContextUtils
Composes the double array from a genotype annotation.
getAttributeAsInteger(String) GATKRead
Retrieve the value of a particular attribute typed as an integer.
getAttributeAsInteger(String) SAMRecordToGATKReadAdapter
getAttributeAsObject(Genotype, String, Function<String, T>, T) GATKProtectedVariantContextUtils
Gets an attribute value by transforming the string its string representation using an translation function.
getAttributeAsString(Genotype, String, String) GATKProtectedVariantContextUtils
Returns an attribute as a string.
getAttributeAsString(String) GATKRead
Retrieve the value of a particular attribute typed as a String.
getAttributeAsString(String) SAMRecordToGATKReadAdapter
getAttributeMap() ReducibleAnnotationData
Get the stored raw per-allele data
getAttributesToReverse() AbstractAlignmentMerger
Gets the set of attributes to be reversed on reads marked as negative strand.
getAttributesToReverseComplement() AbstractAlignmentMerger
Gets the set of attributes to be reverse complemented on reads marked as negative strand.
getAuthenticatedGcs(String, String, byte[]) BucketUtils
Get an authenticated GCS-backed NIO FileSystem object representing the selected projected and bucket.
getAuthenticatedGcs(String) BaseTest
Get a FileSystem that uses the explicit credentials instead of the default
credentials.
getAvailableTiles() IlluminaDataProviderFactory
Return the list of tiles available for this flowcell and lane.
getAvgReadLen() ReadMetadata
getBadMappings() AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings
getBadMappingsAsCompactStrings() AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings
getBAMOutputHeader() HaplotypeBAMDestination
Get the SAMFileHeader that is used for writing the output for this destination.
getBandSize() BandPassActivityProfile
Get the size (in bp) of the band pass filter
getBandWidth() BAQ
getBAQTag(GATKRead) BAQ
Get the BAQ attribute from the tag in read.
getBarcode() ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch
getBarcodeValue(SAMRecord) EstimateLibraryComplexity
getBase() ReferenceContext
Get the base at the given locus.
getBase() SAMPileupElement
Get the base
getBase() PileupElement
getBase(int) GATKRead
getBase(int) SAMRecordToGATKReadAdapter
getBaseCounts() 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() PileupElement
Get the Base Deletion quality at this pileup position
getBaseDeletionQualities(GATKRead) ReadUtils
Default utility to query the base deletion quality of a read.
getBaseInsertionQual() PileupElement
Get the Base Insertion quality at this pileup position
getBaseInsertionQualities(GATKRead) ReadUtils
Default utility to query the base insertion quality of a read.
getBaselineIntegerCopyNumberState() IntegerCopyNumberSegment
getBaselineIntegerCopyNumberState() IntervalCopyNumberGenotypingData
getBasePileup() AlignmentContext
getBaseQualities() GATKRead
getBaseQualities(GATKRead, EventType) ReadUtils
getBaseQualities() SAMRecordToGATKReadAdapter
getBaseQualitiesNoCopy() GATKRead
getBaseQualitiesNoCopy() SAMRecordToGATKReadAdapter
getBaseQuality() SAMPileupElement
Get the quality
getBaseQuality(int) GATKRead
getBaseQuality(int) SAMRecordToGATKReadAdapter
getBaseQualityCount() GATKRead
getBaseQualityCount() SAMRecordToGATKReadAdapter
getBaseQualityString(GATKRead) ReadUtils
Returns the base qualities for the read as a string.
getBaseQuals() SAMPileupFeature
Gets the PHRED base qualities.
getBaseQuals() ReadPileup
Returns an array of the quals in this pileup.
getBases() ReferenceContext
Get all reference bases in this context.
getBases(SimpleInterval) ReferenceContext
Get all reference bases in this context with the given window.
getBases(int, int) ReferenceContext
Get all reference bases in this context with the given leading / trailing bases as the window.
getBases() SVFastqUtils.FastqRead
returns bases with values like 'A', 'C', 'G', and 'T'
getBases() Path
The base sequence for this path.
getBases() SAMPileupFeature
Gets the bases in byte array form
Note: this call costs O(n) and allocates fresh array each time
getBases() ReadPileup
Returns an array of the bases in this pileup.
getBases() GATKRead
getBases() SAMRecordToGATKReadAdapter
getBases() ReferenceBases
getBases() BclData
getBases() ReadData
getBasesCoveringRefInterval(int, int, byte[], int, Cigar) 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) 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, Allele, Strand, int, ReferenceContext) FuncotatorUtils
Get a string of bases around a variant (specified by reference and alternate alleles), including the reference allele itself.
getBasesNoCopy() GATKRead
getBasesNoCopy() SAMRecordToGATKReadAdapter
getBasesOfImmediatelyFollowingInsertion() PileupElement
Get the bases for an insertion that immediately follows this alignment state, or null if none exists
getBasesReverseComplement(byte[]) ReadUtils
Returns the reverse complement of the read bases
getBasesReverseComplement(GATKRead) ReadUtils
Returns the reverse complement of the read bases
getBasesStream() SAMPileupFeature
Get the bases as a stream
getBasesString() SAMPileupFeature
Returns pile of observed bases over the genomic location.
getBasesString() GATKRead
getBciFile() BclIndexReader
getBestAvailableSequenceDictionary() AbstractConcordanceWalker
getBestAvailableSequenceDictionary() GATKTool
Returns the "best available" sequence dictionary or null if there is no single best dictionary.
getBestAvailableSequenceDictionary() GATKSparkTool
Returns the "best available" sequence dictionary.
getBestAvailableSequenceDictionary() VariantWalkerSpark
getBestAvailableSequenceDictionary() VariantWalkerBase
Overriding the superclass method to preferentially
choose the sequence dictionary from the driving source of variants.
getBestAvailableSequenceDictionary() GenomicsDBImport
Overriding getBestAvailableSequenceDictionary() to prefer the mergedVCFHeader's
sequence directory, if present, over any other dictionaries
getBetweenNextPosition() PileupElement
Get the cigar elements that occur after the current position but before the next position on the genome
getBetweenPrevPosition() 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.
getBoolean(int) DataLine
Returns the boolean value in a column by its index.
getBoolean(String) DataLine
Returns the boolean value in a column by its index.
getBQSRSpecificReadFilterList() BaseRecalibrator
Return the list of basic, raw read filters used for BQSR contexts, not including WellFormed.
getBreakPointIntervals(int, SAMSequenceDictionary, boolean) SVContext
Returns break point intervals for this structural variant.
getBucket(String) BucketUtils
Given a path of the form "gs://bucket/folder/folder/file", returns "bucket".
getBufferBytes() CapturedStreamOutput
getBufferBytes() StreamOutput
Returns the content as a string.
getBufferedReaderGz(String) PSBuildReferenceTaxonomyUtils
Gets a buffered reader for a gzipped file
getBufferedReaderTarGz(String, String) PSBuildReferenceTaxonomyUtils
Gets a Reader for a file in a gzipped tarball
getBufferSize() OutputStreamSettings
getBufferString() StreamOutput
Returns the content as a string.
getBuilder() GencodeFuncotation
getByteBufferIterator(int, int, File) MMapBackedIteratorFactory
getByteIterator(int, File) MMapBackedIteratorFactory
getBytesAvailableToRead() CircularByteBuffer
Returns the number of bytes that are in the buffer at the time of the method invocation.
getC() FourChannelIntensityData
getCacheHits() CachingIndexedFastaSequenceFile
getCacheMisses() CachingIndexedFastaSequenceFile
getCacheSize() CachingIndexedFastaSequenceFile
getCall() CalledCopyRatioSegment
getCallableRegion() AssemblyRegionTrimmer.Result
Returns the trimmed variant containing region
getCalledHaplotypes() AssemblyBasedCallerGenotypingEngine.CalledHaplotypes
Get the set of haplotypes that we actually called (i.e., underlying one of the VCs in getCalls().
getCallIntegerCopyNumberState() IntegerCopyNumberSegment
getCalls() AssemblyBasedCallerGenotypingEngine.CalledHaplotypes
Get the list of calls made at this location
getCanonicalChromosomes(String, SAMSequenceDictionary) SvDiscoveryUtils
getCanonicalChromosomesBroadcast() SvDiscoveryInputMetaData.ReferenceData
getCapacity() CircularByteBuffer
Returns the total capacity of the buffer (empty+filled).
getCDF() LibraryStatistics
getCDF() IntHistogram
getcDnaChange() GencodeFuncotation
getCds() GencodeGtfExonFeature
getCenter() PosteriorSummary
getChainedPgIds(SAMFileHeader) AbstractMarkDuplicatesCommandLineProgram
We have to re-chain the program groups based on this algorithm.
getChainedPgIds(SAMFileHeader) AbstractMarkDuplicatesCommandLineProgram
We have to re-chain the program groups based on this algorithm.
getChannel(IntensityChannel) FourChannelIntensityData
getChannels() TensorType
getChild() Trio
getChildID() Trio
getChildren() PSTreeNode
getChildrenOf(int) PSTree
getChr() SAMPileupFeature
Deprecated.
getChrom() Snp
getChromosome() GencodeFuncotation
getChromosomeName() GencodeGtfFeature
getCigar() SVFastqUtils.Mapping
Returns the cigar of the primary interval, or the empty cigar if unmapped.
getCigar() Haplotype
Get the cigar for this haplotype.
getCigar() GATKRead
getCigar() SAMRecordToGATKReadAdapter
getCigar() SmithWatermanAlignment
getCigarElement(int) GATKRead
Return the cigar element at a given index.
getCigarElement(int) 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() GATKRead
getCigarElements() SAMRecordToGATKReadAdapter
This implementation does not make a new Cigar object but instead provides
an unmodifiable view of the underlying list of CigarElements.
getCigarOperator() 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() BreakpointEvidence.ReadEvidence
getClasses() ClassFinder
Fetches the set of classes discovered so far.
getClassesOfType(Class<?>, List<Class<?>>) ClassUtils
Gets a list of classes that are either the same as, or a subclass/subinterface of a parent target class.
getClassForPluginHelp(String) GATKAnnotationPluginDescriptor
Return the class representing the instance of the plugin specified by pluginName
getClassForPluginHelp(String) GATKReadFilterPluginDescriptor
Return the class object for the plugin with simple class name pluginName
Used for help/usage and documentation generation.
getClassList() Main
The single classes we wish to include in our command line.
getCloudStorageConfiguration(int) BucketUtils
The config we want to use.
getClusterCount() Tile
Returns the number of on this tile.
getClusterDensity() Tile
Returns the cluster density of this tile, in units of [cluster/mm^2].
getCnvCallsBroadcast() SvDiscoveryInputMetaData.SampleSpecificData
getCode() AminoAcid
getCode() GenotypeConcordanceStates.CallState
getCode() GenotypeConcordanceStates.TruthState
getCodecForFile(File) FeatureManager
Utility method that determines the correct codec to use to read Features from the provided file.
getCodecForFile(File, Class<? extends Feature>) 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.
getCodecForFile(Path, Class<? extends Feature>) 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.
getCodingSequence(ReferenceContext, List<? extends Locatable>, Strand) FuncotatorUtils
Deprecated.
getCodingSequenceAlleleStart() SequenceComparison
getCodingSequenceChangeString(SequenceComparison) FuncotatorUtils
Get the coding sequence change string from the given
SequenceComparison
This method is assumed to be called only when the variant occurs in a coding region of the genome.
getCodingSequenceChangeStringForExonSpliceSite(int) FuncotatorUtils
getCodonChange() GencodeFuncotation
getCodonChangeString(SequenceComparison) FuncotatorUtils
getCodons() AminoAcid
getCollector(int, IntervalList) CollectWgsMetrics
getCollector(int, IntervalList) CollectWgsMetricsWithNonZeroCoverage
getColumnFormat() GATKReportColumn
Get the display width for this column.
getColumnInfo() GATKReportTable
getColumnMedians(RealMatrix) MatrixSummaryUtils
Return an array containing the median for each column in the given matrix.
getColumnName() GATKReportColumn
getColumnNames() DelimitedTextFileWithHeaderIterator
getColumnNames() TabbedTextFileWithHeaderParser
getCommand() ProcessSettings
getCommandLine() CommandLineProgram
getCommandLine() CommandLineProgram
getCommandLineName() Main
Returns the command line that will appear in the usage.
getCommandLineParser() CommandLineProgram
getCommandLineParser() CommandLineProgram
getCommandString() ProcessSettings
getComments() AnnotatedIntervalCollection
Creates a copy from the SAM File header or an empty list if no sam file header and no comments.
getCommonContigsByName(SAMSequenceDictionary, SAMSequenceDictionary) SequenceDictionaryUtils
Returns the set of contig names found in both dicts.
getComparator() AbstractLocatableCollection
getComparator(Set<String>) TranscriptSelectionMode
getComplement(byte) BaseUtils
getCompleteHeader() VariantContextTestUtils
Method which returns a complete header with all the GATK and HTSJDK standard header lines for testing purposes
getComplication() NovelAdjacencyAndAltHaplotype
getCompressedBlockSize() BaseBclReader.TileData
getConcordance() AbstractConcordanceWalker.TruthVersusEval
getConcordanceStateArray(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) GenotypeConcordanceScheme
Get the concordance state array associate with the given truth state and call state tuple.
getConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates) GenotypeConcordanceScheme
Get the concordance state array associate with the given truth state and call state tuple.
getConfigfile(Path) DataSourceUtils
Gets the Path config file in the given directory.
getConfigFilenameFromArgs(String[], String) ConfigFactory
Get the configuration file name from the given arguments.
getConfigFilePath(Path) XsvLocatableTableCodec
Gets the path to the corresponding configuration file for the given inputFilePath.
getConfiguration() GenotypingEngine
Returns a reference to the engine configuration
getConsensusCorrection(int) ReadErrorCorrector.CorrectionSet
Get consensus correction for a particular offset.
getConsolidatedPaddedCigar(int) Haplotype
Get the haplotype cigar extended by padSize M at the tail, consolidated into a clean cigar
getContamination() ContaminationRecord
getContig() AbstractConcordanceWalker.TruthVersusEval
getContig() AlignmentContext
getContig() AssemblyRegion
getContig() ReferenceShard
getContig() Shard
getContig() ShardBoundary
getContig() VariantShard
getContig() AlleleFractionSegment
getContig() AllelicCount
getContig() AnnotatedInterval
getContig() CopyRatio
getContig() CopyRatioSegment
getContig() IntegerCopyNumberSegment
getContig() IntervalCopyNumberGenotypingData
getContig() ModeledSegment
getContig() MultidimensionalSegment
getContig() SimpleCount
getContig() AnnotatedInterval
getContig() SequenceComparison
getContig() SVFastqUtils.Mapping
Returns the contig as per the primary interval, or null if unmapped.
getContig() SVInterval
getContig() SVLocation
getContig() MinorAlleleFractionRecord
getContig() PileupSummary
getContig() BasicValidationResult
getContig() ActivityProfile
getContig() GencodeGtfFeature
getContig() SAMPileupFeature
getContig() TableFeature
getContig() XsvTableFeature
getContig() GenomeLoc
getContig() AlignmentStateMachine
Get the contig of the underlying read
getContig() SAMRecordToGATKReadAdapter
getContig() SimpleInterval
getContig() MinimalVariant
getContig() VariantContextVariantAdapter
getContigAlignments() AlignedAssemblyOrExcuse
List is equal in length to the number of contigs in the assembly.
getContigColumn() XsvLocatableTableCodec
getContigColumnName() AnnotatedIntervalHeader
getContigID(String) ReadMetadata
getContigIndex() GenomeLoc
getContigIndex(String) GenomeLocParser
Returns the contig index of a specified string version of the contig
getContigIndexWithoutException(String) GenomeLocParser
getContigInfo(String) GenomeLocParser
get the contig's SAMSequenceRecord
getContigName() AlignedContig
getContigName() AssemblyContigWithFineTunedAlignments
getContigName(int) ReadMetadata
getContigNameMap() ReadMetadata
getContigNames(SAMSequenceDictionary) SequenceDictionaryUtils
getContigNamesList(SAMSequenceDictionary) SequenceDictionaryUtils
getContigSequence() AlignedContig
getContigSequence() AssemblyContigWithFineTunedAlignments
getContigSizes(Path) IntervalUtils
Returns a map of contig names with their sizes.
getContigsWithSignatureClassifiedAsComplex() SvDiscoverFromLocalAssemblyContigAlignmentsSpark.AssemblyContigsClassifiedByAlignmentSignatures
getContigsWithSignatureClassifiedAsSimpleChimera() SvDiscoverFromLocalAssemblyContigAlignmentsSpark.AssemblyContigsClassifiedByAlignmentSignatures
getContigsWithSignatureClassifiedAsUnknown() SvDiscoverFromLocalAssemblyContigAlignmentsSpark.AssemblyContigsClassifiedByAlignmentSignatures
getContingencyStateCounts(GenotypeConcordanceScheme) GenotypeConcordanceCounts
Returns the total number of times each contingency state is encountered, summed across all truth/call state pairs.
getContingencyStateSet(GenotypeConcordanceStates.ContingencyState[]) GenotypeConcordanceScheme
Get the contingency state array as a set
getContingencyStateString(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) GenotypeConcordanceScheme
Get the contingency state array as a parse-able string
getContingencyTable(ReadLikelihoods<Allele>, VariantContext, int) StrandBiasTest
Allocate and fill a 2x2 strand contingency table.
getContingencyTable(ReadLikelihoods<Allele>, VariantContext, int, Collection<String>) StrandBiasTest
Allocate and fill a 2x2 strand contingency table.
getCopyNumber() IntegerCopyNumberState
getCopyNumberPosterior(IntegerCopyNumberState) CopyNumberPosteriorDistribution
Get the probability for a given copy number state
getCopyNumberPosteriorDistribution() IntervalCopyNumberGenotypingData
getCount() SimpleCount
getCount() AggregatedSubHaplotypeFinder
getCount(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) GenotypeConcordanceCounts
Returns the count defined by the truth state set and call state set.
getCount(GenotypeConcordanceStates.TruthAndCallStates) GenotypeConcordanceCounts
Returns the count defined by the truth state set and call state set.
getCountedKmers() KMerCounter
Get an unordered collection of the counted kmers in this counter
getCounterSize() GenotypeConcordanceCounts
getCountMap() AllelePileupCounter
getCounts() SimpleCountCollection
getCounts() ExactACcounts
getCovariateByParsedName(String) StandardCovariateList
getCovariateForTable(NestedIntegerArray<RecalDatum>) RecalibrationTables
getCovariates() BaseRecalibrationEngine
getCovariates() RecalibrationReport
getCovariatesValues() ReadRecalibrationInfo
Get the ReadCovariates object carrying the mapping from offsets -> covariate key sets
getCoverage(String) CoveragePerContig
getCoverage() LibraryStatistics
getCoverage() ReadMetadata
getCoverageByTarget() TargetMetricsCollector.PerUnitTargetMetricCollector
Returns the accumulated coverage per target.
getCurrentCigarElement() AlignmentStateMachine
Get the cigar element we're currently aligning with.
getCurrentCigarElement() PileupElement
Get the cigar element aligning this element to the genome
getCurrentCigarElementOffset() 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() PileupElement
Get the offset of this cigar element in the Cigar of the current read (0-based)
Suppose the cigar is 1M2D3I4D.
getCurrentLine() BasicInputParser
Provides access to the current (just parsed) line in pre-parsed format.
getCurrentLine() DelimitedTextFileWithHeaderIterator.Row
getCurrentLine() TabbedTextFileWithHeaderParser.Row
getCurrentLineNumber() 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() DelimitedTextFileWithHeaderIterator
getCurrentLineNumber() TabbedTextFileWithHeaderParser
getCycleData() CbclReader
getCycleFromDir(File) PerTilePerCycleFileUtil
getCycleIndexRanges() OutputMapping
getCycleIndexRanges() ReadStructure.Substructure
getCycles() ReadStructure.Substructure
getData() ClipReads.ReadClipperWithData
getData() VariantDataManager
getDataSourceInfoString() OutputRenderer
getDataSourceName() GencodeFuncotation
getDataSourceName() TableFuncotation
getDataSourceName() Funcotation
getDataSourceName() XsvTableFeature
getDataType() GATKReportColumn
getDateTimeForDisplay(ZonedDateTime) Utils
Return the given dateTime formatted as string for display.
getDecile10() ModeledSegment.SimplePosteriorSummary
getDecile50() ModeledSegment.SimplePosteriorSummary
getDecile90() ModeledSegment.SimplePosteriorSummary
getDeciles(T) ParameterDecileCollection
getDeciles() PosteriorSummary
getDefaultAlleleFrequency() M2ArgumentCollection
getDefaultCloudIndexPrefetchBufferSize() GATKTool
getDefaultCloudIndexPrefetchBufferSize() GenomicsDBImport
getDefaultCloudPrefetchBufferSize() GATKTool
getDefaultCloudPrefetchBufferSize() GenomicsDBImport
getDefaultHeaders() CommandLineProgram
Returns the (live) list of default metrics headers used by this tool.
getDefaultHeaders() CommandLineProgram
getDefaultInstances() GATKAnnotationPluginDescriptor
Get the list of default plugins used for this instance of this descriptor.
getDefaultInstances() GATKReadFilterPluginDescriptor
Get the list of default plugins used for this instance of this descriptor.
getDefaultPartsDirectory(String) ReadsSparkSink
Gets the default parts directory for a given file by appending .parts/ to the end of it
getDefaultPlatform() NGSPlatform
Returns a representative PL string for this platform
getDefaultReadFilters() AssemblyRegionWalker
Returns the default list of CommandLineReadFilters that are used for this tool.
getDefaultReadFilters() GATKTool
Returns the default list of ReadFilters that are used for this tool.
getDefaultReadFilters() LocusWalker
Returns the default list of CommandLineReadFilters that are used for this tool.
getDefaultReadFilters() ReadWalker
Returns the default list of CommandLineReadFilters that are used for this tool.
getDefaultReadFilters() AssemblyRegionWalkerSpark
getDefaultReadFilters() GATKSparkTool
Returns the default list of ReadFilters that are used for this tool.
getDefaultReadFilters() InsertSizeMetricsCollector
Return the read filter for InsertSizeMetrics collector.
getDefaultReadFilters() AnnotatePairOrientation
getDefaultReadFilters() CollectAllelicCounts
getDefaultReadFilters() CollectReadCounts
getDefaultReadFilters() ExampleCollectMultiMetricsSpark
Return the read filters required for this collector
getDefaultReadFilters() ExampleMultiMetricsCollector
Return the read filter for example metrics collector.
getDefaultReadFilters() ExampleMultiMetricsCollectorSpark
Return the read filters to be used for this collector.
getDefaultReadFilters() ExampleCollectSingleMetricsSpark
Return the read filter required for this collector
getDefaultReadFilters() HaplotypeCallerSpark
getDefaultReadFilters() BaseRecalibratorSpark
getDefaultReadFilters() BwaSpark
getDefaultReadFilters() PileupSpark
getDefaultReadFilters() CollectBaseDistributionByCycleSpark
getDefaultReadFilters() CollectInsertSizeMetricsSpark
Return the read filters required for this collector
getDefaultReadFilters() CollectQualityYieldMetricsSpark
getDefaultReadFilters() InsertSizeMetricsCollectorSpark
Return the read filters to be used for this collector.
getDefaultReadFilters() MeanQualityByCycleSpark
getDefaultReadFilters() MetricsCollectorSpark
Return the read filters used for this collector.
getDefaultReadFilters() MetricsCollectorSparkTool
The following
MetricsCollectorSpark methods must be implemented by subclasses
and should be forwarded to the embedded collector.
getDefaultReadFilters() QualityScoreDistributionSpark
getDefaultReadFilters() SortSamSpark
getDefaultReadFilters() DiscoverVariantsFromContigAlignmentsSAMSpark
getDefaultReadFilters() CpxVariantReInterpreterSpark
getDefaultReadFilters() SvDiscoverFromLocalAssemblyContigAlignmentsSpark
getDefaultReadFilters() MarkDuplicatesSpark
getDefaultReadFilters() VariantAnnotator
getDefaultReadFilters() BaseRecalibrator
getDefaultReadFilters() GetPileupSummaries
getDefaultReadFilters() HaplotypeCaller
getDefaultReadFilters() Mutect2
getDefaultReadFilters() CheckPileup
getDefaultReadFilters() Pileup
getDefaultReadFilters() FilterAlignmentArtifacts
getDefaultReadFilters() RevertBaseQualityScores
getDefaultReadFilters() ASEReadCounter
getDefaultReadFilters() SplitNCigarReads
getDefaultReadFilters() UnmarkDuplicates
getDefaultReadFilters() ValidateBasicSomaticShortMutations
getDefaultReadFilters() CNNScoreVariants
getDefaultToolVCFHeaderLines() GATKTool
getDefaultValue(HybridADVIArgumentCollection.HybridADVIArgument) GermlineCNVHybridADVIArgumentCollection
getDefaultValue(HybridADVIArgumentCollection.HybridADVIArgument) GermlineContigPloidyHybridADVIArgumentCollection
getDefaultValue(HybridADVIArgumentCollection.HybridADVIArgument) HybridADVIArgumentCollection
getDefaultVariantAnnotationGroups() GATKTool
Returns the default list of annotation groups that are used for this tool.
getDefaultVariantAnnotationGroups() GATKSparkTool
getDefaultVariantAnnotationGroups() HaplotypeCallerSpark
getDefaultVariantAnnotationGroups() ReadsPipelineSpark
getDefaultVariantAnnotationGroups() CombineGVCFs
getDefaultVariantAnnotationGroups() GenotypeGVCFs
getDefaultVariantAnnotationGroups() HaplotypeCaller
getDefaultVariantAnnotationGroups() Mutect2
getDefaultVariantAnnotations() GATKTool
Returns the default list of
Annotations that are used for this tool.
getDefaultVariantAnnotations() GATKSparkTool
getDelegatee() ProgressReportingDelegatingCodec
getDeleteOnExit() SamFileTester
getDeletionsKeySet() ReadCovariates
getDeletionsKeySet(int) ReadCovariates
getDenoisedCopyRatios() SVDDenoisedCopyRatioResult
getDensity() TileMetricsOutReader
getDepthHistogram() CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
getDepths() TargetMetricsCollector.Coverage
Gets the coverage depths as an array of ints.
getDescendentScore() PSPathogenTaxonScore
getDescription() CopyNumberProgramGroup
getDescription() CoverageAnalysisProgramGroup
getDescription() ExampleProgramGroup
getDescription() MetagenomicsProgramGroup
getDescription() ShortVariantDiscoveryProgramGroup
getDescription() StructuralVariantDiscoveryProgramGroup
getDescription() TestProgramGroup
getDescription() SVFastqUtils.FastqRead
getDescription() BaseQuality
getDescription() FragmentLength
getDescription() MappingQuality
getDescription() PerAlleleAnnotation
getDescription() ReadPosition
getDescription() BaseCallingProgramGroup
getDescription() DiagnosticsAndQCProgramGroup
getDescription() IntervalsManipulationProgramGroup
getDescription() OtherProgramGroup
getDescription() ReadDataManipulationProgramGroup
getDescription() ReferenceProgramGroup
getDescription() Testing
getDescription() VariantEvaluationProgramGroup
getDescription() VariantFilteringProgramGroup
getDescription() VariantManipulationProgramGroup
getDescriptions() ChromosomeCounts
getDescriptions() Coverage
getDescriptions() DepthPerAlleleBySample
getDescriptions() DepthPerSampleHC
getDescriptions() GenotypeAnnotation
Return the descriptions used for the VCF FORMAT meta field.
getDescriptions() InfoFieldAnnotation
Returns the descriptions used for the VCF INFO meta field.
getDescriptions() MappingQualityZero
getDescriptions() OxoGReadCounts
getDescriptions() PerAlleleAnnotation
getDescriptions() ReferenceBases
getDescriptions() RMSMappingQuality
getDescriptions() StrandArtifact
getDescriptions() StrandBiasBySample
getDescriptions() UniqueAltReadCount
getDescriptorLengths() ReadStructure.Substructure
getDetectedCycles() PerTilePerCycleFileUtil
getDictionaryAsString(SAMSequenceDictionary) 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() AbstractAlignmentMerger
getDictionaryForMergedBam() SamAlignmentMerger
getDictionaryOrderComparator(SAMSequenceDictionary) IntervalUtils
The order of contigs/sequences in the dictionary is the order of the sorting here.
getDifferingPositions(Kmer, int, int[], byte[]) Kmer
Gets a set of differing positions and bases from another k-mer, limiting up to a max distance.
getDimensions() NestedIntegerArray
getDiploidHaplotype(Snp, DiploidGenotype) HaplotypeBlock
Gets the diploid haplotype for this haplotype block given the provided SNP and SNP
genotype.
getDirectory() ProcessSettings
getDisableToolDefaultAnnotations() DefaultGATKVariantAnnotationArgumentCollection
getDisableToolDefaultAnnotations() GATKAnnotationArgumentCollection
Returns true if all tool-default annotations are disabled; false otherwise.
getDisableToolDefaultReadFilters() DefaultGATKReadFilterArgumentCollection
Returns true if all default filters are disabled; false otherwise.
getDisableToolDefaultReadFilters() GATKReadFilterArgumentCollection
Returns true if all default filters are disabled; false otherwise.
getDiscoverStageArgs() SvDiscoveryInputMetaData
getDiscoveryAltCount() BasicValidationResult
getDiscoveryRefCount() BasicValidationResult
getDisplayName() GATKAnnotationPluginDescriptor
Return a display name to identify this plugin to the user
getDisplayName() GATKReadFilterPluginDescriptor
Return a display name to identify this plugin to the user
getDisplayNameForToolClass(Class<?>) Main
getDisplaySummaryForTool(Class<?>, CommandLineProgramProperties) Main
Return a summary string for a command line tool suitable for display.
getDistalTargets(ReadMetadata, int) 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) BreakpointEvidence
Returns the distal interval implicated as a candidate adjacency to the breakpoint by this piece of evidence.
getDistalTargets(ReadMetadata, int) 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() EvidenceTargetLink
Distance between the two intervals.
getDotLabel() BaseEdge
Get the DOT format label for this edge, to be displayed when printing this edge to a DOT file
getDotLabel() MultiSampleEdge
getDouble(int) DataLine
Returns the double value in a column by its index.
getDouble(int, Function<String, RuntimeException>) DataLine
Returns the double value in a column by its index.
getDouble(String) DataLine
Returns the double value in a column by its index.
getDouble(Enum<?>) DataLine
Returns the double value of a column by its name.
getDownsamplingInfo() LocusWalker
getDownsamplingInfo() LocusWalkerSpark
getDownsamplingInfo() AlignmentContextIteratorBuilder
getDrivingFeatureFile() FeatureWalker
Returns the file that contains the driving features.
getDrivingFeatureFile() ExampleFeatureWalker
getDrivingVariantsFeatureInput() VariantWalker
Returns the feature input for the driving variants file.
getDrivingVariantsFeatureInputs() MultiVariantWalker
Returns a list of feature inputs used for the driving variants for this source.
getDuplicatedItems(Collection<T>) Utils
Gets duplicated items in the collection.
getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator, SAMRecordDuplicateComparator) SimpleMarkDuplicatesWithMateCigar
getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator, SAMRecordDuplicateComparator) UmiAwareMarkDuplicatesWithMateCigar
getDupSeqRepeatUnitRefSpan() BreakpointComplications.IntraChrStrandSwitchBreakpointComplications
getEdges() Path
Get the edges of this path in order.
getEffectiveCounts(LikelihoodMatrix<Allele>) SomaticGenotypingEngine
getEffectiveCounts(RealMatrix, double[]) SomaticLikelihoodsEngine
Given data log likelihoods and a Dirichlet prior for a categorical distribution, obtain the array of total
responsibilities for each category
getEigensampleVectors() HDF5SVDReadCountPanelOfNormals
getEigensampleVectors() SVDReadCountPanelOfNormals
Returns a modifiable copy of an array containing the orthnonormal matrix of eigensample vectors.
getElementForPileupElement(PileupElement, int) AS_RankSumTest
getElementForPileupElement(PileupElement, int) BaseQualityRankSumTest
getElementForPileupElement(PileupElement, int) ClippingRankSumTest
getElementForPileupElement(PileupElement, int) LikelihoodRankSumTest
getElementForPileupElement(PileupElement, int) MappingQualityRankSumTest
getElementForPileupElement(PileupElement, int) RankSumTest
Get the element for the given read at the given reference position
This can return an OptionalDouble.empty() if the annotation should not be computed based on the pileups.
getElementForPileupElement(PileupElement, int) ReadPosRankSumTest
getElementForRead(GATKRead, int) AS_BaseQualityRankSumTest
Get the element for the given read at the given reference position
getElementForRead(GATKRead, int) AS_MappingQualityRankSumTest
getElementForRead(GATKRead, int) AS_ReadPosRankSumTest
getElementForRead(GATKRead, int) BaseQualityRankSumTest
getElementForRead(GATKRead, int) ClippingRankSumTest
getElementForRead(GATKRead, int, ReadLikelihoods<Allele>.BestAllele) LikelihoodRankSumTest
getElementForRead(GATKRead, int) LikelihoodRankSumTest
getElementForRead(GATKRead, int) MappingQualityRankSumTest
getElementForRead(GATKRead, int, ReadLikelihoods<Allele>.BestAllele) RankSumTest
Get the element for the given read at the given reference position
getElementForRead(GATKRead, int) RankSumTest
Get the element for the given read at the given reference position
getElementForRead(GATKRead, int) ReadPosRankSumTest
getEmpiricalErrorRate() RecalDatum
Returns the error rate (in real space) of this interval, or 0 if there are no observations
getEmpiricalQuality() RecalDatum
getEmpiricalQuality(double) RecalDatum
getEmpiricalQualityAsByte() RecalDatum
getEnableAllAnnotations() DefaultGATKVariantAnnotationArgumentCollection
getEnableAllAnnotations() GATKAnnotationArgumentCollection
Returns true if all annotations are enabled; false otherwise.
getEncapsulatedSamRecord() SAMRecordToGATKReadAdapter
getEnd() AbstractConcordanceWalker.TruthVersusEval
getEnd() AlignmentContext
getEnd() AssemblyRegion
getEnd() Shard
getEnd() ShardBoundary
getEnd() AlleleFractionSegment
getEnd() AllelicCount
getEnd() AnnotatedInterval
getEnd() CopyRatio
getEnd() CopyRatioSegment
getEnd() IntegerCopyNumberSegment
getEnd() IntervalCopyNumberGenotypingData
getEnd() ModeledSegment
getEnd() MultidimensionalSegment
getEnd() SimpleCount
getEnd() AnnotatedInterval
getEnd() GencodeFuncotation
getEnd() SVContext
The end position of this variant context.
getEnd() SVFastqUtils.Mapping
Returns the primary interval end position, or SAMRecord.NO_ALIGNMENT_START if unmapped.
getEnd() SVInterval
getEnd() MinorAlleleFractionRecord
getEnd() PileupSummary
getEnd() BasicValidationResult
getEnd() ActivityProfile
getEnd() GencodeGtfFeature
getEnd() SAMPileupFeature
getEnd() TableFeature
getEnd() XsvTableFeature
getEnd() GenomeLoc
getEnd() SAMRecordToGATKReadAdapter
getEnd() SimpleInterval
getEnd() MinimalVariant
getEnd() VariantContextVariantAdapter
getEndColumn() XsvLocatableTableCodec
getEndColumnName() AnnotatedIntervalHeader
getEnum(String) FuncotatorArgumentDefinitions.DataSourceType
getEnum(String) GencodeGtfFeature.FeatureTag
getEnum(String) GencodeGtfFeature.FeatureType
getEnum(String) GencodeGtfFeature.GeneTranscriptType
getEnum(String) GencodeGtfFeature.GenomicPhase
getEnum(String) GencodeGtfFeature.LocusLevel
getEnum(String) GencodeGtfFeature.RemapStatus
getEnum(String) GencodeGtfFeature.RemapTargetStatus
getEnum(String) GencodeGtfFeature.TranscriptSupportLevel
getEnvironment() ProcessSettings
getError() ContaminationRecord
getErrorFraction(EventType, int) 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() AlignedAssemblyOrExcuse
Either this is null, or the assembly and list of alignments is null.
getErrorRate() QualQuantizer.QualInterval
getEstimatedQReported() RecalDatum
getEstimatedQReportedAsByte() RecalDatum
getEukaryoticAminoAcidByCodon(String) FuncotatorUtils
Returns the
AminoAcid corresponding to the given three-letter Eukaryotic
codon
The codons given are expected to be valid for Eukaryotic DNA.
getEval() AbstractConcordanceWalker.TruthVersusEval
getEvalHeader() AbstractConcordanceWalker
getEvaluationData() VariantDataManager
getEventMap() Haplotype
getEvidenceTargetLinks() SvDiscoveryInputMetaData.SampleSpecificData
getEvidenceTargetLinks() FindBreakpointEvidenceSpark.AssembledEvidenceResults
getException() ExtractIlluminaBarcodes.PerTileBarcodeExtractor
getExecutableName() PythonExecutorBase.PythonExecutableName
getExistingBaseDeletionQualities(GATKRead) ReadUtils
getExistingBaseInsertionQualities(GATKRead) ReadUtils
getExitValue() ProcessOutput
getExonEndPosition() SequenceComparison
getExonId() GencodeGtfFeature
getExonNumber() GencodeGtfFeature
getExons() GencodeGtfTranscriptFeature
getExonStartPosition() SequenceComparison
getExpectedException() IntegrationTestSpec
getExpectedSortOrder() ExampleCollectMultiMetricsSpark
Return the sort order required/expected by this collector.
getExpectedSortOrder() ExampleCollectSingleMetricsSpark
Return the sort order required/expected by this collector.
getExpectedSortOrder() CollectInsertSizeMetricsSpark
getExpectedSortOrder() CollectQualityYieldMetricsSpark
getExpectedSortOrder() MetricsCollectorSpark
Return the sort order this collect requires.
getExpectedSortOrder() MetricsCollectorSparkTool
getExpectedTiles() IlluminaFileUtil
Return the list of tiles we would expect for this lane based on the metrics found in InterOp/TileMetricsOut.bin
getExtendedSpan() AssemblyRegion
Get the span of this assembly region including the extension value
getExtension() AssemblyRegion
Get the extension applied to this region
The extension is >= 0 bp in size, and indicates how much padding was requested for the region
getExtension() IlluminaLaneMetrics
This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
getExtension() IlluminaPhasingMetrics
This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
getExtension() MendelianViolationMetrics
getF1R2(Genotype) OrientationBiasUtils
getF2R1(Genotype) OrientationBiasUtils
getFalseNegativeCount() FilterAnalysisRecord
getFalseNegatives() ConcordanceSummaryRecord
getFalsePositiveProbability() PSKmerBloomFilter
getFalsePositiveProbability() PSKmerSet
getFalsePositives() ConcordanceSummaryRecord
getFamilies() SampleDB
Returns a map from family ID -> set of family members.
getFamilies(Collection<String>) SampleDB
getFamily(String) SampleDB
Return all samples with a given family ID
getFamilyID() Sample
getFamilyId() PedFile.PedTrio
getFamilyIDs() SampleDB
Returns a sorted set of the family IDs in all samples
getFaqLink() CommandLineProgram
getFastaDictionaryFileName(String) ReferenceUtils
Given a fasta filename, return the name of the corresponding dictionary file.
getFastaIndexFileName(String) ReferenceUtils
Given a fasta filename, return the name of the corresponding index file.
getFather(Sample) SampleDB
Get the sample's father
getFather() Trio
getFeatureCodecClass() FeatureInput
getFeatureContext() AssemblyRegionWalkerContext
getFeatureContext() IntervalWalkerContext
getFeatureContext() LocusWalkerContext
getFeatureContext() ReadWalkerContext
getFeatureContext() VariantWalkerContext
getFeatureIterator(FeatureInput<T>) FeatureManager
Given a FeatureInput argument field from our tool, returns an iterator to its features starting
from the first one.
getFeatureOrderNumber() GencodeGtfFeature
getFeaturePath() FeatureInput
Gets the file backing this source of Features
getFeatures(FeatureInput<T>, SimpleInterval) 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() GencodeGtfFeature
getFeatureType() ProgressReportingDelegatingCodec
getField(String) GencodeFuncotation
getField(String) TableFuncotation
getField(String) Funcotation
getField(String) DelimitedTextFileWithHeaderIterator.Row
getField(String) TabbedTextFileWithHeaderParser.Row
getFieldNames() GencodeFuncotation
getFieldNames() TableFuncotation
getFieldNames() Funcotation
getFields() DelimitedTextFileWithHeaderIterator.Row
getFields() TabbedTextFileWithHeaderParser.Row
getFIFOForWrite() StreamingPythonScriptExecutor
Obtain a temporary FIFO to be used to transfer data to Python.
getFile() AbstractIlluminaPositionFileReader
getFile() TileIndex
getFileExtension() CollectVariantCallingMetrics.VariantCallingDetailMetrics
getFileExtension() CollectVariantCallingMetrics.VariantCallingSummaryMetrics
getFileName() AbstractInputParser
getFileName() BasicInputParser
Gets the name of the file being parsed
getFiles(List<Integer>, int[]) MultiTileBclFileUtil
getFiles() PerTileFileUtil
getFiles(List<Integer>) PerTileFileUtil
getFiles() PerTilePerCycleFileUtil
getFiles(List<Integer>) PerTilePerCycleFileUtil
getFiles(int[]) PerTilePerCycleFileUtil
Returns a cycleIlluminaFileMap with all available tiles but limited to the cycles passed in.
getFiles(List<Integer>, int[]) 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) CbclReader
getFilter() FilterAnalysisRecord
getFilteredBases() CountingFilter
Gets the number of bases that have been filtered out thus far.
getFilteredCount() CountingReadFilter
getFilteredCount() CountingVariantFilter
getFilteredRecords() CountingFilter
Gets the number of records that have been filtered out thus far.
getFilteredSize() BandPassActivityProfile
Get the filter size (which is the size of each wing of the band, minus the center point)
getFilterLine(String) GATKSVVCFHeaderLines
getFilterLine(String) GATKVCFHeaderLines
getFilterLines() GATKSVVCFHeaderLines
getFilters() BasicValidationResult
getFinalRecalibrationTables() BaseRecalibrationEngine
Get the final recalibration tables, after finalizeData() has been called
This returns the finalized recalibration table collected by this engine.
getFinalSampleDB() SampleDBBuilder
getFinalVariantReadPosition(GATKRead, int) ReadPosRankSumTest
Get the position of a variant within a read with respect to the closer end, accounting for hard clipped bases and low quality ends
Used by ReadPosRankSum annotations
getFingerprintFile() MatchResults
getFingerprintIdDetailsStringFunction(CrosscheckMetric.DataType) CrosscheckFingerprints
getFingerprintPanels() Snp
getFirstAlignedBaseOffset(GATKRead) ReadUtils
Returns the offset (0-based index) of the first base in the read that is aligned against the reference.
getFirstAlignedReadPosition(GATKRead) ReadUtils
Returns the first position (1-based) on the original read in 5to3 prime orientation that is aligned
against a base on the reference.
getFirstContig() ReadMetadata.PartitionStatistics
getFirstContigID() ReadMetadata.PartitionBounds
getFirstInsertionOffset(GATKRead) ReadUtils
If a read starts in INSERTION, returns the first element length.
getFirstLocation() ReadMetadata.PartitionStatistics
getFirstOfPair(int) HitsForInsert
getFirstRefIndex() EmptyFragment
getFirstRefIndex() Fragment
getFirstRefIndex() Pair
getFirstRefIndex() PairedEnds
getFirstSnp() HaplotypeBlock
Gets the arbitrarily first SNP in the haplotype.
getFirstStart() ReadMetadata.PartitionBounds
getFirstStartPosition() EmptyFragment
getFirstStartPosition() Fragment
getFirstStartPosition() Pair
getFirstStartPosition() PairedEnds
getFirstVertex() Path
Get the first vertex in this path
getFloatIterator(int, File) MMapBackedIteratorFactory
getForceSort() SamAlignmentMerger
getForceSort() SamAlignmentMerger
getFormat() GATKReportColumn
getFormatLine(String) GATKSVVCFHeaderLines
getFormatLine(String) GATKVCFHeaderLines
getFormatLines() GATKSVVCFHeaderLines
getForwardBases() ReferenceContext
Get the bases in this context, from the beginning of the interval to the end of the window.
getFounderGenotypes(VariantContext) PedigreeAnnotation
getFounderIds() SampleDB
getFraction(int) IntHistogram.CDF
getFractionUnexpectedAlleleObs() HaplotypeProbabilitiesFromSequence
getFragment(int) HitsForInsert
getFragmentLength() GATKRead
Returns the observed length of the read's fragment (equivalent to TLEN in SAM).
getFragmentLength() SAMRecordToGATKReadAdapter
getFragmentOrdinal() BreakpointEvidence.ReadEvidence
getFullPath() Resource
getFullReference(IndexedFastaSequenceFile) AssemblyRegion
See #getActiveRegionReference but using the span including regions not the extended span
getFullReference(IndexedFastaSequenceFile, int) AssemblyRegion
See #getActiveRegionReference but using the span including regions not the extended span
getFullReferenceWithPadding() AssemblyResultSet
Returns the current full reference with padding.
getFuncotatorLargeDataValidationTestInputPath() BaseTest
A path where the test inputs for the Funcotator LargeDataValidationTest are stored.
getFunctionValueAccuracy() UnivariateSolverSpecifications
getG() FourChannelIntensityData
getGA4GHEnd() SimpleInterval
getGA4GHStart() SimpleInterval
getGapExtensionProb() BAQ
getGapOpenProb() BAQ
getGATKConfig() ConfigFactory
Quick way to get the GATK configuration.
getGCContent() AnnotationSet
getGcContent() GencodeFuncotation
getGcContent() SequenceComparison
getGCPTestInputPath() BaseTest
A GCS path where the test inputs are stored.
getGCPTestProject() BaseTest
name of the google cloud project that stores the data and will run the code
getGCPTestStaging() BaseTest
A writable GCS path where java files can be cached and temporary test files can be written,
of the form gs://bucket/, or gs://bucket/path/.
getGene() Gene.Transcript
getGeneId() GencodeGtfFeature
getGeneName() GencodeGtfFeature
getGenesForPickTranscripts() 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() GencodeGtfFeature
getGeneTranscriptType() GencodeFuncotation
getGeneType() GencodeGtfFeature
getGenomeChange() GencodeFuncotation
getGenomeLocation() Haplotype
Get the span of this haplotype (may be null)
getGenomeLocParser() GenomeLocSortedSet
Gets the GenomeLocParser used to create this sorted set.
getGenomeOffset() AlignmentStateMachine
What is the current offset w.r.t.
getGenomePosition() AlignmentStateMachine
Get the position (1-based as standard) of the current alignment on the genome w.r.t.
getGenomicEndLocation() GencodeGtfFeature
getGenomicPhase() GencodeGtfFeature
getGenomicPosition() GencodeGtfFeature
getGenomicStartLocation() GencodeGtfFeature
getGenomicStrand() GencodeGtfFeature
getGenotypeAnnotations() VariantAnnotatorEngine
Returns the list of genotype annotations that will be applied.
getGenotypeDouble(Genotype, String, double) OrientationBiasUtils
getGenotypeString(Genotype, String) OrientationBiasUtils
Get field value as a string.
getGLModel(VariantContext) HaplotypeCallerGenotypingEngine
getGoodMappings() AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings
getGoogleServiceAccountKeyPath() BaseTest
A local path where the service account credentials are stored
getGraph() AssemblyResult
getGraph() Path
Get the graph of this path
getGroupMap(DocWorkUnit) GATKHelpDoclet
Adds a super-category so that we can custom-order the categories in the doc index
getGroupMap(DocWorkUnit) PicardHelpDoclet
Adds a super-category so that we can custom-order the categories in the doc index
getHaplotype(Snp) HaplotypeMap
Queries a HaplotypeBlock by Snp object.
getHaplotype(String) HaplotypeMap
Queries a HaplotypeBlock by Snp name.
getHaplotype(String, int) HaplotypeMap
Queries a HaplotypeBlock by Snp chromosome and position.
getHaplotype() HaplotypeProbabilities
Returns the haplotype for which the probabilities apply.
getHaplotypeCount() AssemblyResultSet
Returns the number of haplotypes in the assembly result set.
getHaplotypeFrequencies() HaplotypeBlock
Gets the set of haplotype frequencies.
getHaplotypeFrequency(int) HaplotypeBlock
Gets the frequency of the i'th diploid haplotype where haplotypes are ordered accorinding
to DiploidHaplotype.
getHaplotypeList() AssemblyResultSet
Returns the haplotypes as a list.
getHaplotypeReadGroupID() HaplotypeBAMDestination
Get the read group ID that is used by this writer when writing halpotypes as reads.
getHaplotypes() HaplotypeMap
Returns an unmodifiable collection of all the haplotype blocks in the map.
getHaplotypeSampleTag() HaplotypeBAMDestination
Get the sample tag that is used by this writer when writing halpotypes as reads.
getHeadAlignment() AlignedContig
getHeadAlignment() AssemblyContigWithFineTunedAlignments
getHeader() AssemblyRegion
Returns the header for the reads in this region.
getHeader(FeatureInput<T>) FeatureContext
Gets the header associated with the provided FeatureInput
getHeader() FeatureDataSource
Gets the header associated with this data source
getHeader(FeatureInput<T>) FeatureManager
Get the header associated with a particular FeatureInput
getHeader() MultiVariantDataSource
Gets the merged header associated with this data source
getHeader() ReadsDataSource
Returns the SAM header for this data source.
getHeader(String, String) ReadsSparkSource
Loads the header using Hadoop-BAM.
getHeader(String) VariantsSparkSource
getHeader() BwaSparkEngine
getHeader() SVFastqUtils.FastqRead
Returns the header line of this Fastq read starting with '@' followed by the read id and description separated by tab characters.
getHeader() TableFeature
Gets the column names.
getHeader() XsvTableFeature
getHeader() ArtificialBAMBuilder
getHeader() ArtificialReadIterator
getHeader() SamFileTester
getHeader() FingerprintChecker
getHeader() HaplotypeMap
getHeader() AbstractAlignmentMerger
getHeaderBroadcast() SvDiscoveryInputMetaData.SampleSpecificData
getHeaderForFeatures(FeatureInput<T>) GATKTool
Returns the header for the specified source of Features
getHeaderForReads() GATKTool
Returns the SAM header for the reads data source.
getHeaderForReads() GATKSparkTool
getHeaderForSAMWriter() GATKTool
Returns the SAM header suitable for writing SAM/BAM/CRAM files produced by this tool.
getHeaderForVariants() MultiVariantWalker
Gets the header associated with our driving source of variants as a VCFHeader.
getHeaderForVariants() VariantWalkerSpark
Gets the header associated with our driving source of variants as a VCFHeader.
getHeaderForVariants() VariantWalker
Gets the header associated with our driving source of variants as a VCFHeader.
getHeaderForVariants() VariantWalkerBase
Return the VCFHeader to be used for the driving variants for this tool.
getHeaderSize() CbclReader
getHeaderWithoutLocationColumns() XsvLocatableTableCodec
getHeaderWithoutLocationColumns() XsvTableFeature
Get the header from this
XsvTableFeature without the columns that contain location information.
getHelpDoc() TensorType
getHelpDoc() FilterSamReads.Filter
getHelpDoc() RevertSam.FileType
getHelpDoc() IntervalListTools.Action
getHet(int, int) GenotypeConcordanceStates.CallState
getHetCount(Allele) HeterozygosityCalculator
Get the count of heterozygotes in vc for a specific altAllele (both reference and non-reference hets, e.g.
getHeterogyzousGenotype() Snp
getHets() GenotypeCounts
getHighQualityDepthHistogram() AbstractWgsMetricsCollector
getHistogram(long[], String, String) AbstractWgsMetricsCollector
getHom(int) GenotypeConcordanceStates.CallState
getHom(int) GenotypeConcordanceStates.TruthState
getHomologyForwardStrandRep() BreakpointComplications
getHomozygousAllele1Genotype() Snp
getHomozygousAllele2Genotype() Snp
getHoms() GenotypeCounts
getHugoSymbol() GencodeFuncotation
getId() SVFastqUtils.FastqRead
getId() SeqVertex
Get the unique ID for this SeqVertex
getId() FalsePositiveRecord
getID(SAMReadGroupRecord) ReadGroupCovariate
Get the ID of the readgroup.
getID() Sample
getId() UniqueIDWrapper
getIdealSpan() AssemblyRegionTrimmer.Result
Returns the ideal trimming span.
getIDString(NovelAdjacencyAndAltHaplotype, boolean) BreakEndVariantType
getIndelCounter() GenotypeConcordance
getIndelFalsePositiveRate() FalsePositiveRecord
getIndelFalsePositives() FalsePositiveRecord
getIndentString(int) CountingReadFilter
getIndentString(int) CountingVariantFilter
getIndex(SVInterval) SVIntervalTree
Find the rank of the specified interval.
getIndex() MarkDuplicatesSparkUtils.IndexPair
getIndex() UnivariateSolverJobDescription
getIndexTemplateName() GATKHelpDoclet
Return the name of the freemarker template to be used for the index generated by Barclay.
getIndexTemplateName() PicardHelpDoclet
Return the name of the freemarker template to be used for the index generated by Barclay.
getIndices() ReadStructure.Substructure
getIndividualId() PedFile.PedTrio
getInfo() Fingerprint
getInfoAnnotations() VariantAnnotatorEngine
Returns the list of info annotations that will be applied.
getInfoLine(String) GATKSVVCFHeaderLines
getInfoLine(String) GATKVCFHeaderLines
getInfoLines() GATKSVVCFHeaderLines
getInfoString() DataSourceFuncotationFactory
getInfoString() GencodeFuncotationFactory
getInitialGuess() UnivariateSolverJobDescription
getInput() SamFileTester
getInputArguments() ExampleCollectMultiMetricsSpark
Return the embedded argument collection.
getInputArguments() ExampleCollectSingleMetricsSpark
Return the embedded argument collection.
getInputArguments() CollectInsertSizeMetricsSpark
getInputArguments() CollectQualityYieldMetricsSpark
getInputArguments() MetricsCollectorSparkTool
To be implemented by subclasses; return the fully initialized and populated
argument collection that will be passed to the collector
getInputBuffer() InputStreamSettings
getInputFile() InputStreamSettings
getInputFile() FingerprintResults
getInputStream() ReadEndsForMarkDuplicatesCodec
getInputStream() ReadEndsForMarkDuplicatesCodec
getInputStream() RepresentativeReadIndexerCodec
getInsertedSequence() SVContext
Returns the inserted sequence.
getInsertedSequenceForwardStrandRep() BreakpointComplications
getInsertionMappings() AssemblyContigWithFineTunedAlignments
getInsertionsKeySet() ReadCovariates
getInsertionsKeySet(int) ReadCovariates
getInstance() RMSMappingQuality
getInstance(VariantContext, int, int) AFCalculatorProvider
Returns a AF calculator capable to handle a particular variant-context.
getInstance(int, int) AFCalculatorProvider
Returns a AF calculator given the required homogeneous ploidy and maximum alt allele count.
getInstance(VariantContext, int, int) ConcurrentAFCalculatorProvider
getInstance(int, int) ConcurrentAFCalculatorProvider
getInstance(VariantContext, int, int) FixedAFCalculatorProvider
getInstance(int, int) FixedAFCalculatorProvider
getInstance(int, int) GeneralPloidyFailOverAFCalculatorProvider
Returns a AF calculator given the required homogeneous ploidy and maximum alt allele count.
getInstance(int, int) GenotypeLikelihoodCalculators
Returns an instance given its ploidy and the number of alleles.
getInstance(String) BwaMemIndexCache
Returns a BwaMemIndex instance that corresponds to given index image file.
getInstance() ConfigFactory
getInstance() SmithWatermanJavaAligner
return the stateless singleton instance of SmithWatermanJavaAligner
getInt(int) DataLine
Returns the int value in a column by its index.
getInt(String) DataLine
Returns the int value in a column by its index.
getInt(Enum<?>) DataLine
Returns the int value of a column by its name.
getIntegerCopyNumberStateList() CopyNumberPosteriorDistribution
getIntegerField(String) DelimitedTextFileWithHeaderIterator.Row
getIntegerField(String) TabbedTextFileWithHeaderParser.Row
getIntegerIterator(int, File) MMapBackedIteratorFactory
getIntermediateStopSites(SimpleInterval, int) CombineGVCFs
getInternalVariantId() SvType
getInterval() FeatureContext
Gets our query interval (the interval that all Features returned by this FeatureContext overlap).
getInterval() ReadsContext
Gets the interval spanned by this context (returned reads will overlap this interval).
getInterval() ReferenceContext
Get the location on the reference represented by this context, without including
any extra bases of requested context around this interval.
getInterval() Shard
getInterval() ShardBoundary
getInterval() ShardBoundaryShard
getInterval() ShardToMultiIntervalShardAdapter
getInterval() IntervalWalkerContext
getInterval() AlleleFractionSegment
getInterval() AllelicCount
getInterval() AnnotatedInterval
getInterval() CopyRatio
getInterval() CopyRatioSegment
getInterval() IntegerCopyNumberSegment
getInterval() IntervalCopyNumberGenotypingData
getInterval() ModeledSegment
getInterval() MultidimensionalSegment
getInterval() SimpleCount
getInterval() AnnotatedInterval
Returns a copy
getInterval() DownsampleableSparkReadShard
getInterval() StrandedInterval
getInterval() SVIntervalTree.Entry
getInterval() BasicValidationResult
getInterval() ReferenceBases
getIntervalExclusionPadding() IntervalArgumentCollection
Get the interval exclusion padding specified on the command line.
getIntervalFile() CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
getIntervalFile() IntervalArgumentCollection
getIntervalId() KmerAndInterval
getIntervalId() QNameAndInterval
getIntervalList() HaplotypeMap
Returns an IntervalList with an entry for every SNP in every Haplotype in the map.
getIntervalMergingRule() IntervalArgumentCollection
Get the interval merging rule specified on the command line.
getIntervalPadding() IntervalArgumentCollection
Get the interval padding specified on the command line.
getIntervals(SAMSequenceDictionary) IntervalArgumentCollection
Get the intervals specified on the command line.
getIntervals() MultiIntervalLocalReadShard
getIntervals() MultiIntervalShard
getIntervals() ShardToMultiIntervalShardAdapter
getIntervals() GATKSparkTool
getIntervals(JavaSparkContext) IntervalWalkerSpark
Loads intervals and the corresponding reads, reference and features into a JavaRDD.
getIntervals() AbstractLocatableCollection
getIntervalSetRule() IntervalArgumentCollection
Get the interval set rule specified on the command line.
getIntervalsForTraversal() TraversalParameters
getIntervalsToExamine() CollectWgsMetrics
Gets the intervals over which we will calculate metrics.
getIntervalStrings() IntervalArgumentCollection
Subclasses must provide a -L argument and override this to return the results of that argument.
getIntervalStrings() OptionalIntervalArgumentCollection
getIntervalStrings() RequiredIntervalArgumentCollection
getIntervalsWithFlanks(GenomeLocParser, List<GenomeLoc>, int) IntervalUtils
Returns a list of intervals between the passed int locs.
getIntervalsWithFlanks(List<SimpleInterval>, int, SAMSequenceDictionary) IntervalUtils
Pads the provided intervals by the specified amount, sorts the resulting intervals, and merges intervals
that are adjacent/overlapping after padding.
getKBest(int) AggregatedSubHaplotypeFinder
getKernel() BandPassActivityProfile
Get the kernel of this band pass filter.
getKey() KmerAndInterval
getKey() QNameAndInterval
getKey() KmerAndCount
getKey() KV
getKeyNames() AS_BaseQualityRankSumTest
getKeyNames() AS_FisherStrand
getKeyNames() AS_InbreedingCoeff
getKeyNames() AS_MappingQualityRankSumTest
getKeyNames() AS_QualByDepth
getKeyNames() AS_ReadPosRankSumTest
getKeyNames() AS_RMSMappingQuality
getKeyNames() AS_StrandOddsRatio
getKeyNames() BaseQualityRankSumTest
getKeyNames() ChromosomeCounts
getKeyNames() ClippingRankSumTest
getKeyNames() Coverage
getKeyNames() DepthPerAlleleBySample
getKeyNames() DepthPerSampleHC
getKeyNames() ExcessHet
getKeyNames() FisherStrand
getKeyNames() GenotypeSummaries
getKeyNames() InbreedingCoeff
getKeyNames() LikelihoodRankSumTest
getKeyNames() MappingQualityRankSumTest
getKeyNames() MappingQualityZero
getKeyNames() OxoGReadCounts
getKeyNames() PerAlleleAnnotation
getKeyNames() PossibleDeNovo
getKeyNames() QualByDepth
getKeyNames() ReadPosRankSumTest
getKeyNames() ReferenceBases
getKeyNames() RMSMappingQuality
getKeyNames() SampleList
getKeyNames() StrandArtifact
getKeyNames() StrandBiasBySample
getKeyNames() StrandOddsRatio
getKeyNames() TandemRepeat
getKeyNames() UniqueAltReadCount
getKeyNames() VariantAnnotation
Return the keys
getKeySet(int, EventType) ReadCovariates
Get the keys for all covariates at read position for error model
getKeySet(EventType) ReadCovariates
getKingdomTaxonId() PSPathogenTaxonScore
getKmerCount(Kmer) KMerCounter
Get the count of kmer in this kmer counter
getKmers(Collection<SeqVertex>) GraphUtils
Get the list of kmers as byte[] from the vertices in the graph
getKmerSize() AssemblyResult
getKmerSize() BaseGraph
How big of a kmer did we use to create this graph?
getKmerSize() KmerSearchableGraph
The kmer-size of indexed kmers.
getKmerSize() MultiDeBruijnVertex
Get the kmer size for this DeBruijnVertex
getKmersWithCountsAtLeast(int) KMerCounter
Get kmers that have minCount or greater in this counter
getKvReadContextData() ReadsPreprocessingPipelineTestData
getKvReadiVariantBroken() ReadsPreprocessingPipelineTestData
The dataflow version is currently broken (Issue #795).
getKvReadiVariantFixed() ReadsPreprocessingPipelineTestData
getKvReadsRefBases() ReadsPreprocessingPipelineTestData
getKvReadVariant() ReadsPreprocessingPipelineTestData
getKvRefBasesiReads() ReadsPreprocessingPipelineTestData
getKvRefShardiReads() ReadsPreprocessingPipelineTestData
getKvVariantShardRead() ReadsPreprocessingPipelineTestData
getKvVariantShardVariant() ReadsPreprocessingPipelineTestData
getLane() ClusterData
getLane() IlluminaFileUtil
Return the lane we're inspecting
getLane() AbstractIlluminaPositionFileReader
getLaneNumber() TileMetricsOutReader.IlluminaLaneTileCode
getLaneNumber() TileMetricsOutReader.IlluminaTileMetrics
getLaneNumber() Tile
Returns the number of this tile's parent lane.
getLaneTileCode() TileMetricsOutReader.IlluminaTileMetrics
getLastAlignedReadPosition(GATKRead) ReadUtils
Returns the last position (1-based) on the original unclipped nor reverse-complemented read that is mapped against the reference.
getLastContig() ReadMetadata.PartitionStatistics
getLastContigID() ReadMetadata.PartitionBounds
getLastEnd() ReadMetadata.PartitionBounds
getLastInsertionOffset(GATKRead) ReadUtils
If a read ends in INSERTION, returns the last element length.
getLastLocation() ReadMetadata.PartitionStatistics
getLastThreeFields(String, char, int[]) ReadNameParser
Given a string, splits the string by the delimiter, and returns the the last three fields parsed as integers.
getLastVertex() Path
Get the final vertex of the path
getLCA(Collection<Integer>) PSTree
Get lowest common ancester of the set of given nodes.
getLeft() PairedStrandedIntervals
getLeftClipPoint(byte[]) BaseQualityClipReadTransformer
Returns left clip point or -1 if no clip
getLeftJustifiedLeftRefLoc() NovelAdjacencyAndAltHaplotype
getLeftJustifiedRightRefLoc() NovelAdjacencyAndAltHaplotype
getLegalSizeAbove(long, double) SetSizeUtils
Computes next largest legal table size for a given number of elements, accounting for load factor
getLegalSizeAbove(long) SetSizeUtils
getLegalSizeBelow(long, double) SetSizeUtils
Computes next smallest legal table size for a given number of elements, accounting for load factor
getLegalSizeBelow(long) SetSizeUtils
getLength() PSTreeNode
getLength() SVInterval
getLength() TextMDCodec.DeletionMDElement
getLength() TextMDCodec.MatchMDElement
getLength() TextMDCodec.MDElement
getLength() TextMDCodec.MismatchMDElement
getLength() ClippingOp
getLength() GATKRead
getLength() SAMRecordToGATKReadAdapter
getLengthForDupTandem(NovelAdjacencyAndAltHaplotype) NovelAdjacencyAndAltHaplotype
Clean expansion of repeat 1 -> 2, or
complex expansion, or
expansion of 1 repeat on ref to 2 repeats on alt with inserted sequence in between the 2 repeats
getLengthOf(int) PSTree
getLengthOfImmediatelyFollowingIndel() 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.
getLetter() AminoAcid
getLevel() ContaminationRecord
getLibrary(GATKRead, SAMFileHeader) ReadUtils
Returns the library associated with the provided read's read group.
getLibraryId(SAMRecord) LibraryIdGenerator
Get the library ID for the given SAM record.
getLibraryId() ReadEnds
getLibraryId() Pair
getLibraryId(SAMRecord) LibraryIdGenerator
Get the library ID for the given SAM record.
getLibraryId() PhysicalLocationForMateCigar
getLibraryId() ReadEnds
getLibraryId() PhysicalLocation
getLibraryId() PhysicalLocationInt
getLibraryIdGenerator() MarkDuplicatesWithMateCigarIterator
getLibraryIdsMap() LibraryIdGenerator
getLibraryIdsMap() LibraryIdGenerator
getLibraryName(String) ReadMetadata
getLibraryName() RScriptLibrary
getLibraryName(SAMFileHeader, SAMRecord) LibraryIdGenerator
Gets the library name from the header for the record.
getLibraryName(SAMFileHeader, String) LibraryIdGenerator
Gets the library name from the header for the read group id.
getLibraryName(SAMFileHeader, SAMRecord) LibraryIdGenerator
Gets the library name from the header for the record.
getLibraryNameToStatisticsMap() ReadMetadata.PartitionStatistics
getLibraryStatistics(String) ReadMetadata
getLikelihoods() HaplotypeProbabilities
Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidence
getLikelihoods() HaplotypeProbabilitiesFromGenotype
getLikelihoods() HaplotypeProbabilityOfNormalGivenTumor
getLineNumber() DataLine
Returns the line number for this data-line.
getLoc() ActivityProfileState
Get the locus associated with the ActivityProfileState
getLocation() AlignmentContext
getLocation() BreakpointEvidence
getLocation() TableFeature
Gets the position for the feature.
getLocation() GenomeLoc
getLocation() Haplotype
Get the span of this haplotype (may be null)
getLocation() HasGenomeLocation
getLocation() AlignmentStateMachine
Gets #getGenomePosition but as a 1 bp GenomeLoc
getLocation() ReadPileup
getLocations(ReadEndsForMateCigar) MarkQueue
Returns the nonDuplicateReadEndsSet of read ends that should be considered for tracking optical duplicates.
getLocationSet() ReadEndsForMateCigar
getLocForOffset(SimpleInterval, int) ActivityProfile
Helper function that gets the interval for a site offset from relativeLoc, protecting ourselves from
falling off the edge of the contig.
getLociToGenotype(Collection<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.
getLocusIterator(SamReader) CollectWgsMetrics
Creates AbstractLocusIterator implementation according to this#USE_FAST_ALGORITHM value.
getLocusLevel() GencodeFuncotation
getLocusLevel() GencodeGtfFeature
getLocusResults() MatchResults
getLOD() MatchResults
getLodMostProbableGenotype() HaplotypeProbabilities
Returns the LOD score between the most probable haplotype and the second most probable.
getLodNT() MatchResults
getLodTN() MatchResults
getLog10LikelihoodOfAFEq0() AFCalculationResult
Get the log10 unnormalized -- across all ACs -- likelihood of AC == 0 for all alleles
getLog10LikelihoodOfAFGT0() AFCalculationResult
Get the log10 unnormalized -- across all ACs -- likelihood of AC > 0 for any alleles
getLog10Likelihoods() ExactACset
getLog10PNonRef(VariantContext, int, int, double[]) AFCalculator
Compute the probability of the alleles segregating given the genotype likelihoods of the samples in vc
getLog10PNonRef(VariantContext) AlleleFrequencyCalculator
getLog10PNonRef(VariantContext, int, int, double[]) AlleleFrequencyCalculator
Compute the probability of the alleles segregating given the genotype likelihoods of the samples in vc
getLog10PosteriorOfAFEq0() AFCalculationResult
Get the log10 normalized -- across all ACs -- posterior probability of AC == 0 for all alleles
getLog10PosteriorOfAFEq0ForAllele(Allele) 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.
getLog10PosteriorOfAFGT0() AFCalculationResult
Get the log10 normalized -- across all ACs -- posterior probability of AC > 0 for any alleles
getLog10PriorOfAFEq0() AFCalculationResult
Get the log10 unnormalized -- across all ACs -- prior probability of AC == 0 for all alleles
getLog10PriorOfAFGT0() AFCalculationResult
Get the log10 unnormalized -- across all ACs -- prior probability of AC > 0
getLog2CopyRatioSimplePosteriorSummary() ModeledSegment
getLog2CopyRatioValue() CopyRatio
getLog2CopyRatioValues() CopyRatioCollection
getLog_of_base() MathUtil.LogMath
getLogLikelihoodArray() PairHMM
Return the results of the computeLogLikelihoods function
getLogLikelihoods() HaplotypeProbabilities
getLogLikelihoods() HaplotypeProbabilitiesFromContaminatorSequence
getLogProbabilityForIndex(int) ProbabilityVector
Return log Probability for original index i
getLogValue(double) MathUtil.LogMath
Returns the log-representation of the provided decimal value.
getLogValue(double[]) MathUtil.LogMath
Returns the log-representation of the provided decimal array.
getLong() SVKmerShort
getLong(int) DataLine
Returns the long value in a column by its index.
getLong(String) DataLine
Returns the long value in a column by its index.
getLong(Enum<?>) DataLine
Returns the long value in a column by its name expressed as
an enum constant.
getLongIterator(int, File) MMapBackedIteratorFactory
getLower() PosteriorSummary
getMaf() HaplotypeBlock
Returns the minor allele frequency of this haplotype.
getMaf() Snp
getMapping() SVFastqUtils.FastqRead
getMappingQual() PileupElement
Get the mapping quality of the read of this element
getMappingQuality() BreakpointEvidence.ReadEvidence
getMappingQuality() GATKRead
getMappingQuality() SAMRecordToGATKReadAdapter
getMappingQuals() ReadPileup
Get an array of the mapping qualities.
getMappingsDiffer() SamComparison
getMappingsDiffer() CompareSAMs
getMappingsMatch() SamComparison
getMappingsMatch() CompareSAMs
getMask() PSKmerBloomFilter
getMask() PSKmerSet
getMask(byte[], int) SVKmerShort
getMaskedBaseCount(byte[], int, int) BaitDesigner
Returns the total of soft or hard masked bases in the interval of bases.
getMaskedKmersFromLocalReference(ReferenceFileSource, int, int, SVKmerShort) PSKmerUtils
Gets all kmers from a given reference as a Collection of long arrays, while logging handy progress messages.
getMasterSequenceDictionary() GATKTool
Returns the master sequence dictionary if it has been set, otherwise null.
getMatchedBarcode() ClusterData
getMatchesLessDeletions(Cigar, int) PSUtils
getMatchResults() FingerprintResults
getMateContig() GATKRead
getMateContig() SAMRecordToGATKReadAdapter
getMateForwardStrand(GATKRead) BreakpointEvidence.DiscordantReadPairEvidence
getMateReferenceIndex(GATKRead, SAMFileHeader) ReadUtils
Returns the reference index in the given header of the contig of the read's mate,
or SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX if the read's mate is unmapped.
getMateRefLoc(NovelAdjacencyAndAltHaplotype, boolean) BreakEndVariantType
getMaternalID() Sample
getMaternalID() Trio
getMaternalId() PedFile.PedTrio
getMateStart() GATKRead
getMateStart() SAMRecordToGATKReadAdapter
getMateTargetInterval(GATKRead, ReadMetadata) BreakpointEvidence.DiscordantReadPairEvidence
Finds the coordinates implicated by the read's mate as being part of the breakpoint, ie.
getMax() UnivariateSolverJobDescription
getMaxEvaluations() UnivariateSolverJobDescription
getMaximumKmerSize() AssemblyResultSet
Returns the maximum kmerSize available.
getMaximumTrackedValue() IntHistogram
getMaxMedianFragmentSize() ReadMetadata
getMaxNonOutlierFragmentSize() LibraryStatistics
getMaxPairErrorRate() AdapterMarker
getMaxProbPropagationDistance() 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() 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.
getMaxReadLength(List<GATKRead>) ReadUtils
Calculate the maximum read length from the given list of reads.
getMaxReadsInPartition() ReadMetadata
getMaxSingleEndErrorRate() AdapterMarker
getMaxVal() ProbabilityVector
getMayBeNullGoodMappingToNonCanonicalChromosome() AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings
getMeanBaseQuality() LibraryStatistics
getMeanBaseQuality() ReadMetadata
getMeanLog2CopyRatio() CopyRatioSegment
getMeanLog2CopyRatio() MultidimensionalSegment
getMeanVector() VariantDataManager
getMedian() LibraryStatistics
getMedianPartitionSpan() ReadMetadata
getMedianPhasingMap() LanePhasingMetricsCollector
getMedianPrePhasingMap() LanePhasingMetricsCollector
getMedianShift() MannWhitneyU.Result
getMedianValue(List<T>) Utils
Streams and sorts a collection of objects and returns the integer median entry of the sorted list
getMergedCountingReadFilter(SAMFileHeader) GATKReadFilterPluginDescriptor
Merge the default filters with the users's command line read filter requests, then initialize
the resulting filters.
getMergedReadFilter(SAMFileHeader) 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>) GATKReadFilterPluginDescriptor
Merge the default filters with the users's command line read filter requests, then initialize
the resulting filters.
getMessage(Throwable) UserException
getMessage(int) RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
getMetadata() AbstractRecordCollection
getMetadataType() AbstractLocatableCollection
getMetadataType() AbstractRecordCollection
getMetadataType() AbstractSampleLocatableCollection
getMetadataType() AbstractSampleRecordCollection
getMetadataType() CoveragePerContigCollection
getMetricCode() TileMetricsOutReader.IlluminaLaneTileCode
getMetricCode() TileMetricsOutReader.IlluminaTileMetrics
getMetrics(CountingFilter, CountingFilter, CountingPairedFilter) AbstractWgsMetricsCollector
Creates CollectWgsMetrics.WgsMetrics - the object holding the result of CollectWgsMetrics
getMetrics() ExtractIlluminaBarcodes.PerTileBarcodeExtractor
getMetricsByLibrary(String) LibraryIdGenerator
getMetricsByLibrary(String) LibraryIdGenerator
getMetricsByLibraryMap() LibraryIdGenerator
getMetricsByLibraryMap() LibraryIdGenerator
getMetricsCode() IlluminaMetricsCode
getMetricsFile() CommandLineProgram
Gets a MetricsFile with default headers already written into it.
getMetricsFile() CommandLineProgram
Gets a MetricsFile with default headers already written into it.
getMetricValue() TileMetricsOutReader.IlluminaTileMetrics
getMidpoint() 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() 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.
getMin() UnivariateSolverJobDescription
getMinBaseQual() BAQ
getMinBaseQualityToUseInAssembly() ReadThreadingAssembler
getMinEvidenceMapQ() SVReadFilter
getMinEvidenceMatchLength() SVReadFilter
getMiniCluster(Configuration) MiniClusterUtils
getMiniCluster() MiniClusterUtils
getMinimaIndices() PersistenceOptimizer
Returns an unmodifiable list of the indices of the local minima, sorted first by decreasing topological persistence
and then by increasing index.
getMinimumKmerSize() AssemblyResultSet
Returns the minimum kmerSize available.
getMinorAlleleFraction() MinorAlleleFractionRecord
getMinorAlleleFraction() PileupSummary
getMinorAlleleFractionSimplePosteriorSummary() ModeledSegment
getMinPairMatchBases() AdapterMarker
getMinSingleEndMatchBases() AdapterMarker
getMinVal() ProbabilityVector
getMinValidationReadCount() BasicValidationResult
getMismatchCount(GATKRead, byte[], int) AlignmentUtils
getMismatchCount(GATKRead, byte[], int, int, int) AlignmentUtils
Count how many bases mismatch the reference.
getMismatchesKeySet() ReadCovariates
getMismatchesKeySet(int) ReadCovariates
getMissingLeft() SamComparison
getMissingLeft() CompareSAMs
getMissingRight() SamComparison
getMissingRight() CompareSAMs
getMitochondrialAminoAcidByCodon(String, boolean) FuncotatorUtils
Returns the
AminoAcid corresponding to the given three-letter Mitochondrial
codon.
getMixingFraction() MixingFraction
getModeledSegments() MultidimensionalModeller
getMostLikelyGenotype(Snp) HaplotypeProbabilities
Gets the genotype for this Snp given the most likely haplotype.
getMostLikelyHaplotype() HaplotypeProbabilities
Gets the most likely haplotype given the probabilities.
getMother(Sample) SampleDB
Get the sample's mother
getMother() Trio
getMultiplicity() BaseEdge
Get the number of observations of paths connecting two vertices
getName() CopyNumberProgramGroup
getName() CoverageAnalysisProgramGroup
getName() ExampleProgramGroup
getName() MetagenomicsProgramGroup
getName() ShortVariantDiscoveryProgramGroup
getName() StructuralVariantDiscoveryProgramGroup
getName() TestProgramGroup
getName() FeatureDataSource
Get the logical name of this data source.
getName() FeatureInput
Gets the logical name of this Feature source.
getName() CountingReadFilter.CountingAndReadFilter
getName() CountingReadFilter
getName() CountingVariantFilter.CountingAndVariantFilter
getName() CountingVariantFilter
getName() MultiVariantDataSource
Get the logical name of this data source.
getName() AminoAcid
getName() DataSourceFuncotationFactory
getName() CosmicFuncotationFactory
getName() GencodeFuncotationFactory
getName() VcfFuncotationFactory
getName() LocatableXsvFuncotationFactory
getName() SimpleKeyXsvFuncotationFactory
getName() PSPathogenReferenceTaxonProperties
getName() PSTreeNode
getName() SVFastqUtils.FastqRead
getName() TrancheManager.SelectionMetric
getName() GencodeGtfFeature.OptionalField
getName() GATKDocWorkUnit
getName() AdapterPair
getName() IlluminaAdapterPair
getName() Parameter
getName() GATKRead
getName() MarkDuplicatesSparkRecord
getName() SAMRecordToGATKReadAdapter
getName() QualQuantizer.QualInterval
getName() BaseCallingProgramGroup
getName() DiagnosticsAndQCProgramGroup
getName() IntervalsManipulationProgramGroup
getName() OtherProgramGroup
getName() ReadDataManipulationProgramGroup
getName() ReferenceProgramGroup
getName() Testing
getName() VariantEvaluationProgramGroup
getName() VariantFilteringProgramGroup
getName() VariantManipulationProgramGroup
getName() Snp
getName() AdapterPair
getName() IlluminaUtil.IlluminaAdapterPair
getNameFormat() GATKReportColumnFormat
getNameOf(int) PSTree
getNBases() ReadMetadata.LibraryRawStatistics
getNcbiBuild() GencodeFuncotation
getNearProbeDistance() TargetMetricsCollector
Gets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.
getNegativeMAD() LibraryStatistics
getNeighborhood(VariantContext, int) EventMap
Get all of the variant contexts starting at leftMost that are within maxBP of each other
getNextOnGenomeCigarElement() PileupElement
Get the cigar element of the next genomic aligned position
getNextReadPair(PeekableIterator<SAMRecord>) QuerySortedReadPairIteratorUtil
Get the next read pair (where both have the same read name).
getNextReferenceVertex(V) BaseGraph
Traverse the graph and get the next reference vertex if it exists
getNextReferenceVertex(V, boolean, Optional<E>) BaseGraph
Traverse the graph and get the next reference vertex if it exists
getnLoci() ArtificialBAMBuilder
getNObservations(int) IntHistogram
getNodeIDs() PSTree
getNoise() ReadData
getNoMatchMetric() ExtractIlluminaBarcodes.PerTileBarcodeExtractor
getNonLogValue(double) MathUtil.LogMath
Returns the decimal representation of the provided log values.
getNonNullEnvironmentVariable(String) BaseTest
getNonOverlappingAltAlleleBaseString(Allele, Allele, boolean) FuncotatorUtils
Get the string of bases that are different from the given alleles.
getNovelAdjacencyReferenceLocations() SimpleNovelAdjacencyAndChimericAlignmentEvidence
getNPartitions() ReadMetadata
getNReads() LibraryStatistics
getNReads() ReadMetadata
getNReads() ReadMetadata.LibraryRawStatistics
getNReads() ReadMetadata.PartitionStatistics
getnReadsPerLocus() ArtificialBAMBuilder
getNRefBases() ReadMetadata
getNSamples() ArtificialBAMBuilder
getNumAdaptersToKeep() AdapterMarker
getNumAlignedBases(GATKRead) ReadPosRankSumTest
getNumAlignedBases(SAMRecord) RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
getNumAlignedBasesCountingSoftClips(GATKRead) 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) AlignmentUtils
Returns number of alignment blocks (continuous stretches of aligned bases) in the specified alignment.
getNumArtifactMode() OrientationSampleTransitionSummary
getNumArtifactModeFiltered() OrientationSampleTransitionSummary
getNumBasesPassingMinimumBaseQuality(SAMRecord, AlignmentBlock, int) TargetMetricsCollector
Get the the number of bases in the given alignment block and record that have base quality greater or equal to the minimum
getNumberOfClusters(File) BclReader
getNumberOfDiscardedItems() Downsampler
Returns the number of items discarded (so far) during the downsampling process
getNumberOfElements(Predicate<PileupElement>) ReadPileup
Returns the number of elements that satisfy the predicate.
getNumberOfEvents() EventMap
How many events do we have?
getNumberOfOpticalDuplicateClusters() LibraryIdGenerator
getNumberOfOpticalDuplicateClusters() LibraryIdGenerator
getNumberOfRecords() SamFileTester
getNumClippedBases(boolean, Cigar) SvCigarUtils
Returns the number of clipped bases, including both soft and hard, represented in cigarAlong5to3DirectionOfContig
from the start or from the end
getNumClippedBases(boolean, List<CigarElement>) SvCigarUtils
Returns the number of clipped bases, including both soft and hard, represented in cigarElements
from the start or from the end
getNumClippedBasesAtEnd(GATKRead) ReadPosRankSumTest
getNumClippedBasesAtStart(GATKRead) ReadPosRankSumTest
getNumClustersInTile() TileIndex.TileIndexRecord
getNumColumns() GATKReportTable
getNumDescriptors() ReadStructure
getNumDuplicates() MarkDuplicatesWithMateCigarIterator
getNumDuplicates() MarkQueue
Returns the number of duplicates detected
getNumEigensamples() HDF5SVDReadCountPanelOfNormals
getNumEigensamples() SVDReadCountPanelOfNormals
Returns the number of eigensamples.
getNumericalMean() BetaBinomialDistribution
getNumericalVariance() BetaBinomialDistribution
getNumHardClippedBases(GATKRead) AlignmentUtils
Count the number of bases hard clipped from read
If read's cigar is null, return 0
getNumHardClippingBases(boolean, List<CigarElement>) SvCigarUtils
getNumMismatches() RecalDatum
getNumNonRefPassingVariants() OrientationSampleTransitionSummary
getNumNotArtifactMode() OrientationSampleTransitionSummary
getNumObservations() RecalDatum
getNumOfTies() MannWhitneyU.RankedData
getNumPoints() AlleleFractionSegment
getNumPoints() CopyRatioSegment
getNumPoints() IntegerCopyNumberSegment
getNumPointsAlleleFraction() ModeledSegment
getNumPointsAlleleFraction() MultidimensionalSegment
getNumPointsCopyRatio() ModeledSegment
getNumPointsCopyRatio() MultidimensionalSegment
getNumReads() ClusterData
getNumReadsProcessed() BaseRecalibrationEngine
getNumRecordsWithNoMateCigar() MarkDuplicatesWithMateCigarIterator
Useful for statistics after the iterator has been exhausted and closed.
getNumRows() GATKReportTable
getNumSoftClippingBases(boolean, List<CigarElement>) SvCigarUtils
getNumTandemRepeatUnits(VariantContext, byte[]) GATKVariantContextUtils
getNumTandemRepeatUnits(byte[], byte[], byte[]) GATKVariantContextUtils
getNumTiles() BclIndexReader
getNumTiles() TileIndex
getObq() OrientationSampleTransitionSummary
getObsAllele1() HaplotypeProbabilities
Returns the number of observations of alleles supporting the first/major haplotype allele.
getObsAllele1() HaplotypeProbabilitiesFromSequence
Returns the number of bases/reads that support the first allele.
getObsAllele1() HaplotypeProbabilityOfNormalGivenTumor
getObsAllele2() HaplotypeProbabilities
Returns the number of observations of alleles supporting the second/minor haplotype allele.
getObsAllele2() HaplotypeProbabilitiesFromSequence
Returns the number of bases/reads that support the second allele.
getObsAllele2() HaplotypeProbabilityOfNormalGivenTumor
getOffset(Locatable) ActivityProfileState
The offset of state w.r.t.
getOffset() PileupElement
Get the offset of the this element into the read that aligns that read's base to this genomic position.
getOffsetInCurrentCigar() 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() 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.
getOffsets() ReadPileup
Returns a list of the offsets in this pileup.
getOps() ReadClipper
Check the list of operations set up for this read.
getOpticalDupesByLibraryId() MarkDuplicatesWithMateCigarIterator
getOpticalDuplicatesByLibraryIdMap() LibraryIdGenerator
getOpticalDuplicatesByLibraryIdMap() LibraryIdGenerator
getOptimalNumberOfBits(long, double) LongBloomFilter
getOptionalDouble(Map<String, String>, String, double) Tranche
getOptionalField(String) GencodeGtfFeature
getOptionalFields() GencodeGtfFeature
getOptionalIntAttribute(SAMRecord, String) ReadUtils
Encapsulates a integer attribute into an OptionalInt instance.
getOptionalIntAttribute(GATKRead, String) ReadUtils
Encapsulates a integer attribute into an OptionalInt instance.
getOptionalInteger(Map<String, String>, String, int) Tranche
getOrCreate(Class<? extends T>, Map<?, ?>...) ConfigFactory
Wrapper around ConfigCache.getOrCreate(Class, Map[]) which will ensure that
path variables specified in Config.Sources annotations are resolved prior
to creation.
getOrCreate(Factory, Class<? extends T>, Map<?, ?>...) ConfigFactory
Wrapper around ConfigCache.getOrCreate(Factory, Class, Map[]) which will ensure that
path variables specified in Config.Sources annotations are resolved prior
to creation.
getOrCreate(Object, Class<? extends T>, Map<?, ?>...) ConfigFactory
Wrapper around ConfigCache.getOrCreate(Object, Class, Map[]) which will ensure that
path variables specified in Config.Sources annotations are resolved prior
to creation.
getOrCreate(Factory, Object, Class<? extends T>, Map<?, ?>...) ConfigFactory
Wrapper around ConfigCache.getOrCreate(Factory, Object, Class, Map[]) which will ensure that
path variables specified in Config.Sources annotations are resolved prior
to creation.
getOrderedMates(NovelAdjacencyAndAltHaplotype, ReferenceMultiSource) BreakEndVariantType.InvSuspectBND
getOrderedMates(NovelAdjacencyAndAltHaplotype, ReferenceMultiSource, SAMSequenceDictionary) BreakEndVariantType.TransLocBND
getOrientationByte(boolean, boolean) ReadEnds
Returns a single byte that encodes the orientation of the two reads in a pair.
getOrientationByte(boolean, boolean) ReadEnds
Returns a single byte that encodes the orientation of the two reads in a pair.
getOrientationForOpticalDuplicates() Pair
Returns the pair orientation suitable for optical duplicates,
which always goes by the first then the second end for the strands.
getOrientationForPCRDuplicates() EmptyFragment
getOrientationForPCRDuplicates() Fragment
getOrientationForPCRDuplicates() Pair
getOrientationForPCRDuplicates() 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) ReadUtils
Retrieve the original base qualities of the given read, if present,
as stored in the OQ attribute.
getOriginalIntervalGCContent() HDF5SVDReadCountPanelOfNormals
getOriginalIntervalGCContent() SVDReadCountPanelOfNormals
getOriginalIntervals() HDF5SVDReadCountPanelOfNormals
getOriginalIntervals() 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() HDF5SVDReadCountPanelOfNormals
getOriginalReadCounts() 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() QualQuantizer
getOtherAltCount() PileupSummary
getOtherTranscripts() GencodeFuncotation
getOutput() SamFileTester
getOutputCycles() OutputMapping
getOutputDescriptors() OutputMapping
getOutputDir() SamFileTester
getOutputFile() OutputStreamSettings
getOutputFileName(File) CalculateReadGroupChecksum
Creates a file name (not including the path) for an RG MD5 file based on the name of the input file.
getOutputIndexForCycle(int) 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() SvDiscoveryInputMetaData
getOutputReadLengths() OutputMapping
getOutputReadStructure() IlluminaDataProviderFactory
Sometimes (in the case of skipped reads) the logical read structure of the output cluster data is different from the input
readStructure
getOutputReadStructure() OutputMapping
getOutputStream() ReadEndsForMarkDuplicatesCodec
getOutputStream() ReadEndsForMarkDuplicatesCodec
getOutputStream() RepresentativeReadIndexerCodec
getOutputString() CalledCopyRatioSegment.Call
getOverlapDetector() AbstractLocatableCollection
getOverlapNames() VariantOverlapAnnotator
Get the collection of names of overlap sets ued by this annotator.
getOverlapping(SimpleInterval) IntervalsSkipList
Returns all the intervals that overlap with the query.
getOverlapping(SimpleInterval) IntervalsSkipListOneContig
Returns all the intervals that overlap with the query.
getOverlapping(GenomeLoc) GenomeLocSortedSet
Return a list of intervals overlapping loc
getOverlappingExonPositions(Allele, Allele, String, int, int, Strand, List<? extends Locatable>) FuncotatorUtils
Get the overlapping exon start/stop as a
SimpleInterval for the given altAllele / reference.
getOverlappingFragmentFilteredPileup(SAMFileHeader) ReadPileup
Returns a new ReadPileup where only one read from an overlapping read
pair is retained.
getOverlappingFragmentFilteredPileup(boolean, Comparator<PileupElement>, SAMFileHeader) ReadPileup
Returns a new ReadPileup where only one read from an overlapping read
pair is retained.
getOverlappingFullSearch(GenomeLoc) 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() FragmentCollection
Gets the T elements containing overlapping elements, in no particular order
The returned collection is unmodifiable.
getOverlappingReferenceBases() ReadContextData
getOverlappingVariants() ReadContextData
getP() MannWhitneyU.Result
getPackageList() Main
The packages we wish to include in our command line.
getPackageList() PicardCommandLine
The packages we wish to include in our command line
getPackageNames() GATKAnnotationPluginDescriptor
A list of package names which will be searched for plugins managed by the descriptor.
getPackageNames() GATKReadFilterPluginDescriptor
A list of package names which will be searched for plugins managed by the descriptor.
getPaddedInterval() Shard
getPaddedInterval() ShardBoundary
getPaddedInterval() ShardBoundaryShard
getPaddedInterval() ShardToMultiIntervalShardAdapter
getPaddedInterval() DownsampleableSparkReadShard
getPaddedIntervals() MultiIntervalLocalReadShard
getPaddedIntervals() MultiIntervalShard
getPaddedIntervals() ShardToMultiIntervalShardAdapter
getPaddedReferenceLoc(AssemblyRegion, int, ReferenceSequenceFile) AssemblyBasedCallerUtils
getPaddedReferenceLoc() AssemblyResultSet
Returns the padded reference location.
getPadding() AssemblyRegionTrimmer.Result
Returns the required padding around callable variation.
getPairedReads() PSPairedUnpairedSplitterSpark
getPairedStrandedIntervals() EvidenceTargetLink
getPairedStrandedIntervals(ReadMetadata, SAMSequenceDictionary, int) SVContext
getPairHMMArgs() PairHMMNativeArgumentCollection
getPanelIntervalFractionalMedians() HDF5SVDReadCountPanelOfNormals
getPanelIntervalFractionalMedians() SVDReadCountPanelOfNormals
getPanelIntervals() HDF5SVDReadCountPanelOfNormals
getPanelIntervals() SVDReadCountPanelOfNormals
Returns a modifiable copy of the list of the intervals contained in this PoN after all filtering has been applied.
getParallelReads(String, String, TraversalParameters) ReadsSparkSource
Loads Reads using Hadoop-BAM.
getParallelReads(String, String, TraversalParameters, long) ReadsSparkSource
Loads Reads using Hadoop-BAM.
getParallelReads(String, String) ReadsSparkSource
Loads Reads using Hadoop-BAM.
getParallelReads(String, String, int) ReadsSparkSource
Loads Reads using Hadoop-BAM.
getParallelVariantContexts(String, List<SimpleInterval>) VariantsSparkSource
Loads variants in parallel using Hadoop-BAM for vcfs and bcfs.
getParallelVariants(String, List<SimpleInterval>) VariantsSparkSource
Loads variants in parallel using Hadoop-BAM for vcfs and bcfs.
getParallelVariants(List<String>, List<SimpleInterval>) VariantsSparkSource
Loads variants from multiple inputs in parallel using Hadoop-BAM for vcfs and bcfs.
getParent() PSPathogenReferenceTaxonProperties
getParent() PSTreeNode
getParentOf(int) PSTree
getParents(Sample) SampleDB
Get the sample's father and mother
getParentsRefRefChildHet() MendelianViolation
getPartition(Object) ComplexityPartitioner
getPartitionBounds(int) ReadMetadata
getPartitionIndex() MarkDuplicatesSparkRecord
getPassthrough(GATKRead, int) MarkDuplicatesSparkRecord
getPaternalID() Sample
getPaternalID() Trio
getPaternalId() PedFile.PedTrio
getPath(String) IOUtils
Converts the given URI to a Path object.
getPath() Resource
getPathOf(int) PSTree
Returns path of node id's from the input id to the root.
getPathOnGcs(String) BucketUtils
String -> Path.
getPathWithoutBucket(String) BucketUtils
Given a path of the form "gs://bucket/folder/folder/file", returns "folder/folder/file".
getPenalty() QualQuantizer.QualInterval
getPersistences() PersistenceOptimizer
getPerTilePerCycleFiles() 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
getPhasingCode(int, IlluminaMetricsCode) IlluminaMetricsCode
Phasing codes are between 200 and 299 (inclusive).
getPhasingMap() Tile
getPhasingMetricsForTiles(long, Collection<Tile>, boolean) IlluminaPhasingMetrics
Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them
getPhasingValue() TilePhasingValue
getPhenotype() PedFile.PedTrio
getPileup(Locatable, Iterable<GATKRead>) GATKProtectedVariantContextUtils
Get the pileup of reads covering a locus.
getPileupContingencyTable(Map<String, List<PileupElement>>, Allele, List<Allele>, int, int) StrandBiasTest
Allocate and fill a 2x2 strand contingency table.
getPileupForLane(String) ReadPileup
Make a new pileup from elements whose reads have read groups that agree with the given lane ID.
getPileupForSample(String, SAMFileHeader) ReadPileup
Make a new pileup from elements whose reads belong to the given sample.
getPileupString() SAMPileupFeature
Format in a samtools-like string.
getPileupString(char) ReadPileup
Format, assuming a single-sample, in a samtools-like string.
GetPileupSummaries org.broadinstitute.hellbender.tools.walkers.contamination
Summarizes counts of reads that support reference, alternate and other alleles for given sites.
GetPileupSummaries() GetPileupSummaries
getPinv() SimpleSVD
getPinv() SVD
Get the pseudoinverse as calculated using the SVD
getPlatform(GATKRead, SAMFileHeader) ReadUtils
Returns the platform associated with the provided read's read group.
getPlatformUnit(GATKRead, SAMFileHeader) ReadUtils
Returns the platform unit associated with the provided read's read group.
getPlatformUnit() FingerprintIdDetails
getPloidyModel() HaplotypeCallerGenotypingEngine
Returns the ploidy-model used by this genotyping engine.
getPluginBaseClass() GATKAnnotationPluginDescriptor
getPluginBaseClass() GATKReadFilterPluginDescriptor
getPluginDescriptors() CommandLineProgram
Return the list of GATKCommandLinePluginDescriptors to be used for this CLP.
getPluginDescriptors() GATKTool
Return the list of GATKCommandLinePluginDescriptors to be used for this tool.
getPluginDescriptors() GATKSparkTool
Return the list of GATKCommandLinePluginDescriptor objects to be used for this CLP.
getPluginDescriptors() CountVariantsSpark
Return the list of GATKCommandLinePluginDescriptor objects to be used for this CLP.
getPoorQualityFrequencies() 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.
getPopulationAFAnnotation(List<VariantContext>, List<Allele>, double) GermlineProbabilityCalculator
getPopulationLikelihood() MatchResults
getPos() Snp
getPosition() AlignmentContext
getPosition() SVLocation
getPositionInfo() CbclData
getPositiveMAD() LibraryStatistics
getPosteriorProbabilities() HaplotypeProbabilities
Returns the posterior probabilities using the population frequency as a prior.
getPower() BasicValidationResult
getPrecision() ConcordanceSummaryRecord
getPrePhasingMap() Tile
getPrePhasingValue() TilePhasingValue
getPreviousOnGenomeCigarElement() 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) BaseGraph
Traverse the graph and get the previous reference vertex if it exists
getPrimaryInterval() SVFastqUtils.Mapping
getPrintableId() Fingerprint
getPriorProbablities() HaplotypeProbabilities
getProbabilitiesAsArray() ActivityProfile
Get the probabilities of the states as a single linear array of doubles
getProbabilityVector() ProbabilityVector
getProbeIntervals() CollectHsMetrics
getProbeIntervals() CollectTargetedMetrics
getProbeIntervals() CollectTargetedPcrMetrics
getProbeSetName() CollectHsMetrics
getProbeSetName() CollectTargetedMetrics
getProbeSetName() CollectTargetedPcrMetrics
getProcess() StreamingPythonScriptExecutor
Get the Process object associated with this executor.
getProcess() ProcessControllerBase
getProcessOutputByLine() StreamingProcessController
Blocking call to retrieve output from the remote process by line.
getProcessOutputByPrompt() StreamingProcessController
Blocking call to retrieve output from the remote process by prompt synchronization.
getProgramName() SparkCommandLineProgram
Returns the program's name.
getProgramProperty(Class<?>) Main
getProgramProperty(Class) PicardCommandLine
getProgramRecord() AbstractAlignmentMerger
getProgramRecord() AbstractAlignmentMerger
getProgressMeterRecordLabel() AssemblyRegionWalker
getProgressMeterRecordLabel() FeatureWalker
getProgressMeterRecordLabel() GATKTool
getProgressMeterRecordLabel() IntervalWalker
getProgressMeterRecordLabel() LocusWalker
getProgressMeterRecordLabel() ReadWalker
getProgressMeterRecordLabel() VariantWalkerBase
getProgressMeterRecordLabel() GenomicsDBImport
getProteinChange() GencodeFuncotation
getProteinChangeEndPosition(Integer, Integer) FuncotatorUtils
Get the Protein change end position (1-based, inclusive) given the protein change start position and aligned alternate allele length.
getProteinChangeEndPosition() SequenceComparison
getProteinChangePosition(Integer) FuncotatorUtils
Get the Protein change start position (1-based, inclusive) given the aligned position of the coding sequence.
getProteinChangeStartPosition() SequenceComparison
getProteinChangeString(SequenceComparison) FuncotatorUtils
getPruneFactor() ReadThreadingAssembler
getPruningMultiplicity() BaseEdge
A special assessor that returns the multiplicity that should be used by pruning algorithm
getPruningMultiplicity() MultiSampleEdge
getQName() QNameAndInterval
getQual() PileupElement
Get the base quality score of the base at this aligned position on the genome
getQual() QualQuantizer.QualInterval
getQual(EventType, int) ReadRecalibrationInfo
Get the qual score for event type at offset
getQualities() BclData
getQualities() ReadData
getQualityAllCalled() IntegerCopyNumberSegment
getQualityEnd() IntegerCopyNumberSegment
getQualityScoreCovariate() StandardCovariateList
getQualityScoreTable() RecalibrationTables
getQualitySomeCalled() IntegerCopyNumberSegment
getQualityStart() IntegerCopyNumberSegment
getQuals() SVFastqUtils.FastqRead
returns phred-scaled quals with no bias
getQualsStream() SAMPileupFeature
Get the qualities as a stream
getQualsString() SAMPileupFeature
Returns pile of obseved qualities over the genomic location
Note: this call costs O(n) and allocates fresh array each time
getQuantizationInfo() RecalibrationReport
getQuantizationLevels() QuantizationInfo
getQuantizedQuals() QuantizationInfo
getQuerynameSortedAlignedRecords() AbstractAlignmentMerger
getQuerynameSortedAlignedRecords() SamAlignmentMerger
Reads the aligned SAM records into a SortingCollection and returns an iterator over that collection
getQuerynameSortedAlignedRecords() AbstractAlignmentMerger
getQuerynameSortedAlignedRecords() SamAlignmentMerger
Reads the aligned SAM records into a SortingCollection and returns an iterator over that collection
getRAC() RecalibrationReport
getRandomDataForPlotting(int, List<VariantDatum>, List<VariantDatum>, List<VariantDatum>) VariantDataManager
getRandomDataGenerator() Utils
getRandomGenerator() Utils
getRank() PSPathogenReferenceTaxonProperties
getRank() PSTreeNode
getRank() MannWhitneyU.RankedData
getRankOf(int) PSTree
getRateFactor() PairHMMLikelihoodCalculationEngine.PCRErrorModel
getRawData() ReducibleAnnotationData
getRawDescriptions() AS_QualByDepth
getRawDescriptions() ReducibleAnnotation
Returns the descriptions used for the VCF INFO meta field corresponding to the annotations raw key.
getRawDescriptions() RMSMappingQuality
getRawIntensities() ReadData
getRawKeyName() AS_BaseQualityRankSumTest
getRawKeyName() AS_MappingQualityRankSumTest
getRawKeyName() AS_QualByDepth
getRawKeyName() AS_ReadPosRankSumTest
getRawKeyName() AS_RMSMappingQuality
getRawKeyName() AS_StrandBiasTest
getRawKeyName() ReducibleAnnotation
getRawKeyName() RMSMappingQuality
getRead() ReadWalkerContext
getRead(int) SubsettedLikelihoodMatrix
getRead() ReadClipper
The original read.
getRead(int) LikelihoodMatrix
Returns the allele given its index.
getRead() AlignmentStateMachine
Get the read we are aligning to the genome
getRead() PileupElement
Get the read for this pileup element.
getRead() ReadRecalibrationInfo
Get the read involved in this recalibration info
getRead(int) ClusterData
getReadBarcodeValue(SAMRecord, String) EstimateLibraryComplexity
getReadBaseQuality(GATKRead, int) BaseQualityRankSumTest
getReadCoordinateForReferenceCoordinate(GATKRead, int, ReadUtils.ClippingTail) ReadUtils
getReadCoordinateForReferenceCoordinate(GATKRead, int) ReadUtils
Returns the read coordinate corresponding to the requested reference coordinate.
getReadCoordinateForReferenceCoordinate(int, Cigar, int, ReadUtils.ClippingTail, boolean) ReadUtils
getReadCoordinateForReferenceCoordinateUpToEndOfRead(GATKRead, int, ReadUtils.ClippingTail) ReadUtils
getReadEnds() PhysicalLocationForMateCigarSet
Gets the set of read ends
getReadEndSetForOpticalDuplicates() ReadEndsForMateCigar
Gets the read ends for optical duplicate tracking
getReadFiles() OptionalReadInputArgumentCollection
getReadFiles() ReadInputArgumentCollection
Get the list of BAM/SAM/CRAM files specified at the command line
getReadFiles() RequiredReadInputArgumentCollection
getReadFilesNames() OptionalReadInputArgumentCollection
getReadFilesNames() ReadInputArgumentCollection
Get the list of BAM/SAM/CRAM filenames specified at the command line
getReadFilesNames() RequiredReadInputArgumentCollection
getReadGroup() GATKRead
getReadGroup() ReadEnds
getReadGroup() Pair
getReadGroup() SAMRecordToGATKReadAdapter
getReadGroup() FingerprintResults
getReadGroup() PhysicalLocationForMateCigar
getReadGroup() ReadEnds
getReadGroup() PhysicalLocation
getReadGroup() PhysicalLocationInt
getReadGroupCovariate() StandardCovariateList
getReadGroupIDs() ReadPileup
Gets a set of the read groups represented in this pileup.
getReadGroupIDs(SAMFileHeader) ReadGroupCovariate
getReadGroupLibraryName(SAMReadGroupRecord) LibraryIdGenerator
getReadGroupLibraryName(SAMReadGroupRecord) LibraryIdGenerator
getReadGroups() GATKReport
Gets the unique read groups in the table
getReadGroupTable() RecalibrationTables
getReadIndexPaths() ReadInputArgumentCollection
getReadIntervals() ReadsPreprocessingPipelineTestData
getReadLength() ArtificialBAMBuilder
getReadMetadata() SvDiscoveryInputMetaData.SampleSpecificData
getReadMetadata() FindBreakpointEvidenceSpark.AssembledEvidenceResults
getReadName() HitsForInsert
getReadOffset() AlignmentStateMachine
What is our current offset in the read's bases that aligns us with the reference genome?
getReadPairs() EvidenceTargetLink
getReadPairTemplateNames() EvidenceTargetLink
getReadPaths() OptionalReadInputArgumentCollection
getReadPaths() ReadInputArgumentCollection
Get the list of BAM/SAM/CRAM files specified at the command line.
getReadPaths() RequiredReadInputArgumentCollection
getReadPosition(GATKRead, int) ReadPosRankSumTest
getReads() AssemblyRegion
Get an unmodifiable copy of the list of reads currently in this assembly region.
getReads() GATKSparkTool
getReads(JavaSparkContext) ReadWalkerSpark
Loads reads and the corresponding reference and features into a JavaRDD for the intervals specified.
getReads(JavaSparkContext, int) NioBam
Parses the BAM file into SAMRecords.
getReads() ReadPileup
Returns a list of the reads in this pileup.
getReads() ReadsPreprocessingPipelineTestData
getReadsContext() IntervalWalkerContext
getReadsContext() VariantWalkerContext
getReadSourceName() GATKSparkTool
Returns the name of the source of reads data.
getReadSpanLoc() AssemblyRegion
The span of this assembly region, including the bp covered by all reads in this
region.
getReadStartFrequency() LibraryStatistics
getReadStartLength() ReadsPreprocessingPipelineTestData
getReadToMateMap(ReadsContext, int) ReadUtils
Create a map of reads overlapping interval to their mates by looking for all possible mates within some
maximum fragment size.
getReadType() ReadData
getReadValidationStringency() ReadInputArgumentCollection
Get the read validation stringency specified at the command line, or the default value if none was specified
at the command line.
getRealignments() RealignmentEngine.RealignmentResult
getReasonForAlignmentClassificationFailure() AssemblyContigWithFineTunedAlignments
getRecalibrationTables() BaseRecalibrationEngine
Get a possibly not-final recalibration table, to deal with distributed execution.
getRecalibrationTables() RecalibrationReport
getRecommendedNumReducers() GATKSparkTool
Return the recommended number of reducers for a pipeline processing the reads.
getRecord() ReadEndsForMateCigar
getRecordIterator() SamFileTester
getRecordReadName() ReadEndsForMateCigar
getRecords() AbstractRecordCollection
getRecords() AnnotatedIntervalCollection
getRecordWriter(TaskAttemptContext) ReadsSparkSink.SparkBAMOutputFormat
getRecordWriter(TaskAttemptContext) ReadsSparkSink.SparkCRAMOutputFormat
getRecordWriter(TaskAttemptContext) ReadsSparkSink.SparkHeaderlessSAMOutputFormat
getRecordWriter(TaskAttemptContext) ReadsSparkSink.SparkSAMOutputFormat
getRecordWriter(TaskAttemptContext, Path) VariantsSparkSink.SparkHeaderlessVCFOutputFormat
getRecordWriter(TaskAttemptContext, OutputStream) VariantsSparkSink.SparkHeaderlessVCFOutputFormat
getRecordWriter(TaskAttemptContext) VariantsSparkSink.SparkHeaderlessVCFOutputFormat
getRecordWriter(TaskAttemptContext) VariantsSparkSink.SparkVCFOutputFormat
getRef() PerAlleleCollection
getRef() SAMPileupFeature
Returns the reference basse
getRefAllele() GencodeFuncotation
getRefAllele() AlleleSpecificAnnotationData
Get the reference allele for this allele-specific data.
getRefAllele() PerAlleleCollection
getRefCount() PileupSummary
getReference() GATKSparkTool
getReference() BasicValidationResult
getReference() ArtificialBAMBuilder
getReferenceAllele() SequenceComparison
getReferenceAminoAcidSequence() SequenceComparison
getReferenceBases(SimpleInterval) ReferenceFileSource
getReferenceBases(SimpleInterval) ReferenceHadoopSource
getReferenceBases(SimpleInterval) ReferenceMultiSource
Return reference bases for the given interval.
getReferenceBases(SimpleInterval) ReferenceSource
getReferenceBases(SimpleInterval) ReferenceTwoBitSource
Gets the reference bases spanning the requested interval.
getReferenceBases() SequenceComparison
getReferenceBasesRDD(JavaSparkContext, int, ReferenceMultiSource, SAMSequenceDictionary, int, int) SVReferenceUtils
Create an RDD from the reference sequences.
getReferenceBroadcast() SvDiscoveryInputMetaData.ReferenceData
getReferenceBytes(V, V, boolean, boolean) BaseGraph
Walk along the reference path in the graph and pull out the corresponding bases
getReferenceCodingSequence() SequenceComparison
Return the
ReferenceSequence containing the coding region for the transcript of this
SequenceComparison.
getReferenceContext() AssemblyRegionWalkerContext
getReferenceContext() IntervalWalkerContext
getReferenceContext() LocusWalkerContext
getReferenceContext() ReadWalkerContext
getReferenceContext() VariantWalkerContext
getReferenceContext() GencodeFuncotation
getReferenceData() SvDiscoveryInputMetaData
getReferenceDictionary() GATKTool
Returns the reference sequence dictionary if there is a reference (hasReference() == true), otherwise null.
getReferenceFile() CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
getReferenceFile() CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
getReferenceFile() OptionalReferenceArgumentCollection
getReferenceFile() ReferenceArgumentCollection
getReferenceFile() RequiredReferenceArgumentCollection
getReferenceFile() CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
getReferenceFile() ReorderSam.ReorderSamReferenceArgumentCollection
getReferenceFile() ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
getReferenceFileName() OptionalReferenceInputArgumentCollection
getReferenceFileName() ReferenceInputArgumentCollection
Get the name of the reference file specified at the command line.
getReferenceFileName() RequiredReferenceInputArgumentCollection
getReferenceHaplotype() AssemblyResultSet
Query the reference haplotype in the result set.
getReferenceIndex(GATKRead, SAMFileHeader) ReadUtils
Returns the reference index in the given header of the read's contig,
or SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX if the read is unmapped.
getReferenceLength() PSPathogenTaxonScore
getReferencePath() ReferenceInputArgumentCollection
Get the Path to the reference, may be null
getReferenceSequence() SAMRecordAndReference
getReferenceSequence() SAMRecordAndReference
getReferenceSequenceDictionary(SAMSequenceDictionary) ReferenceFileSource
getReferenceSequenceDictionary(SAMSequenceDictionary) ReferenceHadoopSource
getReferenceSequenceDictionary(SAMSequenceDictionary) ReferenceMultiSource
Return a sequence dictionary for the reference.
getReferenceSequenceDictionary(SAMSequenceDictionary) ReferenceSource
getReferenceSequenceDictionary(SAMSequenceDictionary) ReferenceTwoBitSource
getReferenceSequenceDictionary() GATKSparkTool
getReferenceSequenceDictionaryBroadcast() SvDiscoveryInputMetaData.ReferenceData
getReferenceSinkVertex() BaseGraph
getReferenceSourceVertex() BaseGraph
getReferenceWindow() SequenceComparison
getReferenceWindowForRead(GATKRead, int) BAQ
Given a read, get an interval representing the span of reference bases required by BAQ for that read
getReferenceWindowFunction() ReferenceMultiSource
getReferenceWindowFunction() GATKSparkTool
Window function that controls how much reference context to return for each read when
using the reference source returned by
GATKSparkTool.getReference().
getReferenceWindowFunction() BaseRecalibratorSpark
getReferenceWindowFunction() BQSRPipelineSpark
getReferenceWindowFunction() ReadsPipelineSpark
getRefFrequency() PileupSummary
getRefNucleotide() AllelicCount
getRefReadCount() AllelicCount
getRefs() GenotypeCounts
getRegionForGenotyping() AssemblyResultSet
Returns the current region for genotyping.
getReInterpretMultiSegmentsCalls() SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants
getReInterpretZeroOrOneSegmentCalls() SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants
getRelativeAccuracy() UnivariateSolverSpecifications
getRelativeClass() Resource
getRepresentativeRead() HitsForInsert
getRepresentativeSnp() HaplotypeProbabilities
Returns a representative SNP for this haplotype.
getRepresentativeSnp() HaplotypeProbabilitiesFromGenotype
Returns the SNP who's genotype was used to construct the likelihoods.
getRepresentativeSnp() HaplotypeProbabilityOfNormalGivenTumor
getRequestedExpressions() VariantAnnotatorEngine
getRequiredDouble(Map<String, String>, String) Tranche
getRequiredInteger(Map<String, String>, String) Tranche
getResolvedInstances() GATKAnnotationPluginDescriptor
Merge the default annotations with the users's command line annotation requests, then initialize
the resulting annotations.
getResolvedInstances() GATKReadFilterPluginDescriptor
getResolvedIntervals(String, SAMSequenceDictionary) 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) Resource
Given a resource path that is either on the file system or in a jar, return a File.
getResourceContentsAsStream() Resource
Get the contents of this resource as an InputStream
getResourcePath() RScriptLibrary
getResultFromFinalState(VariantContext, double[], StateTracker) AFCalculator
Convert the final state of the state tracker into our result as an AFCalculationResult
Assumes that stateTracker has been updated accordingly
getResultFromFinalState(VariantContext, double[], StateTracker) AlleleFrequencyCalculator
getResultState() ActivityProfileState
getResultValue() ActivityProfileState
getRight() PairedStrandedIntervals
getRightClipPoint(byte[]) BaseQualityClipReadTransformer
Returns right clip point or -1 if no clip
getRowMedians(RealMatrix) MatrixSummaryUtils
Return an array containing the median for each row in the given matrix.
getRowVariances(RealMatrix) MatrixSummaryUtils
Return an array containing the variance for each row in the given matrix.
getRunFile(File, Pattern) ParameterizedFileUtil
getRunning() ProcessControllerBase
getRunningMetric(int) TrancheManager.SelectionMetric
getRunningMetric(int) TrancheManager.TruthSensitivityMetric
getSafeNonExistentFile(String) BaseTest
Return a File object representing a file with the given name and extension that is guaranteed not to exist.
getSafeNonExistentPath(String) BaseTest
Return a Path object representing a file with the given name and extension that is guaranteed not to exist.
getSamFileHeader() AnnotatedIntervalCollection
Can return null
getSamFileHeader() AnnotatedIntervalHeader
Can be null
getSamFileHeader() CollectWgsMetrics
This method should only be called after this.getSamReader() is called.
getSAMFileWriter(String, SAMFileHeader, boolean) SVFileUtils
Supported format: BAM and SAM.
getSAMFlagsForRead(GATKRead) ReadUtils
Construct a set of SAM bitwise flags from a GATKRead
getSample() OrientationSampleTransitionSummary
getSample(int) GenotypingData
getSample(int) GenotypingLikelihoods
getSample(int) HeterogeneousPloidyModel
getSample(int) HomogeneousPloidyModel
getSample() MixingFraction
getSample(int) IndexedSampleList
getSample(int) ReadLikelihoods
Returns sample name given its index.
getSample(int) SampleList
Returns the element given its index within the set.
getSample(String) SampleDB
Get a sample by its ID
If an alias is passed in, return the main sample object
getSample() Fingerprint
getSample() FingerprintIdDetails
getSample() MatchResults
getSampleAlias() FingerprintResults
getSampleContamination() StandardCallerArgumentCollection
Returns an unmodifiable view of the map of SampleId -> contamination.
getSampleCount() HeterozygosityCalculator
getSampleId() SvDiscoveryInputMetaData.SampleSpecificData
getSampleId(SAMFileHeader) SVUtils
getSampleLikelihood() MatchResults
getSampleName() SampleLocatableMetadata
getSampleName() SampleMetadata
getSampleName() SimpleSampleLocatableMetadata
getSampleName() SimpleSampleMetadata
getSampleName() CoveragePerContig
GetSampleName org.broadinstitute.hellbender.tools
Emit a single sample name from the bam header into an output file.
GetSampleName() GetSampleName
getSampleName(GATKRead, SAMFileHeader) ReadUtils
Returns the sample name associated with the provided read's read group.
getSamples() MultiVariantDataSource
Return lexicographically sorted set of uniquified sample names merged from across input data sources
getSamples(V, Class<U>, int) GibbsSampler
Returns a list of samples for a specified model parameter, discarding the first numBurnIn samples.
getSamples(SAMFileHeader) ReadPileup
Gets a set of the samples represented in this pileup.
getSamples() ArtificialBAMBuilder
getSamples() SampleDB
getSamplesForVariants() MultiVariantWalker
Get in name-sorted order a list of samples merged from the driving variants files.
getSamplesFromHeader(SAMFileHeader) ReadUtils
Pull out the sample names from a SAMFileHeader
note that we use a TreeSet so that they are sorted
getSampleSpecificData() SvDiscoveryInputMetaData
getSamReader() CollectWgsMetrics
Gets the SamReader from which records will be examined.
getSamReader() CollectWgsMetricsWithNonZeroCoverage
getSAMReadGroupRecord(GATKRead, SAMFileHeader) ReadUtils
Returns a SAMReadGroupRecord object corresponding to the provided read's read group.
getSamRecord() SAMRecordAndReference
getSamRecord() SAMRecordAndReference
getSamRecordIndex() ReadEndsForMateCigar
A number of convenience functions
getSamRecordSetBuilder() SamFileTester
getSAMString() GATKRead
Get a string representation of this read in SAM string format, terminated with '\n'.
getSAMString() SAMRecordToGATKReadAdapter
getSanitizedUMI(SAMRecord, String) UmiUtil
Returns an instance of the UMI without dashes
getSAtagForGoodMappingToNonCanonicalChromosome() AssemblyContigWithFineTunedAlignments
getScatteredFileName(File, long, String) IntervalListTools
getScheme(boolean) GenotypeConcordanceSchemeFactory
getScore() Path
Get the total score of this path (bigger is better)
getScore() Haplotype
Get the score (an estimate of the support) of this haplotype
getScore() EmptyFragment
getScore() Fragment
getScore() Pair
getScore() PairedEnds
getScoreNormalized() PSPathogenTaxonScore
getScriptException(String) PythonExecutorBase
Return an exception specific to this executor type, to be thrown on error conditions.
getScriptException(String) RScriptExecutor
Return an exception specific to this executor type, to be thrown on error conditions.
getScriptException(String) ScriptExecutor
Called by the script executor when error is encountered.
getSecondaryVariantClassification() GencodeFuncotation
getSecondOfPair(int) HitsForInsert
getSecondsInAssembly() AlignedAssemblyOrExcuse
getSegment() MinorAlleleFractionRecord
getSelenocysteines() GencodeGtfTranscriptFeature
getSelfScore() PSPathogenTaxonScore
getSensitivity() ConcordanceSummaryRecord
getSensitivity(GenotypeConcordanceScheme, GenotypeConcordanceStates.TruthState[]) GenotypeConcordanceCounts
Returns the sensitivity defined by the scheme across the subset of truth states.
getSentinel() 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.
getSequence(String) HaplotypeCallerSpark.ReferenceMultiSourceAdapter
getSequence() BaseVertex
Get the sequence of bases contained in this vertex
Do not modify these bytes in any way!
getSequenceDictionary() FeatureDataSource
Returns the sequence dictionary for this source of Features.
getSequenceDictionary() MultiVariantDataSource
Returns the aggregate sequence dictionary for this source of Variants.
getSequenceDictionary() ReadsDataSource
Get the sequence dictionary for this ReadsDataSource
getSequenceDictionary() ReferenceDataSource
Get the sequence dictionary for this reference
getSequenceDictionary() ReferenceFileSource
Get the sequence dictionary for this reference
getSequenceDictionary() ReferenceMemorySource
Get the sequence dictionary for this reference
getSequenceDictionary() HDF5SVDReadCountPanelOfNormals
getSequenceDictionary() SVDReadCountPanelOfNormals
Returns the sequence dictionary common to all of the read counts used to build the PoN.
getSequenceDictionary() LocatableMetadata
getSequenceDictionary() SampleLocatableMetadata
getSequenceDictionary() SimpleLocatableMetadata
getSequenceDictionary() SimpleSampleLocatableMetadata
getSequenceDictionary() HaplotypeCallerSpark.ReferenceMultiSourceAdapter
getSequenceDictionary() GenomeLocParser
Return the master sequence dictionary used within this GenomeLocParser
getSequenceDictionaryForDrivingVariants() MultiVariantWalker
getSequenceDictionaryForDrivingVariants() VariantWalker
getSequenceDictionaryForDrivingVariants() VariantWalkerBase
Return the primary sequence dictionary to be used for the driving variants for this tool.
getSequenceDictionaryValidationArgumentCollection() GATKTool
getSequenceDictionaryValidationArgumentCollection() GATKSparkTool
subclasses can override this to provide different default behavior for sequence dictionary validation
getSequenceDictionaryValidationArgumentCollection() BwaSpark
getSequenceDictionaryValidationArgumentCollection() BwaAndMarkDuplicatesPipelineSpark
getSequencerType() NGSPlatform
The broad "type" of sequencer this platform represents (discrete or flow)
getSequenceString() BaseVertex
Get a string representation of the bases in this vertex
getSequentialFileList(File) FastqToSam
Get a list of FASTQs that are sequentially numbered based on the first (base) fastq.
getSets() LargeLongHopscotchSet
getSeverity() GencodeFuncotation.VariantClassification
getSex() Sample
getSex() PedFile.PedTrio
getShardedCollectionSortOrder(List<? extends AbstractLocatableCollection<METADATA, RECORD>>) AbstractLocatableCollection
Gets a list of locatable collections and returns the ascending sort order of collections.
getShardNumber() ReferenceShard
getShardNumber() VariantShard
getShardNumberFromInterval(Locatable) ReferenceShard
getShardNumberFromInterval returns the ReferenceShard that overlap the read's start position.
getSigma() BandPassActivityProfile
Get the Gaussian kernel sigma value
getSingletonReads() FragmentCollection
Gets the T elements not containing overlapping elements, in no particular order.
getSingletonSample(VariantContext) CallingMetricAccumulator
getSingularValues() HDF5SVDReadCountPanelOfNormals
getSingularValues() SVDReadCountPanelOfNormals
Returns a modifiable copy of an array of the singular values of the eigensamples in decreasing order.
getSingularValues() SimpleSVD
getSingularValues() SVD
Get the singular values as an array.
getSinks() BaseGraph
Get the set of sink vertices of this graph
getSizeOf() ReadEndsForMarkDuplicates
getSizeOf() ReadEndsForMarkDuplicatesWithBarcodes
getSizeOnRead() AlignmentInterval
getSkipNLoci() ArtificialBAMBuilder
getSnp(String) HaplotypeBlock
Gets a SNP by name if it belongs to this haplotype.
getSnp(String, int) HaplotypeMap
Queries a Snp by chromosome and position.
getSnpCounter() GenotypeConcordance
getSnpFalsePositiveRate() FalsePositiveRecord
getSnpFalsePositives() FalsePositiveRecord
getSnpGenotype(Snp, DiploidHaplotype) HaplotypeBlock
Gets the expected genotype of the provided SNP given the provided haplotype of this
haplotype block.
getSnps() HaplotypeBlock
Returns an unmodifiable, unordered, collection of all SNPs in this haplotype block.
getSNPSubstitutionType(VariantContext) GATKVariantContextUtils
Returns the type of the substitution (transition vs transversion) represented by this variant.
getSoftEnd() GATKRead
Calculates the reference coordinate for the end of the read taking into account soft clips but not hard clips.
getSoftEnd(GATKRead) ReadUtils
Calculates the reference coordinate for the end of the read taking into account soft clips but not hard clips.
getSoftEnd() SAMRecordToGATKReadAdapter
getSoftStart() GATKRead
Calculates the reference coordinate for the beginning of the read taking into account soft clips but not hard clips.
getSoftStart(GATKRead) ReadUtils
Calculates the reference coordinate for the beginning of the read taking into account soft clips but not hard clips.
getSoftStart() SAMRecordToGATKReadAdapter
getSolexaQualityCharFromFourQualities(String[], int, FormatUtil) 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, ...].
getSortedSampleSet(Map<String, VCFHeader>, GATKVariantContextUtils.GenotypeMergeType) VcfUtils
getSource() ChannelAsSeekableStream
getSource() TableReader
Returns the reader source name.
getSource() Fingerprint
getSourceContig() AssemblyContigWithFineTunedAlignments
getSources() BaseGraph
Get the set of source vertices of this graph
getSpan() AssemblyRegion
Get the raw span of this assembly region (excluding the extension)
getSpan() ReadMetadata.PartitionBounds
getSpan() ReadMetadata.PartitionStatistics
getSpan() 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>) IntervalUtils
getSpanningInterval returns interval that covers all of the locations passed in.
getSparkContext(String, Map<String, String>, String) SparkContextFactory
Get a JavaSparkContext.
getSparkMaster() SparkCommandLineArgumentCollection
getSparkProperties() SparkCommandLineArgumentCollection
getSpecificity(GenotypeConcordanceScheme, GenotypeConcordanceStates.TruthState[]) GenotypeConcordanceCounts
Returns the specificity defined by the scheme across the subset of truth states.
getSplicesForTesting() OverhangFixingManager
For testing purposes only
getSplitBy(GATKRead, SAMFileHeader) ReaderSplitter
Returns the value from this record for this splitter.
getSplitBy(GATKRead, SAMFileHeader) ReadGroupSplitter
getSplitByFunction() LibraryNameSplitter
getSplitByFunction() ReadGroupIdSplitter
getSplitByFunction() ReadGroupSplitter
getSplitByFunction() SampleNameSplitter
getSpliteratorForDrivingVariants() MultiVariantWalker
getSpliteratorForDrivingVariants() VariantWalker
getSpliteratorForDrivingVariants() VariantWalkerBase
Return a spliterator to be used to iterate over the elements of the driving variants.
getSplitReads() EvidenceTargetLink
getSplitReadTemplateNames() EvidenceTargetLink
getSplitsBy(SAMFileHeader) ReaderSplitter
Returns the values from the header that will be used to split the reader.
getSplitsBy(SAMFileHeader) ReadGroupSplitter
getStandardBQSRReadFilterList() BaseRecalibrator
Return the full list of raw read filters used for BQSR contexts, including WellFormed.
getStandardCovariateClassNames() StandardCovariateList
Returns the list of simple class names of standard covariates.
getStandardHaplotypeCallerAnnotationGroups() HaplotypeCallerEngine
getStandardizedCopyRatios() SVDDenoisedCopyRatioResult
getStandardMutect2AnnotationGroups() Mutect2Engine
getStandardUsagePreamble() CommandLineProgram
getStandardUsagePreamble(Class<?>) 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() AbstractConcordanceWalker.TruthVersusEval
getStart() AlignmentContext
getStart() AssemblyRegion
getStart() Shard
getStart() ShardBoundary
getStart() AlleleFractionSegment
getStart() AllelicCount
getStart() AnnotatedInterval
getStart() CopyRatio
getStart() CopyRatioSegment
getStart() IntegerCopyNumberSegment
getStart() IntervalCopyNumberGenotypingData
getStart() ModeledSegment
getStart() MultidimensionalSegment
getStart() SimpleCount
getStart() AnnotatedInterval
getStart() GencodeFuncotation
getStart() SVFastqUtils.Mapping
Returns the primary interval start position, or SAMRecord.NO_ALIGNMENT_START if unmapped.
getStart() SVInterval
getStart() MinorAlleleFractionRecord
getStart() PileupSummary
getStart() BasicValidationResult
getStart() GencodeGtfFeature
getStart() SAMPileupFeature
getStart() TableFeature
getStart() XsvTableFeature
getStart() GenomeLoc
getStart() SAMRecordToGATKReadAdapter
getStart() SimpleInterval
Gets the 1-based start position of the interval on the contig.
getStart() MinimalVariant
getStart() VariantContextVariantAdapter
getStartCodon() GencodeGtfExonFeature
getStartColumn() XsvLocatableTableCodec
getStartColumnName() AnnotatedIntervalHeader
getStartLocation() SVInterval
getStartLocation() GenomeLoc
getStartPosition() Haplotype
getStartPositionInTranscript(Locatable, List<? extends Locatable>, Strand) FuncotatorUtils
Gets the position describing where the given allele and variant lie inside the given transcript using transcript-based coordinates.
getStartPositions() EventMap
Get the starting positions of events in this event map
getStateList() ActivityProfile
Get the list of activity profile results in this object
getStateTracker(boolean, int) AFCalculator
Retrieves the state tracker.
getStateTracker(boolean, int) AlleleFrequencyCalculator
getStatistics() SeekableByteChannelPrefetcher
getStatus() AssemblyResult
getStderr() ProcessOutput
getStderrSettings() ProcessSettings
getStdinSettings() ProcessSettings
getStdout() ProcessOutput
getStdoutSettings() ProcessSettings
getStop() GenomeLoc
getStopCodon() GencodeGtfExonFeature
getStopLocation() GenomeLoc
getStopPosition() Haplotype
getStrand() SequenceComparison
getStrand() StrandedInterval
getStrandCorrectedAllele(Allele, Strand) FuncotatorUtils
Get the strand-corrected (reverse complemented) Allele for the given Allele and Strand.
getStrandCountsFromLikelihoodMap(VariantContext, ReadLikelihoods<Allele>, ReducibleAnnotationData<List<Integer>>, int) AS_StrandBiasTest
Allocate and fill a 2x2 strand contingency table.
getStrandedOffset(boolean, int, int) ContextCovariate
Helper method: computes the correct offset to use in computations of covariate values.
getStrandedUnclippedStart(GATKRead) 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.
getStrandSwitch() NovelAdjacencyAndAltHaplotype
getStratifiedPileups(Locatable) ReadLikelihoods
Collect a map stratified per-sample of the base pileups at the provided Location
NOTE: Since we shouldn't need to use the pileup if we have more reliable liklihoods, we want to discourage their use
getStratifiedPileups(Locatable) UnfilledReadsLikelihoods
Collect a map stratified per-sample of the base pileups at the provided Location
getStreamLocations() InputStreamSettings
getStreamLocations() OutputStreamSettings
getString() ArgumentsBuilder
getStructuralVariantLength() SVContext
Returns the absolute structural variant length as recorded in the SVLEN annotation.
getSubsequenceAt(String, long, long) HaplotypeCallerSpark.ReferenceMultiSourceAdapter
getSubsequenceAt(String, long, long) 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) ReferenceBases
getSubset returns only the bases of the interval passed in.
getSuffix() 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
getSuffixString() MultiDeBruijnVertex
Get the string representation of the suffix of this DeBruijnVertex
getSuggestedAlternateCommand(Set<Class<?>>, String) Main
When a command does not match any known command, searches for similar commands, using the same method as GIT *
getSum(Set<GenotypeConcordanceStates.TruthState>, Set<GenotypeConcordanceStates.CallState>) GenotypeConcordanceCounts
Returns the sum of all pairs of tuples defined by the truth state set and call state set.
getSum() GenotypeConcordanceCounts
Returns the sum of all pairs of tuples defined by the truth state set and call state set.
getSummaryLine() CountingReadFilter
getSummaryLine() CountingVariantFilter
getSummaryLineForLevel(int) CountingReadFilter
getSummaryLineForLevel(int) CountingVariantFilter
getSuperCategoryMap() HelpConstants
getSuperCategoryProperty(String) 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) 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() SVFastqUtils.Mapping
getSupportedFuncotationFields() DataSourceFuncotationFactory
getSupportedFuncotationFields() CosmicFuncotationFactory
getSupportedFuncotationFields() GencodeFuncotationFactory
getSupportedFuncotationFields() VcfFuncotationFactory
getSupportedFuncotationFields() LocatableXsvFuncotationFactory
getSupportedFuncotationFields() SimpleKeyXsvFuncotationFactory
getSupportInformation() CommandLineProgram
getSupportingContigIds() SVContext
Returns the ids of the assembled contig that support this context's structural variant.
getSupportingStates() AssemblyRegion
An ordered list (by genomic coordinate) of the ActivityProfileStates that went
into this active region.
getSupportLowerBound() BetaBinomialDistribution
getSupportUpperBound() BetaBinomialDistribution
getSVLength() SvType
getSymbAltAlleleLine(String) GATKSVVCFHeaderLines
getSymbAltAlleleLines() GATKSVVCFHeaderLines
getT() FourChannelIntensityData
getTabixFormat() ProgressReportingDelegatingCodec
getTabixFormat() SAMPileupCodec
getTable(int) RecalibrationTables
getTable(String) GATKReport
Return a table with a given name
getTableForCovariate(Covariate) RecalibrationTables
getTableFromSamples(GenotypesContext, int) StrandBiasTest
Create the contingency table by retrieving the per-sample strand bias annotation and adding them together
getTableName() GATKReportTable
getTables() GATKReport
getTagFilterPrefix() GATKHelpDocWorkUnitHandler
getTagFilterPrefix() PicardHelpDocWorkUnitHandler
getTailAlignment() AlignedContig
getTailAlignment() AssemblyContigWithFineTunedAlignments
getTarget() TrancheManager.SelectionMetric
getTarget() TrancheManager.TruthSensitivityMetric
getTargetPartitionSize() 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() FalsePositiveRecord
getTempFilePath(String, String) BucketUtils
Get a temporary file path based on the prefix and extension provided.
getTemplateName() BreakpointEvidence.ReadEvidence
getTemplateName(DocWorkUnit) GATKHelpDocWorkUnitHandler
getTemplateName(DocWorkUnit) PicardHelpDocWorkUnitHandler
getTemplateSize() BreakpointEvidence.ReadEvidence
getTempPath(MiniDFSCluster, String, String) MiniClusterUtils
getTestedClassName() BaseTest
Returns the name of the class being tested.
getTestedToolName() CommandLineProgramTester
Returns the name for the tested tool.
getTestedToolName() CleanSamTester
getTestFile(String) BaseTest
getTests(Class<?>) BaseTest.TestDataProvider
Return all of the data providers in the form expected by TestNG of type class C
getTestSparkContext() SparkContextFactory
Get the test JavaSparkContext if it has been registered, otherwise returns null.
getTestSparkContext(Map<String, String>) SparkContextFactory
Get the test JavaSparkContext if it has been registered, otherwise returns null.
getTheoreticalFPP(long) LongBloomFilter
getThreadingGraph() AssemblyResult
getThreadLocal() ProcessController
Returns a thread local ProcessController.
getThreshold(double) TrancheManager.SelectionMetric
getThreshold(double) TrancheManager.TruthSensitivityMetric
getThresholdForSelectingAdaptersToKeep() AdapterMarker
getTies() MannWhitneyU.TestStatistic
getTile() ReadEnds
getTile() Pair
getTile() CbclData
getTile() ClusterData
getTile() AbstractIlluminaPositionFileReader
getTile() PhysicalLocation
getTile() PhysicalLocationInt
getTiledFiles(File, Pattern) NewIlluminaBasecallsConverter
getTiledFiles(File, Pattern) ParameterizedFileUtil
Return all files that match pattern of the given file type in the given base directory
getTileFromReadName(String) IlluminaUtil
Parse the tile # from the read name.
getTileInfo() BaseBclReader.CycleData
getTileNum() BaseBclReader.TileData
getTileNumber() TileMetricsOutReader.IlluminaLaneTileCode
getTileNumber() TileMetricsOutReader.IlluminaTileMetrics
getTileNumber() Tile
Returns the number/name of this tile.
getTileOfNextCluster() MultiTileParser
getTileOfNextCluster() PerTileParser
Return the tile of the NEXT ILLUMINA_DATA object to be returned by the method next.
getTiles() MultiTileBclFileUtil
getTiles() MultiTileFileUtil
getTiles() ParameterizedFileUtil
Return a list of all tiles available for this file format and run
getTiles() PerTilePerCycleFileUtil
Discover all files of this type in expectedBase that match pattern and construct a list of tiles
available based on these files.
getTiles() TileIndex
getTileTemplateRead() TilePhasingValue
getToCoverage() LIBSDownsamplingInfo
getToMarkQueueMinimumDistance() MarkQueue
Returns the minimum genomic distance such that we can be assured that all duplicates have been considered.
getToolDeprecationInfo(String) DeprecatedToolsRegistry
Utility method to pull up the version number at which a tool was deprecated and the suggested replacement, if any
getToolDeprecationMessage(String) Main
Get deprecation message for a tool
getToolkitName() CommandLineProgram
getToolkitShortName() GATKTool
getToolLogger() SvDiscoveryInputMetaData
getToolName() GATKTool
Returns the name of this tool.
getToolReturnCode() PicardNonZeroExitException
getToolStatusWarning(boolean) CommandLineProgram
If this tool is either Experimental or Beta, return a warning message advising against use in production
environment.
getToolTestDataDir() BaseTest
Returns the location of the resource directory for the command line program.
getTotal() TargetMetricsCollector.Coverage
getTotalBaseQuality() ReadMetadata.LibraryRawStatistics
getTotalCount() PileupSummary
getTotalCycles() ReadStructure.Substructure
getTotalHardClipping(Cigar) SvCigarUtils
getTotalInserts() PerUnitInsertSizeMetricsCollector
getTotalInserts() InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
getTotalLength() PSPathogenReferenceTaxonProperties
getTotalObs() HaplotypeProbabilities
Returns the total number of observations of any allele.
getTotalObs() HaplotypeProbabilitiesFromSequence
Gets the total number of observations presented at this locus.
getTotalObs() HaplotypeProbabilityOfNormalGivenTumor
getTotalObservations() IntHistogram.CDF
getTotalObservations() IntHistogram
getTotalOutputCycles() OutputMapping
getTotalReadCount() AllelicCount
getTotalReads() PSPathogenTaxonScore
getTrainingData() VariantDataManager
getTrancheIndex() Tranche
getTrancheIndex() VQSLODTranche
getTrancheString(T) Tranche
getTranscriptAlleleStart() SequenceComparison
getTranscriptAlleleStartPosition(VariantContext, List<? extends Locatable>, Strand) FuncotatorUtils
Get the position (1-based, inclusive) of the given VariantContext start relative to the transcript it appears in.
getTranscriptCodingSequence() SequenceComparison
Return the
ReferenceSequence containing the coding region for the transcript of this
SequenceComparison.
getTranscriptCoordinate(int) Gene.Transcript
Given a coordinate on the genome (same chromosome) give the corresponding coordinate in the transcript.
getTranscriptExonNumber() GencodeFuncotation
getTranscriptId() GencodeGtfFeature
getTranscriptIdWithoutVersionNumber(String) FuncotatorUtils
Removes the transcript ID version number from the given transcript ID (if it exists).
getTranscriptLength() GencodeFuncotation
getTranscriptName() GencodeGtfFeature
getTranscriptPos() GencodeFuncotation
getTranscripts() GencodeGtfGeneFeature
getTranscriptStatus() GencodeGtfFeature
getTranscriptStrand() GencodeFuncotation
getTranscriptType() GencodeGtfFeature
getTransformedReadStream(ReadFilter) GATKTool
Returns a stream over the reads, which are:
1.
getTransientAttribute(Object) SAMRecordToGATKReadAdapter
This is used to access the transient attribute store in the underlying SAMRecord.
getTraversalParameters(SAMSequenceDictionary) 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.
getTrios(boolean) SampleDB
Returns all the trios present in the sample database.
getTrios() SampleDB
Returns all the trios present in the db.
getTrueNegativeCount() FilterAnalysisRecord
getTruePositives() ConcordanceSummaryRecord
getTrueU() MannWhitneyU.TestStatistic
getTruth() AbstractConcordanceWalker.TruthVersusEval
getTruthHeader() AbstractConcordanceWalker
getTruthIfPresentElseEval() AbstractConcordanceWalker.TruthVersusEval
getTruthSensitivity() Tranche
getTumorSeqAllele2() GencodeFuncotation
getType() DataSourceFuncotationFactory
getType() CosmicFuncotationFactory
getType() GencodeFuncotationFactory
getType() VcfFuncotationFactory
getType() LocatableXsvFuncotationFactory
getType() SimpleKeyXsvFuncotationFactory
getType() EmptyFragment
getType() Fragment
getType() MarkDuplicatesSparkRecord
getType() Pair
getType() Passthrough
getTypeSpecificAttributes() SvType
getU() MannWhitneyU.Result
getU() SimpleSVD
getU() 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() MannWhitneyU.TestStatistic
getU2() MannWhitneyU.TestStatistic
getUcscGenomeVersion() GencodeGtfFeature
getUnambiguousReads() PSPathogenTaxonScore
getUnclippedEnd() GATKRead
Returns the alignment end (1-based, inclusive) adjusted for clipped bases.
getUnclippedEnd() SAMRecordToGATKReadAdapter
getUnclippedReadLength(Cigar) SvCigarUtils
getUnclippedStart() GATKRead
Returns the alignment start (1-based, inclusive) adjusted for clipped bases.
getUnclippedStart() SAMRecordToGATKReadAdapter
getUnclippedStartPosition() EmptyFragment
getUnclippedStartPosition() Fragment
getUnclippedStartPosition() Pair
getUnclippedStartPosition() PairedEnds
getUncompressedProbabilityVector() ProbabilityVector
getUnfilteredBaseQHistogram() AbstractWgsMetricsCollector
getUnfilteredDepthHistogram() AbstractWgsMetricsCollector
getUnfilteredReads() GATKSparkTool
Loads the reads into a JavaRDD using the intervals specified, and returns them
without applying any filtering.
getUniqueFalseNegativeCount() FilterAnalysisRecord
getUniqueNameSuffix() 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() 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.
getUniqueReadThreadingGraph(int) AssemblyResultSet
Returns a read-threading graph in the assembly set that has a particular kmerSize.
getUniqueTrueNegativeCount() FilterAnalysisRecord
getUnknownCommandMessage(Set<Class<?>>, String) Main
When a command does not match any known command, searches for a deprecation message, if any, or for similar
commands.
getUnmappedBoth() SamComparison
getUnmappedBoth() CompareSAMs
getUnmappedLeft() SamComparison
getUnmappedLeft() CompareSAMs
getUnmappedRight() SamComparison
getUnmappedRight() CompareSAMs
getUnpairedReads() PSPairedUnpairedSplitterSpark
getUpdatedGenotypes(VariantContext, Genotype, Genotype, Genotype, ArrayList<Genotype>) FamilyLikelihoods
Applies the trio genotype combination to the given trio.
getUpdateMethod() ParameterizedModel
getUpper() PosteriorSummary
getUsableExtension() AssemblyRegionTrimmer.Result
Returns the maximum extension around the original active region span considered for the trimmed
variation region.
getUsage() CommandLineProgram
getUserDisabledAnnotationNames() DefaultGATKVariantAnnotationArgumentCollection
getUserDisabledAnnotationNames() GATKAnnotationArgumentCollection
Returns the disabled annotation names.
getUserDisabledReadFilterNames() DefaultGATKReadFilterArgumentCollection
Returns the set of filters disabled by the user.
getUserDisabledReadFilterNames() GATKReadFilterArgumentCollection
Returns the disabled read filter names.
getUserEnabledAnnotationGroups() DefaultGATKVariantAnnotationArgumentCollection
getUserEnabledAnnotationGroups() GATKAnnotationArgumentCollection
Returns the enabled annotation.
getUserEnabledAnnotationNames() DefaultGATKVariantAnnotationArgumentCollection
getUserEnabledAnnotationNames() GATKAnnotationArgumentCollection
Returns the enabled annotation.
getUserEnabledReadFilterNames() DefaultGATKReadFilterArgumentCollection
Returns the list with the read filters provided by the user, preserving the order.
getUserEnabledReadFilterNames() GATKReadFilterArgumentCollection
Returns the enabled filter names.
getUtil(IlluminaFileUtil.SupportedIlluminaFormat) IlluminaFileUtil
Given a file type, get the Parameterized File Util object associated with it
getUtrs() GencodeGtfTranscriptFeature
getV() SimpleSVD
getV() SVD
Get the V matrix of a Singular Value Decomposition.
getValidationAltCount() BasicValidationResult
getValidationRefCount() BasicValidationResult
getValidationStringency() FingerprintChecker
getValue() KmerAndInterval
getValue() QNameAndInterval
getValue() KmerAndCount
getValue() SVIntervalTree.Entry
getValue() MarkDuplicatesSparkUtils.IndexPair
getValue() GencodeGtfFeature.OptionalField
getValue(int) TableFeature
Gets the value associated with the ith column (first column is 0).
getValue() KV
getValue() Parameter
getValueCounts() CompressedDataList
getValueFormat() GATKReportColumnFormat
getValueForRead(GATKRead, VariantContext) BaseQuality
getValueForRead(GATKRead, VariantContext) FragmentLength
getValueForRead(GATKRead, VariantContext) MappingQuality
getValueForRead(GATKRead, VariantContext) PerAlleleAnnotation
getValueForRead(GATKRead, VariantContext) ReadPosition
getValues(FeatureInput<T>) FeatureContext
Gets all Features from the source represented by the provided FeatureInput argument that overlap
this FeatureContext's query interval.
getValues(FeatureInput<T>, int, int) 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>, SimpleInterval) FeatureContext
Gets all Features from the source represented by the provided FeatureInput argument that overlap the given interval.
getValues(FeatureInput<T>, int) 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(Collection<FeatureInput<T>>) 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) 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() XsvTableFeature
getValuesTo(int) TableFeature
Gets all the values from the first column (0) to the last one specified (exclusive).
getValuesWithoutLocationColumns() XsvTableFeature
Get the data from this
XsvTableFeature without the columns that contain location information.
getVar(int, int) GenotypeConcordanceStates.TruthState
getVarianceVector() VariantDataManager
getVariant() VariantWalkerContext
getVariantClassification() GencodeFuncotation
getVariantContexts() EventMap
Get the variant contexts in order of start position in this event map
getVariants(JavaSparkContext) VariantWalkerSpark
Loads variants and the corresponding reads, reference and features into a JavaRDD for the intervals specified.
getVariants() ReadsPreprocessingPipelineTestData
getVariantSequenceDictionaries() FeatureManager
Returns the list of sequence dictionaries retrieved from the VCF headers of variant Feature inputs.
getVariantShardsFromInterval(Locatable) VariantShard
getVariantShardsFromInterval calculates *all* shards overlapping location.
getVariantsList(List<String>) VariantsSource
getVariantsList grabs the variants from local files (or perhaps eventually buckets).
getVariantsListAs(List<String>, Function<VariantContext, T>) VariantsSource
getVariantsListAs grabs the variants from local files (or perhaps eventually buckets), applies
the wrapper function to each object, and returns them as a list of objects of the type returned
by the wrapper function
getVariantType() GencodeFuncotation
getVariantType() ConcordanceSummaryRecord
getVariantTypeFromOrdinal(int) VariantType
Gets the enum for a given ordinal
getVariationEvents(int) AssemblyResultSet
Returns a sorted set of variant events that best explain the haplotypes found by the assembly
across kmerSizes.
getVc() ReferenceConfidenceVariantContextMerger.VCWithNewAlleles
getVCFAnnotationDescriptions() VariantAnnotatorEngine
Returns the set of descriptions to be added to the VCFHeader line (for all annotations in this engine).
getVCFAnnotationDescriptions(boolean) VariantAnnotatorEngine
Returns the set of descriptions to be added to the VCFHeader line (for all annotations in this engine).
getVCFHeaderLines() ReferenceConfidenceModel
getVcfKey() BaseQuality
getVcfKey() FragmentLength
getVcfKey() MappingQuality
getVcfKey() PerAlleleAnnotation
getVcfKey() ReadPosition
getVCsAtThisLocation(List<Haplotype>, int, List<VariantContext>) AssemblyBasedCallerGenotypingEngine
getVersion() CommandLineProgram
getVersion() HDF5SVDReadCountPanelOfNormals
getVersion() SVDReadCountPanelOfNormals
Returns the PoN version.
getVersion() DataSourceFuncotationFactory
getVersion() Funcotator
getVersion() GATKReport
getVersion() CommandLineProgram
getVertices() Path
Get the list of vertices in this path in order defined by the edges of the path
getWeight() BreakpointEvidence
getWidth() GATKReportColumnFormat
getWindow() ReferenceContext
Get the full expanded window of bases spanned by this context, including any extra
bases of requested context around the current interval.
getWordCount() AbstractInputParser
getWordStarts(String) TextFormattingUtils
Returns the word starting positions within line, excluding the first position 0.
getWorkingDir(MiniDFSCluster) MiniClusterUtils
getWrapped() UniqueIDWrapper
getWriter(File) ConcordanceSummaryRecord
getX() ReadEnds
getX() Pair
getX() ClusterData
getX() PhysicalLocation
getX() PhysicalLocationInt
getXCoordinate() CbclData
getY() ReadEnds
getY() Pair
getY() ClusterData
getY() PhysicalLocation
getY() PhysicalLocationInt
getYCoordinate() CbclData
getZ() MannWhitneyU.Result
getZeroBasedTileNumber() TileIndex.TileIndexRecord
getZishScore(int) LibraryStatistics
getZishScore(String, int) ReadMetadata
ggaExtension AssemblyRegionTrimmerArgumentCollection
GibbsBuilder(S2, T2) ParameterizedModel.GibbsBuilder
GibbsSampler V extends java.lang.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>) GibbsSampler
Constructs a GibbsSampler given the total number of samples (including burn-in) and a
ParameterizedModel.
GLmodel UnifiedArgumentCollection
GLOBAL_PSI_SCALE_LONG_NAME GermlineContigPloidyModelArgumentCollection
globalPriorIndel CalculateGenotypePosteriors
Prior indel pseudocounts for Dirichlet distribution of allele frequencies.
globalPriorSnp CalculateGenotypePosteriors
Prior SNP pseudocounts for Dirichlet distribution of allele frequencies.
globalQScorePrior 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).
GMMFromTables(GATKReportTable, GATKReportTable, GATKReportTable, int, int) VariantRecalibrator
Rebuild a Gaussian Mixture Model from gaussian means and co-variates stored in a GATKReportTables
GOOD_CIGAR ReadFilterLibrary
GoodAndBadMappings(List<AlignmentInterval>) AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings
GoodAndBadMappings(List<AlignmentInterval>, List<AlignmentInterval>, AlignmentInterval) AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings
GoodAndBadMappings(List<AlignmentInterval>, List<AlignmentInterval>) AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings
GoodCigarReadFilter() ReadFilterLibrary.GoodCigarReadFilter
goodLog10Probability(double) MathUtils
Checks that the result is a well-formed log10 probability
goodLog10ProbVector(double[], int, boolean) MathUtils
Check that the log10 prob vector vector is well formed
goodNonCanonicalMappingSATag SimpleChimera
goodProbability(double) MathUtils
Checks that the result is a well-formed probability
GQ_MEAN_KEY GATKVCFConstants
GQ_STDEV_KEY GATKVCFConstants
grabCount() KmerAndCount
granularity CreateHadoopBamSplittingIndex
graph() KBestHaplotype
Returns the original graph searched.
Graph() GraphUtils.Graph
graphEquals(BaseGraph<T, E>, BaseGraph<T, E>) 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 ReadThreadingAssemblerArgumentCollection
This argument is meant for debugging and is not immediately useful for normal analysis use.
GraphUtils org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
Utility functions used in the graphs package
GraphUtils picard.util
Created by farjoun on 11/2/16.
GraphUtils() GraphUtils
GraphUtils.Graph Node extends java.lang.Comparable<Node >> - Class in picard.util
groupIntervalsByContig(List<SimpleInterval>) IntervalUtils
Accepts a sorted List of intervals, and returns a List of Lists of intervals grouped by contig,
one List per contig.
gunzip(File, File) IOUtils
Un-gzips the input file to the output file.
gunzipToTempIfNeeded(File) IOUtils
Un-gzips the input file to a output file but only if the file's name ends with '.gz'.
GVCF_FILE_EXTENSION IndexFeatureFile
GVCF_INPUT CollectVariantCallingMetrics
GVCF_VALIDATE ValidateVariants
GVCFGQBands 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.
GvcfKeyIgnoringVCFRecordWriter(Path, VCFHeader, boolean, TaskAttemptContext) VariantsSparkSink.GvcfKeyIgnoringVCFRecordWriter
GvcfKeyIgnoringVCFRecordWriter(OutputStream, VCFHeader, boolean, TaskAttemptContext) VariantsSparkSink.GvcfKeyIgnoringVCFRecordWriter
GvcfMetricAccumulator picard.vcf
An accumulator for collecting metrics about a single-sample GVCF.
GvcfMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets) GvcfMetricAccumulator
gvcfToHeaderSampleMapFile FixCallSetSampleOrdering
GVCFWriter org.broadinstitute.hellbender.utils.variant.writers
Genome-wide VCF writer
GVCFWriter(VariantContextWriter, List<Integer>, int) GVCFWriter
Create a new GVCF writer
Should be a non-empty list of boundaries.
id() AggregatedSubHaplotypeFinder
ID_COLUMN_NAME FalsePositiveRecord
idealSpan AssemblyRegionTrimmer.Result
The ideal trimmer variant region span including the extension.
identifyContaminant(Path, double, int) FingerprintChecker
Generates a per-sample Fingerprint for the contaminant in the supplied SAM file.
IdentifyContaminant 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() IdentifyContaminant
identity() ReadTransformer
IDENTITY_FUNCTION ReferenceWindowFunctions
A function for requesting only reference bases that directly overlap each read.
IDENTITY_MARGIN_LONG_NAME PSScoreArgumentCollection
IDENTITY_MARGIN_SHORT_NAME PSScoreArgumentCollection
identityMargin PSScoreArgumentCollection
For reads having multiple alignments, the best hit is always counted as long as it is above the identity score
threshold.
idx SVKmerizer
IGNORE ValidateSamFile
IGNORE_FILTER_STATUS GenotypeConcordance
IGNORE_LANE_INFO UnifiedArgumentCollection
IGNORE_MISSING_MATES FixMateInformation
IGNORE_READ_GROUPS CheckFingerprint
IGNORE_SAFETY_CHECKS_LONG_NAME GatherVcfsCloud
IGNORE_SEQUENCE CollectRnaSeqMetrics
IGNORE_SNP_ALLELES UnifiedArgumentCollection
IGNORE_UNEXPECTED_BARCODES IlluminaBasecallsToFastq
IGNORE_UNEXPECTED_BARCODES IlluminaBasecallsToSam
IGNORE_VARIANTS_THAT_START_OUTSIDE_INTERVAL MultiVariantWalkerGroupedOnStart
IGNORE_WARNINGS ValidateSamFile
ignoreAlignment(SAMRecord) AbstractAlignmentMerger
ignoreAlignment(SAMRecord) SamAlignmentMerger
For now, we only ignore those alignments that have more than maxGaps insertions
or deletions.
ignoreAlignment(SAMRecord) AbstractAlignmentMerger
ignoreAlignment(SAMRecord) SamAlignmentMerger
ignoreCrossContigID(int) ReadMetadata
IGNORED_READS RnaSeqMetrics
Number of primary alignments that are mapped to a sequence specified on command-line as IGNORED_SEQUENCE.
ignoreExceptions ScriptExecutor
ignoreInputSamples 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 CalculateGenotypePosteriors
Don't add input sample ACs for variants not seen in the supporting panel.
ignoreLastModificationTime 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 CheckPileup
ignoreSafetyChecks GatherVcfsCloud
IGV_HEADER_DELIMITER TableCodec
IGVUtils org.broadinstitute.hellbender.utils
Utilities for interacting with IGV-specific formats.
ILLUMINA_ALLEGED_MINIMUM_QUALITY BclQualityEvaluationStrategy
IlluminaAdapterPair org.broadinstitute.hellbender.utils.illumina
Describes adapters used on each pair of strands
IlluminaBasecallingMetrics picard.illumina
Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis.
IlluminaBasecallingMetrics() IlluminaBasecallingMetrics
IlluminaBasecallsConverter CLUSTER_OUTPUT_RECORD > - Class in picard.illumina
Manages the conversion of Illumina basecalls into some output format.
IlluminaBasecallsConverter(File, int, ReadStructure, Map<String, ? extends BasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>>, boolean, int, List<File>, int, boolean, Integer, Integer, Comparator<CLUSTER_OUTPUT_RECORD>, SortingCollection.Codec<CLUSTER_OUTPUT_RECORD>, Class<CLUSTER_OUTPUT_RECORD>, BclQualityEvaluationStrategy, boolean, boolean, boolean) IlluminaBasecallsConverter
IlluminaBasecallsConverter(File, File, int, ReadStructure, Map<String, ? extends BasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>>, boolean, int, List<File>, int, boolean, Integer, Integer, Comparator<CLUSTER_OUTPUT_RECORD>, SortingCollection.Codec<CLUSTER_OUTPUT_RECORD>, Class<CLUSTER_OUTPUT_RECORD>, BclQualityEvaluationStrategy, boolean, boolean, boolean) IlluminaBasecallsConverter
IlluminaBasecallsToFastq picard.illumina
IlluminaBasecallsToFastq() IlluminaBasecallsToFastq
IlluminaBasecallsToFastq.ReadNameFormat picard.illumina
Simple switch to control the read name format to emit.
IlluminaBasecallsToSam picard.illumina
IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into
SAM or BAM file format.
IlluminaBasecallsToSam() IlluminaBasecallsToSam
IlluminaDataProvider picard.illumina.parser
Parse various formats and versions of Illumina Basecall files, and use them the to populate
ClusterData objects.
IlluminaDataProviderFactory 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, IlluminaDataType...) IlluminaDataProviderFactory
Create factory with the specified options, one that favors using QSeqs over all other files
IlluminaDataProviderFactory(File, File, int, ReadStructure, BclQualityEvaluationStrategy, IlluminaDataType...) IlluminaDataProviderFactory
Create factory with the specified options, one that favors using QSeqs over all other files
IlluminaDataProviderFactory(File, File, int, ReadStructure, BclQualityEvaluationStrategy) IlluminaDataProviderFactory
IlluminaDataType picard.illumina.parser
List of data types of interest when parsing Illumina data.
IlluminaFileUtil picard.illumina.parser
General utils for dealing with IlluminaFiles as well as utils for specific, support formats.
IlluminaFileUtil(File, int) IlluminaFileUtil
IlluminaFileUtil(File, File, int) IlluminaFileUtil
IlluminaFileUtil.SupportedIlluminaFormat picard.illumina.parser
IlluminaLaneMetrics picard.illumina
Embodies characteristics that describe a lane.
IlluminaLaneMetrics() IlluminaLaneMetrics
IlluminaLaneMetricsCollector() CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
IlluminaLaneTileCode(int, int, int) TileMetricsOutReader.IlluminaLaneTileCode
IlluminaMetricsCode 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 picard.illumina
Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.
IlluminaPhasingMetrics() IlluminaPhasingMetrics
IlluminaReadNameEncoder picard.fastq
A read name encoder following the encoding initially produced by picard fastq writers.
IlluminaReadNameEncoder(String) IlluminaReadNameEncoder
IlluminaTileMetrics(ByteBuffer, TileMetricsOutReader.TileMetricsVersion) TileMetricsOutReader.IlluminaTileMetrics
IlluminaTileMetrics(int, int, int, float) TileMetricsOutReader.IlluminaTileMetrics
IlluminaUtil picard.util
Misc utilities for working with Illumina specific files and data
IlluminaUtil() IlluminaUtil
IlluminaUtil.IlluminaAdapterPair picard.util
Describes adapters used on each pair of strands
IMPRECISE GATKSVVCFConstants
ImpreciseDeletion(EvidenceTargetLink, int, ReadMetadata) SimpleSVType.ImpreciseDeletion
impreciseDupAffectedRefRange BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications
ImpreciseVariantDetector org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
ImpreciseVariantDetector() ImpreciseVariantDetector
impreciseVariantEvidenceThreshold StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection
IMPUTE_ZEROS_LONG_NAME CreateReadCountPanelOfNormals
in ReadEndsForMarkDuplicatesCodec
in RepresentativeReadIndexerCodec
IN_PON_VCF_ATTRIBUTE GATKVCFConstants
INBREEDING_COEFFICIENT_KEY GATKVCFConstants
InbreedingCoeff org.broadinstitute.hellbender.tools.walkers.annotator
Likelihood-based test for the consanguinuity among samples
InbreedingCoeff() InbreedingCoeff
InbreedingCoeff(Set<String>) InbreedingCoeff
InbreedingCoeff(File) InbreedingCoeff
incAll(int) CountSet
Increase (or decrease) all elements in the set by a number.
INCLUDE_BQ_HISTOGRAM CollectWgsMetrics
INCLUDE_DUPLICATES CollectSequencingArtifactMetrics
INCLUDE_DUPLICATES CollectInsertSizeMetrics
INCLUDE_FILTERED IntervalListTools
INCLUDE_FILTERED VcfToIntervalList
INCLUDE_FILTERED_SHORT_NAME VcfToIntervalList
INCLUDE_NO_CALLS QualityScoreDistribution
INCLUDE_NON_PF_READS CollectSequencingArtifactMetrics
INCLUDE_NON_PF_READS CollectOxoGMetrics
INCLUDE_NON_PF_READS BamToBfq
INCLUDE_NON_PF_READS IlluminaBasecallsToFastq
INCLUDE_NON_PF_READS IlluminaBasecallsToSam
INCLUDE_NON_PF_READS SamToFastq
INCLUDE_NON_PRIMARY_ALIGNMENTS SamToFastq
INCLUDE_SECONDARY_ALIGNMENTS CollectQualityYieldMetrics
INCLUDE_SECONDARY_ALIGNMENTS MergeBamAlignment
INCLUDE_SUPPLEMENTAL_ALIGNMENTS CollectQualityYieldMetrics
INCLUDE_UNPAIRED CollectSequencingArtifactMetrics
INCLUDE_UNPAIRED CollectMultipleMetrics
includeDeletions() LocusWalker
Does this tool require deletions in the AlignmentContext? Tools that don't should override to return false.
includeDeletions() Pileup
includeMappingLocation StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
includeMatching(Collection<String>, Collection<String>, boolean) SelectVariants
Returns a new set of values including only values listed by filters/expressions
includeNoCalls QualityScoreDistributionSpark
includeNs() LocusWalker
Does this tool require Ns in the AlignmentContext? Tools that do should override to return true.
includePluginClass(Class<?>) GATKAnnotationPluginDescriptor
includePluginClass(Class<?>) GATKReadFilterPluginDescriptor
includeReadsWithDeletionsInIsActivePileups() AssemblyRegionWalker
includeReadsWithDeletionsInIsActivePileups() AssemblyRegionWalkerSpark
subclasses can override this to control if reads with deletions should be included in isActive pileups
includeReadsWithDeletionsInIsActivePileups() ExampleAssemblyRegionWalker
includeReadsWithDeletionsInIsActivePileups() ExampleAssemblyRegionWalkerSpark
includeReadsWithDeletionsInIsActivePileups() HaplotypeCaller
includeReadsWithDeletionsInIsActivePileups() Mutect2
includeRefAllele() FragmentLength
includeRefAllele() PerAlleleAnnotation
includeSupplementalAlignments CollectQualityYieldMetrics.QualityYieldMetricsCollector
incMultiplicity(int) BaseEdge
Increase the multiplicity of this edge by incr
incMultiplicity(int) MultiSampleEdge
incNQClippedBases(int) ClipReads.ClippingData
incNRangeClippedBases(int) ClipReads.ClippingData
incomingEdgeOf(V) BaseGraph
Get the incoming edge of v.
incomingVerticesOf(V) BaseGraph
Get the set of vertices connected to v by incoming edges
IncompatibleRecalibrationTableParameters(String) UserException.IncompatibleRecalibrationTableParameters
IncompatibleSequenceDictionaries(String, String, SAMSequenceDictionary, String, SAMSequenceDictionary) UserException.IncompatibleSequenceDictionaries
INCORRECT_STRAND_READS RnaSeqMetrics
Number of aligned reads that are mapped to the incorrect strand.
increase(int) GenotypeAlleleCounts
Increases the allele counts a number of times.
increase() GenotypeAlleleCounts
Updates the genotype counts to match the next genotype.
increment(long, double) RecalDatum
increment(boolean) RecalDatum
increment(Object, String) GATKReportTable
Increment the value for a given position in the table.
increment(int) CounterManager.Counter
Increments value corresponding to reference sequence index
increment(GenotypeConcordanceStates.TruthAndCallStates) GenotypeConcordanceCounts
Increments a count for the truth/call state tuple.
increment(GenotypeConcordanceStates.TruthAndCallStates, double) GenotypeConcordanceCounts
incrementDatumOrPutIfNecessary2keys(NestedIntegerArray<RecalDatum>, byte, double, int, int) 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) 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) 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() FilterAnalysisRecord
incrementNumberOfDiscardedItems(int) Downsampler
Increments the number of discarded items by the given value.
incrementNumMismatches(double) RecalDatum
incrementNumObservations(long) RecalDatum
incrementReadCount() TargetMetricsCollector.Coverage
Increments the # of reads mapping to this target.
incrementTrueNegative() FilterAnalysisRecord
incrementUniqueFalseNegative() FilterAnalysisRecord
incrementUniqueTrueNegative() FilterAnalysisRecord
incSeqClippedBases(String, int) ClipReads.ClippingData
INDEL_COLUMN_NAME FalsePositiveRecord
INDEL_CONTINUATION_QUAL Mutect2Engine
INDEL_FPR_COLUMN_NAME FalsePositiveRecord
INDEL_GAP_CONTINUATION_PENALTY UnifiedArgumentCollection
INDEL_GAP_OPEN_PENALTY UnifiedArgumentCollection
INDEL_HAPLOTYPE_SIZE UnifiedArgumentCollection
INDEL_HETEROZYGOSITY HomoSapiensConstants
Standard heterozygous rate for INDEL variation.
INDEL_OUTPUT SplitVcfs
INDEL_START_QUAL Mutect2Engine
INDEL_START_TOLERANCE_LONG_NAME FilterAlignmentArtifacts
indelCounter GenotypeConcordance
indelHeterozygosity GenotypeCalculationArgumentCollection
This argument informs the prior probability of having an indel at a site.
indelHeterozygosity HaplotypeCallerGenotypingEngine
indelPadding AssemblyRegionTrimmerArgumentCollection
Include at least this many bases around an event for calling it
indels DbSnpBitSetUtil.DbSnpBitSets
indels DbSnpBitSetUtil.DbSnpBitSets
INDELS_CONTEXT_SIZE RecalibrationArgumentCollection
The context covariate will use a context of this size to calculate its covariate value for base insertions and deletions.
indelSizeToEliminateInRefModel HaplotypeCallerArgumentCollection
This parameter determines the maximum size of an indel considered as potentially segregating in the
reference model.
indelToMatch PairHMMModel
Position in the transition probability array for the Indel-to-Match transition.
IndependentAllelesDiploidExactAFCalculator org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
Computes the conditional bi-allelic exact results
Suppose vc contains 2 alt allele: A* with C and T.
IndependentReplicateMetric picard.analysis.replicates
A class to store information relevant for biological rate estimation
IndependentReplicateMetric() IndependentReplicateMetric
independentReplicationRateFromBiDups IndependentReplicateMetric
independentReplicationRateFromTriDups IndependentReplicateMetric
independentReplicationRateFromUmi IndependentReplicateMetric
IndependentSampleGenotypesModel 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() IndependentSampleGenotypesModel
IndependentSampleGenotypesModel(int, int) IndependentSampleGenotypesModel
Initialize model with given maximum allele count and ploidy for caching
index() GenotypeAlleleCounts
Returns the index of this genotype allele count within all possible genotypes with the same ploidy.
index() GATKReportTable.TableDataHeaderFields
index() GATKReportTable.TableNameHeaderFields
INDEX_VALIDATION_STRINGENCY ValidateSamFile
indexByClass(Class<? extends Covariate>) StandardCovariateList
Returns the index of the covariate by class name or -1 if not found.
IndexedAlleleList A extends htsjdk.variant.variantcontext.Allele> - Class in org.broadinstitute.hellbender.utils.genotyper
Allele list implementation using and indexed-set.
IndexedAlleleList() IndexedAlleleList
Constructs a new empty allele-list
IndexedAlleleList(A...) IndexedAlleleList
Constructs a new allele-list from an array of alleles.
IndexedAlleleList(Collection<A>) IndexedAlleleList
Constructs a new allele-list from a collection of alleles.
IndexedSampleList org.broadinstitute.hellbender.utils.genotyper
Simple implementation of a sample-list using an indexed-set.
IndexedSampleList() IndexedSampleList
Constructs an empty sample-list.
IndexedSampleList(Collection<String>) IndexedSampleList
Constructs a sample-list from a collection of samples.
IndexedSampleList(String...) IndexedSampleList
Constructs a sample-list from an array 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) IndexedSet
Creates an empty indexed set indicating the expected number of elements.
IndexedSet(Collection<E>) IndexedSet
Creates a new sample list from a existing collection of elements.
IndexedSet(E...) IndexedSet
Creates a new sample list from a existing array of elements.
IndexFeatureFile 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() IndexFeatureFile
indexImageFile BwaArgumentCollection
The BWA-MEM index image file name that you've distributed to each executor.
indexImageFile PSFilterArgumentCollection
This file should be generated using BwaMemIndexImageCreator.
indexOf(Object) IndexedSet
Returns the index of an object.
indexOf(String) TableColumnCollection
Returns the index of a column by its name.
indexOfAllele(A) GenotypingData
indexOfAllele(A) GenotypingLikelihoods
indexOfAllele(A) SubsettedLikelihoodMatrix
indexOfAllele(A) AlleleList.ActualPermutation
indexOfAllele(A) AlleleList
Returns the index of the given Allele in this AlleleList.
indexOfAllele(A) AlleleList.NonPermutation
indexOfAllele(A) IndexedAlleleList
indexOfAllele(A) LikelihoodMatrix
Queries the index of an allele in the matrix.
indexOfAllele(A) ReadLikelihoods
Returns the index of an allele within the likelihood collection.
indexOfAllele(VariantContext, Allele, boolean, boolean, boolean) GATKVariantContextUtils
Returns the absolute 0-based index of an allele.
indexOfAltAllele(VariantContext, Allele, boolean) GATKVariantContextUtils
Returns the relative 0-based index of an alternative allele.
indexOfMax(double[]) MathUtil
Returns the index of the largest element in the array.
indexOfMax(long[]) MathUtil
Returns the index of the largest element in the array.
indexOfMin(int[]) MathUtil
Returns the index of the smallest element in the array.
indexOfMin(double[]) MathUtil
Returns the index of the smallest element in the array.
indexOfRead(GATKRead) SubsettedLikelihoodMatrix
indexOfRead(GATKRead) LikelihoodMatrix
Queries the index of a read in the matrix.
indexOfReference() AlleleList
Resolves the index of the reference allele in an allele-list.
indexOfSample(String) GenotypingData
indexOfSample(String) GenotypingLikelihoods
indexOfSample(String) HeterogeneousPloidyModel
indexOfSample(String) HomogeneousPloidyModel
indexOfSample(String) IndexedSampleList
indexOfSample(String) ReadLikelihoods
Returns the index of a sample within the likelihood collection.
indexOfSample(String) SampleList
Returns the index of an object.
IndexRange org.broadinstitute.hellbender.utils
Represents 0-based integer index range.
IndexRange(int, int) IndexRange
Creates a new range given its from and to indices.
IndexUtils org.broadinstitute.hellbender.utils
indicatesRefSeqDuplicatedOnAlt() BreakpointComplications
To be overridden as appropriate.
indicatesRefSeqDuplicatedOnAlt() BreakpointComplications.IntraChrStrandSwitchBreakpointComplications
indicesAvailable() ReadsDataSource
Are indices available for all files?
inferArtifactName() SequencingArtifactMetrics.BaitBiasSummaryMetrics
Label the artifacts corresponding to known error modes.
inferArtifactName() SequencingArtifactMetrics.PreAdapterSummaryMetrics
Label the artifacts corresponding to known error modes.
INFERRED_UMI_ENTROPY UmiMetrics
Entropy (in base 4) of the inferred UMI sequences, indicating the
effective number of bases in the inferred UMIs.
INFERRED_UNIQUE_UMIS UmiMetrics
Number of different inferred UMI sequences derived
InfoFieldAnnotation org.broadinstitute.hellbender.tools.walkers.annotator
Annotations relevant to the INFO field of the variant file (ie annotations for sites).
InfoFieldAnnotation() InfoFieldAnnotation
INFORMATIVE_THRESHOLD ReadLikelihoods.BestAllele
INIT_ARD_REL_UNEXPLAINED_VARIANCE_LONG_NAME GermlineDenoisingModelArgumentCollection
INITIAL_TEMPERATURE_LONG_NAME HybridADVIArgumentCollection
INITIAL_TUMOR_LOD_LONG_NAME M2ArgumentCollection
INITIAL_TUMOR_LOD_SHORT_NAME M2ArgumentCollection
initialize(InsertSizeMetricsArgumentCollection, SAMFileHeader) InsertSizeMetricsCollector
initialize(ExampleMultiMetricsArgumentCollection, SAMFileHeader, List<Header>) ExampleCollectMultiMetricsSpark
Initialize the collector with it's input arguments.
initialize(ExampleMultiMetricsArgumentCollection, SAMFileHeader) ExampleMultiMetricsCollector
initialize(ExampleMultiMetricsArgumentCollection, SAMFileHeader, List<Header>) ExampleMultiMetricsCollectorSpark
Initialize the collector with input arguments.
initialize(ExampleSingleMetricsArgumentCollection, SAMFileHeader, List<Header>) ExampleCollectSingleMetricsSpark
Initialize the collector with it's input arguments.
initialize(ExampleSingleMetricsArgumentCollection, SAMFileHeader, List<Header>) ExampleSingleMetricsCollectorSpark
Initialize the collector with input arguments;
initialize(InsertSizeMetricsArgumentCollection, SAMFileHeader, List<Header>) CollectInsertSizeMetricsSpark
initialize(QualityYieldMetricsArgumentCollection, SAMFileHeader, List<Header>) CollectQualityYieldMetricsSpark
initialize(InsertSizeMetricsArgumentCollection, SAMFileHeader, List<Header>) InsertSizeMetricsCollectorSpark
Initialize the collector with input arguments;
initialize(T, SAMFileHeader, List<Header>) 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>) MetricsCollectorSparkTool
initialize(QualityYieldMetricsArgumentCollection, SAMFileHeader, List<Header>) QualityYieldMetricsCollectorSpark
Initialize the collector with input arguments;
initialize(AssemblyRegionTrimmerArgumentCollection, SAMSequenceDictionary, boolean, boolean, boolean) AssemblyRegionTrimmer
Initializes the trimmer.
initialize(IndexedFastaSequenceFile) OverhangFixingManager.Splice
initialize(int, int) 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) 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(List<Haplotype>, Map<String, List<GATKRead>>, int, int) 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) 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() MultiTileBclParser
initialize() PathHelper.PathProviders
initializeAdditionalWriters() SamToFastq
initializeAdditionalWriters() SamToFastqWithTags
initializeAnnotationOverrides(LinkedHashMap<String, String>) DataSourceFuncotationFactory
initializeConfigurationsFromCommandLineArgs(String[], String) ConfigFactory
Get the configuration filename from the command-line (if it exists) and create a configuration for it.
initializeConfigurationsFromCommandLineArgs(String[], String, Class<? extends T>) ConfigFactory
Get the configuration from filename the command-line (if it exists) and create a configuration for it of the given type.
initialized PairHMM
initializeDefaultMapWithKeys() MafOutputRenderer
initializeDrivingVariants() MultiVariantWalker
initializeDrivingVariants() VariantWalker
initializeDrivingVariants() 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.
initializeLog10Priors(byte[], byte[], byte[], int) Log10PairHMM
Initializes the matrix that holds all the constants related to the editing
distance between the read and the haplotype.
initializeLog10Probabilities(byte[], byte[], byte[]) Log10PairHMM
Initializes the matrix that holds all the constants related to quality scores.
initializeNewRawAnnotationData(List<Allele>) AS_RankSumTest
Initializing a AlleleSpecificAnnotationData> object for annotateRawData() to be used for
the per-read data generated by calculateRawData().
initialTumorLod M2ArgumentCollection
Only variants with estimated tumor LODs exceeding this threshold will be considered active.
initiateScheme() GA4GHScheme
initiateScheme() GA4GHSchemeWithMissingAsHomRef
initiateScheme() GenotypeConcordanceScheme
initilizeAll() PathHelper
calls PathProviders::initialize() for all PathProviders.
injectDefaultVerbosity(List<String>) CommandLineProgramTester
Inject the verbosity parameter into the list.
injectSystemPropertiesFromConfig(T) ConfigFactory
Injects system properties from the given configuration file.
inPlaceCombine(RecalibrationTables, RecalibrationTables) RecalibrationTables
Combines the right table into the left table, in-place (without making a copy)
input CountVariantsSpark
INPUT EstimateLibraryComplexityGATK
INPUT AbstractMarkDuplicatesCommandLineProgram
INPUT CollectJumpingLibraryMetrics
INPUT CollectMultipleMetrics
INPUT CollectOxoGMetrics
INPUT CollectRrbsMetrics
INPUT CollectWgsMetrics
INPUT CollectTargetedMetrics
INPUT CollectIndependentReplicateMetrics
INPUT SinglePassSamProgram
INPUT BamToBfq
INPUT CheckFingerprint
INPUT ClusterCrosscheckMetrics
INPUT CrosscheckFingerprints
INPUT IdentifyContaminant
INPUT CollectIlluminaBasecallingMetrics
INPUT MarkIlluminaAdapters
INPUT NonNFastaSize
INPUT NormalizeFasta
INPUT AddCommentsToBam
INPUT AddOrReplaceReadGroups
INPUT BamIndexStats
INPUT BuildBamIndex
INPUT CalculateReadGroupChecksum
INPUT CheckTerminatorBlock
INPUT CleanSam
INPUT DownsampleSam
INPUT FilterSamReads
INPUT FixMateInformation
INPUT GatherBamFiles
INPUT EstimateLibraryComplexity
INPUT AbstractMarkDuplicatesCommandLineProgram
INPUT MergeSamFiles
INPUT PositionBasedDownsampleSam
INPUT ReorderSam
INPUT ReplaceSamHeader
INPUT RevertOriginalBaseQualitiesAndAddMateCigar
INPUT RevertSam
INPUT SamFormatConverter
INPUT SamToFastq
INPUT SetNmMdAndUqTags
INPUT SortSam
INPUT SplitSamByLibrary
INPUT SplitSamByNumberOfReads
INPUT ValidateSamFile
INPUT ViewSam
INPUT BedToIntervalList
INPUT IntervalListToBed
INPUT IntervalListTools
INPUT LiftOverIntervalList
INPUT AccumulateVariantCallingMetrics
INPUT CollectVariantCallingMetrics
INPUT FilterVcf
INPUT FixVcfHeader
INPUT GatherVcfs
INPUT LiftoverVcf
INPUT MakeSitesOnlyVcf
INPUT FindMendelianViolations
INPUT MergeVcfs
INPUT RenameSampleInVcf
INPUT SortVcf
INPUT SplitVcfs
INPUT UpdateVcfSequenceDictionary
INPUT VcfFormatConverter
INPUT VcfToIntervalList
input2 CompareDuplicatesSpark
INPUT_2_LONG_NAME CompareDuplicatesSpark
INPUT_2_SHORT_NAME CompareDuplicatesSpark
INPUT_BASE ConvertSequencingArtifactToOxoG
INPUT_CALL_HEADER TagGermlineEvents
INPUT_GCS_PATH_LONG_NAME ParallelCopyGCSDirectoryIntoHDFSSpark
INPUT_GLOB ParallelCopyGCSDirectoryIntoHDFSSpark
INPUT_GLOB_ALL_FILES ParallelCopyGCSDirectoryIntoHDFSSpark
INPUT_LONG_NAME StandardArgumentDefinitions
INPUT_MODEL_INTERVAL_FILE GermlineCNVCaller
INPUT_SAMPLE_MAP CrosscheckFingerprints
INPUT_SHORT_NAME StandardArgumentDefinitions
INPUT_SHORT_NAME StandardOptionDefinitions
INPUT_VCFS_LIST_LONG_NAME CreateSomaticPanelOfNormals
INPUT_VCFS_LIST_SHORT_NAME CreateSomaticPanelOfNormals
inputBam CreateHadoopBamSplittingIndex
inputPaired PathSeqBwaSpark
inputPrior GenotypeCalculationArgumentCollection
By default, the prior specified with the argument --heterozygosity/-hets is used for variant discovery at a particular locus, using an infinite sites model,
see e.g.
inputReports GatherBQSRReports
inputReports GatherTranches
inputs GatherVcfsCloud
InputStreamSettings org.broadinstitute.hellbender.utils.runtime
Settings that define text to write to the process stdin.
InputStreamSettings() InputStreamSettings
inputUnpaired PathSeqBwaSpark
inRange(double, double, double, String) ParamUtils
Checks that the input is within range and returns the same value or throws an IllegalArgumentException
inRange(long, double, double, String) ParamUtils
Checks that the input is within range and returns the same value or throws an IllegalArgumentException
inRange(long, long, long, String) ParamUtils
Checks that the input is within range and returns the same value or throws an IllegalArgumentException
inRange(int, int, int, String) ParamUtils
Checks that the input int value is within range and returns the same value or throws an IllegalArgumentException
inRange(DoubleRange, double, String) ParamUtils
Validates the value of a parameter.
inRange(IntRange, int, String) ParamUtils
Validates the value of a parameter.
insertAllele(Allele, Allele, int, int) Haplotype
INSERTED_SEQUENCE GATKSVVCFConstants
INSERTED_SEQUENCE_LENGTH GATKSVVCFConstants
INSERTED_SEQUENCE_MAPPINGS GATKSVVCFConstants
insertedSequenceForwardStrandRep BreakpointComplications
Insertion(NovelAdjacencyAndAltHaplotype, int) SimpleSVType.Insertion
insertionMappings SimpleChimera
INSERTIONS_DEFAULT_QUALITY RecalibrationArgumentCollection
A default base qualities to use as a prior (reported quality) in the insertion covariate model.
insertionToInsertion PairHMMModel
Position in the transition probability array for the Insertion-to-Insertion transition.
InsertSizeMetrics 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() InsertSizeMetrics
InsertSizeMetrics 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() InsertSizeMetrics
InsertSizeMetricsArgumentCollection org.broadinstitute.hellbender.metrics
ArgumentCollection for InsertSizeMetrics collectors.
InsertSizeMetricsArgumentCollection() InsertSizeMetricsArgumentCollection
InsertSizeMetricsCollector org.broadinstitute.hellbender.metrics
Collects InsertSizeMetrics on the specified accumulationLevels
InsertSizeMetricsCollector() InsertSizeMetricsCollector
InsertSizeMetricsCollector picard.analysis.directed
Collects InsertSizeMetrics on the specified accumulationLevels using
InsertSizeMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, double, Integer, double, boolean) InsertSizeMetricsCollector
InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector 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 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() InsertSizeMetricsCollectorSpark
INSTANCE MarkDuplicatesSparkUtils.PairedEndsCoordinateComparator
instanceMain(String[]) CommandLineProgram
instanceMain(String[]) PicardCommandLineProgram
instanceMain(String[]) PicardCommandLineProgramExecutor
Entry point for Picard tools that are called from GATK.
instanceMain(String[], List<String>, List<Class<? extends CommandLineProgram>>, String) Main
The main method.
instanceMain(String[]) Main
This method is not intended to be used outside of the GATK framework and tests.
instanceMain(String[]) CommandLineProgram
instanceMain(String[], List<String>, String) PicardCommandLine
The main method.
instanceMain(String[]) PicardCommandLine
For testing
instanceMainPostParseArgs() CommandLineProgram
instanceMainWithExit(String[]) CommandLineProgram
int1() FindBreakpointEvidenceSpark.IntPair
int2() FindBreakpointEvidenceSpark.IntPair
IntBiConsumer org.broadinstitute.hellbender.utils.functional
Created by davidben on 8/19/16.
IntegerCopyNumberSegment org.broadinstitute.hellbender.tools.copynumber.formats.records
A genotyped integer copy-number segment.
IntegerCopyNumberSegment(SimpleInterval, IntegerCopyNumberState, IntegerCopyNumberState, int, double, double, double, double) IntegerCopyNumberSegment
IntegerCopyNumberSegmentCollection org.broadinstitute.hellbender.tools.copynumber.formats.collections
IntegerCopyNumberSegmentCollection(File) IntegerCopyNumberSegmentCollection
IntegerCopyNumberSegmentCollection(SampleLocatableMetadata, List<IntegerCopyNumberSegment>) IntegerCopyNumberSegmentCollection
IntegerCopyNumberState org.broadinstitute.hellbender.tools.copynumber.gcnv
This class represents integer copy number states.
IntegerCopyNumberState(int) IntegerCopyNumberState
integrate(DoubleFunction<Double>, double, double, int) IntegrationUtils
integrate2d(ToDoubleBiFunction<Double, Double>, double, double, int, double, double, int) IntegrationUtils
IntegrationTestSpec org.broadinstitute.hellbender.utils.test
IntegrationTestSpec(String, List<String>) IntegrationTestSpec
IntegrationTestSpec(String, int, Class<?>) IntegrationTestSpec
IntegrationUtils org.broadinstitute.hellbender.utils
Created by tsato on 5/1/17.
IntegrationUtils() IntegrationUtils
IntensityChannel 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.
INTERGENIC_BASES RnaSeqMetrics
Number of bases in primary alignments that do not align to any gene.
INTERLEAVE SamToFastq
INTEROP_SUBDIRECTORY_NAME TileMetricsUtil
The path to the directory containing the tile metrics file relative to the basecalling directory.
intersect(SVInterval) SVInterval
intersect(GenomeLoc) GenomeLoc
intersect(Locatable) SimpleInterval
Returns the intersection of the two intervals.
INTERSECT_INTERVALS GenotypeConcordance
interval ContextShard
INTERVAL_CONTIG_NAMES_SUB_PATH HDF5Utils
INTERVAL_EXCLUSION_PADDING_LONG_NAME IntervalArgumentCollection
INTERVAL_FILE_EXTENSIONS IntervalUtils
Recognized extensions for interval files
INTERVAL_GC_CONTENT_KEY GATKVCFConstants
INTERVAL_LIST ExtractSequences
INTERVAL_LIST FilterSamReads
INTERVAL_LIST ViewSam
INTERVAL_LIST_FILE_NAME GermlineCNVNamingConstants
INTERVAL_MATRIX_SUB_PATH HDF5Utils
INTERVAL_MERGING_RULE_LONG_NAME IntervalArgumentCollection
INTERVAL_PADDING_LONG_NAME IntervalArgumentCollection
INTERVAL_PSI_SCALE_LONG_NAME GermlineDenoisingModelArgumentCollection
INTERVAL_SET_RULE_LONG_NAME IntervalArgumentCollection
INTERVAL_VARIANT_ID_FIELD_SEPARATOR GATKSVVCFConstants
IntervalAlignmentContextIterator 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) IntervalAlignmentContextIterator
IntervalArgumentCollection org.broadinstitute.hellbender.cmdline.argumentcollections
Intended to be used as an @ArgumentCollection for specifying intervals at the command line.
IntervalArgumentCollection() IntervalArgumentCollection
intervalArgumentCollection GATKTool
intervalArgumentCollection GATKSparkTool
intervalArgumentCollection GermlineCNVCaller
IntervalArgumentCollection picard.cmdline.argumentcollections
Base interface for an interval argument collection.
intervalArugmentCollection CollectWgsMetrics
IntervalCopyNumberGenotypingData 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) IntervalCopyNumberGenotypingData
IntervalCoverageFinder org.broadinstitute.hellbender.tools.spark.sv.evidence
Class to find the coverage of the intervals.
IntervalCoverageFinder(ReadMetadata, List<SVInterval>, Iterator<GATKRead>, SVReadFilter) IntervalCoverageFinder
intervalExclusionPadding IntervalArgumentCollection
Use this to add padding to the intervals specified using -XL.
intervalFile StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
intervalFileToList(GenomeLocParser, String) IntervalUtils
Read a file of genome locations to process.
intervalIsOnDictionaryContig(SimpleInterval, SAMSequenceDictionary) IntervalUtils
Determines whether the provided interval is within the bounds of its assigned contig according to the provided dictionary
IntervalListScatterer picard.util
IntervalListScatterer(IntervalListScatterer.Mode) IntervalListScatterer
IntervalListScatterer.Mode picard.util
IntervalListToBed picard.util
Trivially simple command line program to convert an IntervalList file to a BED file.
IntervalListToBed() IntervalListToBed
IntervalListTools picard.util
Performs various IntervalList manipulations.
IntervalListTools() IntervalListTools
IntervalListTools.Action picard.util
IntervalLocusIterator org.broadinstitute.hellbender.utils.iterators
Returns a SimpleInterval for each locus in a set of intervals.
IntervalLocusIterator(Iterator<SimpleInterval>) IntervalLocusIterator
intervalMergingRule IntervalArgumentCollection
By default, the program merges abutting intervals (i.e.
IntervalMergingRule org.broadinstitute.hellbender.utils
a class we use to determine the merging rules for intervals passed to the GATK
intervalOnlyAssembly StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
IntervalOverlappingIterator T extends htsjdk.samtools.util.Locatable> - Class in org.broadinstitute.hellbender.utils.iterators
Wraps an iterator of Locatable with a list of sorted intervals
to return only the objects which overlaps with them
IntervalOverlappingIterator(Iterator<T>, List<SimpleInterval>, SAMSequenceDictionary) IntervalOverlappingIterator
Wraps an iterator to be filtered by a sorted list of intervals
intervalPadding IntervalArgumentCollection
Use this to add padding to the intervals specified using -L.
intervals AbstractWgsMetricsCollector
INTERVALS CollectSequencingArtifactMetrics
INTERVALS CollectMultipleMetrics
INTERVALS CollectOxoGMetrics
INTERVALS CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
INTERVALS CollectWgsMetrics
intervals CollectWgsMetrics.WgsMetrics
The intervals over which this metric was computed.
INTERVALS NonNFastaSize
INTERVALS MergeSamFiles
INTERVALS GenotypeConcordance
INTERVALS_LONG_NAME StandardArgumentDefinitions
INTERVALS_SHORT_NAME StandardArgumentDefinitions
intervalSetRule IntervalArgumentCollection
By default, the program will take the UNION of all intervals specified using -L and/or -XL.
IntervalSetRule org.broadinstitute.hellbender.utils
set operators for combining lists of intervals
intervalShardPadding IntervalWalkerSpark
intervalSize(List<GenomeLoc>) IntervalUtils
IntervalsManipulationProgramGroup picard.cmdline.programgroups
Tools that process genomic intervals in various formats.
IntervalsManipulationProgramGroup() IntervalsManipulationProgramGroup
IntervalsSkipList T extends htsjdk.samtools.util.Locatable> - Class in org.broadinstitute.hellbender.utils.collections
Holds many intervals in memory, with an efficient operation to get
intervals that overlap a given query interval.
IntervalsSkipList(Iterable<T>) IntervalsSkipList
Creates an IntervalsSkipList that holds a copy of the given intervals, sorted
and indexed.
IntervalsSkipListOneContig T extends htsjdk.samtools.util.Locatable> - Class in org.broadinstitute.hellbender.utils.collections
Holds many intervals in memory, with an efficient operation to get
intervals that overlap a given query interval.
IntervalsSkipListOneContig(Iterable<T>) IntervalsSkipListOneContig
Creates an IntervalsSkipList that holds a copy of the given intervals, sorted
and indexed.
intervalsSpecified() IntervalArgumentCollection
Have any intervals been specified for inclusion or exclusion
intervalStrings OptionalIntervalArgumentCollection
intervalStrings RequiredIntervalArgumentCollection
IntervalUtils org.broadinstitute.hellbender.utils
Parse text representations of interval strings that
can appear in GATK-based applications.
IntervalUtils() IntervalUtils
IntervalUtils.IntervalBreakpointType org.broadinstitute.hellbender.utils
An enum to classify breakpoints whether the breakpoint is the start or end of a region.
IntervalWalker 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() IntervalWalker
IntervalWalkerContext org.broadinstitute.hellbender.engine.spark
IntervalWalkerContext(SimpleInterval, ReadsContext, ReferenceContext, FeatureContext) IntervalWalkerContext
IntervalWalkerSpark org.broadinstitute.hellbender.engine.spark
IntervalWalkerSpark() IntervalWalkerSpark
IntHistogram org.broadinstitute.hellbender.tools.spark.utils
Histogram of observations on a compact set of non-negative integer values.
IntHistogram(int) IntHistogram
IntHistogram.CDF org.broadinstitute.hellbender.tools.spark.utils
IntHistogram.CDF.Serializer org.broadinstitute.hellbender.tools.spark.utils
IntHistogram.Serializer org.broadinstitute.hellbender.tools.spark.utils
IntPair(int, int) FindBreakpointEvidenceSpark.IntPair
INTRONIC_BASES RnaSeqMetrics
Number of bases in primary alignments that align to an intronic base for some gene, and not a coding or UTR base.
IntToDoubleBiFunction org.broadinstitute.hellbender.utils.functional
Created by davidben on 8/19/16.
INV33 GATKSVVCFConstants
INV33_BND BreakEndVariantType.InvSuspectBND
INV55 GATKSVVCFConstants
INV55_BND BreakEndVariantType.InvSuspectBND
INV_LOG_10 MathUtils
INV_LOG_2 MathUtils
INV_LOG_2 ParamUtils
INV_SQRT_2_PI MathUtils
INVALID_ELEMENT_FROM_READ RankSumTest
INVALID_TABLE_NAME_REGEX GATKReportTable
REGEX that matches any table with an invalid name
INVALIDATE_LONG_NAME VariantFiltration
Inversion(NovelAdjacencyAndAltHaplotype, int) SimpleSVType.Inversion
INVERT IntervalListTools
INVERT_GT_LONG_NAME VariantFiltration
INVERT_LONG_NAME VariantFiltration
invertCigar(Cigar) CigarUtils
Inverts the order of the operators in the cigar.
invertFilterExpression VariantFiltration
Invert the selection criteria for --filter-expression
invertGenotypeFilterExpression VariantFiltration
Invert the selection criteria for --genotype-filter-expression
IO_SIZE FifoBuffer
IOUtils org.broadinstitute.hellbender.utils.io
IOUtils() IOUtils
IS_BISULFITE_SEQUENCE MergeBamAlignment
IS_BISULFITE_SEQUENCE SetNmMdAndUqTags
IS_BISULFITE_SEQUENCED CollectAlignmentSummaryMetrics
IS_BISULFITE_SEQUENCED CollectGcBiasMetrics
IS_BISULFITE_SEQUENCED ValidateSamFile
IS_ENOUGH_VALIDATION_COVERAGE ValidateBasicSomaticShortMutations
IS_HOST_ALIGNED_LONG_NAME PSFilterArgumentCollection
IS_HOST_ALIGNED_SHORT_NAME PSFilterArgumentCollection
IS_NOT_NOISE ValidateBasicSomaticShortMutations
IS_NOVASEQ CollectIlluminaLaneMetrics
IS_ORIENTATION_BIAS_ARTIFACT_MODE OrientationBiasFilterConstants
IS_ORIENTATION_BIAS_CUT OrientationBiasFilterConstants
IS_ORIENTATION_BIAS_RC_ARTIFACT_MODE OrientationBiasFilterConstants
isAbleToValidateGenotype(Genotype, Allele) BasicSomaticShortMutationValidator
isAcceptableFeatureType(Class<? extends Feature>) FeatureWalker
Returns whether the given class of features is acceptable for this walker.
isAcceptableFeatureType(Class<? extends Feature>) ExampleFeatureWalker
isActive() AssemblyRegion
Does this region represent an active region (all isActiveProbs above threshold) or
an inactive region (all isActiveProbs below threshold)?
isActive(AlignmentContext, ReferenceContext, FeatureContext) 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) 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) Mutect2Engine
isActiveProb() ActivityProfileState
isAdapterSequence(byte[]) 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>) RecalibrationTables
isAfter(Locatable, Locatable, SAMSequenceDictionary) IntervalUtils
Tests whether the first Locatable starts after the end of the second Locatable
isAfterDeletionEnd() PileupElement
Is the current element immediately after a deletion, but itself not a deletion?
Suppose we are aligning a read with cigar 1M2D3M.
isAfterInsertion() PileupElement
Does an insertion occur immediately before the current position on the genome?
isAfterSoftClip() PileupElement
Does a soft-clipping event occur immediately before the current position on the genome?
isAllRegularBases(byte[]) BaseUtils
isAntiTraining TrainingSet
isAppendFile() OutputStreamSettings
isAvailable() PathHelper.PathProviders
isBamFileName(String) IOUtils
Returns true if the file's extension is BAM.
isBaseInsideAdaptor(GATKRead, long) 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(GenomeLoc) GenomeLoc
Tests whether this contig is completely before contig 'that'.
isBefore(Locatable, Locatable, SAMSequenceDictionary) IntervalUtils
Tests whether the first Locatable ends before the start of the second Locatable
isBeforeDeletionStart() PileupElement
Is the current element immediately before a deletion, but itself not a deletion?
Suppose we are aligning a read with cigar 3M2D1M.
isBeforeInsertion() PileupElement
Does an insertion occur immediately after the current position on the genome?
isBeforeSoftClip() PileupElement
Does a soft-clipping event occur immediately after the current position on the genome?
isBetaFeature() CommandLineProgram
isBetween(GenomeLoc, GenomeLoc) GenomeLoc
isBlank(byte[]) AbstractInputParser
Determines whether a given line is a comment
isBlockGzipped(File) BclReader
isBreakEndOnly() BreakEndVariantType
isBreakEndOnly() SimpleSVType
isBreakEndOnly() SvType
isBufferTruncated() CapturedStreamOutput
isBufferTruncated() StreamOutput
Returns true if the buffer was truncated.
isCalledAlt(double) VariantCallContext
isCalledRef(double) VariantCallContext
isChimeric(SAMRecord, int, Set<SamPairUtil.PairOrientation>) ChimeraUtil
Checks whether the given read is part of a chimeric pair.
isChimeric(SAMRecord, SAMRecord, int, Set<SamPairUtil.PairOrientation>) ChimeraUtil
Checks whether the given read is part of a chimeric pair.
isClipOverlappingReads() AbstractAlignmentMerger
isClipOverlappingReads() AbstractAlignmentMerger
isClosed() CircularByteBuffer
Returns true if the buffer is closed, false otherwise.
isCloudStorageUrl(String) BucketUtils
isCloudStorageUrl(Path) BucketUtils
isClusterRecord() TileMetricsOutReader.IlluminaTileMetrics
isComment(byte[]) AbstractInputParser
Determines whether a given line is a comment
isCommentLine(String[]) TableReader
Checks whether a line is a comment line or not.
isCompatibleWithSparkBroadcast() ReferenceMultiSource
Returns whether this reference source can be used with Spark broadcast.
isCompatibleWithSparkBroadcast() ReferenceSource
Returns whether this reference source can be used with Spark broadcast.
isComplexIndel(Allele, Allele) GATKProtectedVariantContextUtils
This method should only be run on variants that are known to be indels.
isConcrete() Nucleotide
Checks whether the nucleotide refer to a concrete (rather than ambiguous) base.
isConsensus TrainingSet
isContaminant(HitsForInsert) AbstractAlignmentMerger
isContaminant(HitsForInsert) SamAlignmentMerger
Criteria for contaminant reads:
1.
isCramFile(File) IOUtils
Returns true if the file's extension is CRAM.
isCramFile(Path) IOUtils
Returns true if the file's extension is CRAM.
isCramFileName(String) IOUtils
Returns true if the file's extension is CRAM.
isDbSnpSite(String, int) DbSnpBitSetUtil
Returns true if there is a dbSnp entry at pos in sequenceName, otherwise false
isDbSnpSite(String, int) DbSnpBitSetUtil
Returns true if there is a dbSnp entry at pos in sequenceName, otherwise false
isDebug() ReadThreadingAssembler
isDebugGraphTransformations() ReadThreadingAssembler
isDeletion() PileupElement
Is this element a deletion w.r.t.
isDeletion(String, String) GATKVariantContextUtils
Determines whether the given reference and alternate alleles constitute a deletion mutation.
isDeletion(Allele, Allele) GATKVariantContextUtils
Determines whether the given reference and alternate alleles constitute a deletion mutation.
isDelimiter(byte) AbstractInputParser
Determines whether a given character is a delimiter
isDelimiter(byte) CsvInputParser
Determines whether a given character is a delimiter
isDelimiter(byte) TabbedInputParser
Determines whether a given character is a delimiter
isDependentArgumentAllowed(Class<?>) GATKAnnotationPluginDescriptor
isDependentArgumentAllowed(Class<?>) GATKReadFilterPluginDescriptor
isDifferentByKSStatistic(IntHistogram, float) 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) GenotypeUtils
Returns true of the genotype is a called diploid genotype with likelihoods.
isDisabledFilter(String) GATKReadFilterPluginDescriptor
Determine if a particular ReadFilter was disabled on the command line, either directly of by disabling all
tool defaults.
isDisjointFrom(SVInterval) SVInterval
isDoingExactLog10Calculations() Log10PairHMM
Is this HMM using exact log calculations?
isDone(LineIterator) GencodeGtfCodec
isDone(B) ProgressReportingDelegatingCodec
isDuplicate() GATKRead
isDuplicate() SAMRecordToGATKReadAdapter
isEmitEmptyLoci() AlignmentContextIteratorBuilder
isEmpty() FeatureManager
Does this manager have no sources of Features to query?
isEmpty() HopscotchCollection
isEmpty() LargeLongHopscotchSet
isEmpty() LongBloomFilter
isEmpty() LongHopscotchSet
isEmpty() 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() ActivityProfile
Is this profile empty? (ie., does it contain no ActivityProfileStates?)
isEmpty() CountSet
isEmpty() CompressedDataList
isEmpty() GenomeLocSortedSet
determine if the collection is empty
isEmpty() Histogram
isEmpty() ReadPileup
isEmpty() GATKRead
isEmpty(SAMRecord) ReadUtils
isEmpty() RecalibrationReport
isEmpty() RecalibrationTables
isEmpty() ReadStructure.Substructure
isEmpty() MarkQueue
isEnoughValidationReads() BasicValidationResult
isEvidence(GATKRead) SVReadFilter
isEvidenceUpstreamOfBreakpoint() 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() BreakpointEvidence.ReadEvidence
isExpected() CrosscheckMetric.FingerprintResult
isExperimentalFeature() CommandLineProgram
isF2R1(GATKRead) OxoGReadCounts
isFeatureFile(Path) FeatureManager
isFileUrl(String) BucketUtils
isFinalized() AssemblyRegion
isFinite(double, String) ParamUtils
Checks that the input is not infinity nor NaN or throws an IllegalArgumentException
isFirstOfPair() GATKRead
isFirstOfPair() SAMRecordToGATKReadAdapter
isForwardStrand() SVFastqUtils.Mapping
isFrameshift(Allele, Allele) GATKVariantContextUtils
Determines whether the given reference and alternate alleles constitute a frameshift mutation.
isFrameshift(String, String) GATKVariantContextUtils
Determines whether the given reference and alternate alleles constitute a frameshift mutation.
isFrameshift(int, int, int) GATKVariantContextUtils
Determines whether the given reference and alternate alleles constitute a frameshift mutation.
isFuncotationInTranscriptList(GencodeFuncotation, Set<String>) FuncotatorUtils
Determines whether the given funcotation has a transcript ID that is in the given acceptableTranscripts.
isGenomicsDBPath(String) FeatureDataSource
isGenotypeInTransition(Genotype, Transition) OrientationBiasUtils
Complement of the artifact mode is NOT considered.
isGenotypeInTransitionsWithComplement(Genotype, Collection<Transition>) OrientationBiasUtils
isGenotypeInTransitionWithComplement(Genotype, Transition) OrientationBiasUtils
isGood() RealignmentEngine.RealignmentResult
isGood(Cigar) CigarUtils
A good Cigar object obeys the following rules:
- is valid as per SAM spec Cigar.isValid(String, long).
isGzipped(File) BclReader
isHadoopUrl(String) BucketUtils
Returns true if the given path is a HDFS (Hadoop filesystem) URL.
isHeaderLine(String[]) TableReader
Determines whether a line is a repetition of the header.
isHet() DiploidGenotype
isHeterozygous() DiploidGenotype
isHetRef(byte) DiploidGenotype
isHom() DiploidGenotype
isHomogeneous() HeterogeneousPloidyModel
isHomogeneous() HomogeneousPloidyModel
isHomogeneous() PloidyModel
Checks whether the ploidy is homogeneous across all samples.
isHomomozygous() DiploidGenotype
isHomRef(byte) DiploidGenotype
isHomVar(byte) DiploidGenotype
isImpreciseDeletion() EvidenceTargetLink
isIncludeDeletions() AlignmentContextIteratorBuilder
isIncludeNs() AlignmentContextIteratorBuilder
isIndel() GATKVariant
isIndel(String, String) GATKVariantContextUtils
Determines whether the given reference and alternate alleles constitute an insertion or deletion mutation.
isIndel(Allele, Allele) GATKVariantContextUtils
Determines whether the given reference and alternate alleles constitute an insertion or deletion mutation.
isIndel() MinimalVariant
isIndel() VariantContextVariantAdapter
isIndexed() HaplotypeCallerSpark.ReferenceMultiSourceAdapter
isInformative() ReadLikelihoods.BestAllele
isInformative(double[]) GATKVariantContextUtils
isInFrameWithEndOfRegion(int, int) FuncotatorUtils
Calculates whether the given startPosition (1-based, inclusive) is in frame relative to the end of the region.
isInsertion(Allele, Allele) GATKVariantContextUtils
Determines whether the given reference and alternate alleles constitute an insertion mutation.
isInsertion(String, String) GATKVariantContextUtils
Determines whether the given reference and alternate alleles constitute an insertion mutation.
isInsideDeletion(Cigar, int) AlignmentUtils
Is the offset inside a deletion?
isInsideRead(GATKRead, int) ReadUtils
Is a base inside a read?
isIntervalFile(String) IntervalUtils
Check if string argument was intended as a file
Accepted file extensions: .bed .list, .picard, .interval_list, .intervals.
isIntervalFile(String, boolean) IntervalUtils
isKeepAlignerProperPairFlags() AbstractAlignmentMerger
isKeepUniqueReadListInLibs() AlignmentContextIteratorBuilder
isKept(int) Permutation
Given an index of the original list, return whether this index is found at any position of the permuted list.
isKept(int) AlleleList.ActualPermutation
isKept(int) AlleleList.NonPermutation
isKnown TrainingSet
isKnown(String) NGSPlatform
checks whether or not the requested platform is listed in the set (and is not unknown)
isLeftEdge() AlignmentStateMachine
Is this the left edge state? I.e., one that is before or after the current read?
isLeftOverhang(GenomeLoc, GenomeLoc) OverhangFixingManager
Is this a proper overhang on the left side of the read?
isLowComplexity() 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(GATKRead) SVReadFilter
isMapped() SVFastqUtils.Mapping
isMappedPrimary(GATKRead) SVReadFilter
isMappedToPrimaryContig(GATKRead, ReadMetadata) SVReadFilter
isMatch() CrosscheckMetric.FingerprintResult
isMatched() ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch
isMissing(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) GenotypeConcordanceCounts
Returns true if EITHER the truth or call state is MISSING.
isNBase(byte) BaseUtils
isNegativeOrZero(double, String) ParamUtils
Checks that the input is positive or zero and returns the same value or throws an IllegalArgumentException
isNeitherIncompleteNorSimpleTranslocation() SimpleChimera
isNextToSoftClip() PileupElement
Does a soft-clipping event occur immediately before or after the current position on the genome?
isNonEmpty(Collection<?>) Utils
Checks that a Collection is not null and that it is not empty.
isNonPermuted() Permutation
Checks whether this is a trivial permutation where the resulting element list is the same as original.
isNonPermuted() AlleleList.ActualPermutation
isNonPermuted() AlleleList.NonPermutation
isNonPrimary(GATKRead) ReadUtils
isNotFailure() AlignedAssemblyOrExcuse
isOpen() SeekableByteChannelPrefetcher
Tells whether or not this channel is open.
isOpen() XorWrapper
isOpticalDuplicate ReadEnds
A *transient* flag marking this read end as being an optical duplicate.
isOutOfNoiseFloor() BasicValidationResult
isOutputAvailable() StreamingPythonScriptExecutor
See if any output is currently available.
isOutputAvailable() StreamingProcessController
Non-blocking call to see if output is available.
isPaired() GATKRead
isPaired() ReadEnds
isPaired() HitsForInsert
isPaired() SAMRecordToGATKReadAdapter
isPaired() ReadEnds
isPaired() ReadEndsForMateCigar
isPartial() Permutation
Checks whether this permutation is a partial one of the original list.
isPartial() AlleleList.ActualPermutation
isPartial() AlleleList.NonPermutation
isPast(GenomeLoc) GenomeLoc
Tests whether this contig is completely after contig 'that'.
isPerformDownsampling() LIBSDownsamplingInfo
isPf() CbclData
isPf() ClusterData
isPhasing(IlluminaMetricsCode) IlluminaMetricsCode
isPolymorphic(Allele, double) AFCalculationResult
Are we sufficiently confident in being non-ref that the site is considered polymorphic?
We are non-ref if the probability of being non-ref > the emit confidence (often an argument).
isPolymorphicPhredScaledQual(Allele, double) AFCalculationResult
Same as #isPolymorphic but takes a phred-scaled quality score as input
isPopulatePaTag() AbstractAlignmentMerger.UnmappingReadStrategy
isPositionInFrame(int) FuncotatorUtils
Gets whether the given position is in-frame.
isPositive(long, String) ParamUtils
Checks that the input is greater than zero and returns the same value or throws an IllegalArgumentException
isPositive(int, String) ParamUtils
Checks that the input int value is greater than zero and returns the same value or
throws an IllegalArgumentException
isPositive(double, String) ParamUtils
Checks that the input is greater than zero and returns the same value or throws an IllegalArgumentException
isPositiveOrZero(double, String) ParamUtils
Checks that the input is positive or zero and returns the same value or throws an IllegalArgumentException
isPositiveOrZero(long, String) ParamUtils
Checks that the input is positive or zero and returns the same value or throws an IllegalArgumentException
isPositiveOrZero(int, String) ParamUtils
Checks that the input is positive or zero and returns the same value or throws an IllegalArgumentException
isPreservingCase() CachingIndexedFastaSequenceFile
Is this CachingIndexedFastaReader keeping the original case of bases in the fasta, or is
everything being made upper case?
isPrimaryLine(GATKRead) SVReadFilter
isProperlyPaired() GATKRead
isProperlyPaired() SAMRecordToGATKReadAdapter
isQualityScoreTable(NestedIntegerArray<RecalDatum>) RecalibrationTables
isRead1ReverseStrand() EmptyFragment
isRead1ReverseStrand() Fragment
isRead1ReverseStrand() Pair
isRead1ReverseStrand() PairedEnds
isReadGroupTable(NestedIntegerArray<RecalDatum>) RecalibrationTables
isReadNameGroupedBam(SAMFileHeader) 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() TensorType
isRecoverDanglingBranches() ReadThreadingAssembler
isRedirectErrorStream() ProcessSettings
isRef() BaseEdge
Does this edge indicate a path through the reference graph?
isReference() AggregatedSubHaplotypeFinder
isReference() KBestHaplotype
Indicates whether this result is the reference haplotype.
isReferenceNode(V) BaseGraph
isRefSink(V) BaseGraph
isRefSource(V) BaseGraph
isRegularBase(byte) BaseUtils
Returns true iff the base represented by the byte is a 'regular' base (ACGT or *).
isRemoteStorageUrl(String) BucketUtils
Returns true if the given path is a GCS or HDFS (Hadoop filesystem) URL.
isRepeatAllele(Allele, Allele, String) GATKVariantContextUtils
Helper function for isTandemRepeat that checks that allele matches somewhere on the reference
isRequestedReducibleRawKey(String) VariantAnnotatorEngine
Method which checks if a key is a raw key of the requested reducible annotations
isReservedTag(String) AbstractAlignmentMerger
isReservedTag(String) AbstractAlignmentMerger
isResetMappingInformation() AbstractAlignmentMerger.UnmappingReadStrategy
isReverseStrand() GATKRead
isReverseStrand() SAMRecordToGATKReadAdapter
isRightAlign(String) GATKReportColumn
Check if the value can be right aligned.
isRightEdge() AlignmentStateMachine
Are we on the right edge? I.e., is the current state off the right of the alignment?
isRightOverhang(GenomeLoc, GenomeLoc) OverhangFixingManager
Is this a proper overhang on the right side of the read?
isSameBlock(GATKRead) KSWindowFinder
isSameDictionary(SAMSequenceDictionary, SAMSequenceDictionary) CopyNumberArgumentValidationUtils
Compares two non-null sequence dictionaries using sequence index, name, and length only.
isSameFormat(GATKReport) GATKReport
Returns whether or not the two reports have the same format, from columns, to tables, to reports, and everything
in between.
isSameFormat(GATKReportTable) GATKReportTable
Returns whether or not the two tables have the same format including columns and everything in between.
isSampleContaminationPresent() StandardCallerArgumentCollection
Returns true if there is some sample contamination present, false otherwise.
isSecondaryAlignment() GATKRead
isSecondaryAlignment() SAMRecordToGATKReadAdapter
isSecondOfPair() GATKRead
isSecondOfPair() SAMRecordToGATKReadAdapter
isSequenceDictionaryFromIndex(SAMSequenceDictionary) IndexUtils
isSequenceDictionaryUsingB37Reference(SAMSequenceDictionary) FuncotatorUtils
Returns if the given SAMSequenceDictionary is for the B37 Human Genome Reference.
isSink(V) BaseGraph
isSkipBlankLines() AbstractInputParser
isSnp() GATKVariant
isSnp() MinimalVariant
isSnp() VariantContextVariantAdapter
isSoloTranscript() Gene.Transcript
isSource(V) BaseGraph
isSpanningDeletion(Allele) GATKVCFConstants
isSpecialFile(File) IOUtils
Returns true if the file is a special file.
isStop() AminoAcid
isSupplementaryAlignment() GATKRead
isSupplementaryAlignment() SAMRecordToGATKReadAdapter
isSupportConnected() BetaBinomialDistribution
isTandemRepeat(VariantContext, byte[]) 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) SVReadFilter
isTestable(GATKRead) KSWindowFinder
isTheUpstreamMate BreakEndVariantType
Technically, a BND-formatted variant should have two VCF records, for mates, hence we also have this field.
isTheUpstreamMate() BreakEndVariantType
isTraining TrainingSet
isTransition(byte, byte) BaseUtils
isTransition(VariantContext) GATKVariantContextUtils
If this is a BiAllelic SNP, is it a transition?
isTreatGroupedDelimitersAsOne() AbstractInputParser
isTruth TrainingSet
isTwoBit(String) ReferenceTwoBitSource
isUnmapped() AlignedContig
isUnmapped(GenomeLoc) GenomeLoc
isUnmapped() GenomeLoc
Return true if this GenomeLoc represents the UNMAPPED location
isUnmapped() GATKRead
isUnmapped() SAMRecordToGATKReadAdapter
isUnmappedGenomeLocString(String) GenomeLocParser
isUpstreamOf(SVInterval) SVInterval
isUsableBaseForAnnotation(PileupElement) PileupElement
Can the base in this pileup element be used in comparative tests?
isUsableRead(GATKRead, int) AS_ReadPosRankSumTest
isUsableRead(GATKRead) OxoGReadCounts
isUsableRead(GATKRead, int) RankSumTest
Can the read be used in comparative tests between ref / alt bases?
isUsableRead(GATKRead, int) ReadPosRankSumTest
isValid(String, int, int) SimpleInterval
Test that these are valid values for constructing a SimpleInterval:
contig cannot be null
start must be >= 1
end must be >= start
isValidated() BreakpointEvidence
isValidBase(byte) DiploidGenotype
isValidDirectory(Path) DataSourceUtils
isValidGenomeLoc(String, int, int, boolean) GenomeLocParser
Would a genome loc created with the given parameters be valid w.r.t.
isValidGenomeLoc(String, int, int) GenomeLocParser
isValidLength(int) IndexRange
Checks whether this range is valid for a collection or array of a given size.
isVar(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) GenotypeConcordanceCounts
Returns true if EITHER the truth or call state is a VAR.
isVariantFile(File) VcfUtils
Checks if the suffix is one of those that are allowed for the various
formats that contain variants (currently vcf and bcf)
isVariationPresent() AssemblyRegionTrimmer.Result
Checks whether there is any variation present in the target region.
isVariationPresent() AssemblyResultSet
Checks whether there is any variation present in the assembly result set.
isViolation(Sample, Sample, Sample, VariantContext) MendelianViolation
isViolation(Genotype, Genotype, Genotype) MendelianViolation
Evaluate the genotypes of mom, dad, and child to detect Mendelian violations
isWithinInterval(Locatable) MultiVariantWalkerGroupedOnStart
isXnp(Allele, Allele) GATKVariantContextUtils
Determines whether the given reference and alternate alleles constitute a polymorphism in one or more nucleotides (XNP).
isXnp(String, String) GATKVariantContextUtils
Determines whether the given reference and alternate alleles constitute a polymorphism in one or more nucleotides (XNP).
iterator() 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)
Calling this method invalidates (closes) any previous iterator obtained from this method.
iterator() MultiIntervalLocalReadShard
iterator() 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() ReadsContext
Get an iterator over the reads in this context.
iterator(SimpleInterval) ReadsContext
Get an iterator over the reads of the backing data source over a given interval.
iterator() ReadsDataSource
Iterate over all reads in this data source.
iterator() ReferenceContext
Get an iterator over the reference bases in this context.
iterator() ReferenceFileSource
Start an iteration over the entire reference.
iterator() ReferenceMemorySource
Start an iteration over the entire reference.
iterator() ShardBoundaryShard
iterator() ShardToMultiIntervalShardAdapter
iterator() DownsampleableSparkReadShard
iterator() HaplotypeCallerSpark.ReferenceMultiSourceAdapter
iterator() PSKmerSet
iterator() IntervalCoverageFinder
iterator() KmerCleaner
iterator() ReadsForQNamesFinder
iterator() PairedStrandedIntervalTree
iterator() SVIntervalTree
Return an iterator over the entire tree.
iterator(SVInterval) SVIntervalTree
Return an iterator over all intervals greater than or equal to the specified interval.
iterator() HopscotchCollection
iterator() LargeLongHopscotchSet
iterator() LongHopscotchSet
iterator() KBestHaplotypeFinder
iterator(int) KBestHaplotypeFinder
Returns an iterator on the first k best haplotypes.
iterator() CountSet
iterator() IndexedSet
iterator() CompressedDataList
iterator() ReadsDownsamplingIterator
iterator() GenomeLocSortedSet
get an iterator over this collection
iterator() ReadFilteringIterator
iterator() ReadTransformingIterator
iterator() SamReaderQueryingIterator
iterator() SAMRecordToReadIterator
iterator() PathLineIterator
iterator() ReadsIterable
iterator() ReadPileup
The best way to access PileupElements where you only care about the bases and quals in the pileup.
iterator() ArtificialReadIterator
return this iterator, for the iterable interface
iterator AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
iterator() StandardCovariateList
Returns a new iterator over all covariates in this list.
iterator() RecalibrationTables
iterator() XReadLines
I'm an iterator too...
iterator() TableReader
Returns an iterator on the remaining records in
the input.
iterator() Gene
iterator() BaseIlluminaDataProvider
iterator() ReadStructure.Substructure
iterator() TileIndex
iterator AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
iterator() AbstractInputParser
iterator() TabbedTextFileWithHeaderParser
Creates the iterator object.
IteratorFilter(Iterator<T>, Predicate<T>) SVUtils.IteratorFilter
Iterators picard.util
Iterators() Iterators
iterators() VariantIteratorProducer
Renders the embodied regions of the VCF files in the form of CloseableIterators over
VariantContexts.
iteratorSize(Iterator<T>) SVUtils
count the number of items available from an iterator
iteratorSize(LongIterator) SVUtils
M2ArgumentCollection org.broadinstitute.hellbender.tools.walkers.mutect
M2ArgumentCollection() M2ArgumentCollection
M2FiltersArgumentCollection org.broadinstitute.hellbender.tools.walkers.mutect
M2FiltersArgumentCollection() M2FiltersArgumentCollection
MACHINE_NAME IlluminaBasecallsToFastq
MAD_COVERAGE CollectWgsMetrics.WgsMetrics
The median absolute deviation of coverage of the genome after all filters are applied.
MafOutputRenderer 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>) MafOutputRenderer
Main org.broadinstitute.hellbender
This is the main class of Hellbender and is the way of executing individual command line programs.
Main() Main
main(String[]) Main
The entry point to GATK from commandline.
main(String[]) CollectAlignmentSummaryMetrics
Required main method implementation.
main(String[]) CollectBaseDistributionByCycle
main(String[]) CollectGcBiasMetrics
main(String[]) CollectInsertSizeMetrics
Required main method implementation.
main(String[]) CollectJumpingLibraryMetrics
Stock main method.
main(String[]) CollectMultipleMetrics
main(String[]) CollectRnaSeqMetrics
Required main method implementation.
main(String[]) CollectRrbsMetrics
main(String[]) CollectWgsMetrics
main(String[]) CollectWgsMetricsWithNonZeroCoverage
main(String[]) CompareMetrics
main(String[]) CollectHsMetrics
Stock main method.
main(String[]) CollectTargetedPcrMetrics
Stock main method.
main(String[]) MeanQualityByCycle
Required main method.
main(String[]) QualityScoreDistribution
Required main method.
main(String[]) PicardCommandLine
Override this if you want to include different java packages to search for classes that extend CommandLineProgram.
main(String[]) BamToBfq
main(String[]) CheckIlluminaDirectory
Required main method implementation.
main(String[]) CollectIlluminaBasecallingMetrics
main(String[]) CollectIlluminaLaneMetrics
main(String[]) ExtractIlluminaBarcodes
main(String[]) IlluminaBasecallsToFastq
main(String[]) IlluminaBasecallsToSam
main(String[]) MarkIlluminaAdapters
main(String[]) CollectHiSeqXPfFailMetrics
Stock main method.
main(String[]) ExtractSequences
main(String[]) NonNFastaSize
main(String[]) NormalizeFasta
main(String[]) AddCommentsToBam
main(String[]) BamIndexStats
Stock main method for a command line program.
main(String[]) BuildBamIndex
Stock main method for a command line program.
main(String[]) CalculateReadGroupChecksum
main(String[]) CheckTerminatorBlock
main(String[]) CleanSam
main(String[]) CompareSAMs
main(String[]) CreateSequenceDictionary
main(String[]) DuplicationMetrics
main(String[]) FastqToSam
Stock main method.
main(String[]) FixMateInformation
main(String[]) GatherBamFiles
main(String[]) EstimateLibraryComplexity
Stock main method.
main(String[]) MarkDuplicates
Stock main method.
main(String[]) MarkDuplicatesWithMateCigar
Stock main method.
main(String[]) SimpleMarkDuplicatesWithMateCigar
Stock main method.
main(String[]) MergeSamFiles
Required main method implementation.
main(String[]) ReplaceSamHeader
main(String[]) RevertOriginalBaseQualitiesAndAddMateCigar
Default main method impl.
main(String[]) SamFormatConverter
main(String[]) SamToFastq
main(String[]) SetNmMdAndUqTags
main(String[]) SplitSamByLibrary
main(String[]) ValidateSamFile
main(String[]) ViewSam
main(String[]) Test
main(String[]) BaitDesigner
Stock main method.
main(String[]) BedToIntervalList
main(String[]) FifoBuffer
main(String[]) ScatterIntervalsByNs
main(String[]) CollectVariantCallingMetrics
main(String[]) FilterVcf
main(String[]) FixVcfHeader
main(String[]) GatherVcfs
main(String[]) GenotypeConcordance
main(String[]) MakeSitesOnlyVcf
main(String[]) MergeVcfs
main(String[]) RenameSampleInVcf
main(String[]) SortVcf
main(String[]) SplitVcfs
main(String[]) UpdateVcfSequenceDictionary
main(String[]) VcfFormatConverter
main(String[]) VcfToIntervalList
mainEntry(String[]) Main
makeAllReadCollector() MultiLevelCollector
makeAllReadCollector() 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() TargetMetricsCollector
makeAllReadCollector() MultiLevelCollector
makeAnnotatedCall(byte[], SimpleInterval, FeatureContext, SAMFileHeader, VariantContext, ReadLikelihoods<Allele>, VariantContext) HaplotypeCallerGenotypingEngine
makeArg(SAMRecord, ReferenceSequence) InsertSizeMetricsCollector
makeArg(SAMRecord, ReferenceSequence) MultiLevelCollector
makeArg(SAMRecord, ReferenceSequence) MultiLevelReducibleCollector
Convert the current SAMRecord and the ReferenceSequence for that record into an ARGTYPE object.
makeArg(SAMRecord, ReferenceSequence) SAMRecordAndReferenceMultiLevelCollector
makeArg(SAMRecord, ReferenceSequence) SAMRecordMultiLevelCollector
makeArg(SAMRecord, ReferenceSequence) 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) InsertSizeMetricsCollector
makeArg(SAMRecord, ReferenceSequence) GcBiasMetricsCollector
makeArg(SAMRecord, ReferenceSequence) MultiLevelCollector
makeArg(SAMRecord, ReferenceSequence) SAMRecordAndReferenceMultiLevelCollector
makeArg(SAMRecord, ReferenceSequence) SAMRecordMultiLevelCollector
makeBAMFile(File) ArtificialBAMBuilder
Write the reads from this builder to output, creating an index as well
makeBarcodeRegex(int) ParameterizedFileUtil
makeBlock(VariantContext, VariantContext) 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.
makeCalls() SimpleCopyRatioCaller
makeChildCollector(String, String, String) InsertSizeMetricsCollector
makeChildCollector(String, String, String) MultiLevelCollector
Construct a PerUnitMetricCollector with the given arguments.
makeChildCollector(String, String, String) MultiLevelReducibleCollector
Construct a PerUnitMetricCollector with the given arguments.
makeChildCollector(String, String, String) ExampleMultiMetricsCollector
Make an PerUnitExampleMultiMetricsCollector with the given arguments
makeChildCollector(String, String, String) AlignmentSummaryMetricsCollector
makeChildCollector(String, String, String) InsertSizeMetricsCollector
Make an InsertSizeCollector with the given arguments
makeChildCollector(String, String, String) RnaSeqMetricsCollector
makeChildCollector(String, String, String) TargetMetricsCollector
makeChildCollector(String, String, String) GcBiasMetricsCollector
makeChildCollector(String, String, String) RrbsMetricsCollector
makeChildCollector(String, String, String) MultiLevelCollector
Construct a PerUnitMetricCollector with the given arguments.
makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) CollectHsMetrics
makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) CollectTargetedMetrics
A factory method for the TargetMetricsCollector to use this time.
makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) CollectTargetedPcrMetrics
makeCombinedAnnotationString(List<Allele>, Map<Allele, Histogram>) AS_RankSumTest
makeCommandLineArgs(List<String>) CommandLineProgramTester
For testing support.
makeCommandLineArgs(List<String>, String) CommandLineProgramTester
For testing support.
makeCycleFileParser(List<File>, PerTileCycleParser.CycleFilesParser<BclData>) MultiTileBclParser
makeCycleFileParser(List<File>) MultiTileBclParser
makeDataProvider(List<File>, List<AbstractIlluminaPositionFileReader.PositionInfo>, File[], int, File) IlluminaDataProviderFactory
Call this method to create a ClusterData iterator over all clusters for a given tile.
makeDataProvider() IlluminaDataProviderFactory
makeDataProvider(List<Integer>) IlluminaDataProviderFactory
Call this method to create a ClusterData iterator over the specified tiles.
makeEvalVariantFilter() AbstractConcordanceWalker
makeExceptionMsg() AbstractIlluminaPositionFileReader
Create a string that will be included in any NoSuchElementException thrown by the next() method
makeExceptionMsg() ClocsFileReader
makeExceptionMsg() LocsFileReader
makeExceptionMsg() PosFileReader
makeFilePathAbsolute(String) BucketUtils
Changes relative local file paths to be absolute file paths.
makeFilteredPileup(Predicate<PileupElement>) ReadPileup
Make a new pileup consisting of elements of this pileup that satisfy the predicate.
makeFinalizedAnnotationString(int, Map<Allele, Double>) RMSMappingQuality
makeFromAlleles(String, String, int, List<String>) GATKVariantContextUtils
For testing purposes only.
makeGenomicsDBUri(File) GenomicsDBTestUtils
makeGenotypeCall(int, GenotypeBuilder, GenotypeAssignmentMethod, double[], List<Allele>) GATKVariantContextUtils
makeIgnoredSequenceIndicesSet(SAMFileHeader, Set<String>) RnaSeqMetricsCollector
makeIndexableSourceFromStream(InputStream) GencodeGtfCodec
makeIndexableSourceFromStream(InputStream) ProgressReportingDelegatingCodec
makeInstance(String, String, File, File, Set<MetricAccumulationLevel>, File, File, boolean) CollectMultipleMetrics.ProgramInterface
makeInstance(String, String, File, File, Set<MetricAccumulationLevel>, File, File) CollectMultipleMetrics.ProgramInterface
makeInstancesOfSubclasses(Class<? extends T>, Package) ClassUtils
Finds and creates objects of all concrete subclasses of the given class in the package.
makeInterpretation(JavaRDD<AssemblyContigWithFineTunedAlignments>, SvDiscoveryInputMetaData) CpxVariantInterpreter
makeInterpretation(JavaRDD<AssemblyContigWithFineTunedAlignments>, SvDiscoveryInputMetaData) SimpleNovelAdjacencyInterpreter
makeIntervalArgumentCollection() CollectWgsMetrics
makeItSo(File, File, boolean, long, Collection<SinglePassSamProgram>) SinglePassSamProgram
makeItSo(FastqReader, FastqReader, SAMFileWriter) FastqToSam
Handles the FastqToSam execution on the FastqReader(s).
makeKernel(int, double) BandPassActivityProfile
makeLaneTileRegex(String, int) ParameterizedFileUtil
Return a regex string for finding Lane and Tile given a file extension pattern
makeLibraryCollector(SAMReadGroupRecord) MultiLevelCollector
makeLibraryCollector(SAMReadGroupRecord) MultiLevelReducibleCollector
makeLibraryCollector(SAMReadGroupRecord) MultiLevelCollector
makeMergedVariantContext(List<VariantContext>) AssemblyBasedCallerUtils
makeNewHMM(PairHMMNativeArguments) PairHMM.Implementation
makeOREdge(Collection<BaseEdge>, int) BaseEdge
Create a new BaseEdge with the given multiplicity.
makeOverlapDetector(File, SAMFileHeader, File, Log) RnaSeqMetricsCollector
makePermutations(List<T>, int, boolean) 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) IlluminaUtil
Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
makePhredBinaryFromSolexaQualityAscii_1_3(String, int, int) IlluminaUtil
Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
makePileupElement() AlignmentStateMachine
Create a new PileupElement based on the current state of this element
Must not be a left or right edge
makePostReadFilterTransformer() GATKTool
Returns the post-filter read transformer (simple or composite) that will be applied to the reads after filtering.
makePostReadFilterTransformer() ApplyBQSR
Returns the BQSR post-transformer.
makePostReadFilterTransformer() SplitNCigarReads
makePreReadFilterTransformer() GATKTool
Returns the pre-filter read transformer (simple or composite) that will be applied to the reads before filtering.
makePreReadFilterTransformer() SplitNCigarReads
makePrintStreamMaybeGzipped(File) IOUtils
Makes a print stream for a file, gzipping on the fly if the file's name ends with '.gz'.
makeQualityScoreTable() 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>) AS_RankSumTest
makeRawAnnotationString(List<Allele>, Map<Allele, List<Integer>>) AS_StrandBiasTest
makeRawAnnotationString(List<Allele>, Map<Allele, Number>) RMSMappingQuality
makeRead(String, KV<Integer, Integer>, int, Class<?>) ReadsPreprocessingPipelineTestData
makeRead creates a read backed by either SAMRecord or Google model Read.
makeRead(String, int, int, int, Class<?>) ReadsPreprocessingPipelineTestData
makeRead creates a read backed by either SAMRecord or Google model Read.
makeReaderMaybeGzipped(File) IOUtils
Makes a reader for a file, unzipping if the file's name ends with '.gz'.
makeReaderMaybeGzipped(InputStream, boolean) IOUtils
makes a reader for an inputStream wrapping it in an appropriate unzipper if necessary
makeReadFilter() GATKTool
Returns a read filter (simple or composite) that can be applied to reads.
makeReadFilter() GATKSparkTool
makeReadFilter(SAMFileHeader) GATKSparkTool
makeReadFromCigar(String) ReadClipperTestUtils
Make a read from the CIGAR string
makeReadFromCigar(Cigar) ReadClipperTestUtils
Make a read from the CIGAR.
makeReadFromCigar(String, int) ReadClipperTestUtils
Make a read from the CIGAR
makeReadGroupCollector(SAMReadGroupRecord) MultiLevelCollector
makeReadGroupCollector(SAMReadGroupRecord) MultiLevelReducibleCollector
makeReadGroupCollector(SAMReadGroupRecord) MultiLevelCollector
makeReads() ArtificialBAMBuilder
Create a read stream based on the parameters.
makeReducedAnnotationString(VariantContext, Map<Allele, Double>) AS_StrandBiasTest
makeReferenceArgumentCollection() CollectAlignmentSummaryMetrics
makeReferenceArgumentCollection() CollectRrbsMetrics
makeReferenceArgumentCollection() CommandLineProgram
makeReferenceArgumentCollection() CreateSequenceDictionary
makeReferenceArgumentCollection() DownsampleSam
makeReferenceArgumentCollection() ReorderSam
makeReferenceArgumentCollection() ScatterIntervalsByNs
makeReferenceArgumentCollection() LiftoverVcf
makeReferenceShardBoundaryReads(int, int, Class<?>) ReadsPreprocessingPipelineTestData
Generates a List of artificial reads located in significant positions relative to reference shard
boundaries.
makeSampleCollector(SAMReadGroupRecord) MultiLevelCollector
makeSampleCollector(SAMReadGroupRecord) MultiLevelReducibleCollector
makeSampleCollector(SAMReadGroupRecord) MultiLevelCollector
makeSeekable(List<File>, BclQualityEvaluationStrategy, int[]) BclReader
makeSequenceDictionary(File) CreateSequenceDictionary
Deprecated.
MakeSitesOnlyVcf picard.vcf
Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.
MakeSitesOnlyVcf() MakeSitesOnlyVcf
makeSourceFromStream(InputStream) GencodeGtfCodec
makeSourceFromStream(InputStream) ProgressReportingDelegatingCodec
makeStandardHCReadFilters() HaplotypeCallerEngine
makeStandardMutect2ReadFilters() Mutect2Engine
makeTemporaryBAMFile() ArtificialBAMBuilder
Make an indexed BAM file contains the reads in the builder, marking it for deleteOnExit()
makeTileIterator(File) PerTileParser
Factory method for the iterator of each tile
makeTileIterator(File) PosParser
Make an CloseableIterator
based on the given file and fileType specified at construction.
makeTruthVariantFilter() AbstractConcordanceWalker
makeTruthVariantFilter() Concordance
makeValueObjectForAnnotation(int[][]) FisherStrand
makeValueObjectForAnnotation(double) FisherStrand
makeVariantAnnotations() GATKTool
Returns a list of annotations that can be applied to VariantContexts.
makeVariantAnnotations() GATKSparkTool
makeVariantAnnotations() HaplotypeCallerSpark
makeVariantAnnotations() ReadsPipelineSpark
makeVariantAnnotations() 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.
makeVariantFilter() VariantWalkerSpark
makeVariantFilter() VariantWalkerBase
makeVariantFilter() SelectVariants
Create filters for variant types, ids, and genomic intervals.
makeVariantFilter() CNNScoreVariants
makeVCFHeader(SAMSequenceDictionary, Set<VCFHeaderLine>) HaplotypeCallerEngine
Create a VCF header.
makeVCFWriter(String, SAMSequenceDictionary, boolean, boolean, boolean) HaplotypeCallerEngine
Create a VCF or GVCF writer as appropriate, given our arguments
makeVectorTable(String, String, List<String>, double[], String, String) VariantRecalibrator
makeZippedInputStream(InputStream) IOUtils
creates an input stream from a zipped stream
MALE_CHROMS FindMendelianViolations
MalformedBAM(GATKRead, String) UserException.MalformedBAM
MalformedBAM(File, String) UserException.MalformedBAM
MalformedBAM(String, String) UserException.MalformedBAM
MalformedFile(String) UserException.MalformedFile
MalformedFile(File, String) UserException.MalformedFile
MalformedFile(File, String, Exception) UserException.MalformedFile
MalformedFile(Path, String) UserException.MalformedFile
MalformedFile(Path, String, Exception) UserException.MalformedFile
MalformedGenomeLoc(String) UserException.MalformedGenomeLoc
MalformedGenomeLoc(String, Exception) UserException.MalformedGenomeLoc
MalformedRead(GATKRead, String) UserException.MalformedRead
MalformedRead(String, String) UserException.MalformedRead
MANDATORY_PROPERTIES SparkContextFactory
MannWhitneyU org.broadinstitute.hellbender.utils
Imported with changes from Picard private.
MannWhitneyU() MannWhitneyU
MannWhitneyU.RankedData org.broadinstitute.hellbender.utils
The ranked data in one list and a list of the number of ties.
MannWhitneyU.Result org.broadinstitute.hellbender.utils
The results of performing a rank sum test.
MannWhitneyU.TestStatistic 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 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 OutputRenderer
manualAnnotationSerializedString OutputRenderer
MAP_ALLELE_FRACTIONS_KEY StrandArtifact
MAP_NAME_VALUE_DELIMITER FuncotatorArgumentDefinitions
MAP_QUAL_RANK_SUM_KEY GATKVCFConstants
MAPPED ReadFilterLibrary
MAPPED_READS PSScoreMetrics
The number of non-host reads mapped to a pathogen
mappedAndUnmappedReadIterator(int, int, int, int) ArtificialReadUtils
create an iterator containing the specified read piles
MappedReadFilter() ReadFilterLibrary.MappedReadFilter
mappedReadIterator(int, int, int) ArtificialReadUtils
create an iterator containing the specified read piles
Mapping(String) SVFastqUtils.Mapping
Mapping(GATKRead) SVFastqUtils.Mapping
MAPPING_ERROR_RATE_LONG_NAME GermlineContigPloidyModelArgumentCollection
MAPPING_ERROR_RATE_LONG_NAME GermlineDenoisingModelArgumentCollection
MAPPING_QUALITIES GATKSVVCFConstants
MAPPING_QUALITY_AVAILABLE ReadFilterLibrary
MAPPING_QUALITY_NOT_ZERO ReadFilterLibrary
MAPPING_QUALITY_UNAVAILABLE QualityUtils
MAPPING_QUALITY_ZERO_BY_SAMPLE_KEY GATKVCFConstants
MappingQuality org.broadinstitute.hellbender.tools.walkers.annotator
Median mapping quality of reads supporting each alt allele.
MappingQuality() MappingQuality
MappingQualityAvailableReadFilter() ReadFilterLibrary.MappingQualityAvailableReadFilter
MappingQualityNotZeroReadFilter() ReadFilterLibrary.MappingQualityNotZeroReadFilter
MappingQualityRankSumTest org.broadinstitute.hellbender.tools.walkers.annotator
Rank Sum Test for mapping qualities of REF versus ALT reads
MappingQualityRankSumTest() MappingQualityRankSumTest
MappingQualityReadFilter org.broadinstitute.hellbender.engine.filters
Keep only reads with mapping qualities within a specified range.
MappingQualityReadFilter() MappingQualityReadFilter
MappingQualityReadFilter(int) MappingQualityReadFilter
MappingQualityReadFilter(int, Integer) MappingQualityReadFilter
MappingQualityReadTransformer 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) MappingQualityReadTransformer
MappingQualityZero org.broadinstitute.hellbender.tools.walkers.annotator
Count of all reads with MAPQ = 0 across all samples
MappingQualityZero() MappingQualityZero
mapQual AlignmentInterval
Mapping quality, SAMRecord.NO_MAPPING_QUALITY if unspecified.
mapQualTieBreaker ReadPileup
mapToDouble(IntToDoubleFunction) IndexRange
Apply an int -> double function to this range, producing a double[]
mapToInteger(IntUnaryOperator) IndexRange
Apply an int -> int function to this range, producing an int[]
margin AddContextDataToReadSparkOptimized
marginalize(Map<B, List<A>>) ReadLikelihoods
Perform marginalization from an allele set to another (smaller one) taking the maximum value
for each read in the original allele subset.
marginalize(Map<B, List<A>>, Locatable) ReadLikelihoods
Perform marginalization from an allele set to another (smaller one) taking the maximum value
for each read in the original allele subset.
mark(JavaRDD<GATKRead>, SAMFileHeader, MarkDuplicatesScoringStrategy, OpticalDuplicateFinder, int, boolean) MarkDuplicatesSpark
Main method for marking duplicates, takes an JavaRDD of GATKRead and an associated SAMFileHeader with corresponding
sorting information and returns a new JavaRDD\ 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.
MarkDuplicates picard.sam.markduplicates
A better duplication marking algorithm that handles all cases including clipped
and gapped alignments.
MarkDuplicates() MarkDuplicates
MarkDuplicates.DuplicateTaggingPolicy picard.sam.markduplicates
Enum used to control how duplicates are flagged in the DT optional tag on each read.
MarkDuplicates.DuplicateType picard.sam.markduplicates
Enum for the possible values that a duplicate read can be tagged with in the DT attribute.
MarkDuplicatesGATK org.broadinstitute.hellbender.tools.walkers.markduplicates
A better duplication marking algorithm that handles all cases including clipped
and gapped alignments.
MarkDuplicatesGATK() MarkDuplicatesGATK
MarkDuplicatesScoringStrategy 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 org.broadinstitute.hellbender.tools.spark.transforms.markduplicates
MarkDuplicatesSpark() MarkDuplicatesSpark
MarkDuplicatesSparkArgumentCollection org.broadinstitute.hellbender.cmdline.argumentcollections
An argument collection for use with tools that mark optical
duplicates.
MarkDuplicatesSparkArgumentCollection() MarkDuplicatesSparkArgumentCollection
markDuplicatesSparkArgumentCollection BwaAndMarkDuplicatesPipelineSpark
markDuplicatesSparkArgumentCollection ReadsPipelineSpark
markDuplicatesSparkArgumentCollection MarkDuplicatesSpark
MarkDuplicatesSparkRecord org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
A common interface for the data types that represent reads for mark duplicates spark.
MarkDuplicatesSparkRecord.Type org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
MarkDuplicatesSparkUtils org.broadinstitute.hellbender.tools.spark.transforms.markduplicates
Utility classes and functions for Mark Duplicates.
MarkDuplicatesSparkUtils() 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.PairedEndsCoordinateComparator org.broadinstitute.hellbender.tools.spark.transforms.markduplicates
Comparator for sorting Reads by coordinate.
MarkDuplicatesWithMateCigar picard.sam.markduplicates
An even better duplication marking algorithm that handles all cases including clipped
and gapped alignments.
MarkDuplicatesWithMateCigar() MarkDuplicatesWithMateCigar
MarkDuplicatesWithMateCigarIterator 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>) MarkDuplicatesWithMateCigarIterator
Initializes the mark duplicates iterator.
MarkedOpticalDuplicateReadFilter org.broadinstitute.hellbender.tools.spark.pathseq
MarkedOpticalDuplicateReadFilter() MarkedOpticalDuplicateReadFilter
MarkIlluminaAdapters picard.illumina
Command line program to mark the location of adapter sequences.
MarkIlluminaAdapters() MarkIlluminaAdapters
MarkQueue picard.sam.markduplicates.util
This is the mark queue.
MarkQueue(DuplicateScoringStrategy.ScoringStrategy) MarkQueue
mask(SVKmerShort) SVKmerShort
mask VariantFiltration
Any variant which overlaps entries from the provided mask file will be filtered.
MASK_EXTENSION_LONG_NAME VariantFiltration
MASK_NAME_LONG_NAME VariantFiltration
maskExtension VariantFiltration
maskName VariantFiltration
When using the -mask argument, the maskName will be annotated in the variant record.
MATCHED_NORMAL_LONG_NAME CalculateContamination
MATCHED_NORMAL_SEGMENT_FILE_LONG_NAME TagGermlineEvents
MATCHED_NORMAL_SHORT_NAME CalculateContamination
matches(GATKRead) ArtificialReadQueryIterator
given a read and the query type, check if it matches our regions
matches(int, String) TableColumnCollection
Checks a column names matches given one.
matchesAll(int, String...) TableColumnCollection
Checks an array of column matches the column names starting from a given index.
matchesExactly(String...) TableColumnCollection
Checks whether columns contain all the names in an array and no other and in the very same order.
MATCHING_DICTIONARY_TAGS MergeBamAlignment
MatchingBasesAndQualsReadFilter() ReadFilterLibrary.MatchingBasesAndQualsReadFilter
matchingRef() Transition
Return the ref:ref transition corresponding to this ref:alt transition.
MatchMDElement(int) TextMDCodec.MatchMDElement
matchPattern ParameterizedFileUtil
A pattern that will match files of this type for this lane
MatchResults picard.fingerprint
Represents the results of a fingerprint comparison between one dataset and a specific
fingerprint file.
matchToDeletion PairHMMModel
Position in the transition probability array for the Match-to-Deletion transition.
matchToInsertion PairHMMModel
Position in the transition probability array for the Match-to-Insertion transition.
matchToMatch PairHMMModel
Position in the transition probability array for the Match-to-Match transition.
matchToMatchProb(byte, byte) PairHMMModel
Returns the probability that neither of two event takes place.
matchToMatchProb(int, int) PairHMMModel
Returns the probability that neither of two events, insertion and deletion, takes place.
matchToMatchProbLog10(byte, byte) PairHMMModel
Returns the log10 probability that neither of two events, insertion and deletion, takes place.
matchToMatchProbLog10(int, int) PairHMMModel
Returns the log-probability that neither of two events takes place.
MATE_ALIGNMENT_LENGTH_UNCERTAINTY BreakpointEvidence.DiscordantReadPairEvidence
MATE_DIFFERENT_STRAND ReadFilterLibrary
MATE_ON_SAME_CONTIG_OR_NO_MAPPED_MATE ReadFilterLibrary
MateDifferentStrandReadFilter() ReadFilterLibrary.MateDifferentStrandReadFilter
mateIsReverseStrand() GATKRead
mateIsReverseStrand() SAMRecordToGATKReadAdapter
mateIsUnmapped() GATKRead
mateIsUnmapped() SAMRecordToGATKReadAdapter
MateOnSameContigOrNoMappedMateReadFilter() ReadFilterLibrary.MateOnSameContigOrNoMappedMateReadFilter
MathUtil picard.util
General math utilities
MathUtil.LogMath picard.util
A collection of common math operations that work with log values.
MathUtils org.broadinstitute.hellbender.utils
MathUtils is a static class (no instantiation allowed!) with some useful math methods.
MathUtils.IntToDoubleArrayFunction org.broadinstitute.hellbender.utils
MathUtils.RunningAverage org.broadinstitute.hellbender.utils
A utility class that computes on the fly average and standard deviation for a stream of numbers.
MATRIX_OUTPUT CollectIndependentReplicateMetrics
MATRIX_OUTPUT CrosscheckFingerprints
MatrixSummaryUtils org.broadinstitute.hellbender.utils
Static class for implementing some matrix summary stats that are not in Apache, Spark, etc
max() SVIntervalTree
Find the greatest interval in the tree.
max(SVInterval) SVIntervalTree
Find the latest interval in the tree less than or equal to the specified interval.
max() CountSet
Returns the largest integer value in the set.
max(GenomeLoc) GenomeLoc
Returns the maximum GenomeLoc of this and other
max(double[]) MathUtil
Returns the largest value stored in the array.
max(long[]) MathUtil
Returns the largest value stored in the array.
MAX_ADAPTER_MISMATCHES_LONG_NAME PSFilterArgumentCollection
MAX_ADAPTER_MISMATCHES_SHORT_NAME PSFilterArgumentCollection
MAX_ADVI_ITER_FIRST_EPOCH_LONG_NAME HybridADVIArgumentCollection
MAX_ADVI_ITER_SUBSEQUENT_EPOCHS_LONG_NAME HybridADVIArgumentCollection
MAX_ALIGN_LENGTH GATKSVVCFConstants
MAX_ALT_ALLELE_COUNT_LONG_NAME M2FiltersArgumentCollection
MAX_ALT_FRACTION_IN_NORMAL Mutect2Engine
MAX_ALT_HITS_LONG_NAME PSBwaArgumentCollection
MAX_ALT_HITS_SHORT_NAME PSBwaArgumentCollection
MAX_ALTERNATE_ALLELES 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.
MAX_APPARENT_BASES_PER_WINDOW KSWindowFinder
MAX_ASSEMBLY_LONG_NAME AssemblyRegionWalker
max_attempts VariantRecalibrator
The statistical model being built by this tool may fail due to simple statistical sampling
issues.
MAX_BASE_SCORE PreAdapterOrientationScorer
Defined by convention that the Phred quality score is 100.0, so this value ensures that the Phred calculation will
be 100.0.
MAX_BIAS_FACTORS_LONG_NAME GermlineDenoisingModelArgumentCollection
MAX_CALLING_ITERS_LONG_NAME HybridADVIArgumentCollection
MAX_CONTAMINATION_PROBABILITY_LONG_NAME M2FiltersArgumentCollection
MAX_COPY_NUMBER_LONG_NAME GermlineCallingArgumentCollection
MAX_DELETION_FRACTION UnifiedArgumentCollection
If the fraction of reads with deletions spanning a locus is greater than this value, the site will not be considered callable and will be skipped.
MAX_DIFF_RATE EstimateLibraryComplexityGATK
MAX_DIFF_RATE EstimateLibraryComplexity
MAX_DISCARD_FRACTION RevertSam
MAX_DUST_SCORE StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
MAX_EDIT_DISTANCE_TO_JOIN UmiAwareMarkDuplicatesWithMateCigar
MAX_ERROR_RATE ClippingUtility
The default value used for the maximum error rate when matching read bases to clippable sequence.
MAX_ERROR_RATE_PE MarkIlluminaAdapters
MAX_ERROR_RATE_SE MarkIlluminaAdapters
MAX_EVENTS_IN_REGION_LONG_NAME M2FiltersArgumentCollection
MAX_FAILED_REALIGNMENTS_LONG_NAME FilterAlignmentArtifacts
MAX_FILE_HANDLES_FOR_READ_ENDS_MAP MarkDuplicatesGATK
MAX_FILE_HANDLES_FOR_READ_ENDS_MAP MarkDuplicates
MAX_FILTER_SIZE BandPassActivityProfile
MAX_FRAGMENT_LENGTH_NAME ReadFilterArgumentDefinitions
MAX_FS FilterVcf
MAX_GATK_USABLE_Q_SCORE 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 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.
MAX_GERMLINE_POSTERIOR_LONG_NAME M2FiltersArgumentCollection
MAX_GROUP_RATIO EstimateLibraryComplexityGATK
MAX_GROUP_RATIO EstimateLibraryComplexity
MAX_INSERT_SIZE InsertSizeMetrics
The maximum measure insert size by alignment.
MAX_INSERT_SIZE CollectAlignmentSummaryMetrics
MAX_INSERT_SIZE InsertSizeMetrics
The maximum measure insert size by alignment.
MAX_INSERTIONS_OR_DELETIONS MergeBamAlignment
MAX_KMER_FREQ FindBadGenomicKmersSpark
MAX_MASKED_BASES_LONG_NAME PSFilterArgumentCollection
MAX_MASKED_BASES_SHORT_NAME PSFilterArgumentCollection
MAX_MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_LONG_NAME M2FiltersArgumentCollection
MAX_MISMATCH_RATE CollectRrbsMetrics
MAX_MISMATCHES ExtractIlluminaBarcodes
MAX_MNP_DISTANCE_LONG_NAME HaplotypeCallerArgumentCollection
MAX_MNP_DISTANCE_LONG_NAME M2ArgumentCollection
MAX_MNP_DISTANCE_SHORT_NAME HaplotypeCallerArgumentCollection
MAX_MNP_DISTANCE_SHORT_NAME M2ArgumentCollection
MAX_N_INDEL_INFORMATIVE_READS ReferenceConfidenceModel
MAX_NO_CALLS ExtractIlluminaBarcodes
MAX_NORMAL_QUAL_SUM Mutect2Engine
MAX_NUMBER_OF_VALUES_PER_HDF5_MATRIX HDF5Utils
MAX_OPEN_TEMP_FILES ValidateSamFile
MAX_OPTICAL_DUPLICATE_SET_SIZE AbstractOpticalDuplicateFinderCommandLineProgram
MAX_OUTPUT ValidateSamFile
MAX_PE_ERROR_RATE ClippingUtility
The default value used for the maximum error rate when matching paired end read bases to clippable sequence.
MAX_POPULATION_AF_LONG_NAME M2ArgumentCollection
MAX_POPULATION_AF_SHORT_NAME M2ArgumentCollection
MAX_POS AbstractIlluminaPositionFileReader
MAX_PROB_BELOW_ONE MathUtil
The double value closest to 1 while still being less than 1.
MAX_Q FastqToSam
MAX_QUAL QualityUtils
Maximum sense quality value.
MAX_READ_LENGTH EstimateLibraryComplexity
MAX_READ_LENGTH_ARG_NAME ReadFilterArgumentDefinitions
MAX_READS_IN_RAM_PER_TILE IlluminaBasecallsToFastq
MAX_READS_IN_RAM_PER_TILE IlluminaBasecallsToSam
MAX_REASONABLE_Q_SCORE QualityUtils
bams containing quals above this value are extremely suspicious and we should warn the user
MAX_RECALIBRATED_Q_SCORE RecalDatum
MAX_RECORDS_IN_RAM PicardCommandLineProgram
MAX_RECORDS_IN_RAM AbstractAlignmentMerger
MAX_RECORDS_IN_RAM CommandLineProgram
MAX_RECORDS_IN_RAM AbstractAlignmentMerger
MAX_RECORDS_TO_EXAMINE RevertOriginalBaseQualitiesAndAddMateCigar
MAX_SAM_QUAL_SCORE QualityUtils
Maximum quality score that can be encoded in a SAM/BAM file
MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP MarkDuplicatesGATK
If more than this many sequences in SAM file, don't spill to disk because there will not
be enough file handles.
MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 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 GetPileupSummaries
MAX_SITE_AF_SHORT_NAME GetPileupSummaries
MAX_SPLICES_TO_KEEP OverhangFixingManager
MAX_STARTS_LONG_NAME AssemblyRegionWalker
MAX_STRAND_ARTIFACT_PROBABILITY_LONG_NAME M2FiltersArgumentCollection
MAX_SUSPICIOUS_READS_PER_ALIGNMENT_START_LONG_NAME M2ArgumentCollection
MAX_TARGET_COVERAGE HsMetrics
The maximum coverage of reads that mapped to target regions of an experiment.
MAX_TARGET_COVERAGE TargetedPcrMetrics
The maximum coverage of reads that mapped to target regions of an experiment.
MAX_TARGET_COVERAGE TargetMetrics
The maximum coverage of reads that mapped to target regions of an experiment.
MAX_TO_MERGE ScatterIntervalsByNs
MAX_TRAINING_EPOCHS_LONG_NAME HybridADVIArgumentCollection
maxAdapterMismatches PSFilterArgumentCollection
maxAlternateHits PSBwaArgumentCollection
The maximum number of alternate alignments for each read, i.e.
maxAmbiguousBaseFraction AmbiguousBaseReadFilter
maxAmbiguousBases AmbiguousBaseReadFilter
maxAmbiguousBases PSFilterArgumentCollection
This is the threshold for filtering reads based on the number of 'N' values present in the sequence.
maxAssemblyRegionSize AssemblyRegionWalker
maxAssemblyRegionSize AssemblyRegionWalkerSpark
maxAssemblyRegionSize HaplotypeCallerSpark.ShardingArgumentCollection
maxCallableImpreciseVariantDeletionSize StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection
maxContaminationProbability M2FiltersArgumentCollection
maxDepthPerSample LocusWalker
maxDepthPerSample LocusWalkerSpark
maxDifference(List<Double>, List<Double>) MathUtils
Find the maximum difference between entries of two arrays.
maxDUSTScore StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
maxElementIndex(double[]) MathUtils
maxElementIndex(double[], int, int) MathUtils
maxElementIndex(double[], int) MathUtils
maxEnd() SVIntervalTree
Return the interval having the largest ending value.
maxEventsInRegion M2FiltersArgumentCollection
maxFASTQSize StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
maxFragmentLength FragmentLengthReadFilter
maxGermlinePosterior M2FiltersArgumentCollection
maxHaplotypeLength PairHMM
MAXIMUM_CHUNK_SIZE CreateReadCountPanelOfNormals
MAXIMUM_CYCLE_VALUE RecalibrationArgumentCollection
The cycle covariate will generate an error if it encounters a cycle greater than this value.
MAXIMUM_INSERT_SIZE CollectSequencingArtifactMetrics
MAXIMUM_INSERT_SIZE CollectOxoGMetrics
MAXIMUM_MAPPING_QUALITY_NAME ReadFilterArgumentDefinitions
MAXIMUM_NUMBER_OF_SEGMENTS_PER_CHROMOSOME_LONG_NAME ModelSegments
MAXIMUM_NUMBER_OF_SMOOTHING_ITERATIONS_LONG_NAME ModelSegments
MAXIMUM_STRONG_REF_GENOTYPE_PER_PLOIDY GenotypeLikelihoodCalculators
Maximum possible number of genotypes that this calculator can handle.
MAXIMUM_ZEROS_IN_INTERVAL_PERCENTAGE_LONG_NAME CreateReadCountPanelOfNormals
MAXIMUM_ZEROS_IN_SAMPLE_PERCENTAGE_LONG_NAME CreateReadCountPanelOfNormals
maximumAlleleIndex() GenotypeAlleleCounts
Returns the largest allele index present in the genotype.
maximumKeyValue() ContextCovariate
maximumKeyValue() Covariate
Returns the maximum value possible for any key representing this covariate
maximumKeyValue() CycleCovariate
maximumKeyValue() QualityScoreCovariate
maximumKeyValue() ReadGroupCovariate
maximumSpan AssemblyRegionTrimmer.Result
Maximum available range for the trimmed variant region.
maxMADTolerance InsertSizeMetricsArgumentCollection
maxMappingQualityScore MappingQualityReadFilter
maxMedianFragmentLengthDifference M2FiltersArgumentCollection
maxMnpDistance HaplotypeCallerArgumentCollection
Two or more phased substitutions separated by this distance or less are merged into MNPs.
maxMnpDistance M2ArgumentCollection
Two or more phased substitutions separated by this distance or less are merged into MNPs.
maxNumHaplotypesInPopulation ReadThreadingAssemblerArgumentCollection
The assembly graph can be quite complex, and could imply a very large number of possible haplotypes.
maxPopulationAlleleFrequency M2ArgumentCollection
In tumor-only mode, we discard variants with population allele frequencies greater than this threshold.
maxProbPropagationDistance AssemblyRegionWalker
maxProbPropagationDistance AssemblyRegionWalkerSpark
maxProbPropagationDistance HaplotypeCallerSpark.ShardingArgumentCollection
maxProbPropagationDistance ActivityProfile
maxQualityScore UnifiedArgumentCollection
maxReadLength ReadLengthReadFilter
maxReadLength PairHMM
maxReadsPerAlignmentStart AssemblyRegionWalker
maxReadsPerAlignmentStart AssemblyRegionWalkerSpark
maxReadsPerAlignmentStart HaplotypeCallerSpark.ShardingArgumentCollection
maxReasonableFragmentLength RealignmentArgumentCollection
Maximum fragment length to be considered a reasonable pair alignment
maxSuspiciousReadsPerAlignmentStart M2ArgumentCollection
Maximum number of suspicious reads (mediocre mapping quality or too many substitutions) allowed in a downsampling stride.
maxTrackedFragmentLength StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
maybeAdvance() PerTileParser
MDElement(int) TextMDCodec.MDElement
mean(int, boolean) VariantDataManager
mean(double...) MathUtils
mean(double[], int, int) MathUtils
Calculate the mean of an array of doubles.
mean() MathUtils.RunningAverage
mean(double...) MathUtil.LogMath
Computes the mean of the provided log values.
mean(double[], int, int) MathUtil
Calculated the mean of an array of doubles.
MEAN_AMPLICON_COVERAGE TargetedPcrMetrics
The mean read coverage of all amplicon regions in the experiment.
MEAN_BAIT_COVERAGE HsMetrics
The mean coverage of all baits in the experiment.
MEAN_BASE_QUALITY 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_STANDARD_DEVIATION_LONG_NAME GermlineContigPloidyModelArgumentCollection
MEAN_CLUSTERS_PER_TILE IlluminaBasecallingMetrics
The mean number of clusters per tile.
MEAN_COVERAGE CollectWgsMetrics.WgsMetrics
The mean coverage in bases of the genome territory, after all filters are applied.
MEAN_CPG_COVERAGE RrbsSummaryMetrics
Mean coverage of CpG sites
MEAN_INSERT_SIZE InsertSizeMetrics
The mean insert size of the "core" of the distribution.
MEAN_INSERT_SIZE InsertSizeMetrics
The mean insert size of the "core" of the distribution.
MEAN_PCT_PF_CLUSTERS_PER_TILE IlluminaBasecallingMetrics
The mean percentage of pf clusters per tile.
MEAN_PF_CLUSTERS_PER_TILE IlluminaBasecallingMetrics
The mean number of pf clusters per tile.
MEAN_PROBE_COVERAGE TargetMetrics
The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.
MEAN_READ_LENGTH AlignmentSummaryMetrics
The mean read length of the set of reads examined.
MEAN_TARGET_COVERAGE HsMetrics
The mean coverage of a target region.
MEAN_TARGET_COVERAGE TargetedPcrMetrics
The mean read coverage of all target regions in an experiment.
MEAN_TARGET_COVERAGE TargetMetrics
The mean coverage of targets.
MEAN_UMI_LENGTH UmiMetrics
Number of bases in each UMI
MeanQualityByCycle picard.analysis
Program to generate a data table and chart of mean quality by cycle from a
BAM file.
MeanQualityByCycle() MeanQualityByCycle
MeanQualityByCycleSpark 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() MeanQualityByCycleSpark
meanWeights() Dirichlet
median() IntHistogram.CDF
median() Histogram
median(double[]) MannWhitneyU
Finds or calculates the median value of a sorted array of double.
median(int[]) MathUtils
median(Collection<T>) MathUtils
Compute the median of a list of numbers
If values.length is even, this will be the middle value when the elements are sorted
If values.length is odd then it will be the mean of the two values closest to the middle.
median(double...) MathUtil
Calculate the median of an array of doubles.
MEDIAN_3PRIME_BIAS RnaSeqMetrics
The median 3 prime bias of the 1000 most highly expressed transcripts, where 3 prime bias is calculated per
transcript as: mean coverage of the 3 prime-most 100 bases divided by the mean coverage of the whole transcript.
MEDIAN_5PRIME_BIAS RnaSeqMetrics
The median 5 prime bias of the 1000 most highly expressed transcripts.
MEDIAN_5PRIME_TO_3PRIME_BIAS RnaSeqMetrics
The ratio of coverage at the 5 prime end to the 3 prime end based on the 1000 most highly expressed transcripts.
MEDIAN_ABSOLUTE_DEVIATION InsertSizeMetrics
The median absolute deviation of the distribution.
MEDIAN_ABSOLUTE_DEVIATION InsertSizeMetrics
The median absolute deviation of the distribution.
MEDIAN_BASE_QUALITY_FILTER_NAME GATKVCFConstants
MEDIAN_COVERAGE CollectWgsMetrics.WgsMetrics
The median coverage in bases of the genome territory, after all filters are applied.
MEDIAN_CPG_COVERAGE RrbsSummaryMetrics
Median coverage of CpG sites
MEDIAN_CV_COVERAGE RnaSeqMetrics
The median coefficient of variation (CV) or stdev/mean for coverage values of the 1000 most highly expressed transcripts.
MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_FILTER_NAME GATKVCFConstants
MEDIAN_INSERT_SIZE InsertSizeMetrics
The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.
MEDIAN_INSERT_SIZE InsertSizeMetrics
The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.
MEDIAN_MAPPING_QUALITY_FILTER_NAME GATKVCFConstants
MEDIAN_TARGET_COVERAGE HsMetrics
The median coverage of a target region.
MEDIAN_TARGET_COVERAGE TargetedPcrMetrics
The median coverage of reads that mapped to target regions of an experiment.
MEDIAN_TARGET_COVERAGE TargetMetrics
The median coverage of targets.
meetsMinMergableSequenceForEitherPrefixOrSuffix(int) SharedVertexSequenceSplitter
Does either the common suffix or prefix have at least minCommonSequence bases in it?
meetsMinMergableSequenceForPrefix(int) SharedVertexSequenceSplitter
Does the common prefix have at least minCommonSequence bases in it?
meetsMinMergableSequenceForSuffix(int) SharedVertexSequenceSplitter
Does the common suffix have at least minCommonSequence bases in it?
MENDEL_VIOLATION_LR_KEY GATKVCFConstants
MendelianViolation org.broadinstitute.hellbender.utils.samples
Class for the identification and tracking of mendelian violation.
MendelianViolation(double) MendelianViolation
MendelianViolation(double, boolean, boolean) MendelianViolation
MendelianViolationMetrics picard.vcf.MendelianViolations
Describes the type and number of mendelian violations found within a Trio.
MendelianViolationMetrics() MendelianViolationMetrics
MendelianViolationsByFamily picard.vcf.MendelianViolations
Created by farjoun on 6/25/16.
MendelianViolationsByFamily() MendelianViolationsByFamily
merge(FlagStat.FlagStatus) FlagStat.FlagStatus
merge(SeqGraph, SeqVertex) SharedSequenceMerger
Attempt to merge the incoming vertices of v
merge(List<VariantContext>, Locatable, Byte, boolean, boolean) ReferenceConfidenceVariantContextMerger
Merges VariantContexts from gVCFs into a single hybrid.
merge(GenomeLoc) GenomeLoc
Returns a new GenomeLoc that represents the entire span of this and that.
merge(T, T) GenomeLoc
Merges 2 *contiguous* locs into 1
merge(SortedSet<T>) GenomeLoc
Merges a list of *sorted* *contiguous* locs into 1
merge(MathUtils.RunningAverage) MathUtils.RunningAverage
merge(QualQuantizer.QualInterval) 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) CollectWgsMetrics.WgsMetrics
Merges the various PCT_EXC_* metrics.
merge(Collection<? extends MergeableMetricBase>) MergeableMetricBase
for a collection of MergeableMetricBase, merge them all into "this" one.
merge(MergeableMetricBase) MergeableMetricBase
Merge another metric into this one
merge(Fingerprint) Fingerprint
Merges the likelihoods from the supplied Fingerprint into the likelihoods for this fingerprint.
merge(FingerprintIdDetails) FingerprintIdDetails
merge(HaplotypeProbabilities) HaplotypeProbabilities
Merges in the likelihood information from the supplied haplotype probabilities object.
merge(HaplotypeProbabilities) HaplotypeProbabilitiesFromContaminatorSequence
merge(HaplotypeProbabilities) HaplotypeProbabilitiesFromGenotype
merge(HaplotypeProbabilities) HaplotypeProbabilitiesFromSequence
Merges information from another haplotype probabilities object for the same haplotype into
this object.
merge(HaplotypeProbabilities) HaplotypeProbabilityOfNormalGivenTumor
merge(ExtractIlluminaBarcodes.BarcodeMetric) ExtractIlluminaBarcodes.BarcodeMetric
Adds the non-calculated
merge(CollectHiSeqXPfFailMetrics.PFFailSummaryMetric) CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
Adds the non-calculated fields from the other metric to this one.
merge(Collection<CallingMetricAccumulator.Result>) CallingMetricAccumulator.Result
merge(Collection<RESULT>) VariantProcessor.ResultMerger
MERGE_FILTER_IN_ALL GATKVariantContextUtils
MERGE_FILTER_PREFIX GATKVariantContextUtils
MERGE_INTERSECTION GATKVariantContextUtils
MERGE_NEARBY_TARGETS BaitDesigner
MERGE_REF_IN_ALL GATKVariantContextUtils
MERGE_SEQUENCE_DICTIONARIES MergeSamFiles
MergeableMetricBase picard.analysis
An extension of MetricBase that knows how to merge-by-adding fields that are appropriately annotated.
MergeableMetricBase() MergeableMetricBase
MergeableMetricBase.MergeByAdding picard.analysis
Metrics whose values can be merged by adding.
MergeableMetricBase.MergeByAssertEquals picard.analysis
Metrics whose values should be equal when merging.
MergeableMetricBase.MergingIsManual picard.analysis
MergeableMetricBase.NoMergingIsDerived picard.analysis
MergeableMetricBase.NoMergingKeepsValue picard.analysis
Metrics that are not merged.
mergeAlignment(File) AbstractAlignmentMerger
/**
Merges the alignment data with the non-aligned records from the source BAM file.
mergeAlignment(File) SamAlignmentMerger
Merges the alignment from the map file with the non-aligned records from the source BAM file.
mergeAlignment(File) AbstractAlignmentMerger
Merges the alignment data with the non-aligned records from the source BAM file.
mergeAlignment(File) SamAlignmentMerger
Merges the alignment from the map file with the non-aligned records from the source BAM file.
mergeAndConvertTranches(TreeMap<Double, List<VQSLODTranche>>, List<Double>, VariantRecalibratorArgumentCollection.Mode) VQSLODTranche
mergeAndConvertTranches(List<VQSLODTranche>, VariantRecalibratorArgumentCollection.Mode) VQSLODTranche
MergeAnnotatedRegions org.broadinstitute.hellbender.tools.copynumber.utils
MergeAnnotatedRegions() MergeAnnotatedRegions
MergeBamAlignment picard.sam
Summary
MergeBamAlignment() MergeBamAlignment
mergedSampleName(String, String, boolean) GATKVariantContextUtils
mergeFingerprintsBy(Map<FingerprintIdDetails, Fingerprint>, Function<FingerprintIdDetails, String>) CrosscheckFingerprints
mergeIfCan(MergeableMetricBase) MergeableMetricBase
Merges another MergableMetricBase if possible
mergeIntervalLocations(List<GenomeLoc>, IntervalMergingRule) IntervalUtils
merge a list of genome locs that may be overlapping, returning the list of unique genomic locations
mergeListsBySetOperator(List<GenomeLoc>, List<GenomeLoc>, IntervalSetRule) IntervalUtils
merge two interval lists, using an interval set rule
mergeRegions(List<AnnotatedInterval>, SAMSequenceDictionary, String, Consumer<Locatable>) AnnotatedIntervalUtils
Merge AnnotatedIntervals by whether the regions overlap.
MergeSamFiles 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() MergeSamFiles
MergeVcfs picard.vcf
Combines multiple variant files into a single variant file.
MergeVcfs() MergeVcfs
mergeWithContiguous(Locatable) SimpleInterval
Returns a new SimpleInterval that represents the entire span of this and that.
mergeWithNewVCs(List<VariantContext>, ReferenceContext) 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.
Metadata org.broadinstitute.hellbender.tools.copynumber.formats.metadata
Interface for marking objects that contain metadata that can be represented as a SAMFileHeader.
metadata PileupSpark
This enables annotating the pileup to show overlaps with metadata from a Feature file(s).
metadata Pileup
This enables annotating the pileup to show overlaps with metadata from a Feature file(s).
Metadata.Type org.broadinstitute.hellbender.tools.copynumber.formats.metadata
metadataFile StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
MetadataUtils org.broadinstitute.hellbender.tools.copynumber.formats.metadata
MetagenomicsProgramGroup org.broadinstitute.hellbender.cmdline.programgroups
Tools that perform metagenomic analysis, e.g.
MetagenomicsProgramGroup() MetagenomicsProgramGroup
METRIC_ACCUMULATION_LEVEL CollectAlignmentSummaryMetrics
METRIC_ACCUMULATION_LEVEL CollectGcBiasMetrics
METRIC_ACCUMULATION_LEVEL CollectInsertSizeMetrics
METRIC_ACCUMULATION_LEVEL CollectMultipleMetrics
METRIC_ACCUMULATION_LEVEL CollectRnaSeqMetrics
METRIC_ACCUMULATION_LEVEL CollectRrbsMetrics
METRIC_ACCUMULATION_LEVEL CollectTargetedMetrics
METRIC_ACCUMULATION_LEVEL_LONG_NAME StandardArgumentDefinitions
METRIC_ACCUMULATION_LEVEL_SHORT_NAME StandardArgumentDefinitions
metricAccumulationLevel InsertSizeMetricsArgumentCollection
MetricAccumulationLevel org.broadinstitute.hellbender.metrics
For use with Picard metrics programs that may output metrics for multiple levels
of aggregation with an analysis.
MetricAccumulationLevel picard.analysis
For use with Picard metrics programs that may output metrics for multiple levels
of aggregation with an analysis.
MetricAccumulationLevelArgumentCollection org.broadinstitute.hellbender.cmdline.argumentcollections
MetricAccumulationLevelArgumentCollection() MetricAccumulationLevelArgumentCollection
metrics RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
METRICS MarkIlluminaAdapters
METRICS_FILE AbstractMarkDuplicatesCommandLineProgram
METRICS_FILE ExtractIlluminaBarcodes
METRICS_FILE DownsampleSam
METRICS_FILE AbstractMarkDuplicatesCommandLineProgram
METRICS_FILE_LONG_NAME StandardArgumentDefinitions
METRICS_FILE_PREFIX CollectRrbsMetrics
METRICS_FILE_SHORT_NAME StandardArgumentDefinitions
METRICS_FILE_SHORT_NAME StandardOptionDefinitions
MetricsArgumentCollection org.broadinstitute.hellbender.metrics
Base class for defining a set of metrics collector arguments.
MetricsArgumentCollection() MetricsArgumentCollection
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.CollectMultipleMetrics walker tool
- a standalone Spark tool
- the
CollectMultipleMetricsSpark tool
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 extends
MetricBase: defines the aggregate metrics that we're trying to collect
XMetricsArgumentCollection: defines parameters for XMetrics, extends
MetricsArgumentCollection
XMetricsCollector: processes a single read, and has a reduce/combiner
For multi level collectors, XMetricsCollector is composed of several classes:
XMetricsCollector extends
MultiLevelReducibleCollector<
XMetrics, HISTOGRAM_KEY, XMetricsCollectorArgs, XMetricsPerUnitCollector>
XMetricsPerUnitCollector: per level collector, implements
PerUnitMetricCollector (requires a combiner)
XMetricsCollectorArgs per-record argument (type argument for MultiLevelReducibleCollectorMetricsCollectorSpark
CollectXMetrics extends org.broadinstitute.hellbender.metrics.analysis.SinglePassSamProgram
CollectXMetricsSpark extends MetricsCollectorSparkTool
The 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() MetricsCollectorSparkTool
metricsFile MarkDuplicatesSpark
metricsFiles CompareMetrics
MetricsReadFilter 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() MetricsReadFilter
MetricsReadFilter(boolean, boolean) MetricsReadFilter
MetricsUtils org.broadinstitute.hellbender.metrics
Utility methods for dealing with MetricsFile and related classes.
MICROBE_BWA_IMAGE_LONG_NAME PSBwaArgumentCollection
MICROBE_BWA_IMAGE_SHORT_NAME PSBwaArgumentCollection
MICROBE_FASTA_LONG_NAME PSBwaArgumentCollection
MICROBE_FASTA_SHORT_NAME PSBwaArgumentCollection
MICROBE_MIN_SEED_LENGTH_LONG_NAME PSBwaArgumentCollection
MICROBE_MIN_SEED_LENGTH_SHORT_NAME PSBwaArgumentCollection
midpoint() SVInterval
MILLISECONDS_PER_MINUTE ProgressMeter
Number of milliseconds in a minute
MILLISECONDS_PER_SECOND ProgressMeter
Number of milliseconds in a second
min() SVIntervalTree
Find the least interval in the tree.
min(SVInterval) SVIntervalTree
Find the earliest interval in the tree greater than or equal to the specified interval.
min() CountSet
Returns the smallest integer value in the set.
min(double[]) MathUtil
Returns the smallest value stored in the array.
min(int[]) MathUtil
Returns the smallest value stored in the array.
min(short[]) MathUtil
Returns the smallest value stored in the array.
min(byte[]) MathUtil
Returns the smallest value stored in the array.
MIN_AB FilterVcf
MIN_ACCEPTABLE_LOD_SCORE VariantRecalibratorEngine
MIN_ADAPTER_LENGTH_LONG_NAME PSFilterArgumentCollection
MIN_ADAPTER_LENGTH_SHORT_NAME PSFilterArgumentCollection
MIN_ALLELE_FRACTION_FOR_GERMLINE_HOM_ALT Mutect2FilteringEngine
MIN_ASSEMBLY_LONG_NAME AssemblyRegionWalker
MIN_BASE_QUAL MarkDuplicatesScoringStrategy
MIN_BASE_QUALITY_DEFAULT_CUTOFF AnnotatePairOrientation
MIN_BASE_QUALITY_LONG_NAME PSFilterArgumentCollection
MIN_BASE_QUALITY_SCORE_LONG_NAME AssemblyBasedCallerArgumentCollection
MIN_BASE_QUALITY_SHORT_NAME PSFilterArgumentCollection
MIN_BASE_QUALTY_SCORE UnifiedArgumentCollection
The minimum confidence needed in a given base for it to be used in variant calling.
MIN_BASES_TO_SUSPECT_PCR_SLIPPAGE_LONG_NAME M2FiltersArgumentCollection
MIN_CLIPPED_READ_LENGTH_LONG_NAME PSFilterArgumentCollection
MIN_CLIPPED_READ_LENGTH_SHORT_NAME PSFilterArgumentCollection
MIN_COUNT AS_StrandBiasTest
MIN_DP FilterVcf
MIN_DP GenotypeConcordance
MIN_DP FindMendelianViolations
MIN_DP_FORMAT_KEY GATKVCFConstants
MIN_GQ FilterVcf
MIN_GQ GenotypeConcordance
MIN_GQ FindMendelianViolations
MIN_GROUP_COUNT EstimateLibraryComplexity
MIN_HET_FRACTION FindMendelianViolations
MIN_IDENTICAL_BASES EstimateLibraryComplexityGATK
MIN_IDENTICAL_BASES EstimateLibraryComplexity
MIN_INDEL_COUNT_FOR_GENOTYPING UnifiedArgumentCollection
A candidate indel is genotyped (and potentially called) if there are this number of reads with a consensus indel at a site.
MIN_INDEL_FRACTION_PER_SAMPLE UnifiedArgumentCollection
Complementary argument to minIndelCnt.
MIN_INDEL_SPACING_NAME RemoveNearbyIndels
MIN_INSERT_SIZE InsertSizeMetrics
The minimum measured insert size.
MIN_INSERT_SIZE InsertSizeMetrics
The minimum measured insert size.
MIN_LIFTOVER_PCT LiftOverIntervalList
MIN_MAPPING_QUALITY_LONG_NAME GetPileupSummaries
MIN_MAPPING_QUALITY_SHORT_NAME GetPileupSummaries
MIN_MATCH_BASES ClippingUtility
The default value used for the minimum number of contiguous bases to match against.
MIN_MATCH_BASES_PE MarkIlluminaAdapters
MIN_MATCH_BASES_SE MarkIlluminaAdapters
MIN_MATCH_PE_BASES ClippingUtility
The default value used for the minimum number of contiguous bases to match against in a paired end read
MIN_MEAN_QUALITY EstimateLibraryComplexityGATK
MIN_MEAN_QUALITY EstimateLibraryComplexity
MIN_MEDIAN_BASE_QUALITY_LONG_NAME M2FiltersArgumentCollection
MIN_MEDIAN_MAPPING_QUALITY_LONG_NAME M2FiltersArgumentCollection
MIN_MEDIAN_READ_POSITION_LONG_NAME M2FiltersArgumentCollection
MIN_MISMATCH_DELTA ExtractIlluminaBarcodes
MIN_NON_VIRUS_CONTIG_LENGTH_LONG_NAME PathSeqBuildReferenceTaxonomy
MIN_NON_VIRUS_CONTIG_LENGTH_SHORT_NAME PathSeqBuildReferenceTaxonomy
MIN_NUMBER_OF_EVENTS_TO_COMBINE_INTO_BLOCK_SUBSTITUTION EventMap
MIN_PHRED_SCALED_QUAL QualityUtils
MIN_POS 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_PVALUE AS_StrandBiasTest
MIN_Q FastqToSam
MIN_QD FilterVcf
MIN_READ_LENGTH_ARG_NAME ReadFilterArgumentDefinitions
MIN_SAMPLE_COUNT_LONG_NAME CreateSomaticPanelOfNormals
MIN_SAMPLES AS_InbreedingCoeff
MIN_SCORE_IDENTITY_LONG_NAME PSScoreArgumentCollection
MIN_SCORE_IDENTITY_SHORT_NAME PSScoreArgumentCollection
MIN_SITE_AF_LONG_NAME GetPileupSummaries
MIN_SITE_AF_SHORT_NAME GetPileupSummaries
MIN_STRAND_ARTIFACT_ALLELE_FRACTION_LONG_NAME M2FiltersArgumentCollection
MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION HaplotypeCallerEngine
MIN_TRAINING_EPOCHS_LONG_NAME HybridADVIArgumentCollection
MIN_UNCLIPPED_BASES MergeBamAlignment
MIN_USABLE_Q_SCORE QualityUtils
The lowest quality score for a base that is considered reasonable for statistical analysis.
MIN_VAL_COUNT ValidateBasicSomaticShortMutations
minAdapterLength PSFilterArgumentCollection
Adapter trimming will require a match of at least this length to a known adapter.
minAlignerScoreDifference RealignmentArgumentCollection
Minimum difference between best and second-best alignment for a read to be considered well-mapped
minAlignLength StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection
minAssemblyRegionSize AssemblyRegionWalker
minAssemblyRegionSize AssemblyRegionWalkerSpark
minAssemblyRegionSize HaplotypeCallerSpark.ShardingArgumentCollection
minBaseQuality ASEReadCounter
If this argument is enabled, bases with quality scores lower than this threshold will not be counted.
minBaseQualityScore AssemblyBasedCallerArgumentCollection
Bases with a quality below this threshold will not be used for calling.
minBaseQualityToUseInAssembly ReadThreadingAssembler
minBqCutoff ValidateBasicSomaticShortMutations
minCoherentEvidenceWeight StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
minDanglingBranchLength ReadThreadingAssemblerArgumentCollection
When constructing the assembly graph we are often left with "dangling" branches.
minDepthOfNonFilteredBases ASEReadCounter
If this argument is enabled, loci with total depth lower than this threshold after all filters have been applied
will be skipped.
minDistance(GenomeLoc) GenomeLoc
Return the minimum distance between any pair of bases in this and that GenomeLocs:
minEvidenceMapQ StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
minEvidenceMatchLength StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
minEvidenceWeight StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
MiniClusterUtils org.broadinstitute.hellbender.utils.test
Utilities to help manage a MiniDFSCluster for use in tests.
MiniClusterUtils() MiniClusterUtils
MiniClusterUtils.MiniClusterTest org.broadinstitute.hellbender.utils.test
An interface for writing tests that run on a minicluster.
minIdentity PSFilterArgumentCollection
Controls the stringency of read filtering based on alignment to the host reference.
minIdentity PSScoreArgumentCollection
This parameter controls the stringency of the microbe alignment.
MinimalGenotypingEngine 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(UnifiedArgumentCollection, SampleList, AFCalculatorProvider) MinimalGenotypingEngine
Creates a new unified genotyping given the UG configuration parameters and the targeted set of samples
MinimalGenotypingEngine(UnifiedArgumentCollection, SampleList, AFCalculatorProvider, boolean) MinimalGenotypingEngine
Creates a new unified genotyping given the UG configuration parameters and the targeted set of samples
MinimalVariant org.broadinstitute.hellbender.utils.variant
MinimalVariant is a minimal implementation of the
GATKVariant interface.
MinimalVariant(SimpleInterval, boolean, boolean) MinimalVariant
MINIMUM_BAITS_PER_TARGET BaitDesigner
MINIMUM_BARCODE_BQ CollectIndependentReplicateMetrics
MINIMUM_BASE_QUALITY Mutect2Engine
MINIMUM_BASE_QUALITY CollectWgsMetrics
MINIMUM_BASE_QUALITY CollectTargetedMetrics
MINIMUM_BASE_QUALITY ExtractIlluminaBarcodes
MINIMUM_BASE_QUALITY_LONG_NAME CollectAllelicCounts
MINIMUM_BQ CollectIndependentReplicateMetrics
MINIMUM_DISTANCE MarkDuplicatesWithMateCigar
MINIMUM_GENOME_FRACTION CollectGcBiasMetrics
MINIMUM_GQ CollectIndependentReplicateMetrics
MINIMUM_INSERT_SIZE CollectSequencingArtifactMetrics
MINIMUM_INSERT_SIZE CollectOxoGMetrics
MINIMUM_INTERVAL_MEDIAN_PERCENTILE_LONG_NAME CreateReadCountPanelOfNormals
MINIMUM_LENGTH CollectRnaSeqMetrics
MINIMUM_LOD_SHORT_NAME StandardOptionDefinitions
MINIMUM_MAPPING_QUALITY CollectSequencingArtifactMetrics
MINIMUM_MAPPING_QUALITY CollectJumpingLibraryMetrics
MINIMUM_MAPPING_QUALITY CollectOxoGMetrics
MINIMUM_MAPPING_QUALITY CollectWgsMetrics
MINIMUM_MAPPING_QUALITY CollectTargetedMetrics
MINIMUM_MAPPING_QUALITY_NAME ReadFilterArgumentDefinitions
MINIMUM_MAPPING_QUALITY_SHORT_NAME StandardOptionDefinitions
MINIMUM_MQ CollectIndependentReplicateMetrics
MINIMUM_NUM_READS_FOR_SIGNAL_COUNT PowerCalculationUtils
MINIMUM_PCT CollectInsertSizeMetrics
MINIMUM_QUALITY ExtractIlluminaBarcodes
MINIMUM_QUALITY IlluminaBasecallsToFastq
MINIMUM_QUALITY IlluminaBasecallsToSam
MINIMUM_QUALITY_SCORE CollectSequencingArtifactMetrics
MINIMUM_QUALITY_SCORE CollectOxoGMetrics
MINIMUM_READ_LENGTH CollectRrbsMetrics
MINIMUM_TOTAL_ALLELE_COUNT_LONG_NAME ModelSegments
minimumAlleleIndex() GenotypeAlleleCounts
Returns the smallest allele index present in the genotype.
minimumPct InsertSizeMetricsArgumentCollection
minimumSequenceLength OverclippedReadFilter
minIndex(int...) MathUtils
minKmerLength(Collection<byte[]>) GraphUtils
Get the minimum length of a collection of byte[]
minKmersPerInterval StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
minMappingQuality ASEReadCounter
If this argument is enabled, reads with mapping quality values lower than this threshold will not be counted.
minMappingQualityScore MappingQualityReadFilter
minMedianBaseQuality M2FiltersArgumentCollection
minMedianMappingQuality M2FiltersArgumentCollection
minMedianReadPosition M2FiltersArgumentCollection
minNonVirusContigLength PathSeqBuildReferenceTaxonomy
Sequences from non-virus organisms less than this length will be filtered out such that any reads aligning to them will
be ignored.
minObservationsForKmerToBeSolid ReadThreadingAssemblerArgumentCollection
MINOR_ALLELE_FRACTION_PRIOR_ALPHA_LONG_NAME ModelSegments
MINOR_ALLELE_FRACTION_STEP_SIZE CalculateContamination
MinorAlleleFractionRecord org.broadinstitute.hellbender.tools.walkers.contamination
Created by David Benjamin on 2/13/17.
MinorAlleleFractionRecord(SimpleInterval, double) MinorAlleleFractionRecord
minOverlapper(SVInterval) SVIntervalTree
Find the earliest interval in the tree that overlaps the specified interval.
minPcrSlippageBases M2FiltersArgumentCollection
minPower UnifiedArgumentCollection
minPruneFactor ReadThreadingAssemblerArgumentCollection
Paths with fewer supporting kmers than the specified threshold will be pruned from the graph.
minQualityScore UnifiedArgumentCollection
The following argument are for debug-only tweaks when running generalized ploidy with a reference sample
minReadLength ReadLengthReadFilter
minReadLength PSFilterArgumentCollection
Reads are trimmed based on base call quality and low-complexity content.
minSeedLength PSFilterArgumentCollection
Controls the sensitivity of BWA alignment to the host reference.
minSeedLength RealignmentArgumentCollection
BWA-mem minimum seed length
MisencodedBaseQualityReadTransformer 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() MisencodedBaseQualityReadTransformer
MisencodedQualityScoresRead(GATKRead, String) UserException.MisencodedQualityScoresRead
MismatchCount() AlignmentUtils.MismatchCount
mismatches AlignmentInterval
MISMATCHES_CONTEXT_SIZE RecalibrationArgumentCollection
The context covariate will use a context of this size to calculate its covariate value for base mismatches.
MISMATCHES_DEFAULT_QUALITY RecalibrationArgumentCollection
A default base qualities to use as a prior (reported quality) in the mismatch covariate model.
MismatchMDElement() TextMDCodec.MismatchMDElement
mismatchQualities AlignmentUtils.MismatchCount
MISSING_SITES_HOM_REF GenotypeConcordance
MISSING_VAL_LONG_NAME VariantFiltration
MissingContigInSequenceDictionary(String, SAMSequenceDictionary) UserException.MissingContigInSequenceDictionary
MissingIndex(String, String) UserException.MissingIndex
MissingReadField(String) GATKException.MissingReadField
MissingReadField(String, String) GATKException.MissingReadField
MissingReadField(String, GATKRead) GATKException.MissingReadField
MissingReference(String) UserException.MissingReference
MissingReferenceDictFile(Path, Path) UserException.MissingReferenceDictFile
MissingReferenceDictFile(String) UserException.MissingReferenceDictFile
MissingReferenceFaiFile(Path, Path) UserException.MissingReferenceFaiFile
MIXING_FRACTIONS_TABLE_NAME AnnotateVcfWithExpectedAlleleFraction
MixingFraction org.broadinstitute.hellbender.tools.walkers.validation
Simple class for storing a sample and its mixing fraction within a pooled bam.
MixingFraction(String, double) MixingFraction
MLE_ALLELE_COUNT_KEY GATKVCFConstants
MLE_ALLELE_FREQUENCY_KEY GATKVCFConstants
MLE_PER_SAMPLE_ALLELE_COUNT_KEY GATKVCFConstants
MLE_PER_SAMPLE_ALLELE_FRACTION_KEY GATKVCFConstants
mLogLikelihoodArray PairHMM
MMapBackedIteratorFactory 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() MMapBackedIteratorFactory
MODE 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 ValidateSamFile
MODE_INSERT_SIZE InsertSizeMetrics
The MODE insert size of all paired end reads where both ends mapped to the same chromosome.
model() ForwardBackwardAlgorithm.Result
Returns the model passed to the forward-backward algorithm.
MODEL_LONG_NAME CopyNumberStandardArgument
MODEL_PATH_SUFFIX DetermineGermlineContigPloidy
MODEL_PATH_SUFFIX GermlineCNVCaller
MODEL_SHARD_PATH_LONG_NAME PostprocessGermlineCNVCalls
ModeledSegment org.broadinstitute.hellbender.tools.copynumber.formats.records
ModeledSegment(SimpleInterval, int, int, ModeledSegment.SimplePosteriorSummary, ModeledSegment.SimplePosteriorSummary) ModeledSegment
ModeledSegment.SimplePosteriorSummary org.broadinstitute.hellbender.tools.copynumber.formats.records
ModeledSegmentCollection org.broadinstitute.hellbender.tools.copynumber.formats.collections
ModeledSegmentCollection(File) ModeledSegmentCollection
ModeledSegmentCollection(SampleLocatableMetadata, List<ModeledSegment>) ModeledSegmentCollection
ModelSegments org.broadinstitute.hellbender.tools.copynumber
Models segmented copy ratios from denoised read counts and segmented minor-allele fractions from allelic counts.
ModelSegments() ModelSegments
MOLECULAR_BARCODE_NAME IlluminaBasecallingMetrics
The barcode name for which the metrics were calculated.
MOLECULAR_BARCODE_SEQUENCE_1 IlluminaBasecallingMetrics
The barcode sequence for which the metrics were calculated.
MOLECULAR_INDEX_BASE_QUALITY_TAG IlluminaBasecallsToSam
MOLECULAR_INDEX_TAG IlluminaBasecallsToSam
molecularBarcode ReadStructure
MolecularIndex ReadType
MostDistantPrimaryAlignmentSelectionStrategy 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() MostDistantPrimaryAlignmentSelectionStrategy
MostDistantPrimaryAlignmentSelectionStrategy 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() MostDistantPrimaryAlignmentSelectionStrategy
MOTHER MendelianViolationMetrics
The ID of the mother within the trio.
mpileup CheckPileup
This is the existing mpileup against which we'll compare GATK's internal pileup at each genome position in the desired interval.
msBetweenCallsToRead SeekableByteChannelPrefetcher
msCopyingData SeekableByteChannelPrefetcher
msWaitingForData SeekableByteChannelPrefetcher
MTAC Mutect2
MTFAC FilterMutectCalls
MULTIALLELIC_FILTER_NAME GATKVCFConstants
MultiDeBruijnVertex org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
A DeBruijnVertex that supports multiple copies of the same kmer
MultiDeBruijnVertex(byte[], boolean) MultiDeBruijnVertex
Create a new MultiDeBruijnVertex with kmer sequence
MultiDeBruijnVertex(byte[]) MultiDeBruijnVertex
Create a new MultiDeBruijnVertex with kmer sequence
MultidimensionalKernelSegmenter org.broadinstitute.hellbender.tools.copynumber.segmentation
Segments copy-ratio and alternate-allele-fraction data using kernel segmentation.
MultidimensionalKernelSegmenter(CopyRatioCollection, AllelicCountCollection) MultidimensionalKernelSegmenter
MultidimensionalModeller org.broadinstitute.hellbender.tools.copynumber.models
Represents a segmented model for copy ratio and allele fraction.
MultidimensionalModeller(MultidimensionalSegmentCollection, CopyRatioCollection, AllelicCountCollection, AlleleFractionPrior, int, int, int, int) 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.
MultidimensionalSegment org.broadinstitute.hellbender.tools.copynumber.formats.records
MultidimensionalSegment(SimpleInterval, int, int, double) MultidimensionalSegment
MultidimensionalSegment(SimpleInterval, List<CopyRatio>, List<AllelicCount>) MultidimensionalSegment
MultidimensionalSegment(SimpleInterval, Comparator<Locatable>, OverlapDetector<CopyRatio>, OverlapDetector<AllelicCount>) MultidimensionalSegment
MultidimensionalSegmentCollection org.broadinstitute.hellbender.tools.copynumber.formats.collections
MultidimensionalSegmentCollection(File) MultidimensionalSegmentCollection
MultidimensionalSegmentCollection(SampleLocatableMetadata, List<MultidimensionalSegment>) MultidimensionalSegmentCollection
MultiHitAlignedReadIterator org.broadinstitute.hellbender.utils.read.mergealignment
Iterate over queryname-sorted SAM, and return each group of reads with the same queryname.
MultiIntervalLocalReadShard org.broadinstitute.hellbender.engine
A class to represent shards of read data spanning multiple intervals.
MultiIntervalLocalReadShard(List<SimpleInterval>, int, ReadsDataSource) 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) 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 java.lang.Comparable<HISTOGRAM_KEY >,ARGTYPE > - Class in org.broadinstitute.hellbender.metrics
MultiLevelCollector handles accumulating Metrics at different MetricAccumulationLevels(ALL_READS, SAMPLE, LIBRARY, READ_GROUP).
MultiLevelCollector() MultiLevelCollector
MultiLevelCollector METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,Histogram_KEY extends java.lang.Comparable,ARGTYPE > - Class in picard.metrics
MultiLevelCollector handles accumulating Metrics at different MetricAccumulationLevels(ALL_READS, SAMPLE, LIBRARY, READ_GROUP).
MultiLevelCollector() MultiLevelCollector
MultiLevelMetrics org.broadinstitute.hellbender.metrics
MultiLevelMetrics() MultiLevelMetrics
MultilevelMetrics picard.metrics
MultilevelMetrics() MultilevelMetrics
MultiLevelReducibleCollector METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,HISTOGRAM_KEY extends java.lang.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() MultiLevelReducibleCollector
multipleAtWhichToBreakBands CombineGVCFs
To reduce file sizes our gVCFs group similar reference positions into bands.
MULTIPLEX_PARAMS IlluminaBasecallsToFastq
multiply(double[], double[]) MathUtil
Calculates the product of two arrays of the same length.
MultiSampleEdge 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) MultiSampleEdge
Create a new MultiSampleEdge with weight multiplicity and, if isRef == true, indicates a path through the reference
MultiThreadedChunkBased(int, VariantIteratorProducer, VariantProcessor.AccumulatorGenerator<A, R>) VariantAccumulatorExecutor.MultiThreadedChunkBased
multithreadingBy(int) VariantProcessor.Builder
MultiTileBclFileFaker picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
MultiTileBclFileFaker() MultiTileBclFileFaker
MultiTileBclFileUtil picard.illumina.parser
NextSeq-style bcl's have all tiles for a cycle in a single file.
MultiTileBclParser picard.illumina.parser
Parse .bcl.bgzf files that contain multiple tiles in a single file.
MultiTileBclParser(File, int, CycleIlluminaFileMap, OutputMapping, boolean, BclQualityEvaluationStrategy, TileIndex) 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.
MultiTileFilterParser picard.illumina.parser
Read filter file that contains multiple tiles in a single file.
MultiTileFilterParser(TileIndex, List<Integer>, File) MultiTileFilterParser
MultiTileLocsFileFaker picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
MultiTileLocsFileFaker() MultiTileLocsFileFaker
MultiTileLocsParser picard.illumina.parser
Read locs file that contains multiple tiles in a single file.
MultiTileLocsParser(TileIndex, List<Integer>, File, int) 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>) MultiTileParser
MultiVariantDataSource 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) MultiVariantDataSource
Creates a MultiVariantDataSource backed by the provided FeatureInputs.
MultiVariantDataSource(List<FeatureInput<VariantContext>>, int, int, int, Path) MultiVariantDataSource
Creates a MultiVariantDataSource backed by the provided FeatureInputs.
MultiVariantWalker 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() MultiVariantWalker
MultiVariantWalkerGroupedOnStart 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() MultiVariantWalkerGroupedOnStart
Mutect2 org.broadinstitute.hellbender.tools.walkers.mutect
Call somatic short variants via local assembly of haplotypes.
Mutect2() Mutect2
Mutect2Engine org.broadinstitute.hellbender.tools.walkers.mutect
Created by davidben on 9/15/16.
Mutect2Engine(M2ArgumentCollection, boolean, boolean, SAMFileHeader, String, VariantAnnotatorEngine) Mutect2Engine
Create and initialize a new HaplotypeCallerEngine given a collection of HaplotypeCaller arguments, a reads header,
and a reference file
Mutect2FilteringEngine org.broadinstitute.hellbender.tools.walkers.mutect
Created by David Benjamin on 9/15/16.
Mutect2FilteringEngine(M2FiltersArgumentCollection, String) Mutect2FilteringEngine
MUTECT_FILTER_NAMES GATKVCFConstants
MutectDownsampler org.broadinstitute.hellbender.utils.downsampling
MutectDownsampler(int, int, int) MutectDownsampler
P_ACTIVE_LONG_NAME GermlineCallingArgumentCollection
P_ALT_LONG_NAME GermlineCallingArgumentCollection
P_ARTIFACT_FIELD_NAME OrientationBiasFilterConstants
P_VALUE_FOR_NOISE PowerCalculationUtils
PACKED_STRING_REP_SEPARATOR AlignmentInterval
paddedHaplotypeLength PairHMM
paddedMaxHaplotypeLength PairHMM
paddedMaxReadLength PairHMM
paddedReadLength PairHMM
padding AssemblyRegionTrimmer.Result
Required padding around the variant trimming region.
PADDING BaitDesigner
PADDING IntervalListTools
PADDING_IN_BP_LONG_NAME TagGermlineEvents
PADDING_LONG_NAME PreprocessIntervals
Pair org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
Class representing a pair of reads together with accompanying optical duplicate marking information.
Pair(GATKRead, GATKRead, SAMFileHeader, int, MarkDuplicatesScoringStrategy) Pair
Pair.Serializer org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
Serializers for each subclass of PairedEnds which rely on implementations of serializations within each class itself
PAIR_ORIENTATION InsertSizeMetrics
The pair orientation of the reads in this data category.
PAIR_ORIENTATION InsertSizeMetrics
The pair orientation of the reads in this data category.
PAIRED ReadFilterLibrary
PAIRED_INPUT_LONG_NAME PathSeqBwaSpark
PAIRED_INPUT_LONG_NAME PathSeqScoreSpark
PAIRED_INPUT_SHORT_NAME PathSeqBwaSpark
PAIRED_INPUT_SHORT_NAME PathSeqScoreSpark
PAIRED_OUTPUT_LONG_NAME PathSeqBwaSpark
PAIRED_OUTPUT_LONG_NAME PathSeqFilterSpark
PAIRED_OUTPUT_SHORT_NAME PathSeqBwaSpark
PAIRED_OUTPUT_SHORT_NAME PathSeqFilterSpark
PAIRED_RUN BamToBfq
PAIRED_RUN MarkIlluminaAdapters
PAIRED_RUN MergeBamAlignment
Deprecated.
PairedEnds org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
Struct-like class to store information about the paired reads for mark duplicates.
pairedInput PathSeqScoreSpark
PairedReadFilter() ReadFilterLibrary.PairedReadFilter
PairedStrandedIntervals org.broadinstitute.hellbender.tools.spark.sv.utils
PairedStrandedIntervals(StrandedInterval, StrandedInterval) PairedStrandedIntervals
PairedStrandedIntervalTree V > - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
PairedStrandedIntervalTree() PairedStrandedIntervalTree
PairedStrandedIntervalTree(Kryo, Input) PairedStrandedIntervalTree
PairedStrandedIntervalTree.PairedStrandedIntervalTreeIterator org.broadinstitute.hellbender.tools.spark.sv.utils
PairedStrandedIntervalTree.PairedStrandedIntervalTreeOverlapperIterator org.broadinstitute.hellbender.tools.spark.sv.utils
PairedStrandedIntervalTree.Serializer T > - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
PairedStrandedIntervalTreeOverlapperIterator(PairedStrandedIntervalTree<V>, PairedStrandedIntervals) PairedStrandedIntervalTree.PairedStrandedIntervalTreeOverlapperIterator
PairedVariantSubContextIterator 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) PairedVariantSubContextIterator
PairedVariantSubContextIterator.VcfTuple picard.vcf
Little class to hold a pair of VariantContexts that are in sync with one another.
pairHMM UnifiedArgumentCollection
The PairHMM implementation to use for -glm INDEL genotype likelihood calculations.
pairHMM LikelihoodEngineArgumentCollection
The PairHMM implementation to use for genotype likelihood calculations.
PairHMM org.broadinstitute.hellbender.utils.pairhmm
Class for performing the pair HMM for local alignment.
PairHMM() PairHMM
PairHMM.Implementation org.broadinstitute.hellbender.utils.pairhmm
pairHMMComputeTime PairHMM
PairHMMLikelihoodCalculationEngine org.broadinstitute.hellbender.tools.walkers.haplotypecaller
PairHMMLikelihoodCalculationEngine(byte, PairHMMNativeArguments, PairHMM.Implementation, double, PairHMMLikelihoodCalculationEngine.PCRErrorModel) PairHMMLikelihoodCalculationEngine
Create a new PairHMMLikelihoodCalculationEngine using provided parameters and hmm to do its calculations
PairHMMLikelihoodCalculationEngine(byte, PairHMMNativeArguments, PairHMM.Implementation, double, PairHMMLikelihoodCalculationEngine.PCRErrorModel, byte) PairHMMLikelihoodCalculationEngine
Create a new PairHMMLikelihoodCalculationEngine using provided parameters and hmm to do its calculations
PairHMMLikelihoodCalculationEngine.PCRErrorModel org.broadinstitute.hellbender.tools.walkers.haplotypecaller
PairHMMModel org.broadinstitute.hellbender.utils.pairhmm
Helper class that implement calculations required to implement the PairHMM Finite State Automation (FSA) model.
pairHMMNativeArgs LikelihoodEngineArgumentCollection
PairHMMNativeArgumentCollection org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Arguments for native PairHMM implementations
PairHMMNativeArgumentCollection() PairHMMNativeArgumentCollection
PANEL_OF_NORMALS_LONG_NAME M2ArgumentCollection
PANEL_OF_NORMALS_SHORT_NAME M2ArgumentCollection
ParallelCopyGCSDirectoryIntoHDFSSpark org.broadinstitute.hellbender.tools.spark
Parallel copy a file or directory from Google Cloud Storage into the HDFS file system used by Spark
ParallelCopyGCSDirectoryIntoHDFSSpark() ParallelCopyGCSDirectoryIntoHDFSSpark
Parameter T extends java.lang.Enum<T > & ParameterEnum ,U > - Class in org.broadinstitute.hellbender.utils.mcmc
Parameter(T, U) Parameter
PARAMETER_DOC ReadStructure
ParameterDecileCollection T extends java.lang.Enum<T > & ParameterEnum > - Class in org.broadinstitute.hellbender.tools.copynumber.formats.collections
ParameterDecileCollection(SampleMetadata, Map<T, DecileCollection>, Class<T>) ParameterDecileCollection
ParameterDecileCollection(File, Class<T>) ParameterDecileCollection
ParameterEnum org.broadinstitute.hellbender.utils.mcmc
ParameterizedFileUtil picard.illumina.parser
ParameterizedFileUtil(boolean, String, File, FileFaker, int, boolean) ParameterizedFileUtil
ParameterizedFileUtil(boolean, String, File, FileFaker, int) ParameterizedFileUtil
ParameterizedFileUtil(String, String, File, FileFaker, int) ParameterizedFileUtil
ParameterizedModel V1 extends java.lang.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 java.lang.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 org.broadinstitute.hellbender.utils.mcmc
ParameterizedState T extends java.lang.Enum<T > & ParameterEnum > - Class in org.broadinstitute.hellbender.utils.mcmc
Represents a mapped collection of
Parameter objects, i.e., named, ordered, enumerated keys associated with
values of mixed type via a key -> key, value map.
ParameterizedState(List<Parameter<T, ?>>) ParameterizedState
ParameterizedState(ParameterizedState<T>) ParameterizedState
Copy constructor.
ParameterReader T extends java.lang.Enum<T > & ParameterEnum > - Class in org.broadinstitute.hellbender.utils.mcmc
ParameterReader(File, Class<T>) ParameterReader
ParameterSampler U ,V extends java.lang.Enum<V > & ParameterEnum ,S extends ParameterizedState <V >,T extends DataCollection > - Interface in org.broadinstitute.hellbender.utils.mcmc
ParameterTableColumn org.broadinstitute.hellbender.utils.mcmc
ParameterWriter T extends java.lang.Enum<T > & ParameterEnum > - Class in org.broadinstitute.hellbender.utils.mcmc
ParameterWriter(File, String) ParameterWriter
ParamUtils 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) PedReader
parse(String, EnumSet<PedReader.MissingPedField>, SampleDB) PedReader
parse(Reader, EnumSet<PedReader.MissingPedField>, SampleDB) PedReader
parseArgs(String[]) CommandLineProgram
Parse arguments and initialize any values annotated with Argument
parseArgs(String[]) CommandLineProgram
parseArgsForConfigSetup(String[]) 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) SAMPileupCodec
parseCatalog(BufferedReader, Map<String, Tuple2<String, Long>>, Map<Integer, PSPathogenReferenceTaxonProperties>, boolean, Set<String>) PSBuildReferenceTaxonomyUtils
Builds maps of reference contig accessions to their taxonomic ids and vice versa.
parseCommaDelimitedArgList(String) PSUtils
parseFilterLowerLimit(String) ApplyVQSR
parseGenomeLoc(String) 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
parseIntervalArguments(GenomeLocParser, List<String>) IntervalUtils
Turns a set of strings describing intervals into a parsed set of intervals.
parseIntervalArguments(GenomeLocParser, String) IntervalUtils
parseMask(String, int) PSUtils
Parses command-line option for specifying kmer spacing masks
parseMDString(String) TextMDCodec
parseMissingFieldTags(Object, List<String>) PedReader
Parses a list of tags from the command line, assuming it comes from the GATK Engine
tags, and returns the corresponding EnumSet.
parseNameForReport() Covariate
Returns the names of the covariate, which is the simple class name without the "Covariate" part;
parseNamesFile(BufferedReader, Map<Integer, PSPathogenReferenceTaxonProperties>) PSBuildReferenceTaxonomyUtils
Parses scientific name of each taxon and puts it in taxIdToProperties
parseNodesFile(BufferedReader, Map<Integer, PSPathogenReferenceTaxonProperties>) PSBuildReferenceTaxonomyUtils
Gets the rank and parent of each taxon.
parseOneContig(AlignedContig, SAMSequenceDictionary, boolean, int, int, boolean) DiscoverVariantsFromContigAlignmentsSAMSpark
Parse all alignment records for a single locally-assembled contig and generate chimeric alignments if available.
parsePlatformForRead(GATKRead, SAMFileHeader, RecalibrationArgumentCollection) 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) PosteriorProbabilitiesUtils
parsePosteriorsIntoProbSpace(Genotype) PosteriorProbabilitiesUtils
parseRawDataString(ReducibleAnnotationData<Histogram>) AS_RankSumTest
parseRawDataString(ReducibleAnnotationData<Double>) AS_RMSMappingQuality
parseRawDataString(ReducibleAnnotationData<List<Integer>>) AS_StrandBiasTest
parseRawDataString(ReducibleAnnotationData<Number>) RMSMappingQuality
parseReadsAndOptionallySplitGappedAlignments(Iterable<SAMRecord>, int, boolean) SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SAMFormattedContigAlignmentParser
Iterates through the input noSecondaryAlignments, which are assumed to contain no secondary alignment (i.e.
parseReferenceRecords(List<SAMSequenceRecord>, Map<Integer, PSPathogenReferenceTaxonProperties>) PSBuildReferenceTaxonomyUtils
Build set of accessions contained in the reference.
parseTileMetrics(File, Map<Integer, File>, ReadStructure, ValidationStringency) TileMetricsUtil
parseTileMetrics(File, ReadStructure, ValidationStringency) TileMetricsUtil
Returns an unmodifiable collection of tile data read from the provided file.
parseTrainingSets(FeatureContext, VariantContext, VariantDatum, boolean) VariantDataManager
PartitionBounds(int, int, int, int, int) ReadMetadata.PartitionBounds
PartitionCrossingChecker 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() PartitionCrossingChecker
A constructor that will always report onBoundary to be false.
PartitionCrossingChecker(int, ReadMetadata, int) PartitionCrossingChecker
A constructor from the metadata with a specified boundary width.
partitionIndex MarkDuplicatesSparkRecord
PartitionStatistics(Iterator<GATKRead>, SVReadFilter, int, Map<String, String>) ReadMetadata.PartitionStatistics
PASS_FILTER FilterApplyingVariantIterator
The "PASS"ing filter String.
PASSES_VENDOR_QUALITY_CHECK ReadFilterLibrary
passesCallThreshold(double) GenotypingEngine
passesEmitThreshold(double, boolean) GenotypingEngine
passesMinimumThreshold(ReducibleAnnotationData<List<Integer>>, int) AS_StrandBiasTest
Does this strand data array pass the minimum threshold for inclusion?
passesMinimumThreshold(int[], int) StrandBiasTest
Does this strand data array pass the minimum threshold for inclusion?
PassesVendorQualityCheckReadFilter() ReadFilterLibrary.PassesVendorQualityCheckReadFilter
Passthrough 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.
PassThroughDownsampler 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() PassThroughDownsampler
path() KBestHaplotype
Returns the path across the original graph that correspond to the solution haplotype.
Path T 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(T, BaseGraph<T, E>) Path
Create a new Path containing no edges and starting at initialVertex
Path(Path<T, E>, E) Path
Create a new Path extending p with edge
Path(E, Path<T, E>) Path
Prepend a path with an edge.
pathExists(JavaSparkContext, Path) SparkUtils
Determine if the targetPath exists.
PathHelper picard.nio
A class who's purpose is to initialize the various plugins that provide Path support.
PathHelper.PathProviders picard.nio
PathLineIterator org.broadinstitute.hellbender.utils.nio
Iterate through the lines of a Path.
PathLineIterator(Path) 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.
PATHS RuntimeUtils
pathsAreTheSame(Path<T, E>) Path
Check that two paths have the same edges and total score
PathSeqBuildKmers org.broadinstitute.hellbender.tools.spark.pathseq
Produce a set of k-mers from the given host reference.
PathSeqBuildKmers() PathSeqBuildKmers
PathSeqBuildReferenceTaxonomy org.broadinstitute.hellbender.tools.spark.pathseq
Build an annotated taxonomy datafile for a given microbe reference.
PathSeqBuildReferenceTaxonomy() PathSeqBuildReferenceTaxonomy
PathSeqBwaSpark org.broadinstitute.hellbender.tools.spark.pathseq
Align reads to a microbe reference using BWA-MEM and Spark.
PathSeqBwaSpark() PathSeqBwaSpark
PathSeqFilterSpark org.broadinstitute.hellbender.tools.spark.pathseq
Filters low complexity, low quality, duplicate, and host reads.
PathSeqFilterSpark() PathSeqFilterSpark
pathseqGetRecommendedNumReducers(String, int, int) PSUtils
Same as GATKSparkTool's getRecommendedNumReducers(), but can specify input BAM path (for when --input is not used)
PathSeqPipelineSpark org.broadinstitute.hellbender.tools.spark.pathseq
Combined tool that performs all PathSeq steps: read filtering, microbe reference alignment and abundance scoring
PathSeqPipelineSpark() PathSeqPipelineSpark
PathSeqScoreSpark org.broadinstitute.hellbender.tools.spark.pathseq
Classify reads and estimate abundances of each taxon in the reference.
PathSeqScoreSpark() PathSeqScoreSpark
PATTERN Strand
PCR_error UnifiedArgumentCollection
The PCR error rate is independent of the sequencing error rate, which is necessary because we cannot necessarily
distinguish between PCR errors vs.
PCR_SLIPPAGE_P_VALUE_LONG_NAME M2FiltersArgumentCollection
PCR_SLIPPAGE_RATE_LONG_NAME M2FiltersArgumentCollection
pcrErrorModel LikelihoodEngineArgumentCollection
When calculating the likelihood of variants, we can try to correct for PCR errors that cause indel artifacts.
pcrSlippagePValueThreshold M2FiltersArgumentCollection
pcrSlippageRate M2FiltersArgumentCollection
PCT_100X CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 100X sequence coverage in post-filtering bases.
PCT_10X CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 10X sequence coverage in post-filtering bases.
PCT_15X CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 15X sequence coverage in post-filtering bases.
PCT_1X CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 1X sequence coverage in post-filtering bases.
PCT_20X CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 20X sequence coverage in post-filtering bases.
PCT_25X CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 25X sequence coverage in post-filtering bases.
PCT_30X CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 30X sequence coverage in post-filtering bases.
PCT_40X CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 40X sequence coverage in post-filtering bases.
PCT_50X CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 50X sequence coverage in post-filtering bases.
PCT_5X CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.
PCT_60X CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 60X sequence coverage in post-filtering bases.
PCT_70X CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 70X sequence coverage in post-filtering bases.
PCT_80X CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 80X sequence coverage in post-filtering bases.
PCT_90X CollectWgsMetrics.WgsMetrics
The fraction of bases that attained at least 90X sequence coverage in post-filtering bases.
PCT_A BaseDistributionByCycleMetrics
PCT_A BaseDistributionByCycleMetrics
PCT_ADAPTER AlignmentSummaryMetrics
The fraction of PF reads that are unaligned and match to a known adapter sequence right from the
start of the read.
PCT_AMPLIFIED_BASES 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 BaseDistributionByCycleMetrics
PCT_C BaseDistributionByCycleMetrics
PCT_CHIMERAS 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 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 RnaSeqMetrics
Fraction of PF_ALIGNED_BASES that mapped to protein coding regions of genes, CODING_BASES/PF_ALIGNED_BASES
PCT_CONVERTED RrbsCpgDetailMetrics
CpG CONVERTED_BASES / CpG TOTAL_BASES (fraction)
PCT_CORRECT_STRAND_READS 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 RrbsSummaryMetrics
CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction)
PCT_DBSNP CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The fraction of passing bi-allelic SNPs in dbSNP
PCT_DBSNP_INDELS CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The fraction of passing indels in dbSNP
PCT_EXC_BASEQ CollectWgsMetrics.WgsMetrics
The fraction of aligned bases that were filtered out because they were of low base quality (default is < 20).
PCT_EXC_BASEQ HsMetrics
The fraction of aligned bases that were filtered out because they were of low base quality.
PCT_EXC_BASEQ TargetedPcrMetrics
The fraction of aligned bases that were filtered out because they were of low base quality.
PCT_EXC_BASEQ TargetMetrics
The fraction of aligned bases that were filtered out because they were of low base quality.
PCT_EXC_CAPPED CollectWgsMetrics.WgsMetrics
The fraction of aligned bases that were filtered out because they would have raised coverage above the capped value (default cap = 250x).
PCT_EXC_DUPE CollectWgsMetrics.WgsMetrics
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
PCT_EXC_DUPE HsMetrics
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
PCT_EXC_DUPE TargetedPcrMetrics
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
PCT_EXC_DUPE TargetMetrics
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
PCT_EXC_MAPQ CollectWgsMetrics.WgsMetrics
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (default is < 20).
PCT_EXC_MAPQ HsMetrics
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
PCT_EXC_MAPQ TargetedPcrMetrics
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
PCT_EXC_MAPQ TargetMetrics
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
PCT_EXC_OFF_TARGET HsMetrics
The fraction of aligned bases that were filtered out because they did not align over a target base.
PCT_EXC_OFF_TARGET TargetedPcrMetrics
The fraction of bases that were filtered out because they did not map to a base within a target region.
PCT_EXC_OFF_TARGET TargetMetrics
The fraction of aligned bases that were filtered out because they did not align over a target base.
PCT_EXC_OVERLAP CollectWgsMetrics.WgsMetrics
The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
PCT_EXC_OVERLAP HsMetrics
The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
PCT_EXC_OVERLAP TargetedPcrMetrics
The fraction of aligned bases that were filtered out because they were the second observation from an
insert with overlapping reads.
PCT_EXC_OVERLAP TargetMetrics
The fraction of aligned bases that were filtered out because they were the second observation from
an insert with overlapping reads.
PCT_EXC_TOTAL CollectWgsMetrics.WgsMetrics
The total fraction of aligned bases excluded due to all filters.
PCT_EXC_UNPAIRED CollectWgsMetrics.WgsMetrics
The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair.
PCT_G BaseDistributionByCycleMetrics
PCT_G BaseDistributionByCycleMetrics
PCT_GQ0_VARIANTS CollectVariantCallingMetrics.VariantCallingDetailMetrics
The percentage of variants in a particular sample that have a GQ score of 0.
PCT_INTERGENIC_BASES RnaSeqMetrics
Fraction of PF_ALIGNED_BASES that mapped to intergenic regions of genomic DNA, INTERGENIC_BASES/PF_ALIGNED_BASES
PCT_INTRONIC_BASES RnaSeqMetrics
Fraction of PF_ALIGNED_BASES that correspond to gene introns, INTRONIC_BASES/PF_ALIGNED_BASES
PCT_JUMPS 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 ExtractIlluminaBarcodes.BarcodeMetric
The fraction of all reads in the lane that matched to this barcode.
PCT_MRNA_BASES RnaSeqMetrics
Sum of bases mapped to regions corresponding to UTRs and coding regions of mRNA transcripts, PCT_UTR_BASES + PCT_CODING_BASES
PCT_N BaseDistributionByCycleMetrics
PCT_N BaseDistributionByCycleMetrics
PCT_NON_CPG_BASES_CONVERTED RrbsSummaryMetrics
NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction)
PCT_NONJUMPS 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 TargetedPcrMetrics
The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon,
OFF_AMPLICON_BASES/PF_BASES_ALIGNED
PCT_OFF_BAIT HsMetrics
The fraction of PF_BASES_ALIGNED that are mapped away from any baited region, OFF_BAIT_BASES/PF_BASES_ALIGNED.
PCT_OFF_PROBE 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 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 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 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 CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The fraction of PF_READS
PCT_PF_FAIL_UNKNOWN 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 AlignmentSummaryMetrics
The fraction of reads that are PF (PF_READS / TOTAL_READS)
PCT_PF_READS HsMetrics
The fraction of reads passing the vendor's filter, PF_READS/TOTAL_READS.
PCT_PF_READS TargetedPcrMetrics
The fraction of reads passing filter, PF_READS/TOTAL_READS.
PCT_PF_READS TargetMetrics
The fraction of reads passing filter, PF_READS/TOTAL_READS.
PCT_PF_READS_ALIGNED AlignmentSummaryMetrics
The percentage of PF reads that aligned to the reference sequence.
PCT_PF_READS_IMPROPER_PAIRS AlignmentSummaryMetrics
The fraction of (primary) reads that are *not* "properly" aligned in pairs (as per SAM flag 0x2).
PCT_PF_UQ_READS HsMetrics
The fraction of PF_UNIQUE_READS from the TOTAL_READS, PF_UNIQUE_READS/TOTAL_READS.
PCT_PF_UQ_READS TargetedPcrMetrics
The fraction of TOTAL_READS that are unique, PF, and are not duplicates, PF_UNIQUE_READS/TOTAL_READS
PCT_PF_UQ_READS TargetMetrics
The fraction of unique reads passing filter, PF_UNIQUE_READS/TOTAL_READS.
PCT_PF_UQ_READS_ALIGNED HsMetrics
The fraction of PF_UQ_READS_ALIGNED from the total number of PF reads.
PCT_PF_UQ_READS_ALIGNED TargetedPcrMetrics
Fraction of PF_READS that are unique and align to the reference genome, PF_UQ_READS_ALIGNED/PF_READS
PCT_PF_UQ_READS_ALIGNED TargetMetrics
The fraction of unique reads passing filter that align to the reference,
PF_UQ_READS_ALIGNED/PF_UNIQUE_READS.
PCT_R1_TRANSCRIPT_STRAND_READS 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 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 AlignmentSummaryMetrics
The fraction of reads whose mate pair was also aligned to the reference.
PCT_RIBOSOMAL_BASES RnaSeqMetrics
Fraction of PF_ALIGNED_BASES that mapped to regions encoding ribosomal RNA, RIBOSOMAL_BASES/PF_ALIGNED_BASES
PCT_SELECTED_BASES 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 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_T BaseDistributionByCycleMetrics
PCT_T BaseDistributionByCycleMetrics
PCT_TARGET_BASES_100X HsMetrics
The fraction of all target bases achieving 100X or greater coverage.
PCT_TARGET_BASES_100X TargetMetrics
The fraction of all target bases achieving 100X or greater coverage.
PCT_TARGET_BASES_10X HsMetrics
The fraction of all target bases achieving 10X or greater coverage.
PCT_TARGET_BASES_10X TargetedPcrMetrics
The fraction of all target bases achieving 10X or greater coverage depth.
PCT_TARGET_BASES_10X TargetMetrics
The fraction of all target bases achieving 10X or greater coverage.
PCT_TARGET_BASES_1X HsMetrics
The fraction of all target bases achieving 1X or greater coverage.
PCT_TARGET_BASES_1X TargetedPcrMetrics
The fraction of all target bases achieving 1X or greater coverage.
PCT_TARGET_BASES_1X TargetMetrics
The fraction of all target bases achieving 1X or greater coverage.
PCT_TARGET_BASES_20X HsMetrics
The fraction of all target bases achieving 20X or greater coverage.
PCT_TARGET_BASES_20X TargetedPcrMetrics
The fraction of all target bases achieving 20X or greater coverage depth.
PCT_TARGET_BASES_20X TargetMetrics
The fraction of all target bases achieving 20X or greater coverage.
PCT_TARGET_BASES_2X HsMetrics
The fraction of all target bases achieving 2X or greater coverage.
PCT_TARGET_BASES_2X TargetedPcrMetrics
The fraction of all target bases achieving 2X or greater coverage depth.
PCT_TARGET_BASES_2X TargetMetrics
The fraction of all target bases achieving 2X or greater coverage.
PCT_TARGET_BASES_30X HsMetrics
The fraction of all target bases achieving 30X or greater coverage.
PCT_TARGET_BASES_30X TargetedPcrMetrics
The fraction of all target bases achieving 30X or greater coverage depth.
PCT_TARGET_BASES_30X TargetMetrics
The fraction of all target bases achieving 30X or greater coverage.
PCT_TARGET_BASES_40X HsMetrics
The fraction of all target bases achieving 40X or greater coverage.
PCT_TARGET_BASES_40X TargetMetrics
The fraction of all target bases achieving 40X or greater coverage.
PCT_TARGET_BASES_50X HsMetrics
The fraction of all target bases achieving 50X or greater coverage.
PCT_TARGET_BASES_50X TargetMetrics
The fraction of all target bases achieving 50X or greater coverage.
PCT_UMI_WITH_N UmiMetrics
The percentage of reads that contain an UMI that contains at least one N
PCT_USABLE_BASES 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 HsMetrics
The number of aligned, de-duped, on-bait bases out of the PF bases available.
PCT_USABLE_BASES_ON_TARGET HsMetrics
The number of aligned, de-duped, on-target bases out of all of the PF bases available.
PCT_UTR_BASES RnaSeqMetrics
Fraction of PF_ALIGNED_BASES that mapped to untranslated regions (UTR) of genes, UTR_BASES/PF_ALIGNED_BASES
PDF_FILE_EXTENSION CollectRrbsMetrics
pdfFile AnalyzeCovariates
Output report file name.
PedFile 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) PedFile
PedFile.PedTrio picard.pedigree
PEDIGREE_FILE_LONG_NAME StandardArgumentDefinitions
PEDIGREE_FILE_SHORT_NAME StandardArgumentDefinitions
PedigreeAnnotation 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>) PedigreeAnnotation
PedigreeAnnotation(File) PedigreeAnnotation
PedigreeValidationType org.broadinstitute.hellbender.utils.samples
PedReader 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() PedReader
PedReader.Field org.broadinstitute.hellbender.utils.samples
PedReader.MissingPedField 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) PedFile.PedTrio
Constructs a TRIO that cannot be modified after the fact.
peek() ArtificialReadIterator
peek at the next sam record
peek() MarkQueue
Returns the first element in this queue
peekFinalized() Downsampler
Peek at the first finalized item stored in this downsampler (or null if there are no finalized items)
peekFinalized() FractionalDownsampler
peekFinalized() LevelingDownsampler
peekFinalized() MutectDownsampler
peekFinalized() PassThroughDownsampler
peekFinalized() PositionalDownsampler
peekFinalized() ReservoirDownsampler
peekPending() Downsampler
Peek at the first pending item stored in this downsampler (or null if there are no pending items)
peekPending() FractionalDownsampler
peekPending() LevelingDownsampler
peekPending() MutectDownsampler
peekPending() PassThroughDownsampler
peekPending() PositionalDownsampler
peekPending() ReservoirDownsampler
PER_BASE_COVERAGE CollectTargetedMetrics
PER_TARGET_COVERAGE CollectTargetedMetrics
PER_TILE_PATTERN_STRING ParameterizedFileUtil
PerAlleleAnnotation org.broadinstitute.hellbender.tools.walkers.annotator
Apply an annotation based on aggregation data from all reads supporting each allele.
PerAlleleAnnotation() PerAlleleAnnotation
PerAlleleCollection X extends java.lang.Number> - Class in org.broadinstitute.hellbender.tools.walkers.mutect
A container for allele to value mapping.
PerAlleleCollection(PerAlleleCollection.Type) PerAlleleCollection
PerAlleleCollection.Type org.broadinstitute.hellbender.tools.walkers.mutect
PERCENT_DUPLICATION DuplicationMetrics
The fraction of mapped sequence that is marked as duplicate.
percentageOrNull(Long, Long) MathUtil
Obtains percentage of two Longs
PERFECT_MATCHES ExtractIlluminaBarcodes.BarcodeMetric
The number of all reads matching this barcode that matched with 0 errors or no-calls.
performSequenceDictionaryValidation() SequenceDictionaryValidationArgumentCollection.NoValidationCollection
performSequenceDictionaryValidation() SequenceDictionaryValidationArgumentCollection
Should sequence dictionary validation be performed
performSequenceDictionaryValidation() SequenceDictionaryValidationArgumentCollection.StandardValidationCollection
Permutation E > - Interface in org.broadinstitute.hellbender.utils.collections
Represent a permutation of a ordered set or list of elements.
permutation(AlleleList<A>) AlleleList
Returns a permutation between two allele lists.
permutationTest(double[], double[], double) MannWhitneyU
Creates histogram of test statistics from a permutation test.
PersistenceOptimizer org.broadinstitute.hellbender.tools.copynumber.utils.optimization
Given 1-dimensional data, finds all local minima sorted by decreasing topological persistence.
PersistenceOptimizer(double[]) PersistenceOptimizer
Identifies the local minima of data based on topological persistence upon construction.
PerTileBarcodeExtractor(int, File, Map<String, ExtractIlluminaBarcodes.BarcodeMetric>, ExtractIlluminaBarcodes.BarcodeMetric, IlluminaDataProviderFactory, int, int, int, int, List<File>, List<AbstractIlluminaPositionFileReader.PositionInfo>, File[]) ExtractIlluminaBarcodes.PerTileBarcodeExtractor
PerTileBarcodeExtractor(int, File, Map<String, ExtractIlluminaBarcodes.BarcodeMetric>, ExtractIlluminaBarcodes.BarcodeMetric, IlluminaDataProviderFactory, int, int, int, int) ExtractIlluminaBarcodes.PerTileBarcodeExtractor
Constructor
PerTileFileUtil picard.illumina.parser
PerTileFileUtil(String, File, FileFaker, int) PerTileFileUtil
PerTileFileUtil(String, File, FileFaker, int, boolean) PerTileFileUtil
PerTileOrPerRunFileUtil picard.illumina.parser
PerTileOrPerRunFileUtil(String, File, FileFaker, int) 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) PerTileParser
PerTileParser(IlluminaFileMap, int) PerTileParser
PerTilePerCycleFileUtil picard.illumina.parser
PerTilePerCycleFileUtil(String, File, FileFaker, int) PerTilePerCycleFileUtil
PerUnitExampleMultiMetricsCollector 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) PerUnitExampleMultiMetricsCollector
PerUnitGcBiasMetricsCollector(String, String, String) GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
PerUnitInsertSizeMetricsCollector 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, double, double, Integer) PerUnitInsertSizeMetricsCollector
PerUnitInsertSizeMetricsCollector(String, String, String) InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
PerUnitMetricCollector BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends java.lang.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 java.lang.Comparable,ARGTYPE > - Interface in picard.metrics
PerRecordCollector - An interface for classes that collect data in order to generate one or more metrics.
PerUnitRnaSeqMetricsCollector(RnaSeqMetrics, String, String, String, Long) 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.
PerUnitRnaSeqMetricsCollector(String, String, String, Long) RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
PerUnitTargetMetricCollector(String, Set<Interval>, String, String, String, long, long, long, Map<Interval, Double>, int, int, boolean) TargetMetricsCollector.PerUnitTargetMetricCollector
Constructor that parses the squashed reference to genome reference file and stores the
information in a map for later use.
PF_ALIGNED_BASES AlignmentSummaryMetrics
The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence.
PF_ALIGNED_BASES RnaSeqMetrics
The total number of aligned PF bases.
PF_BASES QualityYieldMetrics
The total number of bases in all PF reads
PF_BASES CollectQualityYieldMetrics.QualityYieldMetrics
The total number of bases in all PF reads
PF_BASES TargetedPcrMetrics
The total number of bases within the PF_READS of the SAM or BAM file to be examined
PF_BASES TargetMetrics
The number of bases in the PF_READS of a SAM or BAM file
PF_BASES RnaSeqMetrics
The total number of PF bases including non-aligned reads.
PF_BASES IlluminaBasecallingMetrics
The total number of passing-filter bases assigned to the index.
PF_BASES_ALIGNED HsMetrics
The number of PF unique bases that are aligned to the reference genome with mapping scores > 0.
PF_BASES_ALIGNED TargetedPcrMetrics
The number of bases from PF_READS that align to the reference genome with mapping score > 0
PF_BASES_ALIGNED TargetMetrics
The number of PF_BASES that are aligned with mapping score > 0 to the reference genome.
PF_CLUSTERS IlluminaBasecallingMetrics
The total number of PF clusters assigned to the index.
PF_FAIL_EMPTY CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The number of non-PF reads in this tile that are deemed empty.
PF_FAIL_MISALIGNED CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The number of non-PF reads in this tile that are deemed "misaligned".
PF_FAIL_POLYCLONAL CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The number of non-PF reads in this tile that are deemed multiclonal.
PF_FAIL_READS CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The number of non-PF reads in this tile.
PF_FAIL_UNKNOWN CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The number of non-PF reads in this tile that have not been classified.
PF_HQ_ALIGNED_BASES AlignmentSummaryMetrics
The number of bases aligned to the reference sequence in reads that were mapped at high
quality.
PF_HQ_ALIGNED_Q20_BASES AlignmentSummaryMetrics
The subset of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher.
PF_HQ_ALIGNED_READS 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 AlignmentSummaryMetrics
The fraction of bases that mismatch the reference in PF HQ aligned reads.
PF_HQ_MEDIAN_MISMATCHES 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 AlignmentSummaryMetrics
The number of insertion and deletion events per 100 aligned bases.
PF_MISMATCH_RATE AlignmentSummaryMetrics
The rate of bases mismatching the reference for all bases aligned to the reference sequence.
PF_NOISE_READS AlignmentSummaryMetrics
The number of PF reads that are marked as noise reads.
PF_NORMALIZED_MATCHES ExtractIlluminaBarcodes.BarcodeMetric
The "normalized" matches to each barcode.
PF_ONE_MISMATCH_MATCHES ExtractIlluminaBarcodes.BarcodeMetric
The number of PF reads matching this barcode that matched with 1 error or no-call.
PF_PCT_MATCHES ExtractIlluminaBarcodes.BarcodeMetric
The fraction of PF reads in the lane that matched to this barcode.
PF_PERFECT_MATCHES ExtractIlluminaBarcodes.BarcodeMetric
The number of PF reads matching this barcode that matched with 0 errors or no-calls.
PF_Q20_BASES QualityYieldMetrics
The number of bases in PF reads that achieve quality score 20 or higher
PF_Q20_BASES CollectQualityYieldMetrics.QualityYieldMetrics
The number of bases in PF reads that achieve quality score 20 or higher
PF_Q20_EQUIVALENT_YIELD QualityYieldMetrics
The sum of quality scores of all bases divided by 20
PF_Q20_EQUIVALENT_YIELD CollectQualityYieldMetrics.QualityYieldMetrics
The sum of quality scores of all bases in PF reads divided by 20
PF_Q30_BASES QualityYieldMetrics
The number of bases in PF reads that achieve quality score 30 or higher
PF_Q30_BASES CollectQualityYieldMetrics.QualityYieldMetrics
The number of bases in PF reads that achieve quality score 30 or higher
PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT ExtractIlluminaBarcodes.BarcodeMetric
The rate of PF reads matching this barcode to PF reads matching the most prevelant barcode.
PF_READS QualityYieldMetrics
The number of reads that are PF - pass filter
PF_READS AlignmentSummaryMetrics
The number of PF reads where PF is defined as passing Illumina's filter.
PF_READS CollectQualityYieldMetrics.QualityYieldMetrics
The number of reads that are PF - pass filter
PF_READS HsMetrics
The total number of reads that pass the vendor's filter.
PF_READS TargetedPcrMetrics
The total number of reads passing filter (PF), where the filter(s) can be platform/vendor quality controls
PF_READS TargetMetrics
The number of passing filter reads (PF).
PF_READS ExtractIlluminaBarcodes.BarcodeMetric
The number of PF reads matching this barcode (always less than or equal to READS).
PF_READS IlluminaBasecallingMetrics
The total number of passing-filter reads assigned to the index.
PF_READS_ALIGNED AlignmentSummaryMetrics
The number of PF reads that were aligned to the reference sequence.
PF_READS_IMPROPER_PAIRS AlignmentSummaryMetrics
The number of (primary) aligned reads that are **not** "properly" aligned in pairs (as per SAM flag 0x2).
PF_READS_ONLY CollectBaseDistributionByCycle
PF_READS_ONLY MeanQualityByCycle
PF_READS_ONLY QualityScoreDistribution
PF_READS_ONLY_SHORT_NAME StandardOptionDefinitions
PF_SELECTED_PAIRS TargetedPcrMetrics
Tracks the number of PF read pairs (used to calculate library size)
PF_SELECTED_PAIRS TargetMetrics
Tracks the number of read pairs that we see that are PF (used to calculate library size)
PF_SELECTED_UNIQUE_PAIRS TargetedPcrMetrics
Tracks the number of unique, PF, read pairs, observed (used to calculate library size)
PF_SELECTED_UNIQUE_PAIRS TargetMetrics
Tracks the number of unique PF_SELECTED_PAIRS we see (used to calc library size)
PF_STATUS ViewSam
PF_UNIQUE_READS HsMetrics
The number of PF reads that are not marked as duplicates.
PF_UNIQUE_READS TargetedPcrMetrics
The number of PF_READS that were not marked as sample or optical duplicates.
PF_UNIQUE_READS TargetMetrics
The number of PF_READS that are not marked as duplicates.
PF_UQ_BASES_ALIGNED HsMetrics
The number of bases in the PF_UQ_READS_ALIGNED reads.
PF_UQ_BASES_ALIGNED TargetedPcrMetrics
The number of bases from PF_UNIQUE_READS that align to the reference genome and have a mapping score > 0
PF_UQ_BASES_ALIGNED TargetMetrics
The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
PF_UQ_READS_ALIGNED HsMetrics
The number of PF_UNIQUE_READS that aligned to the reference genome with a mapping score > 0.
PF_UQ_READS_ALIGNED TargetedPcrMetrics
The total number of PF_UNIQUE_READS that align to the reference genome with mapping scores > 0
PF_UQ_READS_ALIGNED TargetMetrics
The number of PF_UNIQUE_READS that are aligned with mapping score > 0 to the reference genome.
PFFailDetailedMetric(Integer, int, int, int, int, CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason) CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
PFFailDetailedMetric() CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
This ctor is necessary for when reading metrics from file
PFFailSummaryMetric(String) CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
PFFailSummaryMetric() CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
This ctor is necessary for when reading metrics from file
pfReadsOnly CollectBaseDistributionByCycleSpark
pfReadsOnly MeanQualityByCycleSpark
pfReadsOnly QualityScoreDistributionSpark
PG_PROGRAM_NAME PositionBasedDownsampleSam
pgIdsSeen AbstractMarkDuplicatesCommandLineProgram
The program groups that have been seen during the course of examining the input records.
pgIdsSeen AbstractMarkDuplicatesCommandLineProgram
The program groups that have been seen during the course of examining the input records.
pgTagArgumentCollection AbstractMarkDuplicatesCommandLineProgram
pgTagArgumentCollection MergeBamAlignment
PGTagArgumentCollection picard.sam.util
Argument Collection which holds parameters common to classes that want to add PG tags to reads in SAM/BAM files
PGTagArgumentCollection() PGTagArgumentCollection
phaseCalls(List<VariantContext>, Set<Haplotype>) AssemblyBasedCallerGenotypingEngine
Tries to phase the individual alleles based on pairwise comparisons to the other alleles based on all called haplotypes
PHASED_HOM_VAR_STRING GenotypeGVCFs
PHASESET_PREFIX HaplotypeMap
PHASING_APPLIED IlluminaPhasingMetrics
Median phasing value across all tiles in a lane, applied to the first and second template reads
phasingWeight EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
PHRED_SCALED_MIN_P_VALUE ExcessHet
PHRED_SCALED_POSTERIORS_KEY GATKVCFConstants
PHRED_TO_LOG_PROB_MULTIPLIER QualityUtils
conversion factor from phred scaled quality to log error probability and vice versa
phredScaleCorrectRate(double) 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 LikelihoodEngineArgumentCollection
The phredScaledGlobalReadMismappingRate reflects the average global mismapping rate of all reads, regardless of their
mapping quality.
phredScaledPrior UnifiedArgumentCollection
phredScaleErrorRate(double) 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) 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) 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.
PhysicalLocation picard.sam.util
Small interface that provides access to the physical location information about a cluster.
PhysicalLocationForMateCigar picard.sam.markduplicates.util
Stores the minimal information needed for optical duplicate detection.
PhysicalLocationForMateCigar(PhysicalLocation) PhysicalLocationForMateCigar
PhysicalLocationForMateCigarSet picard.sam.markduplicates.util
This stores records that are comparable for detecting optical duplicates.
PhysicalLocationForMateCigarSet() PhysicalLocationForMateCigarSet
PhysicalLocationInt picard.sam.util
Small class that provides access to the physical location information about a cluster.
PhysicalLocationInt() PhysicalLocationInt
PhysicalLocationShort picard.sam.util
Small class that provides access to the physical location information about a cluster.
PhysicalLocationShort() PhysicalLocationShort
picard - package picard
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.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.util - package picard.sam.util
picard.util - package picard.util
picard.util.help - package picard.util.help
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
PICARD_TOOL_EXCEPTION Main
Exit value used when a Picard tool returns a non-zero exit code (the actual value is displayed on the command line)
PicardCommandLine picard.cmdline
This is the main class of Picard and is the way of executing individual command line programs.
PicardCommandLine() PicardCommandLine
PicardCommandLineProgram org.broadinstitute.hellbender.cmdline
Base class for all Picard tools.
PicardCommandLineProgram() PicardCommandLineProgram
PicardCommandLineProgramExecutor org.broadinstitute.hellbender.cmdline
Adapter shim for use within GATK to run Picard tools.
PicardCommandLineProgramExecutor(CommandLineProgram) PicardCommandLineProgramExecutor
PicardException picard
Basic Picard runtime exception that, for now, does nothing much
PicardException(String) PicardException
PicardException(String, Throwable) PicardException
PicardHelpDoclet picard.util.help
Custom Barclay-based Javadoc Doclet used for generating Picard help/documentation.
PicardHelpDoclet() PicardHelpDoclet
PicardHelpDocWorkUnitHandler picard.util.help
The Picard Documentation work unit handler class that is the companion to PicardHelpDoclet.
PicardHelpDocWorkUnitHandler(HelpDoclet) PicardHelpDocWorkUnitHandler
PicardNonZeroExitException org.broadinstitute.hellbender.exceptions
Exception used to propagate non-zero return values from Picard tools.
PicardNonZeroExitException(int) PicardNonZeroExitException
pickBestConfigurations(AlignedContig, Set<String>, Double) AssemblyContigAlignmentsConfigPicker
pickPrimaryAlignment(HitsForInsert) BestEndMapqPrimaryAlignmentStrategy
Primary alignment was filtered out.
pickPrimaryAlignment(HitsForInsert) BestMapqPrimaryAlignmentSelectionStrategy
Primary alignment was filtered out.
pickPrimaryAlignment(HitsForInsert) EarliestFragmentPrimaryAlignmentSelectionStrategy
pickPrimaryAlignment(HitsForInsert) MostDistantPrimaryAlignmentSelectionStrategy
pickPrimaryAlignment(HitsForInsert) PrimaryAlignmentSelectionStrategy
When this method returns, one alignment has been marked as primary according to the implementation's strategy.
pickPrimaryAlignment(HitsForInsert) BestEndMapqPrimaryAlignmentStrategy
Primary alignment was filtered out.
pickPrimaryAlignment(HitsForInsert) BestMapqPrimaryAlignmentSelectionStrategy
Primary alignment was filtered out.
pickPrimaryAlignment(HitsForInsert) EarliestFragmentPrimaryAlignmentSelectionStrategy
pickPrimaryAlignment(HitsForInsert) MostDistantPrimaryAlignmentSelectionStrategy
pickPrimaryAlignment(HitsForInsert) PrimaryAlignmentSelectionStrategy
When this method returns, one alignment has been marked as primary according to the implementation's strategy.
pickTranscripts(Map<Gene.Transcript, int[]>) RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
Picks the set of transcripts on which the coverage metrics are to be calculated.
Pileup org.broadinstitute.hellbender.tools.walkers.qc
Prints read alignments in samtools pileup format.
Pileup() Pileup
pileupDiff(ReadPileup, SAMPileupFeature) CheckPileup
PileupElement org.broadinstitute.hellbender.utils.pileup
Represents an individual base in a reads pileup.
PileupElement(GATKRead, int, CigarElement, int, int) PileupElement
Create a new pileup element
PileupElement(PileupElement) PileupElement
Create a new PileupElement that's a copy of toCopy
PileupSpark org.broadinstitute.hellbender.tools.spark
Prints read alignments in samtools pileup format.
PileupSpark() PileupSpark
PileupSummary org.broadinstitute.hellbender.tools.walkers.contamination
Created by David Benjamin on 2/14/17.
PileupSummary(String, int, int, int, int, double) PileupSummary
PileupSummary(VariantContext, ReadPileup) PileupSummary
PL_FILTER_NAME_LONG_NAME ReadFilterArgumentDefinitions
PL_FOR_ALL_SNP_ALLELES_KEY GATKVCFConstants
PLATFORM IlluminaBasecallsToSam
PLATFORM FastqToSam
PLATFORM_MODEL FastqToSam
PLATFORM_UNIT FastqToSam
PlatformReadFilter org.broadinstitute.hellbender.engine.filters
Keep only reads where the the Read Group platform attribute (RG:PL tag) contains the given string.
PlatformReadFilter() PlatformReadFilter
PlatformReadFilter(SAMFileHeader) PlatformReadFilter
PlatformUnitReadFilter org.broadinstitute.hellbender.engine.filters
Filter out reads where the the platform unit attribute (PU tag) contains the given string.
PlatformUnitReadFilter() PlatformUnitReadFilter
PlatformUnitReadFilter(SAMFileHeader) PlatformUnitReadFilter
PLFilterNames PlatformReadFilter
ploidy() GenotypeAlleleCounts
ploidy() GenotypeLikelihoodCalculator
Returns the ploidy for this genotype likelihood calculator.
ploidyModel() GenotypingData
Returns the ploidy model that corresponds to the data provided.
PloidyModel org.broadinstitute.hellbender.tools.walkers.genotyper
Information about the number of chromosome per sample at a given location.
PlotDenoisedCopyRatios org.broadinstitute.hellbender.tools.copynumber.plotting
Creates plots of denoised copy ratios.
PlotDenoisedCopyRatios() PlotDenoisedCopyRatios
PlotModeledSegments org.broadinstitute.hellbender.tools.copynumber.plotting
Creates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates.
PlotModeledSegments() PlotModeledSegments
pluginBaseClass GATKAnnotationPluginDescriptor
pluginPackageName GATKAnnotationPluginDescriptor
pNormalizeLogProbability(double[]) 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[]) MathUtil
Takes a vector of numbers and converts it to a vector of probabilities
that sum to 1 with as much fidelity as possible.
poll(SamRecordTrackingBuffer, SAMFileHeader, OpticalDuplicateFinder, LibraryIdGenerator) MarkQueue
The poll method will return the read end that is *not* the duplicate of all comparable read ends that
have been seen.
pon 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 ExomeStandardArgumentDefinitions
PON_FILE_SHORT_NAME ExomeStandardArgumentDefinitions
PON_FILTER_NAME GATKVCFConstants
POOL_SIZE BaitDesigner
POOLED_BAM_DEPTH_ANNOTATION_NAME AnnotateVcfWithBamDepth
popReadyAssemblyRegions(int, int, int, boolean) 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) IntHistogram.CDF
An observed value for which the specified fraction of the sample population has that value or less.
POPULATION_AF_VCF_ATTRIBUTE GATKVCFConstants
popVariantBubbles StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
PosFileFaker picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
PosFileFaker() PosFileFaker
PosFileReader picard.illumina.parser.readers
The pos file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
PosFileReader(File) PosFileReader
position() ChannelAsSeekableStream
position() SeekableByteChannelPrefetcher
Returns this channel's position.
position(long) SeekableByteChannelPrefetcher
Sets this channel's position.
position() XorWrapper
position(long) XorWrapper
POSITION FingerprintingDetailMetrics
The position of the SNP on the chromosome.
POSITION RrbsCpgDetailMetrics
Position within the sequence of the CpG site
PositionalDownsampler 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) PositionalDownsampler
Construct a PositionalDownsampler
PositionBasedDownsampleSam picard.sam
Summary
PositionBasedDownsampleSam() PositionBasedDownsampleSam
PositionInfo(float, float, int, int) AbstractIlluminaPositionFileReader.PositionInfo
positions() ForwardBackwardAlgorithm.Result
Returns the list of positions passed to the forward-backward algorithm
POSITIVE_LABEL_KEY GATKVCFConstants
PosParser 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, IlluminaFileUtil.SupportedIlluminaFormat) PosParser
PosParser(IlluminaFileMap, int, IlluminaFileUtil.SupportedIlluminaFormat) PosParser
PossibleDeNovo org.broadinstitute.hellbender.tools.walkers.annotator
Existence of a de novo mutation in at least one of the given families
PossibleDeNovo(Set<Trio>, double) PossibleDeNovo
PossibleDeNovo() PossibleDeNovo
This is dummy constructor that will do nothing until https://github.com/broadinstitute/gatk/issues/1880 is addressed
POSTERIOR_PROB_OF_CONTAMINATION_ATTRIBUTE GATKVCFConstants
POSTERIOR_PROBABILITIES_KEY StrandArtifact
PosteriorProbabilitiesOptions(double, double, boolean, boolean, boolean, boolean) PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions
PosteriorProbabilitiesUtils org.broadinstitute.hellbender.tools.walkers.variantutils
PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions org.broadinstitute.hellbender.tools.walkers.variantutils
A class to wrangle all the various and sundry genotype posterior options,
mostly from CalculateGenotypePosteriors
posteriors(double[], double[]) MathUtils
PosteriorSummary org.broadinstitute.hellbender.utils.mcmc
Represents central tendency and upper/lower credible-interval bounds of the posterior of a univariate model parameter,
along with optional deciles.
PosteriorSummary(double, double, double) PosteriorSummary
Constructs a PosteriorSummary with only given central tendency and upper/lower credible-interval bounds.
PosteriorSummaryUtils org.broadinstitute.hellbender.utils.mcmc
Contains methods for computing summary statistics for the posterior of a univariate model parameter.
PostprocessGermlineCNVCalls org.broadinstitute.hellbender.tools.copynumber
PostprocessGermlineCNVCalls() PostprocessGermlineCNVCalls
POWER ValidateBasicSomaticShortMutations
PowerCalculationUtils org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
Ppv(GenotypeConcordanceScheme, GenotypeConcordanceStates.CallState[]) GenotypeConcordanceCounts
Returns the PPV defined by the scheme across the subset of call states.
PRE_ADAPTER_DETAILS_EXT SequencingArtifactMetrics
PRE_ADAPTER_METRIC_FIELD_NAME OrientationBiasFilterConstants
PRE_ADAPTER_METRIC_NOT_ARTIFACT_SCORE OrientationBiasFilterer
PRE_ADAPTER_METRIC_RC_FIELD_NAME OrientationBiasFilterConstants
PRE_ADAPTER_METRICS_DETAIL_FILE_FULL_NAME FilterByOrientationBias
PRE_ADAPTER_METRICS_DETAIL_FILE_SHORT_NAME FilterByOrientationBias
PRE_ADAPTER_SUMMARY_EXT SequencingArtifactMetrics
PRE_TANGENT_NORMALIZED_COUNTS_FILE_LONG_NAME ExomeStandardArgumentDefinitions
PRE_TANGENT_NORMALIZED_COUNTS_FILE_SHORT_NAME ExomeStandardArgumentDefinitions
PreAdapterDetailMetrics() SequencingArtifactMetrics.PreAdapterDetailMetrics
preAdapterMetricsFile FilterByOrientationBias
PreAdapterOrientationScorer org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter
This class handles the reading of a picard metrics file PreAdapterDetailMetrics.
PreAdapterSummaryMetrics() SequencingArtifactMetrics.PreAdapterSummaryMetrics
predecessor(SVKmer.Base, int) SVKmer
predecessor(SVKmer.Base, int) 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) 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 VariantContext Iterator such that only variants that satisfy
all predicates are emitted.
PredicateFilterDecoratingClosableIterator(CloseableIterator<T>, Collection<Predicate<T>>) PredicateFilterDecoratingClosableIterator
PREDICTED_INSERT_SIZE FastqToSam
prepareReadAlleleLikelihoodsForAnnotation(ReadLikelihoods<Haplotype>, Map<String, List<GATKRead>>, boolean, Map<Allele, List<Haplotype>>, ReadLikelihoods<Allele>, VariantContext) AssemblyBasedCallerGenotypingEngine
PREPHASING_APPLIED IlluminaPhasingMetrics
Median pre-phasing value across all tiles in a lane, applied to the first and second template reads
prephasingWeight EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
preprocess(SvDiscoveryInputMetaData, JavaRDD<GATKRead>) 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[]) 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.
PreprocessIntervals org.broadinstitute.hellbender.tools.copynumber
Prepares bins for coverage collection.
PreprocessIntervals() PreprocessIntervals
PRESERVE_QSCORES_LESS_THAN ApplyBQSRArgumentCollection
This flag tells GATK not to modify quality scores less than this value.
PRESERVE_QSCORES_LESS_THAN RecalibrationArgumentCollection
This flag tells GATK not to modify quality scores less than this value.
prettyPrint() EventType
prettyPrintSequenceRecords(SAMSequenceDictionary) ReadUtils
previousHaplotypeBases PairHMM
PRIMARY_ALIGNMENT_STRATEGY MergeBamAlignment
PRIMARY_LINE ReadFilterLibrary
PRIMARY_READS PSFilterMetrics
Number of input reads that are not secondary or supplementary alignments
PrimaryAlignmentKey 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(SAMRecord) PrimaryAlignmentKey
PrimaryAlignmentSelectionStrategy 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 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() ReadFilterLibrary.PrimaryLineReadFilter
primaryReads(JavaRDD<GATKRead>) PSUtils
print(PrintStream) GATKReport
Print all tables contained within this container to a PrintStream
print(PrintStream, GATKReportTable.Sorting) GATKReport
Print all tables contained within this container to a PrintStream
PRINT_DELIM AS_RankSumTest
PRINT_DELIM AS_RMSMappingQuality
PRINT_DELIM AS_StrandBiasTest
PRINT_SUMMARY_LONG_NAME CompareDuplicatesSpark
printDecoratedExceptionMessage(PrintStream, Exception, String) Main
Prints the given message (may be null) to the provided stream, adding adornments and formatting.
printDOT(PrintWriter) KBestHaplotypeFinder
Print a DOT representation of search graph.
printDOT(File) KBestHaplotypeFinder
Print a DOT representation of search graph.
printDOTFile(String) KBestHaplotypeFinder
Print a DOT representation of search graph.
printEfficiency(Level) CachingIndexedFastaSequenceFile
Print the efficiency (hits / queries) to logger with priority
printGraph(File, int) BaseGraph
Print out the graph in the dot language for visualization
printGraph(PrintStream, boolean, int) BaseGraph
printHeader() VQSLODTranche
printIGVFormatHeader(PrintStream, String, String...) IGVUtils
Prints a header for an IGV-format file.
printIGVFormatRow(PrintStream, Locatable, String, double...) IGVUtils
Prints a row in an IGV-format file.
printLibraryVersions() CommandLineProgram
Output versions of important dependencies to the logger.
printOutResults(String) CompareMatrix
PrintReads org.broadinstitute.hellbender.tools
Write reads from SAM format file (SAM/BAM/CRAM) that pass criteria to a new file.
PrintReads() PrintReads
PrintReadsSpark org.broadinstitute.hellbender.tools.spark.pipelines
PrintReadsSpark() PrintReadsSpark
printReport() SamComparison
printSettings() CommandLineProgram
Output a curated set of important settings to the logger.
printStandard(boolean) OutputStreamSettings
printStartupMessage(ZonedDateTime) CommandLineProgram
Prints a user-friendly message on startup with some information about who we are and the
runtime environment.
printSummary CompareDuplicatesSpark
printUnknown(Set<Class<?>>, String) PicardCommandLine
When a command does not match any known command, searches for similar commands, using the same method as GIT
PrintVariantsSpark org.broadinstitute.hellbender.tools.spark.pipelines
Print out variants from a VCF file.
PrintVariantsSpark() PrintVariantsSpark
prior TrainingSet
PRO_ALT_BASES 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 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 CollectHiSeqXPfFailMetrics
probability(int) BetaBinomialDistribution
PROBABILITY DownsampleSam
ProbabilityVector org.broadinstitute.hellbender.utils.genotyper
Represents a 1-dimentional probability distribution.
ProbabilityVector(double[], boolean) ProbabilityVector
Default constructor: take vector in log-space, with support from range [0,len-1]
ProbabilityVector(double[]) ProbabilityVector
ProbabilityVector(ProbabilityVector, boolean) ProbabilityVector
PROBE_SET TargetMetrics
The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection run
PROBE_TERRITORY TargetMetrics
The number of unique bases covered by the intervals of all probes in the probe set
process ProcessControllerBase
process() VariantProcessor
processAlignments(JavaRDD<LocusWalkerContext>, JavaSparkContext) LocusWalkerSpark
Process the alignments and write output.
processAlignments(JavaRDD<LocusWalkerContext>, JavaSparkContext) PileupSpark
processAllCommandLinePrograms(List<String>, BiConsumer<Class<CommandLineProgram>, CommandLineProgramProperties>) PicardCommandLine
Process each CommandLineProgram-derived class given a list of packages.
processAssemblyRegions(JavaRDD<AssemblyRegionWalkerContext>, JavaSparkContext) AssemblyRegionWalkerSpark
Process the assembly regions and write output.
processAssemblyRegions(JavaRDD<AssemblyRegionWalkerContext>, JavaSparkContext) ExampleAssemblyRegionWalkerSpark
processCigarForInitialEvents(int) EventMap
processColumns(TableColumnCollection) TableReader
Process the header line's column names.
processCommentLine(String, long) TableReader
Called with the content of the comment line every time one is found in the input.
ProcessController org.broadinstitute.hellbender.utils.runtime
Facade to Runtime.exec() and java.lang.Process.
ProcessController() ProcessController
ProcessControllerBase CAPTURE_POLICY extends CapturedStreamOutput > - Class in org.broadinstitute.hellbender.utils.runtime
ProcessControllerBase() ProcessControllerBase
ProcessControllerBase.OutputCapture org.broadinstitute.hellbender.utils.runtime
ProcessControllerBase.ProcessStream org.broadinstitute.hellbender.utils.runtime
processFile() WgsMetricsProcessor
Method processes the input data and accumulates result data
processFile() WgsMetricsProcessorImpl
Method gets the data from iterator for each locus and processes it with the help of collector.
processIntervals(JavaRDD<IntervalWalkerContext>, JavaSparkContext) IntervalWalkerSpark
Process the intervals and write output.
processIntervals(JavaRDD<IntervalWalkerContext>, JavaSparkContext) ExampleIntervalWalkerSpark
ProcessOutput org.broadinstitute.hellbender.utils.runtime
ProcessOutput(int, StreamOutput, StreamOutput) ProcessOutput
The output of a process.
processRead(GATKRead, ReferenceDataSource, Iterable<? extends Locatable>) 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) ReadWalkerSpark
Process the reads and write output.
processReads(JavaRDD<ReadWalkerContext>, JavaSparkContext) ExampleReadWalkerWithReferenceSpark
ProcessSettings org.broadinstitute.hellbender.utils.runtime
ProcessSettings(String[]) ProcessSettings
ProcessSettings(String[], boolean, File, Map<String, String>, InputStreamSettings, OutputStreamSettings, OutputStreamSettings) ProcessSettings
processState(ActivityProfileState) 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) BandPassActivityProfile
Band pass the probabilities in the ActivityProfile, producing a new profile that's band pass filtered
processStream CapturedStreamOutput
processVariants(JavaRDD<VariantWalkerContext>, JavaSparkContext) VariantWalkerSpark
Process the variants and write output.
processVariants(JavaRDD<VariantWalkerContext>, JavaSparkContext) ExampleVariantWalkerSpark
processVariants(JavaRDD<VariantWalkerContext>, JavaSparkContext) PrintVariantsSpark
produceAlleles(SimpleInterval, ReferenceMultiSource, SvType) AnnotatedVariantProducer
produceAlleles(byte[], SvType) AnnotatedVariantProducer
produceAnnotatedAndLinkedVcFromNovelAdjacency(Tuple2<SvType, SvType>, SimpleNovelAdjacencyAndChimericAlignmentEvidence, Broadcast<ReferenceMultiSource>, Broadcast<SAMSequenceDictionary>, Broadcast<SVIntervalTree<VariantContext>>, String, String) AnnotatedVariantProducer
Given novel adjacency and inferred variant types that should be linked together,
produce annotated, and linked VCF records.
produceAnnotatedVcFromEvidenceTargetLink(EvidenceTargetLink, SvType, ReadMetadata, ReferenceMultiSource) AnnotatedVariantProducer
produceAnnotatedVcFromInferredTypeAndRefLocations(NovelAdjacencyAndAltHaplotype, SvType, Iterable<SimpleChimera>, Broadcast<ReferenceMultiSource>, Broadcast<SAMSequenceDictionary>, Broadcast<SVIntervalTree<VariantContext>>, String) AnnotatedVariantProducer
producePlot InsertSizeMetricsArgumentCollection
product(double...) MathUtil.LogMath
Computes the sum of the provided log values.
PROFILE_OUT_LONG_NAME AssemblyRegionWalker
PROGRAM CollectMultipleMetrics
PROGRAM_GROUP FastqToSam
PROGRAM_GROUP_COMMAND_LINE AbstractMarkDuplicatesCommandLineProgram
PROGRAM_GROUP_COMMAND_LINE AbstractMarkDuplicatesCommandLineProgram
PROGRAM_GROUP_COMMAND_LINE MergeBamAlignment
PROGRAM_GROUP_NAME AbstractMarkDuplicatesCommandLineProgram
PROGRAM_GROUP_NAME AbstractMarkDuplicatesCommandLineProgram
PROGRAM_GROUP_NAME MergeBamAlignment
PROGRAM_GROUP_VERSION AbstractMarkDuplicatesCommandLineProgram
PROGRAM_GROUP_VERSION AbstractMarkDuplicatesCommandLineProgram
PROGRAM_GROUP_VERSION MergeBamAlignment
PROGRAM_RECORD_ID AbstractMarkDuplicatesCommandLineProgram
PROGRAM_RECORD_ID AbstractMarkDuplicatesCommandLineProgram
PROGRAM_RECORD_ID MergeBamAlignment
PROGRAM_RECORD_ID_SHORT_NAME StandardArgumentDefinitions
PROGRAM_RECORD_ID_SHORT_NAME StandardOptionDefinitions
programName SparkCommandLineProgram
ProgressLogger org.broadinstitute.hellbender.utils.runtime
Facilitate consistent logging output when progressing through a stream of SAM records.
ProgressLogger(Logger, int, String, String) ProgressLogger
Construct a progress logger.
ProgressLogger(Logger, int, String) ProgressLogger
Construct a progress logger.
ProgressLogger(Logger, int) ProgressLogger
Construct a progress logger with the desired log and frequency and the verb "Processed".
ProgressLogger(Logger) ProgressLogger
Construct a progress logger with the desired log, the verb "Processed" and a period of 1m records.
progressMeter GATKTool
Progress meter to print out traversal statistics.
ProgressMeter 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() ProgressMeter
ProgressMeter(double) ProgressMeter
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() ProgressReportingDelegatingCodec
ProgressReportingDelegatingCodec(FeatureCodec<A, B>, double) ProgressReportingDelegatingCodec
promote(int[]) MathUtils
"Promotes" an int[] into a double array with the same values (or as close as precision allows).
promote(int[]) MathUtil
"Promotes" an int[] into a double array with the same values (or as close as precision allows).
PROPAGATION_LONG_NAME AssemblyRegionWalker
PROPERLY_PAIRED ReadFilterLibrary
ProperlyPairedReadFilter() ReadFilterLibrary.ProperlyPairedReadFilter
PropertyUtils picard.util
Utility for loading properties files from resources.
PropertyUtils() PropertyUtils
proportionsAboveThresholds(List<ArrayList<Integer>>, List<Double>) TheoreticalSensitivity
PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN MarkIlluminaAdapters
pruneLowWeightChains(int) BaseGraph
Prune all chains from this graph where all edges in the path have multiplicity < pruneFactor
pruneLowWeightChains(BaseGraph<V, E>) LowWeightChainPruner
Prune graph
pSameAlleleWhenMismatchingUmi IndependentReplicateMetric
pSameUmiInIndependentBiDup IndependentReplicateMetric
PSBuildReferenceTaxonomyUtils org.broadinstitute.hellbender.tools.spark.pathseq
PSBuildReferenceTaxonomyUtils() PSBuildReferenceTaxonomyUtils
PSBwaAligner org.broadinstitute.hellbender.tools.spark.pathseq
Loads Bwa index and aligns reads.
PSBwaAligner(PSBwaArgumentCollection, boolean) PSBwaAligner
PSBwaAlignerSpark org.broadinstitute.hellbender.tools.spark.pathseq
Wrapper class for using the PathSeq Bwa aligner class in Spark.
PSBwaAlignerSpark(JavaSparkContext, PSBwaArgumentCollection) PSBwaAlignerSpark
PSBwaArgumentCollection org.broadinstitute.hellbender.tools.spark.pathseq
PSBwaArgumentCollection() PSBwaArgumentCollection
PSBwaFilter 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) PSBwaFilter
PSBwaUtils org.broadinstitute.hellbender.tools.spark.pathseq
Utility functions for PathSeq Bwa tool
PSBwaUtils() PSBwaUtils
PSEUDO_AUTOSOMAL_REGIONS FindMendelianViolations
PSFilter org.broadinstitute.hellbender.tools.spark.pathseq
Performs PathSeq filtering steps and manages associated resources.
PSFilter(JavaSparkContext, PSFilterArgumentCollection, SAMFileHeader) PSFilter
PSFilterArgumentCollection org.broadinstitute.hellbender.tools.spark.pathseq
PSFilterArgumentCollection() PSFilterArgumentCollection
PSFilterEmptyLogger org.broadinstitute.hellbender.tools.spark.pathseq.loggers
Dummy filter metrics class that does nothing
PSFilterEmptyLogger() PSFilterEmptyLogger
PSFilterFileLogger org.broadinstitute.hellbender.tools.spark.pathseq.loggers
Logs filtering read counts to metrics file
PSFilterFileLogger(MetricsFile<PSFilterMetrics, Long>, String) PSFilterFileLogger
PSFilterLogger org.broadinstitute.hellbender.tools.spark.pathseq.loggers
Interface for filter metrics logging
PSFilterMetrics org.broadinstitute.hellbender.tools.spark.pathseq.loggers
Metrics that are calculated during the PathSeq filter
PSFilterMetrics() PSFilterMetrics
PSKmerBloomFilter org.broadinstitute.hellbender.tools.spark.pathseq
Kmer Bloom Filter class that encapsulates the filter, kmer size, and kmer mask
PSKmerBloomFilter(LongBloomFilter, int, SVKmerShort, long) PSKmerBloomFilter
Note values in the Bloom filter should have been run through PSKmerCollection's canonicalizeAndMask()
PSKmerBloomFilter.Serializer org.broadinstitute.hellbender.tools.spark.pathseq
PSKmerCollection 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() PSKmerCollection
PSKmerSet org.broadinstitute.hellbender.tools.spark.pathseq
Kmer Hopscotch set class that encapsulates the filter, kmer size, and kmer mask
PSKmerSet(LargeLongHopscotchSet, int, SVKmerShort) PSKmerSet
Note values in the input set should have been run through PSKmerCollection's canonicalizeAndMask()
PSKmerSet.Serializer org.broadinstitute.hellbender.tools.spark.pathseq
PSKmerUtils org.broadinstitute.hellbender.tools.spark.pathseq
PathSeq utilities for kmer libraries
PSKmerUtils() PSKmerUtils
PSPairedUnpairedSplitterSpark org.broadinstitute.hellbender.tools.spark.pathseq
Class for separating paired and unpaired reads in an RDD
PSPairedUnpairedSplitterSpark(JavaRDD<GATKRead>, int, boolean) PSPairedUnpairedSplitterSpark
Gets RDDs of the paired and unpaired reads.
PSPathogenAlignmentHit org.broadinstitute.hellbender.tools.spark.pathseq
Stores taxonomic IDs that were hits of a read pair.
PSPathogenAlignmentHit(Collection<Integer>, int) PSPathogenAlignmentHit
PSPathogenReferenceTaxonProperties 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() PSPathogenReferenceTaxonProperties
PSPathogenReferenceTaxonProperties(String) PSPathogenReferenceTaxonProperties
PSPathogenTaxonScore org.broadinstitute.hellbender.tools.spark.pathseq
Pathogen abundance scores assigned to a taxonomic node and reported by the PathSeqScoreSpark tool.
PSPathogenTaxonScore() PSPathogenTaxonScore
PSScoreArgumentCollection org.broadinstitute.hellbender.tools.spark.pathseq
PSScoreArgumentCollection() PSScoreArgumentCollection
PSScoreFileLogger org.broadinstitute.hellbender.tools.spark.pathseq.loggers
Logs number of mapped and unmapped reads to metrics file
PSScoreFileLogger(MetricsFile<PSScoreMetrics, Long>, String) PSScoreFileLogger
PSScoreLogger org.broadinstitute.hellbender.tools.spark.pathseq.loggers
Interface for score metrics logging
PSScoreMetrics org.broadinstitute.hellbender.tools.spark.pathseq.loggers
Metrics that are calculated during the PathSeq scoring
PSScoreMetrics() PSScoreMetrics
PSScorer org.broadinstitute.hellbender.tools.spark.pathseq
PSScorer(PSScoreArgumentCollection) PSScorer
PSTaxonomyConstants org.broadinstitute.hellbender.tools.spark.pathseq
Important NCBI taxonomy database constants
PSTaxonomyConstants() PSTaxonomyConstants
PSTaxonomyDatabase org.broadinstitute.hellbender.tools.spark.pathseq
Helper class for holding taxonomy data used by ClassifyReads
PSTaxonomyDatabase(PSTree, Map<String, Integer>) PSTaxonomyDatabase
PSTaxonomyDatabase.Serializer org.broadinstitute.hellbender.tools.spark.pathseq
PSTree org.broadinstitute.hellbender.tools.spark.pathseq
Represents a taxonomic tree with nodes assigned a name and taxonomic rank (e.g.
PSTree(int) PSTree
PSTree(Kryo, Input) PSTree
PSTree.Serializer org.broadinstitute.hellbender.tools.spark.pathseq
PSTreeNode org.broadinstitute.hellbender.tools.spark.pathseq
Node class for PSTree
PSTreeNode() PSTreeNode
PSTreeNode.Serializer org.broadinstitute.hellbender.tools.spark.pathseq
PSUtils org.broadinstitute.hellbender.tools.spark.pathseq
Common functions for PathSeq
PSUtils() PSUtils
put(PairedStrandedIntervals, V) PairedStrandedIntervalTree
put(SVInterval, V) SVIntervalTree
Put a new interval into the tree (or update the value associated with an existing interval).
put(T, int...) NestedIntegerArray
Insert a value at the position specified by the given keys.
put(int, String, ReadEndsForMarkDuplicates) DiskBasedReadEndsForMarkDuplicatesMap
put(int, String, ReadEndsForMarkDuplicates) ReadEndsForMarkDuplicatesMap
Store the element in the map with the given key.
put(int, int[][][]) CovariateKeyCache
Store the given array in the cache.
put(int, String, ReadEndsForMarkDuplicates) DiskBasedReadEndsForMarkDuplicatesMap
put(int, String, ReadEndsForMarkDuplicates) ReadEndsForMarkDuplicatesMap
Store the element in the map with the given key.
putAttribute(Allele, T) ReducibleAnnotationData
putReadsWithTheSameNameInTheSamePartition(SAMFileHeader, JavaRDD<GATKRead>, JavaSparkContext) SparkUtils
Ensure all reads with the same name appear in the same partition of a queryname sorted RDD.
pValueForContingencyTable(int[][]) FisherStrand
PYTHON_EXTENSION PythonExecutorBase
PYTHON_PROMPT StreamingPythonScriptExecutor
pythonArg HybridADVIArgumentCollection.HybridADVIArgument
PythonExecutorBase org.broadinstitute.hellbender.utils.python
Base class for services for executing Python Scripts.
PythonExecutorBase(boolean) PythonExecutorBase
PythonExecutorBase(PythonExecutorBase.PythonExecutableName, boolean) PythonExecutorBase
PythonExecutorBase.PythonExecutableName org.broadinstitute.hellbender.utils.python
Enum of possible executables that can be launched by this executor.
PythonScriptExecutor org.broadinstitute.hellbender.utils.python
Generic service for executing Python Scripts.
PythonScriptExecutor(boolean) PythonScriptExecutor
PythonScriptExecutor(PythonExecutorBase.PythonExecutableName, boolean) PythonScriptExecutor
PythonScriptExecutorException org.broadinstitute.hellbender.utils.python
Python script execution exception.
PythonScriptExecutorException(String) PythonScriptExecutorException
R ReadEnds
R ReadEnds
R_LIBRARY_SUFFIX RScriptLibrary
RANDOM_SEED DownsampleSam
RANDOM_SEED_FOR_CHAIN_GENERATION HMM
randomIntegerInRange(int, int) MathUtils
Get a random int between min and max (inclusive) using the global GATK random number generator.
RandomLikelihoodCalculationEngine org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Random likelihoods generator, used for testing/benchmarking purposes.
RandomLikelihoodCalculationEngine() RandomLikelihoodCalculationEngine
randomRemotePath(String, String, String) BucketUtils
Picks a random name, by putting some random letters between "prefix" and "suffix".
randomSelect(List<E>, Function<E, Double>, RandomGenerator) MathUtils
randomSublist(List<T>, int) FingerprintChecker
A small utility function to choose n random elements (un-shuffled) from a list
Range 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) Range
rank() KBestHaplotype
The rank of this solution within the list of solutions that resulted from the same search.
RankedData(MannWhitneyU.Rank[], ArrayList<Integer>) MannWhitneyU.RankedData
RankSumTest org.broadinstitute.hellbender.tools.walkers.annotator
Abstract root for all RankSum based annotations
RankSumTest() RankSumTest
rapidParseInt(String) ReadNameParser
Very specialized method to rapidly parse a sequence of digits from a String up until the first
non-digit character.
RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT ExtractIlluminaBarcodes.BarcodeMetric
The rate of all reads matching this barcode to all reads matching the most prevelant barcode.
RAW_DELIM AS_RankSumTest
RAW_MAP_QUAL_RANK_SUM_KEY GATKVCFConstants
RAW_RMS_MAPPING_QUALITY_KEY GATKVCFConstants
rawData ReducibleAnnotationData
rawQuals BAQ.BAQCalculationResult
rawValueAsString(int[][]) AS_StrandBiasTest
RawWgsMetrics() CollectRawWgsMetrics.RawWgsMetrics
RawWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, int, Histogram<Integer>, int) CollectRawWgsMetrics.RawWgsMetrics
RBP_HAPLOTYPE_KEY GATKVCFConstants
RBP_INCONSISTENT_KEY GATKVCFConstants
rCount ArtificialReadIterator
RE_REVERSE SamToFastq
read(Kryo, Input, Class<T>) JsonSerializer
read(Kryo, Input, Class<SAMRecord>) SAMRecordSerializer
read(Kryo, Input, Class<SAMRecordToGATKReadAdapter>) SAMRecordToGATKReadAdapterSerializer
read(HDF5File) HDF5SVDReadCountPanelOfNormals
Create an interface to an HDF5 file.
read(File) SimpleCountCollection
read(Kryo, Input, Class<PSKmerBloomFilter>) PSKmerBloomFilter.Serializer
read(Kryo, Input, Class<PSKmerSet>) PSKmerSet.Serializer
read(Kryo, Input, Class<PSTaxonomyDatabase>) PSTaxonomyDatabase.Serializer
read(Kryo, Input, Class<PSTree>) PSTree.Serializer
read(Kryo, Input, Class<PSTreeNode>) PSTreeNode.Serializer
read(Kryo, Input, Class<AlignedAssembly>) AlignedAssembly.Serializer
read(Kryo, Input, Class<AlignedContig>) AlignedContig.Serializer
read(Kryo, Input, Class<AlignmentInterval>) AlignmentInterval.Serializer
read(Kryo, Input, Class<AssemblyContigWithFineTunedAlignments>) AssemblyContigWithFineTunedAlignments.Serializer
read(Kryo, Input, Class<BreakpointComplications.IntraChrStrandSwitchBreakpointComplications>) BreakpointComplications.IntraChrStrandSwitchBreakpointComplications.Serializer
read(Kryo, Input, Class<BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications>) BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications.Serializer
read(Kryo, Input, Class<BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications>) BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications.Serializer
read(Kryo, Input, Class<NovelAdjacencyAndAltHaplotype>) NovelAdjacencyAndAltHaplotype.Serializer
read(Kryo, Input, Class<SimpleChimera>) SimpleChimera.Serializer
read(Kryo, Input, Class<SimpleNovelAdjacencyAndChimericAlignmentEvidence>) SimpleNovelAdjacencyAndChimericAlignmentEvidence.Serializer
read(Kryo, Input, Class<AlignedAssemblyOrExcuse>) AlignedAssemblyOrExcuse.Serializer
read(Kryo, Input, Class<BreakpointEvidence.ExternalEvidence>) BreakpointEvidence.ExternalEvidence.Serializer
read(Kryo, Input, Class<BreakpointEvidence.InterContigPair>) BreakpointEvidence.InterContigPair.Serializer
read(Kryo, Input, Class<BreakpointEvidence.LargeIndel>) BreakpointEvidence.LargeIndel.Serializer
read(Kryo, Input, Class<BreakpointEvidence.MateUnmapped>) BreakpointEvidence.MateUnmapped.Serializer
read(Kryo, Input, Class<BreakpointEvidence.OutiesPair>) BreakpointEvidence.OutiesPair.Serializer
read(Kryo, Input, Class<BreakpointEvidence.ReadEvidence>) BreakpointEvidence.ReadEvidence.Serializer
read(Kryo, Input, Class<BreakpointEvidence.SameStrandPair>) BreakpointEvidence.SameStrandPair.Serializer
read(Kryo, Input, Class<BreakpointEvidence>) BreakpointEvidence.Serializer
read(Kryo, Input, Class<BreakpointEvidence.SplitRead>) BreakpointEvidence.SplitRead.Serializer
read(Kryo, Input, Class<BreakpointEvidence.TemplateSizeAnomaly>) BreakpointEvidence.TemplateSizeAnomaly.Serializer
read(Kryo, Input, Class<BreakpointEvidence.WeirdTemplateSize>) BreakpointEvidence.WeirdTemplateSize.Serializer
read(Kryo, Input, Class<EvidenceTargetLink>) EvidenceTargetLink.Serializer
read(Kryo, Input, Class<KmerAndInterval>) KmerAndInterval.Serializer
read(Kryo, Input, Class<LibraryStatistics>) LibraryStatistics.Serializer
read(Kryo, Input, Class<QNameAndInterval>) QNameAndInterval.Serializer
read(Kryo, Input, Class<ReadMetadata.LibraryRawStatistics>) ReadMetadata.LibraryRawStatistics.Serializer
read(Kryo, Input, Class<ReadMetadata.PartitionBounds>) ReadMetadata.PartitionBounds.Serializer
read(Kryo, Input, Class<ReadMetadata.PartitionStatistics>) ReadMetadata.PartitionStatistics.Serializer
read(Kryo, Input, Class<ReadMetadata>) ReadMetadata.Serializer
read(Kryo, Input, Class<KmerAndCount>) KmerAndCount.Serializer
read(Kryo, Input, Class<PairedStrandedIntervalTree<T>>) PairedStrandedIntervalTree.Serializer
read(Kryo, Input, Class<Strand>) Strand.Serializer
read(Kryo, Input, Class<StrandedInterval>) StrandedInterval.Serializer
read(Kryo, Input, Class<SVFastqUtils.FastqRead>) SVFastqUtils.FastqRead.Serializer
read(Kryo, Input, Class<SVInterval>) SVInterval.Serializer
read(Kryo, Input, Class<SVIntervalTree<T>>) SVIntervalTree.Serializer
read(Kryo, Input, Class<SVKmerLong>) SVKmerLong.Serializer
read(Kryo, Input, Class<SVKmerShort>) SVKmerShort.Serializer
read(Kryo, Input, Class<HopscotchCollection<T>>) HopscotchCollection.Serializer
read(Kryo, Input, Class<HopscotchMap>) HopscotchMap.Serializer
read(Kryo, Input, Class<HopscotchMultiMap>) HopscotchMultiMap.Serializer
read(Kryo, Input, Class<HopscotchSet>) HopscotchSet.Serializer
read(Kryo, Input, Class<HopscotchUniqueMultiMap>) HopscotchUniqueMultiMap.Serializer
read(Kryo, Input, Class<IntHistogram.CDF>) IntHistogram.CDF.Serializer
read(Kryo, Input, Class<IntHistogram>) IntHistogram.Serializer
read(Kryo, Input, Class<LargeLongHopscotchSet>) LargeLongHopscotchSet.Serializer
read(Kryo, Input, Class<LongBloomFilter>) LongBloomFilter.Serializer
read(Kryo, Input, Class<LongHopscotchSet>) LongHopscotchSet.Serializer
read OverhangFixingManager.SplitRead
read(char[], int, int) LineIteratorReader
Reads lines from the buffer, and if empty from the underlying line-iterator.
read ReadLikelihoods.BestAllele
The query read.
read() ChannelAsSeekableStream
Reads the next byte of data from the input stream.
read(byte[], int, int) ChannelAsSeekableStream
read(ByteBuffer) SeekableByteChannelPrefetcher
Reads a sequence of bytes from this channel into the given buffer.
read(Kryo, Input, Class<Pair>) Pair.Serializer
read() CapturedStreamOutput
Drain the input stream to keep the process from backing up until it's empty.
read() CapturedStreamOutputSnapshot
Drain the input stream to keep the process from backing up until it's empty.
read(ByteBuffer) XorWrapper
read(byte[], int, int) CircularByteBuffer
Read bytes from the buffer into the supplied array.
read1 QuerySortedReadPairIteratorUtil.ReadPair
READ1_ALIGNED_BAM MergeBamAlignment
READ1_MAX_BASES_TO_WRITE SamToFastq
READ1_TRIM MergeBamAlignment
READ1_TRIM SamToFastq
read1Coordinate ReadEnds
read1Coordinate ReadEnds
read1IndexInFile ReadEndsForMarkDuplicates
read1IndexInFile ReadEndsForMarkDuplicates
read1ReferenceIndex ReadEnds
read1ReferenceIndex ReadEnds
read2 QuerySortedReadPairIteratorUtil.ReadPair
READ2_ALIGNED_BAM MergeBamAlignment
READ2_MAX_BASES_TO_WRITE SamToFastq
READ2_TRIM MergeBamAlignment
READ2_TRIM SamToFastq
read2Coordinate ReadEnds
read2Coordinate ReadEnds
read2IndexInFile ReadEndsForMarkDuplicates
read2IndexInFile ReadEndsForMarkDuplicates
read2ReferenceIndex ReadEnds
read2ReferenceIndex ReadEnds
READ_CHUNK_SIZE BamToBfq
READ_END BaseDistributionByCycleMetrics
READ_END BaseDistributionByCycleMetrics
READ_FILTER_LONG_NAME ReadFilterArgumentDefinitions
READ_FILTER_SHORT_NAME ReadFilterArgumentDefinitions
READ_GROUP MultiLevelMetrics
The read group to which these metrics apply.
READ_GROUP SplitReads
READ_GROUP FingerprintingDetailMetrics
The sequencing read group from which sequence data was fingerprinted.
READ_GROUP FingerprintingSummaryMetrics
The read group from which sequence data was drawn for comparison.
READ_GROUP MultilevelMetrics
The read group to which these metrics apply.
READ_GROUP_BLACK_LIST_LONG_NAME ReadFilterArgumentDefinitions
READ_GROUP_ID IlluminaBasecallsToSam
READ_GROUP_ID_SHORT_NAME StandardOptionDefinitions
READ_GROUP_LONG_NAME SplitReads
READ_GROUP_NAME FastqToSam
READ_GROUP_SHORT_NAME SplitReads
READ_INDEX_LONG_NAME StandardArgumentDefinitions
READ_INDEX_SHORT_NAME StandardArgumentDefinitions
READ_LENGTH QualityYieldMetrics
The average read length of all the reads (will be fixed for a lane)
READ_LENGTH CollectQualityYieldMetrics.QualityYieldMetrics
The average read length of all the reads (will be fixed for a lane)
READ_LENGTH CollectWgsMetrics
READ_LIST_FILE FilterSamReads
READ_LONG_NAME ClipReads
READ_NAME_FORMAT IlluminaBasecallsToFastq
READ_NAME_LONG_NAME ReadFilterArgumentDefinitions
READ_NAME_PREFIX BamToBfq
READ_NAME_REGEX OpticalDuplicatesArgumentCollection
READ_NAME_REGEX AbstractOpticalDuplicateFinderCommandLineProgram
READ_NAME_REGEX PositionBasedDownsampleSam
READ_NAME_REGEX_LONG_NAME OpticalDuplicatesArgumentCollection
READ_ONE_BARCODE_TAG EstimateLibraryComplexity
READ_ONE_BARCODE_TAG MarkDuplicates
READ_PAIR_DUPLICATES DuplicationMetrics
The number of read pairs that were marked as duplicates.
READ_PAIR_OPTICAL_DUPLICATES DuplicationMetrics
The number of read pairs duplicates that were caused by optical duplication.
READ_PAIR_SUPPORT GATKSVVCFConstants
READ_PAIRS InsertSizeMetrics
The total number of read pairs that were examined in the entire distribution.
READ_PAIRS InsertSizeMetrics
The total number of read pairs that were examined in the entire distribution.
READ_PAIRS_EXAMINED DuplicationMetrics
The number of mapped read pairs examined.
READ_POS_RANK_SUM_KEY GATKVCFConstants
READ_POSITION_FILTER_NAME GATKVCFConstants
READ_SHORT_NAME ClipReads
READ_STARTS GcBiasDetailMetrics
The number of reads whose start position is at the start of a window of this GC.
READ_STRUCTURE CheckIlluminaDirectory
READ_STRUCTURE CollectIlluminaBasecallingMetrics
READ_STRUCTURE CollectIlluminaLaneMetrics
READ_STRUCTURE ExtractIlluminaBarcodes
READ_STRUCTURE IlluminaBasecallsToFastq
READ_STRUCTURE IlluminaBasecallsToSam
READ_TWO_BARCODE_TAG EstimateLibraryComplexity
READ_TWO_BARCODE_TAG MarkDuplicates
READ_VALIDATION_STRINGENCY_LONG_NAME StandardArgumentDefinitions
READ_VALIDATION_STRINGENCY_SHORT_NAME StandardArgumentDefinitions
readActualHeader(LineIterator) AnnotatedIntervalCodec
readActualHeader(LineIterator) SAMPileupCodec
readActualHeader(LineIterator) TableCodec
readActualHeader(LineIterator) XsvLocatableTableCodec
Read until we get to the header of this xsv
Dev note: We also determine the actual locatable columns here.
readAndMateAreUnmapped(GATKRead) ReadUtils
Helper method for interrogating if a read and its mate (if it exists) are unmapped
readArguments GATKTool
readArguments GATKSparkTool
ReadAttributeTypeMismatch(String, String) GATKException.ReadAttributeTypeMismatch
ReadAttributeTypeMismatch(String, String, Throwable) GATKException.ReadAttributeTypeMismatch
ReadAttributeTypeMismatch(SAMRecord, String, String) GATKException.ReadAttributeTypeMismatch
ReadAttributeTypeMismatch(SAMRecord, String, String, Object) GATKException.ReadAttributeTypeMismatch
ReadAttributeTypeMismatch(SAMRecord, String, String, Throwable) GATKException.ReadAttributeTypeMismatch
readBases BAQ.BAQCalculationResult
readBreakpointsFromTruthVCF(String, SAMSequenceDictionary, int) SVVCFReader
ReadCachingIterator 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>) ReadCachingIterator
readChunkedDoubleMatrix(HDF5File, String) HDF5Utils
ReadClassifier 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>) ReadClassifier
ReadClassifier(ReadData) CollectHiSeqXPfFailMetrics.ReadClassifier
Heart of CLP.
ReadClipper org.broadinstitute.hellbender.utils.clipping
A comprehensive clipping tool.
ReadClipper(GATKRead) ReadClipper
Initializes a ReadClipper object.
ReadClipperTestUtils org.broadinstitute.hellbender.utils.test
ReadClipperTestUtils() ReadClipperTestUtils
ReadClipperWithData(GATKRead, List<ClipReads.SeqToClip>) ClipReads.ReadClipperWithData
ReadConstants org.broadinstitute.hellbender.utils.read
Constants for use with the GATKRead interface
readContext ContextShard
ReadContextData org.broadinstitute.hellbender.engine
ReadContextData is additional data that's useful when processing reads.
ReadContextData(ReferenceBases, Iterable<GATKVariant>) ReadContextData
ReadContextData(ReferenceBases, List<GATKVariant>) ReadContextData
ReadCoordinateComparator org.broadinstitute.hellbender.utils.read
Comparator for sorting Reads by coordinate.
ReadCoordinateComparator(SAMFileHeader) ReadCoordinateComparator
readCount() ReadLikelihoods
Returns the total number of reads in the read-likelihood collection.
readCount TargetMetricsCollector.Coverage
ReadCovariates org.broadinstitute.hellbender.utils.recalibration.covariates
The object temporarily held by a read that describes all of its covariates.
ReadCovariates(int, int, CovariateKeyCache) ReadCovariates
Use an LRU cache to keep cache of keys (int[][][]) arrays for each read length we've seen.
ReadData 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() ReadData
ReadData(ReadType) ReadData
ReadDataManipulationProgramGroup picard.cmdline.programgroups
Tools that manipulate read data in SAM, BAM or CRAM format
ReadDataManipulationProgramGroup() ReadDataManipulationProgramGroup
ReadDescriptor picard.illumina.parser
Represents one set of cycles in an ReadStructure (e.g.
ReadDescriptor(int, ReadType) ReadDescriptor
ReadEnds org.broadinstitute.hellbender.utils.read.markduplicates
Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
ReadEnds() ReadEnds
ReadEnds picard.sam.markduplicates.util
Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
ReadEnds() ReadEnds
ReadEndsForMarkDuplicates org.broadinstitute.hellbender.utils.read.markduplicates
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
ReadEndsForMarkDuplicates() ReadEndsForMarkDuplicates
ReadEndsForMarkDuplicates picard.sam.markduplicates.util
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
ReadEndsForMarkDuplicates() ReadEndsForMarkDuplicates
ReadEndsForMarkDuplicates(ReadEndsForMarkDuplicates) ReadEndsForMarkDuplicates
ReadEndsForMarkDuplicatesCodec org.broadinstitute.hellbender.utils.read.markduplicates
Codec for ReadEnds that just outputs the primitive fields and reads them back.
ReadEndsForMarkDuplicatesCodec() ReadEndsForMarkDuplicatesCodec
ReadEndsForMarkDuplicatesCodec picard.sam.markduplicates.util
Codec for ReadEnds that just outputs the primitive fields and reads them back.
ReadEndsForMarkDuplicatesCodec() ReadEndsForMarkDuplicatesCodec
ReadEndsForMarkDuplicatesMap org.broadinstitute.hellbender.utils.read.markduplicates
Interface for storing and retrieving ReadEnds objects.
ReadEndsForMarkDuplicatesMap picard.sam.markduplicates.util
Interface for storing and retrieving ReadEnds objects.
ReadEndsForMarkDuplicatesWithBarcodes picard.sam.markduplicates.util
ReadEndsForMarkDuplicatesWithBarcodes() ReadEndsForMarkDuplicatesWithBarcodes
ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicates) ReadEndsForMarkDuplicatesWithBarcodes
ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicatesWithBarcodes) ReadEndsForMarkDuplicatesWithBarcodes
ReadEndsForMarkDuplicatesWithBarcodesCodec picard.sam.markduplicates.util
Created by nhomer on 9/13/15.
ReadEndsForMarkDuplicatesWithBarcodesCodec() ReadEndsForMarkDuplicatesWithBarcodesCodec
ReadEndsForMateCigar picard.sam.markduplicates.util
A class to store individual records for MarkDuplicatesWithMateCigar.
ReadEndsForMateCigar(SAMFileHeader, SamRecordWithOrdinal, OpticalDuplicateFinder, short) ReadEndsForMateCigar
Builds a read ends object that represents a single read.
ReadEndsForMateCigar(ReadEndsForMateCigar, SamRecordWithOrdinal) ReadEndsForMateCigar
Creates a shallow copy from the "other"
readEntireVCFIntoMemory(String) VariantContextTestUtils
Reads an entire VCF into memory, returning both its VCFHeader and all VariantContext records in
the vcf.
Reader(File) ConcordanceSummaryRecord.Reader
reader(File, BiFunction<TableColumnCollection, Function<String, RuntimeException>, Function<DataLine, R>>) TableUtils
Creates a new table reader given an record extractor factory based from the columns found in the input.
reader(Reader, BiFunction<TableColumnCollection, Function<String, RuntimeException>, Function<DataLine, R>>) 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>>) TableUtils
Creates a new table reader given an record extractor factory based from the columns found in the input.
ReadErrorCorrector org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Utility class that error-corrects reads.
ReadErrorCorrector(int, int, int, byte, int, boolean, byte, boolean, byte[]) ReadErrorCorrector
Create a new kmer corrector
ReadErrorCorrector(int, byte, int, boolean, byte[]) ReadErrorCorrector
Simple constructor with sensible defaults
ReadErrorCorrector.CorrectionSet org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Wrapper utility class that holds, for each position in read, a list of bytes representing candidate corrections.
ReaderSplitter T > - Class in org.broadinstitute.hellbender.tools.readersplitters
Splits a reader by some value.
ReaderSplitter() ReaderSplitter
readerThreads FixCallSetSampleOrdering
ReadEvidence(GATKRead, ReadMetadata, int) 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) BreakpointEvidence.ReadEvidence
for use when the uncertainty in location has a fixed size
ReadEvidence(Kryo, Input) BreakpointEvidence.ReadEvidence
a technical constructor for use in Kryo (de-)serialization.
readFastqFile(String) SVFastqUtils
readFastqStream(BufferedReader, String) SVFastqUtils
readFileIntoByteArray(File) IOUtils
Reads the entirety of the given file into a byte array.
readFileIntoByteArray(File, int) IOUtils
Reads the entirety of the given file into a byte array using the requested read buffer size.
readFilesNames RequiredReadInputArgumentCollection
ReadFilter org.broadinstitute.hellbender.engine.filters
ReadFilter() ReadFilter
ReadFilter.ReadFilterAnd org.broadinstitute.hellbender.engine.filters
ReadFilter.ReadFilterBinOp org.broadinstitute.hellbender.engine.filters
ReadFilterAnd(ReadFilter, ReadFilter) ReadFilter.ReadFilterAnd
ReadFilterArgumentDefinitions org.broadinstitute.hellbender.cmdline
ReadFilterBinOp(ReadFilter, ReadFilter) ReadFilter.ReadFilterBinOp
ReadFilteringIterator org.broadinstitute.hellbender.utils.iterators
An iterator that filters reads from an existing iterator of reads.
ReadFilteringIterator(Iterator<GATKRead>, ReadFilter) ReadFilteringIterator
Create a ReadFilteringIterator given a pre-existing iterator of reads and a read filter.
ReadFilterLibrary org.broadinstitute.hellbender.engine.filters
Standard ReadFilters
ReadFilterLibrary.AllowAllReadsReadFilter org.broadinstitute.hellbender.engine.filters
Do not filter out any read.
ReadFilterLibrary.CigarContainsNoNOperator org.broadinstitute.hellbender.engine.filters
Filter out reads containing skipped region from the reference (CIGAR strings with 'N' operator).
ReadFilterLibrary.FirstOfPairReadFilter org.broadinstitute.hellbender.engine.filters
Keep only reads that are first of pair (0x1 and 0x40).
ReadFilterLibrary.GoodCigarReadFilter org.broadinstitute.hellbender.engine.filters
Keep only reads containing good CIGAR strings.
ReadFilterLibrary.HasReadGroupReadFilter org.broadinstitute.hellbender.engine.filters
Filter out reads without the SAM record RG (Read Group) tag.
ReadFilterLibrary.MappedReadFilter org.broadinstitute.hellbender.engine.filters
Filter out unmapped reads.
ReadFilterLibrary.MappingQualityAvailableReadFilter org.broadinstitute.hellbender.engine.filters
Filter out reads without available mapping quality (MAPQ=255).
ReadFilterLibrary.MappingQualityNotZeroReadFilter org.broadinstitute.hellbender.engine.filters
Filter out reads with mapping quality equal to zero.
ReadFilterLibrary.MatchingBasesAndQualsReadFilter org.broadinstitute.hellbender.engine.filters
Filter out reads where the bases and qualities do not match in length.
ReadFilterLibrary.MateDifferentStrandReadFilter 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 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.NonZeroFragmentLengthReadFilter org.broadinstitute.hellbender.engine.filters
Filter out reads with fragment length (insert size) different from zero.
ReadFilterLibrary.NonZeroReferenceLengthAlignmentReadFilter org.broadinstitute.hellbender.engine.filters
Filter out reads that do not align to the reference.
ReadFilterLibrary.NotDuplicateReadFilter org.broadinstitute.hellbender.engine.filters
Filter out reads marked as duplicate (0x400).
ReadFilterLibrary.NotSecondaryAlignmentReadFilter org.broadinstitute.hellbender.engine.filters
Filter out reads representing secondary alignments (0x100).
ReadFilterLibrary.NotSupplementaryAlignmentReadFilter org.broadinstitute.hellbender.engine.filters
Filter out reads representing supplementary alignments (0x800).
ReadFilterLibrary.PairedReadFilter org.broadinstitute.hellbender.engine.filters
Filter out unpaired reads (not 0x1).
ReadFilterLibrary.PassesVendorQualityCheckReadFilter org.broadinstitute.hellbender.engine.filters
Filter out reads failing platform/vendor quality checks (0x200).
ReadFilterLibrary.PrimaryLineReadFilter 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 org.broadinstitute.hellbender.engine.filters
Keep only paired reads that are properly paired (0x1 and 0x2).
ReadFilterLibrary.ReadLengthEqualsCigarLengthReadFilter org.broadinstitute.hellbender.engine.filters
Filter out reads where the read and CIGAR do not match in length.
ReadFilterLibrary.SecondOfPairReadFilter org.broadinstitute.hellbender.engine.filters
Keep only paired reads (0x1) that are second of pair (0x80).
ReadFilterLibrary.SeqIsStoredReadFilter org.broadinstitute.hellbender.engine.filters
Keep only reads with sequenced bases.
ReadFilterLibrary.ValidAlignmentEndReadFilter 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 org.broadinstitute.hellbender.engine.filters
Keep only reads with a valid alignment start (POS larger than 0) or is unmapped.
ReadFilterSparkifier org.broadinstitute.hellbender.tools.spark.utils
ReadFilterSparkifier(ReadFilter) ReadFilterSparkifier
readFromFile(File) ContaminationRecord
readFromFile(File) MinorAlleleFractionRecord
readFromFile(File) PileupSummary
readFromFile(File) FilterAnalysisRecord
readGroup ReadGroupReadFilter
readGroup ReadEnds
readGroup ReadEnds
READGROUP_COLUMN_NAME RecalUtils
READGROUP_ID_REGEX AddOrReplaceReadGroups
READGROUP_REPORT_TABLE_TITLE RecalUtils
ReadGroupBlackListReadFilter org.broadinstitute.hellbender.engine.filters
Keep records not matching the read group tag and exact match string.
ReadGroupBlackListReadFilter() ReadGroupBlackListReadFilter
ReadGroupBlackListReadFilter(List<String>, SAMFileHeader) ReadGroupBlackListReadFilter
Creates a filter using the lists of files with blacklisted read groups.
ReadGroupCovariate org.broadinstitute.hellbender.utils.recalibration.covariates
The Read Group covariate.
ReadGroupCovariate(RecalibrationArgumentCollection, List<String>) ReadGroupCovariate
ReadGroupIdSplitter org.broadinstitute.hellbender.tools.readersplitters
Splits readers read group id.
ReadGroupIdSplitter() ReadGroupIdSplitter
ReadGroupReadFilter org.broadinstitute.hellbender.engine.filters
Keep only reads from the specified read group.
ReadGroupReadFilter() ReadGroupReadFilter
ReadGroupSplitter T > - Class in org.broadinstitute.hellbender.tools.readersplitters
Splits a reader based on a value from a read group.
ReadGroupSplitter() ReadGroupSplitter
readHasMappedMate(GATKRead) ReadUtils
readHasMappedMate(SAMRecord) ReadUtils
readHasNoAssignedPosition(GATKRead) ReadUtils
Checks whether the provided read has an assigned position.
readHeader(LineIterator) GencodeGtfCodec
readHeader(B) ProgressReportingDelegatingCodec
readIndexInFile RepresentativeReadIndexer
readIndices ReadInputArgumentCollection
ReadInputArgumentCollection 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() ReadInputArgumentCollection
readIntervalAlignedToRefSpan(SimpleInterval) 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) HDF5Utils
readIntervalsFile(String, Map<String, Integer>) SVFileUtils
Read intervals from file.
readKmerFilter(String) PSKmerUtils
readKmersFile(String, int) SVFileUtils
Read a file of kmers.
readLaneTiles(File, ReadStructure, ValidationStringency, boolean) CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.
READLENGTH_EQUALS_CIGARLENGTH ReadFilterLibrary
ReadLengthEqualsCigarLengthReadFilter() ReadFilterLibrary.ReadLengthEqualsCigarLengthReadFilter
ReadLengthReadFilter org.broadinstitute.hellbender.engine.filters
Keep only reads whose length is ≥ min value and ≤ max value.
ReadLengthReadFilter() ReadLengthReadFilter
ReadLengthReadFilter(int, int) ReadLengthReadFilter
readLengths ReadStructure
ReadLikelihoodCalculationEngine org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Common interface for assembly-haplotype vs reads likelihood engines.
ReadLikelihoodCalculationEngine.Implementation org.broadinstitute.hellbender.tools.walkers.haplotypecaller
readLikelihoods() GenotypingData
Returns read-likelihoods to use for genotyping.
ReadLikelihoods A extends htsjdk.variant.variantcontext.Allele> - Class in org.broadinstitute.hellbender.utils.genotyper
Read-likelihoods container implementation based on integer indexed arrays.
ReadLikelihoods(SampleList, AlleleList<A>, Map<String, List<GATKRead>>) ReadLikelihoods
Constructs a new read-likelihood collection.
ReadLikelihoods.BestAllele org.broadinstitute.hellbender.utils.genotyper
Contains information about the best allele for a read search result.
readLines() XReadLines
Reads all of the lines in the file, and returns them as a list of strings
README_FILE_NAME DataSourceUtils
readMetadata KSWindowFinder
ReadMetadata 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) ReadMetadata
ReadMetadata.LibraryRawStatistics org.broadinstitute.hellbender.tools.spark.sv.evidence
ReadMetadata.LibraryRawStatistics.Serializer org.broadinstitute.hellbender.tools.spark.sv.evidence
ReadMetadata.PartitionBounds 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 org.broadinstitute.hellbender.tools.spark.sv.evidence
ReadMetadata.PartitionStatistics org.broadinstitute.hellbender.tools.spark.sv.evidence
ReadMetadata.PartitionStatistics.Serializer org.broadinstitute.hellbender.tools.spark.sv.evidence
ReadMetadata.Serializer org.broadinstitute.hellbender.tools.spark.sv.evidence
ReadMissingReadGroup(GATKRead) UserException.ReadMissingReadGroup
readMixingFractions(File) MixingFraction
readName ReadNameReadFilter
ReadNameEncoder picard.fastq
ReadNameParser picard.sam.util
Provides access to the physical location information about a cluster.
ReadNameParser() ReadNameParser
Creates are read name parser using the default read name regex and optical duplicate distance.
ReadNameParser(String) ReadNameParser
Creates are read name parser using the given read name regex.
ReadNameParser(String, Log) ReadNameParser
Creates are read name parser using the given read name regex.
ReadNameReadFilter org.broadinstitute.hellbender.engine.filters
Keep only reads with this read name.
ReadNameReadFilter() ReadNameReadFilter
readNextLine() AbstractInputParser
readNextLine() BasicInputParser
Workhorse method that reads the next line from the underlying reader
readObject(ObjectInputStream) ContainsKmerReadFilterSpark
readOneBarcode ReadEndsForMarkDuplicatesWithBarcodes
readOrientationBiasSummaryTable(File) OrientationBiasUtils
readOverlapsRegion(GATKRead) AssemblyRegion
Returns true if read would overlap the extended extent of this region
ReadPair() QuerySortedReadPairIteratorUtil.ReadPair
ReadPileup org.broadinstitute.hellbender.utils.pileup
Represents a pileup of reads at a given position.
ReadPileup(Locatable, List<PileupElement>) ReadPileup
Create a new pileup at loc, using the reads and their corresponding
offsets.
ReadPileup(Locatable, Map<String, ReadPileup>) ReadPileup
Create a new pileup at loc, using an stratified pileup
Note: the current implementation of ReadPileup does not efficiently retrieve the stratified pileup
ReadPileup(Locatable) ReadPileup
Create a new pileup without any aligned reads
ReadPileup(Locatable, List<GATKRead>, int) ReadPileup
Create a new pileup with the given reads.
ReadPileup(Locatable, List<GATKRead>, List<Integer>) ReadPileup
Create a new pileup with the given reads.
ReadPosition org.broadinstitute.hellbender.tools.walkers.annotator
Median distance of variant starts from ends of reads supporting each alt allele.
ReadPosition() ReadPosition
ReadPosRankSumTest org.broadinstitute.hellbender.tools.walkers.annotator
Rank Sum Test for relative positioning of REF versus ALT alleles within reads
ReadPosRankSumTest() ReadPosRankSumTest
ReadQueryNameComparator org.broadinstitute.hellbender.utils.read
compare
GATKRead by queryname
duplicates the exact ordering of
SAMRecordQueryNameComparator
ReadQueryNameComparator() ReadQueryNameComparator
ReadRecalibrationInfo org.broadinstitute.hellbender.utils.recalibration
ReadRecalibrationInfo(GATKRead, ReadCovariates, boolean[], double[], double[], double[]) ReadRecalibrationInfo
readRecord() TableReader
Returns the next record form the source.
readRecord(String) TableReader
Reads the record from a string rather than from the input reader.
reads ContextShard
reads() SubsettedLikelihoodMatrix
reads() LikelihoodMatrix
List of reads in the matrix sorted by their index therein.
READS ExtractIlluminaBarcodes.BarcodeMetric
The total number of reads matching the barcode.
READS CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The total number of reads examined
READS_AFTER_DEDUPLICATION PSFilterMetrics
The number of reads after deduplication
READS_AFTER_HOST_FILTER PSFilterMetrics
The number of reads after host read filtering
READS_AFTER_PREALIGNED_HOST_FILTER PSFilterMetrics
The number of reads after filtering prealigned reads
READS_AFTER_QUALITY_AND_COMPLEXITY_FILTER PSFilterMetrics
The number of reads after low-quality and low-complexity filtering
READS_ALIGNED RrbsSummaryMetrics
Number of mapped reads processed
READS_ALIGNED_IN_PAIRS AlignmentSummaryMetrics
The number of aligned reads whose mate pair was also aligned to the reference.
READS_IGNORED_MISMATCHES RrbsSummaryMetrics
Number of reads discarded for exceeding the mismatch threshold
READS_IGNORED_SHORT RrbsSummaryMetrics
Number of reads discarded due to being too short
READS_PER_PARTITION_LONG_NAME PathSeqPipelineSpark
READS_PER_PARTITION_SHORT_NAME PathSeqPipelineSpark
READS_TO_ALIGN BamToBfq
READS_USED GcBiasDetailMetrics
This option is used to mark including or excluding duplicates.
READS_USED GcBiasSummaryMetrics
This option is used to mark including or excluding duplicates.
READS_WITH_NO_CPG RrbsSummaryMetrics
Number of reads discarded for having no CpG sites
readSampleName(SAMFileHeader) MetadataUtils
readsBySampleIndex ReadLikelihoods
Reads by sample index.
ReadsContext 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() ReadsContext
Create an empty ReadsContext with no backing data source or interval.
ReadsContext(GATKDataSource<GATKRead>, SimpleInterval) ReadsContext
Create a ReadsContext backed by the supplied source of reads.
ReadsContext(GATKDataSource<GATKRead>, SimpleInterval, ReadFilter) ReadsContext
Create a ReadsContext backed by the supplied source of reads.
ReadsDataSource org.broadinstitute.hellbender.engine
Manages traversals and queries over sources of reads (for now, SAM/BAM/CRAM files only).
ReadsDataSource(Path) ReadsDataSource
Initialize this data source with a single SAM/BAM file and validation stringency SILENT.
ReadsDataSource(List<Path>) ReadsDataSource
Initialize this data source with multiple SAM/BAM files and validation stringency SILENT.
ReadsDataSource(Path, SamReaderFactory) ReadsDataSource
Initialize this data source with a single SAM/BAM file and a custom SamReaderFactory
ReadsDataSource(List<Path>, SamReaderFactory) ReadsDataSource
Initialize this data source with multiple SAM/BAM files and a custom SamReaderFactory
ReadsDataSource(List<Path>, List<Path>) ReadsDataSource
Initialize this data source with multiple SAM/BAM/CRAM files, and explicit indices for those files.
ReadsDataSource(List<Path>, List<Path>, SamReaderFactory) ReadsDataSource
Initialize this data source with multiple SAM/BAM/CRAM files, explicit indices for those files,
and a custom SamReaderFactory.
ReadsDataSource(List<Path>, List<Path>, SamReaderFactory, int, int) ReadsDataSource
Initialize this data source with multiple SAM/BAM/CRAM files, explicit indices for those files,
and a custom SamReaderFactory.
ReadsDataSource(List<Path>, List<Path>, SamReaderFactory, Function<SeekableByteChannel, SeekableByteChannel>, Function<SeekableByteChannel, SeekableByteChannel>) ReadsDataSource
Initialize this data source with multiple SAM/BAM/CRAM files, explicit indices for those files,
and a custom SamReaderFactory.
ReadsDownsampler org.broadinstitute.hellbender.utils.downsampling
An extension of the basic downsampler API with reads-specific operations
ReadsDownsampler() ReadsDownsampler
ReadsDownsamplingIterator org.broadinstitute.hellbender.utils.downsampling
Iterator wrapper around our generic ReadsDownsampler) interface.
ReadsDownsamplingIterator(Iterator<GATKRead>, ReadsDownsampler) ReadsDownsamplingIterator
ReadsForQNamesFinder org.broadinstitute.hellbender.tools.spark.sv.evidence
Find > pairs for interesting template names.
ReadsForQNamesFinder(HopscotchUniqueMultiMap<String, Integer, QNameAndInterval>, int, boolean, Iterator<GATKRead>, SVReadFilter) ReadsForQNamesFinder
readShardPadding AssemblyRegionWalkerSpark
readShardPadding LocusWalkerSpark
readShardPadding ReadWalkerSpark
readShardPadding HaplotypeCallerSpark.ShardingArgumentCollection
readShardPadding BaseRecalibratorSpark
readShardPadding BQSRPipelineSpark
readShardSize AssemblyRegionWalkerSpark
readShardSize LocusWalkerSpark
readShardSize ReadWalkerSpark
readShardSize HaplotypeCallerSpark.ShardingArgumentCollection
readShardSize BaseRecalibratorSpark
readShardSize BQSRPipelineSpark
ReadsIterable org.broadinstitute.hellbender.utils.nio
ReadsIterable gives you all the reads for a given genomic interval.
ReadsIterable(String, byte[], QueryInterval) ReadsIterable
ReadsKey org.broadinstitute.hellbender.utils.read.markduplicates
Encodes a unique key for read, read pairs and fragments.
ReadsKey() ReadsKey
readsPerPartition PathSeqPipelineSpark
readsPerPartitionEstimate PSScoreArgumentCollection
This parameter is for fine-tuning memory performance.
readsPerPartitionOutput 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 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() ReadsPipelineSpark
ReadsPreprocessingPipelineTestData org.broadinstitute.hellbender.utils.test
ReadsPreprocessingPipelineTestData contains coordinated test data that can be used in the many transforms that
are a part of the ReadsPreprocessingPipeline.
ReadsPreprocessingPipelineTestData(Class<?>) ReadsPreprocessingPipelineTestData
ReadsPreprocessingPipelineTestData holds a bunch of connected data for testing classes that work with
reads, variants, references bases and pairing those types together.
ReadsSparkSink org.broadinstitute.hellbender.engine.spark.datasources
ReadsSparkSink writes GATKReads to a file.
ReadsSparkSink() ReadsSparkSink
ReadsSparkSink.SparkBAMOutputFormat org.broadinstitute.hellbender.engine.spark.datasources
ReadsSparkSink.SparkCRAMOutputFormat org.broadinstitute.hellbender.engine.spark.datasources
ReadsSparkSink.SparkHeaderlessBAMOutputFormat org.broadinstitute.hellbender.engine.spark.datasources
ReadsSparkSink.SparkHeaderlessCRAMOutputFormat org.broadinstitute.hellbender.engine.spark.datasources
ReadsSparkSink.SparkHeaderlessSAMOutputFormat org.broadinstitute.hellbender.engine.spark.datasources
ReadsSparkSink.SparkSAMOutputFormat org.broadinstitute.hellbender.engine.spark.datasources
ReadsSparkSource org.broadinstitute.hellbender.engine.spark.datasources
Loads the reads from disk either serially (using samReaderFactory) or in parallel using Hadoop-BAM.
ReadsSparkSource(JavaSparkContext) ReadsSparkSource
ReadsSparkSource(JavaSparkContext, ValidationStringency) ReadsSparkSource
readsTaken() ArtificialReadIterator
some instrumentation methods
readStartsWithInsertion(Cigar) ReadUtils
readStartsWithInsertion(Cigar, boolean) ReadUtils
readStartsWithInsertion(List<CigarElement>, boolean) ReadUtils
Checks if a read starts with an insertion.
ReadStrandFilter org.broadinstitute.hellbender.engine.filters
Keep only reads whose strand is either forward (not 0x10) or reverse (0x10), as specified.
ReadStrandFilter() ReadStrandFilter
ReadStrandFilter(boolean) ReadStrandFilter
readStreamIntoByteArray(InputStream, int) IOUtils
Reads all data from the given stream into a byte array using the requested read buffer size.
ReadStructure picard.illumina.parser
Describes the intended logical output structure of clusters of an Illumina run.
ReadStructure(List<ReadDescriptor>) ReadStructure
Copies collection into descriptors (making descriptors unmodifiable) and then calculates relevant statistics about descriptors.
ReadStructure(String) ReadStructure
Converts readStructureString into a List and calls the primary constructor using this List as it's argument.
ReadStructure.Substructure 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
ReadsWriteFormat org.broadinstitute.hellbender.utils.read
Possible output formats when writing reads.
readTaxonomyDatabase(String) PSScorer
Reads taxonomy database that has been serialized to a file
ReadThreadingAssembler org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
ReadThreadingAssembler(int, List<Integer>, boolean, boolean, int) ReadThreadingAssembler
ReadThreadingAssemblerArgumentCollection org.broadinstitute.hellbender.tools.walkers.haplotypecaller
ReadThreadingAssemblerArgumentCollection() ReadThreadingAssemblerArgumentCollection
ReadThreadingGraph org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
Note: not final but only intendent to be subclassed for testing.
ReadThreadingGraph(int) ReadThreadingGraph
Constructs an empty read-threading-grpah provided the kmerSize.
ReadThreadingGraph(int, EdgeFactory<MultiDeBruijnVertex, MultiSampleEdge>) ReadThreadingGraph
Constructs a read-threading-graph for a string representation.
readToAlignmentByteArray(Cigar, byte[]) AlignmentUtils
Generate an array of bases for just those that are aligned to the reference (i.e.
readToFastqSeqId(GATKRead, boolean) SVFastqUtils
Convert a read's name into a FASTQ record sequence ID
readTranches(File) VQSLODTranche
Returns a list of tranches, sorted from most to least specific, read in from file f.
ReadTransformer org.broadinstitute.hellbender.transformers
Classes which perform transformations from GATKRead -> GATKRead should implement this interface by overriding SerializableFunction#apply(GATKRead)
ReadTransformerSparkifier org.broadinstitute.hellbender.tools.spark.utils
ReadTransformerSparkifier(ReadTransformer) ReadTransformerSparkifier
ReadTransformingIterator org.broadinstitute.hellbender.utils.iterators
An iterator that transforms read (i.e.
ReadTransformingIterator(Iterator<GATKRead>, ReadTransformer) ReadTransformingIterator
Create a ReadFilteringIterator given a pre-existing iterator of reads and a read filter.
readTrimThresh PSFilterArgumentCollection
Controls the stingency of base call quality-based read trimming.
readTwoBarcode ReadEndsForMarkDuplicatesWithBarcodes
ReadType picard.illumina.parser
A read type describes a stretch of cycles in an ReadStructure
(e.g.
ReadUtils org.broadinstitute.hellbender.utils.read
A miscellaneous collection of utilities for working with reads, headers, etc.
ReadUtils.ClippingTail org.broadinstitute.hellbender.utils.read
A marker to tell which end of the read has been clipped
readValidationStringency ReadInputArgumentCollection
readValidationStringency CreateHadoopBamSplittingIndex
readValuesFromFile(File) ParamUtils
Reads a double array from the given filename.
ReadWalker 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() ReadWalker
ReadWalkerContext org.broadinstitute.hellbender.engine.spark
ReadWalkerContext(GATKRead, ReferenceContext, FeatureContext) ReadWalkerContext
ReadWalkerSpark org.broadinstitute.hellbender.engine.spark
ReadWalkerSpark() ReadWalkerSpark
realign(GATKRead) RealignmentEngine
realignmentArgumentCollection FilterAlignmentArtifacts
RealignmentArgumentCollection org.broadinstitute.hellbender.tools.walkers.realignmentfilter
RealignmentArgumentCollection() RealignmentArgumentCollection
RealignmentEngine org.broadinstitute.hellbender.tools.walkers.realignmentfilter
RealignmentEngine(RealignmentArgumentCollection) RealignmentEngine
RealignmentEngine.RealignmentResult org.broadinstitute.hellbender.tools.walkers.realignmentfilter
RealignmentResult(boolean, List<BwaMemAlignment>) RealignmentEngine.RealignmentResult
realignReadsToTheirBestHaplotype(ReadLikelihoods<Haplotype>, Haplotype, Locatable, SmithWatermanAligner) AssemblyBasedCallerUtils
Returns a map with the original read as a key and the realigned read as the value.
reallyFilterOut(SAMRecord) CountingDuplicateFilter
reallyFilterOut(SAMRecord) CountingFilter
Return true if we are to filter this record out, false otherwise.
reallyFilterOut(SAMRecord) CountingMapQFilter
reallyFilterOut(SAMRecord) CountingPairedFilter
RECAL_FILE GATKReport
RecalDatum org.broadinstitute.hellbender.utils.recalibration
An individual piece of recalibration data.
RecalDatum(long, double, byte) RecalDatum
Create a new RecalDatum with given observation and mismatch counts, and an reported quality
RecalDatum(RecalDatum) RecalDatum
Copy copy into this recal datum, overwriting all of this objects data
RecalibrationArgumentCollection org.broadinstitute.hellbender.utils.recalibration
A collection of the arguments that are used for BQSR.
RecalibrationArgumentCollection() RecalibrationArgumentCollection
RecalibrationReport org.broadinstitute.hellbender.utils.recalibration
This class has all the static functionality for reading a recalibration report file into memory.
RecalibrationReport(File) RecalibrationReport
RecalibrationReport(InputStream) RecalibrationReport
RecalibrationReport(GATKReport) RecalibrationReport
RecalibrationReport(GATKReport, SortedSet<String>) RecalibrationReport
RecalibrationTables org.broadinstitute.hellbender.utils.recalibration
Utility class to facilitate base quality score recalibration.
RecalibrationTables(StandardCovariateList) RecalibrationTables
RecalibrationTables(StandardCovariateList, int) RecalibrationTables
RecalUtils 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() RecalUtils
reciprocialOverlapFraction(GenomeLoc) GenomeLoc
reciprocialOverlap: what is the min.
reclipCigar(Cigar, GATKRead) CigarUtils
Given a cigar1 and a read with cigar2,
this method creates cigar3 such that it has flanking clip operators from cigar2
and it has all operators from cigar1 in the middle.
reConstructContigFromPickedConfiguration(Tuple2<Tuple2<String, byte[]>, List<AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings>>) AssemblyContigAlignmentsConfigPicker
Reconstructs (possibly more than one)
AlignedContig based on
the given best-scored configuration(s) in
nameSeqAndBestConfigurationsOfOneAssemblyContig.
recordAllValuesInStorage(GATKRead, SAMFileHeader, ReadCovariates, boolean) StandardCovariateList
For each covariate compute the values for all positions in this read and
record the values in the provided storage object.
RECORDS_ONLY ViewSam
recordValues(GATKRead, SAMFileHeader, ReadCovariates, boolean) ContextCovariate
recordValues(GATKRead, SAMFileHeader, ReadCovariates, boolean) Covariate
Calculates covariate values for all positions in the read.
recordValues(GATKRead, SAMFileHeader, ReadCovariates, boolean) CycleCovariate
recordValues(GATKRead, SAMFileHeader, ReadCovariates, boolean) QualityScoreCovariate
recordValues(GATKRead, SAMFileHeader, ReadCovariates, boolean) ReadGroupCovariate
recoverDanglingHeads(int, int, SmithWatermanAligner) ReadThreadingGraph
Try to recover dangling heads
recoverDanglingTails(int, int, SmithWatermanAligner) ReadThreadingGraph
Try to recover dangling tails
reduce(FindBreakpointEvidenceSpark.IntPair, FindBreakpointEvidenceSpark.IntPair) FindBreakpointEvidenceSpark.IntPair
reduce(ReadMetadata.LibraryRawStatistics, ReadMetadata.LibraryRawStatistics) ReadMetadata.LibraryRawStatistics
REDUCED_DELIM AS_RankSumTest
REDUCED_DELIM AS_StrandBiasTest
ReducibleAnnotation 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
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) ReducibleAnnotationData
Create a new ReducibleAnnotationData using the raw data string from a VCF
REF ValidateBasicSomaticShortMutations
ref() Transition
ref() Transition
Gets the reference for the transition.
REF_BASE ErrorSummaryMetrics
The reference base (or it's complement).
REF_BASE SequencingArtifactMetrics.BaitBiasDetailMetrics
The (upper-case) original base on the reference strand.
REF_BASE SequencingArtifactMetrics.BaitBiasSummaryMetrics
The (upper-case) original base on the reference strand.
REF_BASE SequencingArtifactMetrics.PreAdapterDetailMetrics
The (upper-case) original base on the reference strand.
REF_BASE SequencingArtifactMetrics.PreAdapterSummaryMetrics
The (upper-case) original base on the reference strand.
REF_COUNT ErrorSummaryMetrics
The number of reference bases observed.
REF_FLAT CollectRnaSeqMetrics
REF_NONOXO_BASES CollectOxoGMetrics.CpcgMetrics
The number of reference alleles observed as C in read 1 and G in read 2.
REF_OXO_BASES CollectOxoGMetrics.CpcgMetrics
The number of reference alleles observed as G in read 1 and C in read 2.
REF_RECORD_LEN FindBadGenomicKmersSpark
REF_RECORDS_PER_PARTITION FindBadGenomicKmersSpark
REF_TOTAL_BASES CollectOxoGMetrics.CpcgMetrics
The total number of reference alleles observed
refactorNDNtoN(Cigar) NDNCigarReadTransformer
Refactor cigar strings that contain N-D-N elements to one N element (with total length of the three refactored elements).
refBases BAQ.BAQCalculationResult
reference PathSeqBuildKmers
reference OverhangFixingManager.Splice
REFERENCE CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
REFERENCE CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
REFERENCE ReorderSam.ReorderSamReferenceArgumentCollection
REFERENCE ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
REFERENCE_BASES_KEY ReferenceBases
REFERENCE_GENOTYPE_QUALITY GATKVCFConstants
REFERENCE_LONG_NAME StandardArgumentDefinitions
REFERENCE_LONG_NAME PathSeqBuildKmers
REFERENCE_SEQUENCE PicardCommandLineProgram
REFERENCE_SEQUENCE CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
REFERENCE_SEQUENCE OptionalReferenceArgumentCollection
REFERENCE_SEQUENCE RequiredReferenceArgumentCollection
REFERENCE_SEQUENCE CommandLineProgram
REFERENCE_SHARD_SIZE ReferenceShard
REFERENCE_SHORT_NAME StandardArgumentDefinitions
REFERENCE_SHORT_NAME PathSeqBuildKmers
REFERENCE_SHORT_NAME StandardOptionDefinitions
REFERENCE_VERSION_LONG_NAME FuncotatorArgumentDefinitions
referenceAlleleMatchesReferenceForIndel(List<Allele>, ReferenceSequence, int, int) LiftoverUtils
Checks whether the reference allele in the provided variant context actually matches the reference sequence
ReferenceArgumentCollection picard.cmdline.argumentcollections
Base interface for a reference argument collection.
referenceArguments GATKTool
referenceArguments GATKSparkTool
referenceArguments PathSeqBuildReferenceTaxonomy
ReferenceBases org.broadinstitute.hellbender.tools.walkers.annotator
Local reference context at a variant position.
ReferenceBases() ReferenceBases
ReferenceBases org.broadinstitute.hellbender.utils.reference
ReferenceBases stores the bases of the reference genome for a particular interval.
ReferenceBases(byte[], SimpleInterval) ReferenceBases
ReferenceConfidenceMode org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Reference confidence emission modes.
ReferenceConfidenceModel 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) ReferenceConfidenceModel
Create a new ReferenceConfidenceModel
ReferenceConfidenceVariantContextMerger org.broadinstitute.hellbender.tools.walkers
Variant context utilities related to merging variant-context instances.
ReferenceConfidenceVariantContextMerger(VariantAnnotatorEngine, VCFHeader) ReferenceConfidenceVariantContextMerger
ReferenceConfidenceVariantContextMerger.VCWithNewAlleles org.broadinstitute.hellbender.tools.walkers
ReferenceContext 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() ReferenceContext
Create a ReferenceContext with no backing data source.
ReferenceContext(ReferenceDataSource, SimpleInterval) 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) 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) ReferenceContext
Create a windowed ReferenceContext set up to lazily query the provided interval,
expanded by the specified number of bases in each direction.
ReferenceDataSource org.broadinstitute.hellbender.engine
Manages traversals and queries over reference data.
ReferenceDiploidExactAFCalculator org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
Reference implementation of multi-allelic EXACT model.
ReferenceDiploidExactAFCalculator() ReferenceDiploidExactAFCalculator
referenceFasta AbstractAlignmentMerger
referenceFasta AbstractAlignmentMerger
ReferenceFileSource org.broadinstitute.hellbender.engine.datasources
Class to load a reference sequence from a fasta file.
ReferenceFileSource(String) ReferenceFileSource
ReferenceFileSource(Path) ReferenceFileSource
ReferenceFileSource 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) ReferenceFileSource
Initialize this data source using a fasta file.
ReferenceFileSource(Path, boolean) ReferenceFileSource
Initialize this data source using a fasta file.
ReferenceHadoopSource org.broadinstitute.hellbender.engine.datasources
Class to load a reference sequence from a fasta file on HDFS.
ReferenceHadoopSource(String) ReferenceHadoopSource
ReferenceInputArgumentCollection org.broadinstitute.hellbender.cmdline.argumentcollections
An abstract ArgumentCollection for specifying a reference sequence file
ReferenceInputArgumentCollection() ReferenceInputArgumentCollection
ReferenceMemorySource org.broadinstitute.hellbender.engine
Manages traversals and queries over in-memory reference data.
ReferenceMemorySource(ReferenceBases, SAMSequenceDictionary) ReferenceMemorySource
Initialize this data source using ReferenceBases and corresponding sequence dictionary.
ReferenceMultiSource org.broadinstitute.hellbender.engine.datasources
Wrapper to load a reference sequence from the Google Genomics API, or a file stored on HDFS or locally.
ReferenceMultiSource() ReferenceMultiSource
ReferenceMultiSource(String, SerializableFunction<GATKRead, SimpleInterval>) ReferenceMultiSource
ReferenceMultiSourceAdapter(ReferenceMultiSource) HaplotypeCallerSpark.ReferenceMultiSourceAdapter
referencePath PSBwaArgumentCollection
ReferenceProgramGroup picard.cmdline.programgroups
Tools that analyze and manipulate FASTA format references
ReferenceProgramGroup() ReferenceProgramGroup
referenceSampleName UnifiedArgumentCollection
referenceSampleRod UnifiedArgumentCollection
referenceSequence CommandLineProgram
ReferenceShard 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) ReferenceShard
ReferenceSource org.broadinstitute.hellbender.engine.datasources
Internal interface to load a reference sequence.
referenceSpan AlignmentInterval
ReferenceTwoBitSource org.broadinstitute.hellbender.engine.spark.datasources
A ReferenceSource impl that is backed by a .2bit representation of a reference genome.
ReferenceTwoBitSource(String) ReferenceTwoBitSource
ReferenceUtils org.broadinstitute.hellbender.utils.reference
A collection of static methods for dealing with references.
referenceVersion Funcotator
ReferenceWindowFunctions org.broadinstitute.hellbender.engine.datasources
A library of reference window functions suitable for passing in to transforms such as AddContextDataToRead.
ReferenceWindowFunctions() ReferenceWindowFunctions
ReferenceWindowFunctions.FixedWindowFunction org.broadinstitute.hellbender.engine.datasources
A function for requesting a fixed number of extra bases of reference context on either side
of each read.
RefFlatReader picard.annotation
Loads gene annotations from a refFlat file into an OverlapDetector.
RefFlatReader.RefFlatColumns picard.annotation
ReflectionUtil picard.util
Class which contains utility functions that use reflection.
ReflectionUtil() ReflectionUtil
reflectiveCopy(TargetMetrics, MT, String[], String[]) 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.
REFSAMPLE_DEPTH_KEY GATKVCFConstants
REFSEQ_CATALOG_LONG_NAME PathSeqBuildReferenceTaxonomy
REFSEQ_CATALOG_SHORT_NAME PathSeqBuildReferenceTaxonomy
refseqCatalogPath PathSeqBuildReferenceTaxonomy
regionStartLoc ActivityProfile
regionStopLoc ActivityProfile
regionWithHigherCoordOnContig SimpleChimera
regionWithLowerCoordOnContig SimpleChimera
registerClasses(Kryo) GATKRegistrator
REJECT LiftOverIntervalList
REJECT LiftoverVcf
remap(Allele) GATKVariantContextUtils.AlleleMapper
remap(List<Allele>) GATKVariantContextUtils.AlleleMapper
remapAlleles(VariantContext, Allele) 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 finalAlleles set.
remove() AssemblyRegionIterator
remove() PairedStrandedIntervalTree.PairedStrandedIntervalTreeIterator
remove() PairedStrandedIntervalTree.PairedStrandedIntervalTreeOverlapperIterator
remove(SVInterval) SVIntervalTree
Remove an interval from the tree.
remove() SVIntervalTree.ValuesIterator
remove(Object) HopscotchCollection
remove(long) LargeLongHopscotchSet
remove(long) LongHopscotchSet
remove(long, int) LongHopscotchSet
remove() LongIterator
remove(Object) CountSet
remove(int) CountSet
Removes a single integer value for the set.
remove(Object) IndexedSet
Removes an element from the set.
remove() ReadsDownsamplingIterator
remove(GenomeLoc) GenomeLocSortedSet
a simple removal of an interval contained in this list.
remove() AllLocusIterator
remove() ReadCachingIterator
remove() ArtificialReadIterator
remove(int, String) DiskBasedReadEndsForMarkDuplicatesMap
remove(int, String) ReadEndsForMarkDuplicatesMap
Remove element with given key from the map.
remove() MultiHitAlignedReadIterator
Unsupported operation.
remove() XReadLines
remove() IlluminaDataProvider
remove() MultiTileParser
remove() PerTileParser
remove() AbstractIlluminaPositionFileReader
remove() BarcodeFileReader
remove() BclReader
remove() FilterFileReader
remove() TileMetricsOutReader
remove() MarkDuplicatesWithMateCigarIterator
remove(int, String) DiskBasedReadEndsForMarkDuplicatesMap
remove(ReadEndsForMateCigar) PhysicalLocationForMateCigarSet
Removes the end from this set, if present
remove(int, String) ReadEndsForMarkDuplicatesMap
Remove element with given key from the map.
remove() AsyncIterator
remove() DelimitedTextFileWithHeaderIterator
remove() ByIntervalListVariantContextIterator
remove() FilterApplyingVariantIterator
remove() PairedVariantSubContextIterator
remove() PredicateFilterDecoratingClosableIterator
REMOVE_ALIGNMENT_INFORMATION RevertSam
REMOVE_DUPLICATE_INFORMATION PositionBasedDownsampleSam
REMOVE_DUPLICATE_INFORMATION RevertSam
REMOVE_DUPLICATES AbstractMarkDuplicatesCommandLineProgram
REMOVE_DUPLICATES AbstractMarkDuplicatesCommandLineProgram
REMOVE_FILTERED_VARIANTS_LONG_NAME FuncotatorArgumentDefinitions
REMOVE_SEQUENCING_DUPLICATES MarkDuplicates
removeAll(Collection<GATKRead>) AssemblyRegion
Remove all of the reads in readsToRemove from this region
removeAll(Collection<?>) HopscotchCollection
unlike the AbstractCollection implementation, this one iterates over the supplied collection
removeAll(long[]) LargeLongHopscotchSet
removeAll(LongHopscotchSet) LongHopscotchSet
removeAll(long[]) LongHopscotchSet
removeAll(Collection<?>) CountSet
removeChild(int) PSTreeNode
removeEach(Object) HopscotchCollection
remove each of the elements equivalent to the key
removeEldestEntry(Map.Entry<K, V>) LRUCache
removeFilteredVariants Funcotator
removeIncompleteTrios() PedFile
Scans through the pedigrees and removes all entries that do not have both paternal and maternal ids set.
removeLocationSet() ReadEndsForMateCigar
RemoveNearbyIndels org.broadinstitute.hellbender.tools.walkers.validation
Remove indels that are close to another indel from a vcf file.
RemoveNearbyIndels() RemoveNearbyIndels
removeNonUniqueMappings(AssemblyContigWithFineTunedAlignments, int, int) AssemblyContigAlignmentsConfigPicker
Process provided originalConfiguration of an assembly contig and split between good and bad alignments.
removePathsNotConnectedToRef() 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) GATKVariantContextUtils
removeSampleReads(int, Collection<GATKRead>, int) ReadLikelihoods
removeShadowedContigs StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
removeSingletonOrphanVertices() BaseGraph
Remove all vertices in the graph that have in and out degree of 0
removeSingletonOrphanVertices() ReadThreadingGraph
removeStaleAttributesAfterMerge(Map<String, Object>) ReferenceConfidenceVariantContextMerger
Remove the stale attributes from the merged set
removeTag(GATKRead) SATagBuilder
Method that removes all SATag units from the list corresponding to the provided read based on start location
removeTag(SATagBuilder) SATagBuilder
Method that removes all SATag units from the list corresponding to the provided read based on start location
removeTag(String, int) SATagBuilder
Method that searches supplementaryReads for every read matching contig and start and removes them from the list.
removeTrailingDeletions(Cigar) AlignmentUtils
Removing a trailing deletion from the incoming cigar if present
removeUnreachableNodes() PSTree
Deletes nodes unreachable from the root and returns the set of deleted nodes.
removeVertex(MultiDeBruijnVertex) ReadThreadingGraph
removeVerticesNotConnectedToRefRegardlessOfEdgeDirection() 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 picard.vcf
Renames a sample within a VCF or BCF.
RenameSampleInVcf() RenameSampleInVcf
renderPhasingMetricsFilesFromBasecallingDirectory(File) TileMetricsUtil
renderSamFileHeader() XsvLocatableTableCodec
Create a SAM File Header from the preamble.
renderTileMetricsFileFromBasecallingDirectory(File, boolean) TileMetricsUtil
Returns the path to the TileMetrics file given the basecalling directory.
ReorderSam picard.sam
Reorders a SAM/BAM input file according to the order of contigs in a second reference file.
ReorderSam() ReorderSam
ReorderSam.ReorderSamReferenceArgumentCollection picard.sam
ReorderSamReferenceArgumentCollection() ReorderSam.ReorderSamReferenceArgumentCollection
repairSupplementaryTags(List<GATKRead>, SAMFileHeader) SplitNCigarReads
A method that repairs the NH and NM tags for a group of reads
REPEAT_TOLERANCE BaitDesigner
REPEAT_UNIT_KEY GATKVCFConstants
repeatBytes(byte, int) Utils
makes an array filled with n copies of the given byte.
repeatChars(char, int) Utils
makes an array filled with n copies of the given char.
REPEATS_PER_ALLELE_KEY GATKVCFConstants
replace(ReadEndsForMateCigar, ReadEndsForMateCigar) PhysicalLocationForMateCigarSet
Replaces a given end with the other end.
REPLACE_ARGUMENT_NAME UpdateVCFSequenceDictionary
replaceClumpedEventsWithBlockSubstitutions() EventMap
replaceExtension(String, String) IOUtils
replaceExtension(File, String) IOUtils
ReplaceSamHeader picard.sam
ReplaceSamHeader() ReplaceSamHeader
replicationRateFromReplicateSets IndependentReplicateMetric
reportMemoryStats MarkDuplicatesGATK
RepresentativeReadIndexer 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() RepresentativeReadIndexer
RepresentativeReadIndexerCodec picard.sam.markduplicates.util
Codec for read names and integers that outputs the primitive fields and reads them back.
RepresentativeReadIndexerCodec() RepresentativeReadIndexerCodec
representativeReadIndexInFile RepresentativeReadIndexer
requestedAlleleFrequencyCalculationModel StandardCallerArgumentCollection
Controls the model used to calculate the probability that a site is variant plus the various sample genotypes in the data at a given locus.
Require2BitReferenceForBroadcast() UserException.Require2BitReferenceForBroadcast
REQUIRE_INDEX VcfFormatConverter
RequiredFeatureInputArgumentCollection 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() RequiredFeatureInputArgumentCollection
RequiredIntervalArgumentCollection org.broadinstitute.hellbender.cmdline.argumentcollections
An ArgumentCollection that requires one or more intervals be specified with -L at the command line
RequiredIntervalArgumentCollection() RequiredIntervalArgumentCollection
RequiredReadInputArgumentCollection 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() RequiredReadInputArgumentCollection
RequiredReferenceArgumentCollection picard.cmdline.argumentcollections
Argument collection for references that are required (and not common).
RequiredReferenceArgumentCollection() RequiredReferenceArgumentCollection
RequiredReferenceInputArgumentCollection org.broadinstitute.hellbender.cmdline.argumentcollections
An argument collection for use with tools that require a reference file as input.
RequiredReferenceInputArgumentCollection() RequiredReferenceInputArgumentCollection
RequiredVariantInputArgumentCollection 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() RequiredVariantInputArgumentCollection
requiresCoordinateSortOrder() FractionalDownsampler
requiresCoordinateSortOrder() MutectDownsampler
requiresCoordinateSortOrder() PassThroughDownsampler
requiresCoordinateSortOrder() PositionalDownsampler
requiresCoordinateSortOrder() ReadsDownsampler
Does this downsampler require that reads be fed to it in coordinate order?
requiresCoordinateSortOrder() ReservoirDownsampler
requiresFeatures() FeatureWalker
requiresFeatures() GATKTool
Does this tool require features? Traversals types and/or tools that do should override to return true.
requiresFeatures() VariantWalkerBase
requiresIntervals() GATKTool
Does this tool require intervals? Traversals types and/or tools that do should override to return true.
requiresIntervals() IntervalWalker
requiresIntervals() GATKSparkTool
Does this tool require intervals? Tools that do should override to return true.
requiresIntervals() IntervalWalkerSpark
requiresIntervals() AnnotateIntervals
requiresIntervals() CollectAllelicCounts
requiresIntervals() CollectReadCounts
requiresIntervals() GenomicsDBImport
requiresReads() AssemblyRegionWalker
requiresReads() GATKTool
Does this tool require reads? Traversals types and/or tools that do should override to return true.
requiresReads() LocusWalker
LocusWalkers requires read sources
requiresReads() ReadWalker
requiresReads() AssemblyRegionWalkerSpark
requiresReads() GATKSparkTool
Does this tool require reads? Tools that do should override to return true.
requiresReads() LocusWalkerSpark
requiresReads() ReadWalkerSpark
requiresReads() AnnotatePairOrientation
requiresReads() GetSampleName
requiresReads() HaplotypeCallerSpark
requiresReads() ApplyBQSRSpark
requiresReads() BaseRecalibratorSpark
requiresReads() BwaSpark
requiresReads() PathSeqFilterSpark
requiresReads() PathSeqPipelineSpark
requiresReads() PileupSpark
requiresReads() BQSRPipelineSpark
requiresReads() BwaAndMarkDuplicatesPipelineSpark
requiresReads() CountBasesSpark
requiresReads() CountReadsSpark
requiresReads() FlagStatSpark
requiresReads() MetricsCollectorSparkTool
requiresReads() PrintReadsSpark
requiresReads() ReadsPipelineSpark
requiresReads() SortSamSpark
requiresReads() DiscoverVariantsFromContigAlignmentsSAMSpark
requiresReads() CpxVariantReInterpreterSpark
requiresReads() SvDiscoverFromLocalAssemblyContigAlignmentsSpark
requiresReads() CalcMetadataSpark
requiresReads() ExtractSVEvidenceSpark
requiresReads() FindBreakpointEvidenceSpark
requiresReads() StructuralVariationDiscoveryPipelineSpark
requiresReads() ExtractOriginalAlignmentRecordsByNameSpark
requiresReads() MarkDuplicatesSpark
requiresReads() CompareDuplicatesSpark
requiresReads() GetPileupSummaries
requiresReads() FilterAlignmentArtifacts
requiresReads() ValidateBasicSomaticShortMutations
requiresReference() AssemblyRegionWalker
requiresReference() GATKTool
Does this tool require reference data? Traversals types and/or tools that do should override to return true.
requiresReference() MultiVariantWalkerGroupedOnStart
requiresReference() AssemblyRegionWalkerSpark
requiresReference() GATKSparkTool
Does this tool require reference data? Tools that do should override to return true.
requiresReference() AnnotateIntervals
requiresReference() CollectAllelicCounts
requiresReference() PreprocessIntervals
requiresReference() TagGermlineEvents
requiresReference() ExampleReadWalkerWithReferenceSpark
requiresReference() Funcotator
requiresReference() HaplotypeCallerSpark
requiresReference() LeftAlignIndels
requiresReference() BaseRecalibratorSpark
requiresReference() BwaSpark
requiresReference() BQSRPipelineSpark
requiresReference() BwaAndMarkDuplicatesPipelineSpark
requiresReference() MetricsCollectorSpark
Return whether or not this collector requires a reference.
requiresReference() ReadsPipelineSpark
requiresReference() DiscoverVariantsFromContigAlignmentsSAMSpark
requiresReference() CpxVariantReInterpreterSpark
requiresReference() SvDiscoverFromLocalAssemblyContigAlignmentsSpark
requiresReference() FindBadGenomicKmersSpark
requiresReference() StructuralVariationDiscoveryPipelineSpark
requiresReference() BaseRecalibrator
requiresReference() GetPileupSummaries
requiresReference() GenotypeGVCFs
requiresReference() CheckPileup
requiresReference() SplitNCigarReads
requiresReference() ValidateBasicSomaticShortMutations
requiresReference() CNNScoreVariants
requiresReference() CollectSequencingArtifactMetrics
requiresReference() CollectOxoGMetrics
requiresReference() CollectWgsMetrics
requiresReference() CommandLineProgram
requiresReference() IdentifyContaminant
requiresReference() ExtractSequences
requiresReference() MergeBamAlignment
requiresReference() SetNmMdAndUqTags
requiresReference() BaitDesigner
ReservoirDownsampler 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, boolean) ReservoirDownsampler
Construct a ReservoirDownsampler
ReservoirDownsampler(int) ReservoirDownsampler
Construct a ReservoirDownsampler
reset() HaplotypeCallerSpark.ReferenceMultiSourceAdapter
reset() ArtificialReadIterator
reset() ArtificialReadQueryIterator
resetFilteredCount() CountingReadFilter
resetFilteredCount() CountingVariantFilter
resetOriginalBaseQualities(GATKRead) ReadUtils
Resets the quality scores of the reads to the orginal (pre-BQSR) ones.
resetRandomGenerator() Utils
resetRefSeqFileWalker() AbstractAlignmentMerger
resetRefSeqFileWalker() AbstractAlignmentMerger
resetStats() Downsampler
Reset stats in the downsampler such as the number of discarded items *without* clearing the downsampler of items
resolveIncompatibleAlleles(Allele, VariantContext, LinkedHashSet<Allele>) GATKVariantContextUtils
Resource org.broadinstitute.hellbender.utils.io
Stores a resource by path and a relative class.
Resource(String, Class<?>) Resource
Create a resource with a path and a relative class.
resources VariantAnnotator
An external resource VCF file or files from which to annotate.
RESTORE_ORIGINAL_QUALITIES RevertOriginalBaseQualitiesAndAddMateCigar
RESTORE_ORIGINAL_QUALITIES RevertSam
restoreHeaderIfNecessary(GATKRead, SAMFileHeader) ReadUtils
Checks whether read is a headerless SAMRecordToGATKReadAdapter, and if it is, sets its
header to the provided header.
restrictToIntervals ActivityProfile
Result(boolean, boolean, AssemblyRegion, int, int, List<VariantContext>, Pair<SimpleInterval, SimpleInterval>, SimpleInterval, SimpleInterval, SimpleInterval, SimpleInterval) AssemblyRegionTrimmer.Result
Creates a trimming result given all its properties.
Result(double, double, double, double) MannWhitneyU.Result
RESULT CrosscheckMetric
result() CallingMetricAccumulator
result() VariantProcessor.Accumulator
retainAll(Collection<?>) CountSet
retainNodes(Set<Integer>) PSTree
Removes all nodes not in the given set
REV_COMPED_ALLELES LiftoverUtils
REV_CXT_ALT_BASES SequencingArtifactMetrics.BaitBiasDetailMetrics
The number of ~REF_BASE:~ALT_BASE alignments at sites complementary to the given reference context.
REV_CXT_REF_BASES SequencingArtifactMetrics.BaitBiasDetailMetrics
The number of ~REF_BASE:~REF_BASE alignments at sites complementary to the given reference context.
REV_ERROR_RATE 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 AS_StrandBiasTest
reverseComplement(int) SVKmer
reverseComplement(long) SVKmer
reverseComplement(int) SVKmerLong
Returns a new SVKmerLong that's the reverse-complement of this one.
reverseComplement(int) SVKmerShort
Returns a new SVKmerShort that's the reverse-complement of this one.
reverseComplementByteValueAsLong(int) SVKmer
reverseComplementVariantContext(VariantContext, Interval, ReferenceSequence) LiftoverUtils
reverseIterator() SVIntervalTree
Return an iterator over the entire tree that returns intervals in reverse order.
reverseIterator(SVInterval) SVIntervalTree
Return an iterator over all intervals less than or equal to the specified interval, in reverse order.
reverseTrimAlleles(VariantContext) GATKVariantContextUtils
Trim the alleles in inputVC from the reverse direction
RevertBaseQualityScores org.broadinstitute.hellbender.tools.walkers
RevertBaseQualityScores() RevertBaseQualityScores
RevertOriginalBaseQualitiesAndAddMateCigar picard.sam
This tool reverts the original base qualities (if specified) and adds the mate cigar tag to mapped BAMs.
RevertOriginalBaseQualitiesAndAddMateCigar() RevertOriginalBaseQualitiesAndAddMateCigar
RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile picard.sam
Used as a return for the canSkipSAMFile function.
RevertSam picard.sam
Reverts a SAM file by optionally restoring original quality scores and by removing
all alignment information.
RevertSam() RevertSam
RevertSam.FileType picard.sam
revertSamRecord(SAMRecord) RevertSam
Takes an individual SAMRecord and applies the set of changes/reversions to it that
have been requested by program level options.
revertSoftClippedBases(GATKRead) ReadClipper
Reverts ALL soft-clipped bases
reviseAndConditionallyLogQuality(byte) 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>) SVIntervalTree.RevIterator
RExecutor picard.util
Util class for executing R scripts.
RExecutor() RExecutor
RF ReadEnds
RF ReadEnds
RG_TAG SamToFastq
RGCN AddOrReplaceReadGroups
RGDS AddOrReplaceReadGroups
RGDT AddOrReplaceReadGroups
RGFO AddOrReplaceReadGroups
RGID AddOrReplaceReadGroups
RGKS AddOrReplaceReadGroups
RGLB AddOrReplaceReadGroups
RGPG AddOrReplaceReadGroups
RGPI AddOrReplaceReadGroups
RGPL AddOrReplaceReadGroups
RGPM AddOrReplaceReadGroups
RGPU AddOrReplaceReadGroups
RGSM AddOrReplaceReadGroups
rhs ReadFilter.ReadFilterBinOp
RIBOSOMAL_BASES RnaSeqMetrics
Number of bases in primary alignments that align to ribosomal sequence.
RIBOSOMAL_INTERVALS CollectRnaSeqMetrics
ribosomalInitialValue RnaSeqMetricsCollector
RIGHT_FILE CrosscheckMetric
RIGHT_GROUP_VALUE CrosscheckMetric
RIGHT_LANE CrosscheckMetric
RIGHT_LIBRARY CrosscheckMetric
RIGHT_MOLECULAR_BARCODE_SEQUENCE CrosscheckMetric
RIGHT_PRIMER BaitDesigner
RIGHT_RUN_BARCODE CrosscheckMetric
RIGHT_SAMPLE CrosscheckMetric
rightMedianDeviation(int) IntHistogram.CDF
rightVariantContext PairedVariantSubContextIterator.VcfTuple
rms(Collection<Integer>) MathUtils
Computes the root mean square of the given array or 0.0 if the array is empty.
RMSMappingQuality org.broadinstitute.hellbender.tools.walkers.annotator
Root Mean Square of the mapping quality of reads across all samples.
RMSMappingQuality() RMSMappingQuality
RnaSeqMetrics 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() RnaSeqMetrics
RnaSeqMetricsCollector picard.analysis.directed
RnaSeqMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, Long, OverlapDetector<Gene>, OverlapDetector<Interval>, HashSet<Integer>, int, RnaSeqMetricsCollector.StrandSpecificity, double, boolean) RnaSeqMetricsCollector
RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector picard.analysis.directed
RnaSeqMetricsCollector.StrandSpecificity picard.analysis.directed
RobustBrentSolver org.broadinstitute.hellbender.utils.solver
A robust version of the Brent solver that tries to avoid spurious non-bracketing conditions.
RobustBrentSolver(double, double, double, UnivariateFunction, int, int) RobustBrentSolver
round(double, int) MathUtil
Round off the value to the specified precision.
ROUND_DOWN_QUANTIZED_LONG_NAME CompareBaseQualities
roundDown 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 CompareBaseQualities
roundPhred(double, double) MathUtils
Round a Phred scaled score to precision phredScorePrecision
roundToNDecimalPlaces(double, int) MathUtils
Rounds the double to the given number of decimal places.
roundTripInKryo(T, Class<?>, SparkConf) SparkTestUtils
Takes an input object and returns the value of the object after it has been serialized and then deserialized in Kryo.
rowMeans(RealMatrix) MathUtils
rowStdDevs(RealMatrix) MathUtils
Calculates the standard deviation per row from a matrix.
rowSums(RealMatrix) MathUtils
Return an array with row sums in each entry
rowVariances(RealMatrix) MathUtils
RR ReadEnds
RR ReadEnds
RrbsCpgDetailMetrics picard.analysis
Holds information about CpG sites encountered for RRBS processing QC
RrbsCpgDetailMetrics() RrbsCpgDetailMetrics
RrbsMetricsCollector picard.analysis
RrbsMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, int, int, int, double) RrbsMetricsCollector
RrbsSummaryMetrics picard.analysis
Holds summary statistics from RRBS processing QC
RrbsSummaryMetrics() RrbsSummaryMetrics
RRNA_FRAGMENT_PERCENTAGE CollectRnaSeqMetrics
RScriptExecutor org.broadinstitute.hellbender.utils.R
Generic service for executing RScripts
RScriptExecutor() RScriptExecutor
RScriptExecutor(boolean) RScriptExecutor
RScriptExecutorException org.broadinstitute.hellbender.utils.R
RScriptExecutorException(String) RScriptExecutorException
RScriptLibrary org.broadinstitute.hellbender.utils.R
Libraries embedded in the StingUtils package.
run() ExtractIlluminaBarcodes.PerTileBarcodeExtractor
run method which extracts barcodes and accumulates metrics for an entire tile
run() Test
RUN_BARCODE BamToBfq
RUN_BARCODE IlluminaBasecallsToFastq
RUN_BARCODE IlluminaBasecallsToSam
RUN_DATE FastqToSam
RUN_DIRECTORY CollectIlluminaLaneMetrics
RUN_MODE_LONG_NAME GermlineCNVCaller
RUN_START_DATE IlluminaBasecallsToSam
RUN_WITHOUT_DBSNP RecalibrationArgumentCollection
runCommandLine(List<String>) CommandLineProgramTester
Runs the command line implemented by this test.
runCommandLine(List<String>, String) CommandLineProgramTester
runCommandLine(String[]) CommandLineProgramTester
runCommandLine(ArgumentsBuilder) CommandLineProgramTester
runCommandLineProgram(CommandLineProgram, String[]) Main
Run the given command line program with the raw arguments from the command line
runLocalAssembly(AssemblyRegion, Haplotype, byte[], SimpleInterval, List<VariantContext>, ReadErrorCorrector, SAMFileHeader, SmithWatermanAligner) ReadThreadingAssembler
Main entry point into the assembly engine.
runMCMC() GibbsSampler
Runs the Monte Carlo Markov Chain, using the state of the model provided in the constructor to initialize.
running ProcessControllerBase
RunningAverage() MathUtils.RunningAverage
runningOnArchitecture(String) NativeUtils
runningOnLinux() NativeUtils
runningOnMac() NativeUtils
runningOnPPCArchitecture() NativeUtils
boolean : returns whether the current platform is PowerPC, LE only
runOnIsolatedMiniCluster(MiniClusterUtils.MiniClusterTest) MiniClusterUtils
runPipeline(JavaSparkContext) GATKSparkTool
runPipeline(JavaSparkContext) SparkCommandLineProgram
Runs the pipeline.
runPipeline(JavaSparkContext) VariantWalkerSpark
runPipeline(JavaSparkContext) CreateReadCountPanelOfNormals
runPipeline(JavaSparkContext) ExampleNioCountReads
Runs the pipeline.
runPipeline(JavaSparkContext) BaseRecalibratorSparkSharded
runProcess(ProcessController, String[]) BaseTest
run an external process and assert that it finishes with exit code 0
runProcess(ProcessController, String[], String) BaseTest
run an external process and assert that it finishes with exit code 0
runProcess(ProcessController, String[], Map<String, String>, String) BaseTest
run an external process and assert that it finishes with exit code 0
runTest() SamFileTester
Sets up the basic command line arguments for input and output and runs instanceMain.
RuntimeUtils org.broadinstitute.hellbender.utils.runtime
RuntimeUtils() RuntimeUtils
runTool() CommandLineProgram
Template method that runs the startup hook, doWork and then the shutdown hook.
runTool(JavaSparkContext) AssemblyRegionWalkerSpark
runTool(JavaSparkContext) GATKSparkTool
Runs the tool itself after initializing and validating inputs.
runTool(JavaSparkContext) IntervalWalkerSpark
runTool(JavaSparkContext) LocusWalkerSpark
runTool(JavaSparkContext) ReadWalkerSpark
runTool(JavaSparkContext) VariantWalkerSpark
runTool(JavaSparkContext) HaplotypeCallerSpark
runTool(JavaSparkContext) ApplyBQSRSpark
runTool(JavaSparkContext) BaseRecalibratorSpark
runTool(JavaSparkContext) BwaSpark
runTool(JavaSparkContext) ParallelCopyGCSDirectoryIntoHDFSSpark
runTool(JavaSparkContext) PathSeqBwaSpark
runTool(JavaSparkContext) PathSeqFilterSpark
runTool(JavaSparkContext) PathSeqPipelineSpark
runTool(JavaSparkContext) PathSeqScoreSpark
runTool(JavaSparkContext) BQSRPipelineSpark
runTool(JavaSparkContext) BwaAndMarkDuplicatesPipelineSpark
runTool(JavaSparkContext) CountBasesSpark
runTool(JavaSparkContext) CountReadsSpark
runTool(JavaSparkContext) CountVariantsSpark
runTool(JavaSparkContext) FlagStatSpark
runTool(JavaSparkContext) CollectBaseDistributionByCycleSpark
runTool(JavaSparkContext) CollectMultipleMetricsSpark
runTool(JavaSparkContext) MeanQualityByCycleSpark
runTool(JavaSparkContext) MetricsCollectorSparkTool
The runTool method used when metrics collector tools are run
"standalone".
runTool(JavaSparkContext) QualityScoreDistributionSpark
runTool(JavaSparkContext) PrintReadsSpark
runTool(JavaSparkContext) ReadsPipelineSpark
runTool(JavaSparkContext) SortSamSpark
runTool(JavaSparkContext) DiscoverVariantsFromContigAlignmentsSAMSpark
runTool(JavaSparkContext) CpxVariantReInterpreterSpark
runTool(JavaSparkContext) SvDiscoverFromLocalAssemblyContigAlignmentsSpark
runTool(JavaSparkContext) CalcMetadataSpark
runTool(JavaSparkContext) ExtractSVEvidenceSpark
runTool(JavaSparkContext) FindBadGenomicKmersSpark
Get the list of high copy number kmers in the reference, and write them to a file.
runTool(JavaSparkContext) FindBreakpointEvidenceSpark
runTool(JavaSparkContext) StructuralVariationDiscoveryPipelineSpark
runTool(JavaSparkContext) ExtractOriginalAlignmentRecordsByNameSpark
runTool(JavaSparkContext) MarkDuplicatesSpark
runTool(JavaSparkContext) CompareDuplicatesSpark
S_LOCS_FILE AbstractIlluminaPositionFileReader
SA_TAG_FIELD_SEPARATOR AlignmentInterval
String used to separate fields in an alignment-interval string
representation.
SA_TAG_INTERVAL_SEPARATOR_STR AlignmentInterval
String used to separate several alignment-intervals in a
SA Tag like string.
safeCombine(RecalibrationTables, RecalibrationTables) RecalibrationTables
Combines the two tables into a new table (allocating a new table in the process)
SAM_DUPLICATE_READ_FLAG ReadUtils
SAM_FILE_HEADER_START XsvLocatableTableCodec
SAM_FIRST_OF_PAIR_FLAG ReadUtils
SAM_MATE_STRAND_FLAG ReadUtils
SAM_MATE_UNMAPPED_FLAG ReadUtils
SAM_NOT_PRIMARY_ALIGNMENT_FLAG ReadUtils
SAM_PILEUP_FILE_EXTENSIONS SAMPileupCodec
SAM_PROPER_PAIR_FLAG ReadUtils
SAM_READ_FAILS_VENDOR_QUALITY_CHECK_FLAG ReadUtils
SAM_READ_PAIRED_FLAG ReadUtils
SAM_READ_STRAND_FLAG ReadUtils
SAM_READ_UNMAPPED_FLAG ReadUtils
SAM_SECOND_OF_PAIR_FLAG ReadUtils
SAM_SUPPLEMENTARY_ALIGNMENT_FLAG ReadUtils
SamAlignmentMerger 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(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) SamAlignmentMerger
Constructor
SamAlignmentMerger 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, boolean, int) 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>) SamAlignmentMerger
Constructor
SamAssertionUtils org.broadinstitute.hellbender.utils.test
Collection of utilities for making common assertions about SAM files for unit testing purposes.
SamAssertionUtils() SamAssertionUtils
SamComparison org.broadinstitute.hellbender.utils.read
Rudimentary SAM comparer.
SamComparison(SamReader, SamReader) SamComparison
Note: the caller must make sure the SamReaders are closed properly.
SAMFileDestination org.broadinstitute.hellbender.utils.haplotype
Class used to direct output from a HaplotypeBAMWriter to a bam/sam file.
SAMFileDestination(Path, boolean, boolean, SAMFileHeader, String) SAMFileDestination
Create a new file destination.
SAMFileGATKReadWriter org.broadinstitute.hellbender.utils.read
A GATKRead writer that writes to a SAM/BAM file.
SAMFileGATKReadWriter(SAMFileWriter) SAMFileGATKReadWriter
samFiles CompareBaseQualities
samFiles CompareSAMs
SamFileTester org.broadinstitute.hellbender.utils.test.testers
Abstract class for doing basic on the fly SAM file testing.
SamFileTester(int, boolean, int, DuplicateScoringStrategy.ScoringStrategy, SAMFileHeader.SortOrder, boolean) SamFileTester
SamFileTester(int, boolean, int, DuplicateScoringStrategy.ScoringStrategy, SAMFileHeader.SortOrder) SamFileTester
SamFileTester(int, boolean, int, DuplicateScoringStrategy.ScoringStrategy) SamFileTester
SamFileTester(int, boolean, int) SamFileTester
SamFileTester(int, boolean) SamFileTester
SamFormatConverter picard.sam
Converts a BAM file to human-readable SAM output or vice versa
SamFormatConverter() SamFormatConverter
SAMFormattedContigAlignmentParser(JavaRDD<GATKRead>, SAMFileHeader, boolean) SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SAMFormattedContigAlignmentParser
samHeader ReadFilter
samHeader ReadsSparkSink.SparkSAMOutputFormat
samHeader ActivityProfile
SamHeaderAndIterator(SAMFileHeader, CloseableIterator<SAMRecord>, List<SamReader>) AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
SamHeaderAndIterator(SAMFileHeader, CloseableIterator<SAMRecord>) AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
samjdk_compression_level() GATKConfig
samjdk_use_async_io_read_samtools() GATKConfig
samjdk_use_async_io_write_samtools() GATKConfig
samjdk_use_async_io_write_tribble() GATKConfig
SAMPileupCodec org.broadinstitute.hellbender.utils.codecs.sampileup
Decoder for single sample SAM pileup data.
SAMPileupCodec() SAMPileupCodec
SAMPileupElement org.broadinstitute.hellbender.utils.codecs.sampileup
Simple representation of a single base with associated quality from a SAM pileup
SAMPileupFeature org.broadinstitute.hellbender.utils.codecs.sampileup
A tribble feature representing a SAM pileup.
SAMPLE MultiLevelMetrics
The sample to which these metrics apply.
SAMPLE SplitReads
sample ReadLikelihoods.BestAllele
The containing sample.
sample(RandomGenerator, Function<Double, Double>) AdaptiveMetropolisSampler
sample(RandomGenerator, Function<Double, Double>, int, int) AdaptiveMetropolisSampler
Generate multiple samples from the probability density function.
sample(RandomGenerator, S, T) ParameterSampler
sample(double) SliceSampler
Generate a single sample from the probability density function, given an initial value to use in slice construction.
sample(double, int) SliceSampler
Generate multiple samples from the probability density function, given an initial value to use in slice construction.
Sample org.broadinstitute.hellbender.utils.samples
Represents an individual under study.
Sample(String, String, String, String, Sex, Affection) Sample
Sample(String, String, String, String, Sex) Sample
SAMPLE FingerprintingDetailMetrics
The name of the sample who's genotypes the sequence data was compared to.
SAMPLE FingerprintingSummaryMetrics
The sample whose known genotypes the sequence data was compared to.
SAMPLE CollectIndependentReplicateMetrics
SAMPLE MultilevelMetrics
The sample to which these metrics apply.
SAMPLE MakeSitesOnlyVcf
SAMPLE_ALIAS SequencingArtifactMetrics.BaitBiasDetailMetrics
SAMPLE_ALIAS SequencingArtifactMetrics.BaitBiasSummaryMetrics
The name of the sample being assayed.
SAMPLE_ALIAS SequencingArtifactMetrics.PreAdapterDetailMetrics
The name of the sample being assayed.
SAMPLE_ALIAS SequencingArtifactMetrics.PreAdapterSummaryMetrics
The name of the sample being assayed.
SAMPLE_ALIAS CollectOxoGMetrics.CpcgMetrics
The name of the sample being assayed.
SAMPLE_ALIAS IdentifyContaminant
SAMPLE_ALIAS IlluminaBasecallsToSam
SAMPLE_ALIAS RevertSam
SAMPLE_ALIAS CollectVariantCallingMetrics.VariantCallingDetailMetrics
The name of the sample being assayed
SAMPLE_ALIAS_SHORT_NAME StandardArgumentDefinitions
SAMPLE_ALIAS_SHORT_NAME StandardOptionDefinitions
SAMPLE_INDEX_LONG_NAME PostprocessGermlineCNVCalls
SAMPLE_LIST_KEY GATKVCFConstants
SAMPLE_LONG_NAME SplitReads
SAMPLE_NAME ReadFilterArgumentDefinitions
SAMPLE_NAME FastqToSam
SAMPLE_NAME_DISCOVERY_VCF_LONG_NAME ValidateBasicSomaticShortMutations
SAMPLE_NAME_LONG_NAME StandardArgumentDefinitions
SAMPLE_NAME_MAP_LONG_NAME GenomicsDBImport
SAMPLE_NAME_SHORT_NAME StandardArgumentDefinitions
SAMPLE_NAME_TXT_FILE GermlineCNVNamingConstants
SAMPLE_NAME_VALIDATION_CASE ValidateBasicSomaticShortMutations
SAMPLE_NAME_VALIDATION_CONTROL ValidateBasicSomaticShortMutations
SAMPLE_PREFIX GermlineCNVNamingConstants
SAMPLE_PSI_SCALE_LONG_NAME GermlineContigPloidyModelArgumentCollection
SAMPLE_PSI_SCALE_LONG_NAME GermlineDenoisingModelArgumentCollection
SAMPLE_SHORT_NAME SplitReads
SAMPLE_SIZE CollectWgsMetrics
SAMPLE_SIZE CollectTargetedMetrics
sampleBarcodes ReadStructure
sampleCount() SampleDB
Get number of sample objects
sampleCumulativeSums(int, int, boolean) TheoreticalSensitivity.RouletteWheel
SampleDB org.broadinstitute.hellbender.utils.samples
Simple database for managing samples
SampleDBBuilder org.broadinstitute.hellbender.utils.samples
Class for creating a temporary in memory database of samples.
SampleDBBuilder(PedigreeValidationType) SampleDBBuilder
sampleIndicesWithoutReplacement(int, int) MathUtils
Creates a new sample of k ints from [0..n-1], without duplicates.
sampleLikelihoods(int) GenotypingLikelihoods
Returns the genotype-likelihoods of the sample given its index in the collection.
SampleList org.broadinstitute.hellbender.tools.walkers.annotator
List samples that are non-reference at a given variant site
SampleList() SampleList
SampleList org.broadinstitute.hellbender.utils.genotyper
An immutable, indexed set of samples.
SampleLocatableMetadata 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) ReadLikelihoods
Returns a read vs allele likelihood matrix corresponding to a sample.
SampleMetadata org.broadinstitute.hellbender.tools.copynumber.formats.metadata
Interface for marking objects that contain metadata associated with a single sample.
sampleName GermlineCNVVariantComposer
sampleNameMapPath FixCallSetSampleOrdering
SampleNameSplitter org.broadinstitute.hellbender.tools.readersplitters
Splits readers sample names.
SampleNameSplitter() SampleNameSplitter
sampleNameToUse HaplotypeCallerArgumentCollection
You can use this argument to specify that HC should process a single sample out of a multisample BAM file.
samplePloidy GenotypeCalculationArgumentCollection
Sample ploidy - equivalent to number of chromosomes per pool.
samplePloidy(int) GenotypingLikelihoods
Returns the ploidy of the sample given its index in the collection.
samplePloidy(int) HeterogeneousPloidyModel
samplePloidy(int) HomogeneousPloidyModel
samplePloidy(int) PloidyModel
Return the assumed ploidy for a sample given its index.
sampleReadCount(int) ReadLikelihoods
Returns the number of reads that belong to a sample in the read-likelihood collection.
SampleReadFilter org.broadinstitute.hellbender.engine.filters
Keep only reads for a given sample.
SampleReadFilter() SampleReadFilter
SampleReadFilter(SAMFileHeader) SampleReadFilter
sampleReads(int) ReadLikelihoods
Returns the reads that belong to a sample sorted by their index (within that sample).
samples GenotypingEngine
samples ReadLikelihoods
Sample list
samples() ReadLikelihoods
Returns the samples in this read-likelihood collection.
SampleSpecificData(String, Broadcast<SVIntervalTree<VariantContext>>, List<SVInterval>, PairedStrandedIntervalTree<EvidenceTargetLink>, ReadMetadata, Broadcast<SAMFileHeader>) SvDiscoveryInputMetaData.SampleSpecificData
samplesToKeep SampleReadFilter
SamReaderQueryingIterator 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) 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) SamReaderQueryingIterator
Create a SamReaderQueryingIterator given a SamReader and a set of traversal parameters governing
which reads are to be returned during iteration.
SAMRecordAndReference org.broadinstitute.hellbender.metrics
SAMRecordAndReference(SAMRecord, ReferenceSequence) SAMRecordAndReference
SAMRecordAndReference picard.metrics
SAMRecordAndReference(SAMRecord, ReferenceSequence) SAMRecordAndReference
SAMRecordAndReferenceMultiLevelCollector BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends java.lang.Comparable<HKEY >> - Class in org.broadinstitute.hellbender.metrics
SAMRecordAndReferenceMultiLevelCollector() SAMRecordAndReferenceMultiLevelCollector
SAMRecordAndReferenceMultiLevelCollector BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends java.lang.Comparable> - Class in picard.metrics
SAMRecordAndReferenceMultiLevelCollector() SAMRecordAndReferenceMultiLevelCollector
SAMRecordMultiLevelCollector BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends java.lang.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() SAMRecordMultiLevelCollector
SAMRecordMultiLevelCollector BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends java.lang.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() SAMRecordMultiLevelCollector
SAMRecordSerializer org.broadinstitute.hellbender.engine.spark
Efficient serializer for SAMRecords that uses SAMRecordSparkCodec for encoding/decoding.
SAMRecordSerializer() SAMRecordSerializer
SAMRecordSparkCodec htsjdk.samtools
A class that uses a slightly adapted version of BAMRecordCodec for serialization/deserialization of SAMRecords.
SAMRecordSparkCodec() SAMRecordSparkCodec
SAMRecordSparkCodec(SAMRecordFactory) SAMRecordSparkCodec
samRecordToDuplicatesFlagsKey(SAMRecord) SamFileTester
SAMRecordToGATKReadAdapter org.broadinstitute.hellbender.utils.read
Implementation of the
GATKRead interface for the
SAMRecord class.
SAMRecordToGATKReadAdapter(SAMRecord) SAMRecordToGATKReadAdapter
SAMRecordToGATKReadAdapterSerializer org.broadinstitute.hellbender.engine.spark
Efficient serializer for SAMRecordToGATKReadAdapters that uses SAMRecordSparkCodec for encoding/decoding.
SAMRecordToGATKReadAdapterSerializer() SAMRecordToGATKReadAdapterSerializer
SAMRecordToReadIterator org.broadinstitute.hellbender.utils.iterators
Wraps a SAMRecord iterator within an iterator of GATKReads.
SAMRecordToReadIterator(Iterator<SAMRecord>) SAMRecordToReadIterator
samRecordWithOrdinal ReadEndsForMateCigar
SamRecordWithOrdinalAndSetDuplicateReadFlag org.broadinstitute.hellbender.utils.read.markduplicates
This class sets the duplicate read flag as the result state when examining sets of records.
SamRecordWithOrdinalAndSetDuplicateReadFlag() SamRecordWithOrdinalAndSetDuplicateReadFlag
SamRecordWithOrdinalAndSetDuplicateReadFlag(SAMRecord, long) SamRecordWithOrdinalAndSetDuplicateReadFlag
SamRecordWithOrdinalAndSetDuplicateReadFlag picard.sam.markduplicates.util
This class sets the duplicate read flag as the result state when examining sets of records.
SamRecordWithOrdinalAndSetDuplicateReadFlag() SamRecordWithOrdinalAndSetDuplicateReadFlag
SamRecordWithOrdinalAndSetDuplicateReadFlag(SAMRecord, long) SamRecordWithOrdinalAndSetDuplicateReadFlag
samsEqualLenient(File, File, ValidationStringency, File) SamAssertionUtils
Compares SAM/BAM files in a stringent way but not by byte identity (allow reorder of attributes).
samsEqualStringent(File, File, ValidationStringency, File) SamAssertionUtils
Compares SAM/BAM files in a stringent way but not by byte identity (allow reorder of attributes)
Comparing by MD5s is too strict and comparing by SamComparison is too lenient.
samsEqualStringent(Path, Path, ValidationStringency, Path) SamAssertionUtils
Compares SAM/BAM files in a stringent way but not by byte identity (allow reorder of attributes)
Comparing by MD5s is too strict and comparing by SamComparison is too lenient.
SamToFastq 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() SamToFastq
SamToFastqWithTags 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() SamToFastqWithTags
SAMTOOLS_OVERLAP_LOW_CONFIDENCE ReadPileup
Constant used by samtools to downgrade a quality for overlapping reads that disagrees in their base.
SANITIZE RevertSam
SATagBuilder org.broadinstitute.hellbender.utils
A builder class that expands functionality for SA tags.
SATagBuilder(GATKRead) SATagBuilder
saveMetrics(MetricsFile<?, ?>, String) MetricsUtils
saveMetrics(String) ExampleCollectMultiMetricsSpark
Finish the collection process and save any results.
saveMetrics(MetricsFile<ExampleMultiMetrics, Integer>) ExampleMultiMetricsCollector
Finish the metrics collection and save any results to the metrics file.
saveMetrics(String) ExampleMultiMetricsCollectorSpark
Save the metrics out to a file.
saveMetrics(String) ExampleCollectSingleMetricsSpark
Finish the collection process and save any results.
saveMetrics(String) ExampleSingleMetricsCollectorSpark
Write out the results of the metrics collection
saveMetrics(String) CollectInsertSizeMetricsSpark
saveMetrics(String) CollectQualityYieldMetricsSpark
saveMetrics(String) InsertSizeMetricsCollectorSpark
saveMetrics(String) MetricsCollectorSpark
This method is called after collectMetrics has returned and
all Spark partitions have completed metrics collection.
saveMetrics(String) MetricsCollectorSparkTool
saveMetrics(String) QualityYieldMetricsCollectorSpark
Write out the results of the metrics collection
saveMetricsRDD(MetricsFile<GATKDuplicationMetrics, Double>, SAMFileHeader, JavaPairRDD<String, GATKDuplicationMetrics>, String) MarkDuplicatesSparkUtils
Saves the metrics to a file.
saveResults(MetricsFile<?, Integer>, SAMFileHeader, String) CollectBaseDistributionByCycleSpark
saveTextualReport(String, SAMFileHeader, RecalibrationTables, RecalibrationArgumentCollection) BaseRecalibratorEngineSparkWrapper
scaledEvidenceProbabilityUsingGenotypeFrequencies(double[]) 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[]) 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_WINDOW_SIZE CollectGcBiasMetrics
scanDir(File, String) ClassFinder
Scans a directory on the filesystem for classes.
scanJar(File, String) ClassFinder
Scans the entries in a ZIP/JAR file for classes under the parent package.
scatter(IntervalList, int) IntervalListScatterer
scatter(IntervalList, int, boolean) IntervalListScatterer
SCATTER_COUNT IntervalListTools
SCATTER_COUNT_LONG_NAME SplitIntervals
SCATTER_COUNT_SHORT_NAME SplitIntervals
scatterContigIntervals(SAMFileHeader, List<GenomeLoc>, List<File>) IntervalUtils
Splits an interval list into multiple files.
scatterFixedIntervals(SAMFileHeader, List<List<GenomeLoc>>, List<File>) IntervalUtils
Splits an interval list into multiple files.
ScatterIntervalsByNReferenceArgumentCollection() ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
ScatterIntervalsByNs picard.util
A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.
ScatterIntervalsByNs() ScatterIntervalsByNs
ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection picard.util
scheme GenotypeConcordanceScheme
The underlying scheme
sChr ArtificialReadIterator
score(byte[], int, int) AggregatedSubHaplotypeFinder
score() KBestHaplotype
Returns the result haplotype score.
score(byte[]) KBestHaplotypeFinder
Get the score of a give sequence of bases
score(Haplotype) KBestHaplotypeFinder
Get the score of a give sequence of bases
score(GATKRead) MarkDuplicatesScoringStrategy
Given a read, compute the reads's score for mark duplicates.
score ReadEndsForMarkDuplicates
score Fragment
score ReadEndsForMarkDuplicates
SCORE IntervalListToBed
SCORE_GENOME_LENGTH_UNITS PSScorer
SCORE_METRICS_FILE_LONG_NAME PSScoreArgumentCollection
SCORE_METRICS_FILE_SHORT_NAME PSScoreArgumentCollection
SCORE_READS_PER_PARTITION_LONG_NAME PSScoreArgumentCollection
SCORE_READS_PER_PARTITION_SHORT_NAME PSScoreArgumentCollection
SCORE_THRESHOLD_LONG_NAME PSBwaArgumentCollection
SCORE_THRESHOLD_SHORT_NAME PSBwaArgumentCollection
SCORE_WARNINGS_FILE_LONG_NAME PSScoreArgumentCollection
SCORE_WARNINGS_FILE_SHORT_NAME PSScoreArgumentCollection
scoreArgs PathSeqPipelineSpark
scoreArgs PathSeqScoreSpark
scoreMetricsFileUri PSScoreArgumentCollection
If specified, records the following metrics:
Number of reads mapped to the microbial reference
Number of unmapped reads
scoreOrientationBiasMetricsOverContext(List<SequencingArtifactMetrics.PreAdapterDetailMetrics>) PreAdapterOrientationScorer
Scores all modes regardless of whether required in the input.
scoreReads(JavaSparkContext, JavaRDD<GATKRead>, JavaRDD<GATKRead>, SAMFileHeader) PSScorer
SCORES_OUTPUT_LONG_NAME PSScoreArgumentCollection
SCORES_OUTPUT_SHORT_NAME PSScoreArgumentCollection
scoresPath PSScoreArgumentCollection
scoreThreshold PSBwaArgumentCollection
This parameter controls the minimum quality of the BWA alignments for the output.
ScriptExecutor 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) ScriptExecutor
ScriptExecutorException org.broadinstitute.hellbender.utils.runtime
Base type for exceptions thrown by the ScriptExecutor.
ScriptExecutorException(String) ScriptExecutorException
SD_CLUSTERS_PER_TILE IlluminaBasecallingMetrics
The standard deviation of clusters per tile.
SD_COVERAGE CollectWgsMetrics.WgsMetrics
The standard deviation of coverage of the genome after all filters are applied.
SD_PCT_PF_CLUSTERS_PER_TILE IlluminaBasecallingMetrics
The standard deviation in percentage of pf clusters per tile.
SD_PF_CLUSTERS_PER_TILE IlluminaBasecallingMetrics
The standard deviation in number of pf clusters per tile.
sDUST(GATKRead, int, double) DUSTReadTransformer
Wrapper method for runDUST so that we don't have to expose the IntTuple class.
SECOND_END_FASTQ SamToFastq
SECOND_INPUT CrosscheckFingerprints
SECOND_INPUT IntervalListTools
SECOND_INPUT_SAMPLE_MAP CrosscheckFingerprints
SECOND_OF_PAIR ReadFilterLibrary
SECONDARY_OR_SUPPLEMENTARY_RDS DuplicationMetrics
The number of reads that were either secondary or supplementary
SecondOfPairReadFilter() ReadFilterLibrary.SecondOfPairReadFilter
secondPassApply(GATKRead, ReferenceContext, FeatureContext) TwoPassReadWalker
Process an individual read (with optional contextual information) on the second pass through the reads.
secondPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) TwoPassVariantWalker
secondPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) ExampleTwoPassVariantWalker
secondPassApply(GATKRead, ReferenceContext, FeatureContext) SplitNCigarReads
SECONDS_BETWEEN_PROGRESS_UPDATES_NAME GATKTool
secondSmallestMinusSmallest(int[], int) MathUtils
Given an int array returns the difference between the second smallest element
and the smallest element.
seedLength PSBwaArgumentCollection
This parameter controls the sensitivity of the BWA-MEM aligner.
seek(long) ChannelAsSeekableStream
seek(int) DataLine
Changes the index of the next value to set using
append operations.
seek(String) DataLine
Changes the index of the next value to set using
append operations.
seek(Enum<?>) DataLine
Changes the index of the next value to set using
append operations.
seek(List<File>, TileIndex, int) BclReader
SeekableByteChannelPrefetcher org.broadinstitute.hellbender.utils.nio
SeekableByteChannelPrefetcher wraps an existing SeekableByteChannel to add prefetching.
SeekableByteChannelPrefetcher(SeekableByteChannel, int) SeekableByteChannelPrefetcher
seeked ArtificialReadQueryIterator
seekToTile(int) IlluminaDataProvider
Jump so that the next record returned will be from the specified tile.
seekToTile(int) MultiTileParser
seekToTile(int) NewIlluminaDataProvider
seekToTile(int) PerTileParser
SEGMENT_FILE_LONG_NAME ExomeStandardArgumentDefinitions
SEGMENT_FILE_SHORT_NAME ExomeStandardArgumentDefinitions
SEGMENT_GERMLINE_CNV_CALLS_PYTHON_SCRIPT PostprocessGermlineCNVCalls
SEGMENT_SIZE_ARG_LONG_NAME GenomicsDBImport
SegmentedCpxVariantSimpleVariantExtractor org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
For extracting simple variants from input GATK-SV complex variants.
SegmentedCpxVariantSimpleVariantExtractor() SegmentedCpxVariantSimpleVariantExtractor
SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
SEGMENTS_FILE_LONG_NAME CopyNumberStandardArgument
SEGMENTS_FILE_SUFFIX ModelSegments
selectAlleleBiasedReads(Map<A, List<GATKRead>>, double) AlleleBiasedDownsamplingUtils
Computes reads to remove based on an allele biased down-sampling
selectAlleleBiasedReads(Map<A, List<GATKRead>>, int, double) AlleleBiasedDownsamplingUtils
Computes reads to remove based on an allele biased down-sampling
SelectionMetric(String) TrancheManager.SelectionMetric
SelectVariants org.broadinstitute.hellbender.tools.walkers.variantutils
Select a subset of variants from a VCF file
SelectVariants() SelectVariants
selectWorstVariants() VariantDataManager
sendAsynchronousCommand(String) StreamingPythonScriptExecutor
Send a command to the remote process without waiting for a response.
sendSynchronousCommand(String) StreamingPythonScriptExecutor
Send a command to Python, and wait for a response prompt, returning all accumulated output
since the last call to either
separator ASEReadCounter
seq SVKmerizer
seq(double, double, double) MathUtil
Mimic's R's seq() function to produce a sequence of equally spaced numbers.
SEQ_ALT_HAPLOTYPE GATKSVVCFConstants
SEQ_IS_STORED ReadFilterLibrary
seqEquals(BaseVertex) BaseVertex
Are b and this equal according to their base sequences?
SeqGraph org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
A graph that contains base sequence at each node
SeqGraph(int) SeqGraph
Construct an empty SeqGraph where we'll add nodes based on a kmer size of kmer
The kmer size is purely information.
SeqIsStoredReadFilter() ReadFilterLibrary.SeqIsStoredReadFilter
sequence BaseVertex
SEQUENCE_DICTIONARY BedToIntervalList
SEQUENCE_DICTIONARY LiftOverIntervalList
SEQUENCE_DICTIONARY CollectVariantCallingMetrics
SEQUENCE_DICTIONARY MergeVcfs
SEQUENCE_DICTIONARY SortVcf
SEQUENCE_DICTIONARY SplitVcfs
SEQUENCE_DICTIONARY UpdateVcfSequenceDictionary
SEQUENCE_DICTIONARY_NAME StandardArgumentDefinitions
SEQUENCE_DICTIONARY_SHORT_NAME StandardOptionDefinitions
SEQUENCE_NAME RrbsCpgDetailMetrics
Sequence the CpG is seen in
SEQUENCE_NAMES CollectRrbsMetrics
SEQUENCE_TAG_GROUP SamToFastqWithTags
SequenceComparison org.broadinstitute.hellbender.tools.funcotator
A simple data object to hold a comparison between a reference sequence and an alternate allele.
SequenceComparison() SequenceComparison
SequenceDictionaryUtils 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.SequenceDictionaryCompatibility org.broadinstitute.hellbender.utils
SequenceDictionaryValidationArgumentCollection org.broadinstitute.hellbender.cmdline.argumentcollections
interface for argument collections that control how sequence dictionary validation should be handled
SequenceDictionaryValidationArgumentCollection.NoValidationCollection 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 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 GATKSparkTool
sequenceRecordsAreEquivalent(SAMSequenceRecord, SAMSequenceRecord) SequenceDictionaryUtils
Helper routine that returns whether two sequence records are equivalent, defined as having the same name and
lengths.
SequencerFlowClass 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 NGSPlatform
SEQUENCING_CENTER IlluminaBasecallsToSam
SEQUENCING_CENTER FastqToSam
SequencingArtifactMetrics picard.analysis.artifacts
SequencingArtifactMetrics() SequencingArtifactMetrics
SequencingArtifactMetrics.BaitBiasDetailMetrics picard.analysis.artifacts
Bait bias artifacts broken down by context.
SequencingArtifactMetrics.BaitBiasSummaryMetrics picard.analysis.artifacts
Summary analysis of a single bait bias artifact, also known as a reference bias artifact.
SequencingArtifactMetrics.PreAdapterDetailMetrics picard.analysis.artifacts
Pre-adapter artifacts broken down by context.
SequencingArtifactMetrics.PreAdapterSummaryMetrics picard.analysis.artifacts
Summary analysis of a single pre-adapter artifact.
SeqVertex 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[]) SeqVertex
Create a new SeqVertex with sequence and the next available id
SeqVertex(String) SeqVertex
Create a new SeqVertex having bases of sequence.getBytes()
SerializableFunction T ,R > - Interface in org.broadinstitute.hellbender.utils
Represents a Function that is Serializable.
SerializableOpticalDuplicatesFinder org.broadinstitute.hellbender.utils.read.markduplicates
An intermediate class flagged as being serializable so that the Picard OpticalDuplicateFinder can be serialized despite
it not being marked as such.
SerializableOpticalDuplicatesFinder(String, int) SerializableOpticalDuplicatesFinder
SerializableOpticalDuplicatesFinder() SerializableOpticalDuplicatesFinder
serialize(Kryo, Output) PSTaxonomyDatabase
serialize(Kryo, Output) PSTree
serialize(Kryo, Output) BreakpointComplications.IntraChrStrandSwitchBreakpointComplications
serialize(Kryo, Output) BreakpointComplications
serialize(Kryo, Output) BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications
serialize(Kryo, Output) BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications
serialize(Kryo, Output) NovelAdjacencyAndAltHaplotype
serialize(Kryo, Output) SimpleChimera
serialize(Kryo, Output) BreakpointEvidence.DiscordantReadPairEvidence
serialize(Kryo, Output) BreakpointEvidence.LargeIndel
serialize(Kryo, Output) BreakpointEvidence.OutiesPair
serialize(Kryo, Output) BreakpointEvidence.ReadEvidence
serialize(Kryo, Output) BreakpointEvidence
serialize(Kryo, Output) BreakpointEvidence.SplitRead
serialize(Kryo, Output) BreakpointEvidence.TemplateSizeAnomaly
serialize(Kryo, Output) BreakpointEvidence.WeirdTemplateSize
serialize(Kryo, Output) EvidenceTargetLink
serialize(Kryo, Output) KmerAndInterval
serialize(Kryo, Output) KmerAndCount
serialize(Kryo, Output) Strand
serialize(Kryo, Output) SVKmerLong
serialize(Kryo, Output) HopscotchCollection
serialize(Kryo, Output) LargeLongHopscotchSet
serialize(Kryo, Output) LongBloomFilter
serialize(Kryo, Output) LongHopscotchSet
serialize(Kryo, Output) Pair
Serializer() PSKmerBloomFilter.Serializer
Serializer() PSKmerSet.Serializer
Serializer() PSTaxonomyDatabase.Serializer
Serializer() PSTree.Serializer
Serializer() PSTreeNode.Serializer
Serializer() AlignedAssembly.Serializer
Serializer() AlignedContig.Serializer
Serializer() AlignmentInterval.Serializer
Serializer() AssemblyContigWithFineTunedAlignments.Serializer
Serializer() BreakpointComplications.IntraChrStrandSwitchBreakpointComplications.Serializer
Serializer() BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications.Serializer
Serializer() BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications.Serializer
Serializer() NovelAdjacencyAndAltHaplotype.Serializer
Serializer() SimpleChimera.Serializer
Serializer() SimpleNovelAdjacencyAndChimericAlignmentEvidence.Serializer
Serializer() AlignedAssemblyOrExcuse.Serializer
Serializer() BreakpointEvidence.ExternalEvidence.Serializer
Serializer() BreakpointEvidence.InterContigPair.Serializer
Serializer() BreakpointEvidence.LargeIndel.Serializer
Serializer() BreakpointEvidence.MateUnmapped.Serializer
Serializer() BreakpointEvidence.OutiesPair.Serializer
Serializer() BreakpointEvidence.ReadEvidence.Serializer
Serializer() BreakpointEvidence.SameStrandPair.Serializer
Serializer() BreakpointEvidence.Serializer
Serializer() BreakpointEvidence.SplitRead.Serializer
Serializer() BreakpointEvidence.TemplateSizeAnomaly.Serializer
Serializer() BreakpointEvidence.WeirdTemplateSize.Serializer
Serializer() EvidenceTargetLink.Serializer
Serializer() KmerAndInterval.Serializer
Serializer() LibraryStatistics.Serializer
Serializer() QNameAndInterval.Serializer
Serializer() ReadMetadata.LibraryRawStatistics.Serializer
Serializer() ReadMetadata.PartitionBounds.Serializer
Serializer() ReadMetadata.PartitionStatistics.Serializer
Serializer() ReadMetadata.Serializer
Serializer() KmerAndCount.Serializer
Serializer() PairedStrandedIntervalTree.Serializer
Serializer() Strand.Serializer
Serializer() StrandedInterval.Serializer
Serializer() SVFastqUtils.FastqRead.Serializer
Serializer() SVInterval.Serializer
Serializer() SVIntervalTree.Serializer
Serializer() SVKmerLong.Serializer
Serializer() SVKmerShort.Serializer
Serializer() HopscotchCollection.Serializer
Serializer() HopscotchMap.Serializer
Serializer() HopscotchMultiMap.Serializer
Serializer() HopscotchSet.Serializer
Serializer() HopscotchUniqueMultiMap.Serializer
Serializer() IntHistogram.CDF.Serializer
Serializer() IntHistogram.Serializer
Serializer() LargeLongHopscotchSet.Serializer
Serializer() LongBloomFilter.Serializer
Serializer() LongHopscotchSet.Serializer
Serializer() Pair.Serializer
serializeToString() GencodeGtfFeature
serializeToVcfString() GencodeFuncotation
serializeToVcfString() TableFuncotation
serializeToVcfString() Funcotation
Converts this
Funcotation to a string suitable for insertion into a VCF file.
serializeToVcfString(String) Funcotation
TODO: This interface should have nothing specific to a VCF.
serialVersionUID VariantFilter
serialVersionUID QualityYieldMetricsArgumentCollection
serialVersionUID ExampleMultiMetricsArgumentCollection
serialVersionUID ExampleSingleMetricsArgumentCollection
serialVersionUID MetricsCollectorSpark
serialVersionUID DUSTReadTransformer
serialVersionUID ReadTransformer
serialVersionUID StripMateNumberTransformer
serialVersionUID Covariate
set(Allele, X) PerAlleleCollection
Take an allele, REF or ALT, and update its value appropriately
set(Collection<Allele>, Function<Allele, X>) PerAlleleCollection
set(int, int, double) SubsettedLikelihoodMatrix
set(int, E) ExpandingArrayList
set(int, int, double) LikelihoodMatrix
Set the likelihood of a read given an allele through their indices.
set(Object, String, Object) GATKReportTable
Set the value for a given position in the table.
set(int, int, Object) GATKReportTable
Set the value for a given position in the table.
set(String, String) DataLine
Sets the string value in the data-line that correspond to a column by its name.
set(String, boolean) DataLine
Sets the boolean value in the data-line that correspond to a column by its name.
set(String, int) DataLine
Sets the int value in the data-line that correspond to a column by its name.
set(String, long) DataLine
Sets the long value in the data-line that correspond to a column by its name.
set(String, double) DataLine
Sets the double value in the data-line that correspond to a column by its name.
set(int, String) DataLine
Sets the string value of a column given its index.
set(int, int) DataLine
Sets the int value of a column given its index.
set(int, long) DataLine
Sets the long value of a column given its index.
set(int, double) DataLine
Sets the value for a column to a double given its index.
SET_ONLY_UQ SetNmMdAndUqTags
setAdditionalInfo(String) BaseVertex
Set additional debugging information for this vertex
setAddPGTagToReads(boolean) AbstractAlignmentMerger
Set addPGTagToReads.
setAlignedAlternateAllele(String) SequenceComparison
setAlignedAlternateAlleleStop(Integer) SequenceComparison
setAlignedCodingSequenceAlleleStart(Integer) SequenceComparison
setAlignedCodingSequenceAlternateAllele(String) SequenceComparison
setAlignedCodingSequenceReferenceAllele(String) SequenceComparison
setAlignedReferenceAllele(String) SequenceComparison
setAlignedReferenceAlleleStop(Integer) SequenceComparison
setAlignmentStart(int) ArtificialBAMBuilder
setAlignmentStartHapwrtRef(int) Haplotype
setAll(String...) DataLine
Sets all the data-line values at once.
setAlleleStart(Integer) SequenceComparison
setAllowDuplicateReads(boolean) FingerprintChecker
Sets whether duplicate reads should be allowed when calling genotypes from SAM files.
setAlreadyBuilt() ReadThreadingGraph
setAlt(Allele, X) PerAlleleCollection
setAlternateAllele(String) SequenceComparison
setAlternateAminoAcidSequence(String) SequenceComparison
setAnnotationEngine(VariantAnnotatorEngine) GenotypingEngine
Changes the annotation engine for this genotyping-engine.
setAnnotationTranscript(String) GencodeFuncotation
setAnnotationTranscript(String) GencodeFuncotationBuilder
setApplyEamssFiltering(boolean) IlluminaDataProviderFactory
Sets whether or not EAMSS filtering will be applied if parsing BCL files for bases and quality scores.
setApprisRank(GencodeGtfFeature.FeatureTag) GencodeFuncotation
setApprisRank(GencodeGtfFeature.FeatureTag) GencodeFuncotationBuilder
setArtifactMode(Transition) OrientationSampleTransitionSummary
setArtifactModeComplement(Transition) OrientationSampleTransitionSummary
setAttribute(String, Integer) GATKRead
Set an integer-valued attribute on the read.
setAttribute(String, String) GATKRead
Set a String-valued attribute on the read.
setAttribute(String, byte[]) GATKRead
Set a byte array attribute on the read.
setAttribute(String, Integer) SAMRecordToGATKReadAdapter
setAttribute(String, String) SAMRecordToGATKReadAdapter
setAttribute(String, byte[]) SAMRecordToGATKReadAdapter
setAttributeMap(Map<Allele, T>) AlleleSpecificAnnotationData
setAttributeMap(Map<Allele, T>) ReducibleAnnotationData
Assign all of the per-allele raw data at once
setAttributesToReverse(Set<String>) AbstractAlignmentMerger
Sets the set of attributes to be reversed on reads marked as negative strand.
setAttributesToReverseComplement(Set<String>) AbstractAlignmentMerger
Sets the set of attributes to be reverse complemented on reads marked as negative strand.
setBaitSetName(String) TargetMetricsCollector.PerUnitTargetMetricCollector
Sets the name of the bait set explicitly instead of inferring it from the bait file.
setBaseQualities(byte[]) GATKRead
Set the read's base qualities.
setBaseQualities(byte[]) SAMRecordToGATKReadAdapter
setBaseQualityString(GATKRead, String) ReadUtils
Set the base qualities from a string of ASCII encoded values
setBases(byte[]) GATKRead
Set the read's sequence.
setBases(byte[]) SAMRecordToGATKReadAdapter
setBases(byte[]) ReadData
setBigDuplicateSetSize(int) OpticalDuplicateFinder
Sets the size of a set that is big enough to log progress about.
setBufferSize(int) OutputStreamSettings
setcDnaChange(String) GencodeFuncotation
setcDnaChange(String) GencodeFuncotationBuilder
setCds(GencodeGtfCDSFeature) GencodeGtfExonFeature
setChromosome(String) GencodeFuncotation
setChromosome(String) GencodeFuncotationBuilder
setCigar(Cigar) Haplotype
Set the cigar of this haplotype to cigar.
setCigar(Cigar) GATKRead
Set the read's Cigar using an existing Cigar object describing how the read aligns to the reference.
setCigar(String) GATKRead
Set the read's Cigar using a textual cigar String describing how the read aligns to the reference.
setCigar(Cigar) SAMRecordToGATKReadAdapter
setCigar(String) SAMRecordToGATKReadAdapter
setClipOverlappingReads(boolean) AbstractAlignmentMerger
setClipOverlappingReads(boolean) AbstractAlignmentMerger
setCodingSequenceAlleleStart(Integer) SequenceComparison
setCodonChange(String) GencodeFuncotation
setCodonChange(String) GencodeFuncotationBuilder
setCollectorsToRun(List<CollectMultipleMetricsSpark.SparkCollectorProvider>) CollectMultipleMetricsSpark
Use this method when invoking CollectMultipleMetricsSpark programmatically to run programs other
than the ones available via enum.
setCommand(String[]) ProcessSettings
setCompareBamFilesSorted(boolean) IntegrationTestSpec
setContig(String) SequenceComparison
setCounter(long) AbstractWgsMetricsCollector
Sets the counter to the current number of processed loci.
setCovariateIndex(int) ReadCovariates
setData(ClipReads.ClippingData) ClipReads.ReadClipperWithData
setData(List<VariantDatum>) VariantDataManager
setDataSourceName(String) GencodeFuncotation
setDataSourceName(String) GencodeFuncotationBuilder
setDebug(boolean) ReadThreadingAssembler
setDebugGraphOutputPath(File) ReadThreadingAssembler
setDebugGraphTransformations(boolean) ReadThreadingAssembler
setDeciles(DecileCollection) PosteriorSummary
setDefaultHeaders(List<Header>) CommandLineProgram
Replaces the set of default metrics headers by the given argument.
setDefaultHeaders(List<Header>) CommandLineProgram
setDeletionBaseQualities(GATKRead, byte[]) ReadUtils
setDirectory(File) ProcessSettings
setDownsampler(ReadsDownsampler) MultiIntervalLocalReadShard
Reads in this shard will be downsampled using this downsampler before being returned.
setDownsamplingInfo(LIBSDownsamplingInfo) AlignmentContextIteratorBuilder
setEmitEmptyLoci(boolean) AlignmentContextIteratorBuilder
setEmpiricalQuality(double) RecalDatum
setEnabled(boolean) BunnyLog
Pass false to disable all logging via bunnylog
(it's enabled by default).
setEnd(int) GencodeFuncotation
setEnd(int) GencodeFuncotationBuilder
setEnvironment(Map<String, String>) ProcessSettings
setErrorCorrectKmers(boolean) ReadThreadingAssembler
setEstimatedQReported(double) RecalDatum
setEventMap(EventMap) Haplotype
setExonEndPosition(Integer) SequenceComparison
setExonPosition(SimpleInterval) SequenceComparison
setExonStartPosition(Integer) SequenceComparison
setFailsVendorQualityCheck(boolean) GATKRead
Mark the read as failing platform/vendor quality checks
setFailsVendorQualityCheck(boolean) SAMRecordToGATKReadAdapter
setFeatureCodecClass(Class<FeatureCodec<T, ?>>) 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) GencodeGtfFeature
setFieldSerializationOverrideValue(String, String) GencodeFuncotation
setFieldSerializationOverrideValue(String, String) TableFuncotation
setFieldSerializationOverrideValue(String, String) Funcotation
Override the given field with a given value for when it comes time to serialize and write this
Funcotation.
setFieldSerializationOverrideValues(Map<String, String>) Funcotation
Override fields with values as specified by the input map (for when it comes time to serialize and write this
Funcotation).
setFilteredGenotypesToNocall VariantFiltration
If this argument is provided, set filtered genotypes to no-call (./.).
setFilteredGenotypeToNocall(VariantContextBuilder, VariantContext, boolean, BiFunction<VariantContext, Genotype, List<String>>) GATKVariantContextUtils
Set the builder's filtered genotypes to no-call and update AC, AN and AF
setFinalized(boolean) AssemblyRegion
setFounderIds(List<String>) PedigreeAnnotation
setFragmentLength(int) GATKRead
Set the observed length of the read's fragment (equivalent to TLEN in SAM).
setFragmentLength(int) SAMRecordToGATKReadAdapter
setFullReferenceWithPadding(byte[]) AssemblyResultSet
Sets the full reference with padding base sequence.
setGcContent(Double) GencodeFuncotation
setGcContent(Double) GencodeFuncotationBuilder
setGcContent(Double) SequenceComparison
setGeneTranscriptType(GencodeGtfFeature.GeneTranscriptType) GencodeFuncotation
setGeneTranscriptType(GencodeGtfFeature.GeneTranscriptType) GencodeFuncotationBuilder
setGenomeChange(String) GencodeFuncotation
setGenomeChange(String) GencodeFuncotationBuilder
setGenomeLocation(Locatable) Haplotype
setGenotypeQualityFromPLs(GenotypeBuilder, Genotype) GATKProtectedVariantContextUtils
Instead of using the GQ value, it re-calculates the quality from the PL so that it does not need
to be bounded by an artificial maximum such as the standard GQ = 99.
setGenotypingErrorRate(double) FingerprintChecker
Sets the assumed genotyping error rate used when accurate error rates are not available.
setGlobalNIODefaultOptions() BucketUtils
Sets NIO_MAX_REOPENS and generous timeouts as the global default.
setGlobalNIODefaultOptions(int) BucketUtils
setGraphWriter(File) ReadThreadingAssembler
setHeader(SAMFileHeader) ReadFilter
setHeader(SAMFileHeader) WellformedReadFilter
setHeader(SAMFileHeader) ReadsSparkSink.SparkBAMOutputFormat
setHeader(SAMFileHeader) ReadsSparkSink.SparkCRAMOutputFormat
setHeader(SAMFileHeader) ReadsSparkSink.SparkSAMOutputFormat
setHeader(SAMFileHeader) ArtificialBAMBuilder
setHeader(SAMFileHeader) SAMRecordToGATKReadAdapter
setHeader(SAMFileHeader) SamFileTester
setHeader(VCFHeader) GVCFWriter
sethInfo(VCFInfoHeaderLine) VariantAnnotatorEngine.VAExpression
setHugoSymbol(String) GencodeFuncotation
setHugoSymbol(String) GencodeFuncotationBuilder
setIgnoreExceptions(boolean) ScriptExecutor
Set to true to have the ScriptExecutor catch and ignore GATK exceptions.
setIncludeDeletions(boolean) AlignmentContextIteratorBuilder
setIncludeNs(boolean) AlignmentContextIteratorBuilder
setIncludeSecondaryAlignments(boolean) AbstractAlignmentMerger
setIncludeSecondaryAlignments(boolean) AbstractAlignmentMerger
setInputBuffer(String) InputStreamSettings
setInputFile(File) InputStreamSettings
setInputStream(InputStream) SAMRecordSparkCodec
Sets the input stream that records will be read from.
setInputStream(InputStream, String) SAMRecordSparkCodec
Sets the input stream that records will be read from.
setInputStream(InputStream) ReadEndsForMarkDuplicatesCodec
setInputStream(InputStream) ReadEndsForMarkDuplicatesCodec
setInputStream(InputStream) RepresentativeReadIndexerCodec
setInsertionBaseQualities(GATKRead, byte[]) ReadUtils
setIntervalsForTraversal(List<SimpleInterval>) FeatureDataSource
setIntervalsForTraversal(List<SimpleInterval>) MultiVariantDataSource
setIsActiveProb(double) ActivityProfileState
Set the probability that this site is active.
setIsDuplicate(boolean) GATKRead
Mark the read as a PCR or optical duplicate.
setIsDuplicate(boolean) SAMRecordToGATKReadAdapter
setIsFirstOfPair() GATKRead
Mark the read as the first read of a pair.
setIsFirstOfPair() SAMRecordToGATKReadAdapter
setIsPaired(boolean) GATKRead
Mark the read as paired (having a mate) or not paired.
setIsPaired(boolean) SAMRecordToGATKReadAdapter
setIsProperlyPaired(boolean) GATKRead
Mark the read as properly paired (or not properly paired).
setIsProperlyPaired(boolean) SAMRecordToGATKReadAdapter
setIsRef(boolean) BaseEdge
Indicate that this edge follows the reference sequence, or not
setIsReverseStrand(boolean) GATKRead
Mark the read as being on the reverse (or forward) strand.
setIsReverseStrand(boolean) SAMRecordToGATKReadAdapter
setIsSecondaryAlignment(boolean) GATKRead
Mark the read as a secondary alignment (an alternative to the primary alignment)
setIsSecondaryAlignment(boolean) SAMRecordToGATKReadAdapter
setIsSecondOfPair() GATKRead
Mark the read as the second read of a pair.
setIsSecondOfPair() SAMRecordToGATKReadAdapter
setIsSupplementaryAlignment(boolean) GATKRead
Mark the read as a supplementary alignment (used in the representation of a chimeric alignment)
setIsSupplementaryAlignment(boolean) SAMRecordToGATKReadAdapter
setIsUnmapped() GATKRead
Mark the read as unmapped (lacking a defined position on the genome).
setIsUnmapped() SAMRecordToGATKReadAdapter
setKeepAlignerProperPairFlags(boolean) AbstractAlignmentMerger
If true, keep the aligner's idea of proper pairs rather than letting alignment merger decide.
setKeepAlignerProperPairFlags(boolean) AbstractAlignmentMerger
If true, keep the aligner's idea of proper pairs rather than letting alignment merger decide.
setKeepUniqueReadListInLibs(boolean) AlignmentContextIteratorBuilder
setKingdomTaxonId(int) PSPathogenTaxonScore
setLane(int) ClusterData
setLength(long) PSTreeNode
setLengthOf(int, long) PSTree
setLibraryId(short) ReadEnds
setLibraryId(short) Pair
setLibraryId(short) PhysicalLocationForMateCigar
setLibraryId(short) ReadEnds
setLibraryId(short) PhysicalLocation
setLibraryId(short) PhysicalLocationInt
setLocationSet(PhysicalLocationForMateCigarSet) ReadEndsForMateCigar
setLocusLevel(Integer) GencodeFuncotation
setLocusLevel(Integer) GencodeFuncotationBuilder
setLogger(Logger) GenotypingEngine
Changes the logger for this genotyper engine.
setLoggingLevel(Log.LogLevel) LoggingUtils
Propagate the verbosity level to Picard, log4j, the java built in logger, and Kryo's MinLog
setMappingQuality(int) GATKRead
Set the mapping quality of this alignment, representing how likely the read maps to this position as
opposed to other locations.
setMappingQuality(int) SAMRecordToGATKReadAdapter
setMatchedBarcode(String) ClusterData
setMateChanged() OverhangFixingManager.SplitRead
setMateIsReverseStrand(boolean) GATKRead
Mark the read's mate as being on the reverse (or forward) strand.
setMateIsReverseStrand(boolean) SAMRecordToGATKReadAdapter
setMateIsUnmapped() GATKRead
Mark the read's mate as unmapped (lacking a defined position on the genome).
setMateIsUnmapped() SAMRecordToGATKReadAdapter
setMatePosition(String, int) GATKRead
Set the position of the read's mate (the contig and the start position).
setMatePosition(Locatable) GATKRead
Set the position of the read's mate using the position of an existing Locatable.
setMatePosition(String, int) SAMRecordToGATKReadAdapter
setMatePosition(Locatable) SAMRecordToGATKReadAdapter
setMaxDuplicateSetSize(long) OpticalDuplicateFinder
Sets the size of a set that is too big to process.
setmaximalPLDifference(int) FingerprintChecker
Sets the maximal difference in PL scores considered when reading PLs from a VCF.
setMaxPairErrorRate(double) AdapterMarker
setMaxRecordsInRam(int) AbstractAlignmentMerger
Allows the caller to override the maximum records in RAM.
setMaxSingleEndErrorRate(double) AdapterMarker
setMinBaseQualityToUseInAssembly(byte) ReadThreadingAssembler
setMinDanglingBranchLength(int) ReadThreadingAssembler
setMinimumBaseQuality(int) FingerprintChecker
Sets the minimum base quality for bases used when computing a fingerprint from sequence data.
setMinimumMappingQuality(int) FingerprintChecker
Sets the minimum mapping quality for reads used when computing fingerprints from sequence data.
setMinimumSeriesLengthForNormalApproximation(int) MannWhitneyU
Sets the minimum number of values in each data series to use the normal distribution approximation.
setMinPairMatchBases(int) AdapterMarker
setMinSingleEndMatchBases(int) AdapterMarker
setMultiplicity(int) BaseEdge
Set the multiplicity of this edge to value
setName(String) PSPathogenReferenceTaxonProperties
setName(String) PSTreeNode
setName(String) GencodeGtfFeature.OptionalField
setName(String) GATKRead
Set the name of the read (equivalent to QNAME in SAM), or set to null if the read has no name.
setName(String) SAMRecordToGATKReadAdapter
setName(String) BaseTest.TestDataProvider
setNameOf(int, String) PSTree
setNcbiBuild(String) GencodeFuncotation
setNcbiBuild(String) GencodeFuncotationBuilder
setNearProbeDistance(int) TargetMetricsCollector
Sets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.
SetNmAndUqTags picard.sam
Deprecated.
SetNmAndUqTags() SetNmAndUqTags
Deprecated.
SetNmMdAndUqTags picard.sam
Fixes the NM, MD, and UQ tags in a SAM or BAM file.
SetNmMdAndUqTags() SetNmMdAndUqTags
setNoise(FourChannelIntensityData) ReadData
setNoMateCigars(boolean) SamFileTester
setNormalization(Map<String, Double>, Map<String, Double>) VariantDataManager
setNoSideEffects(boolean) 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) AdapterMarker
After seeing the thresholdForSelectingAdapters number of adapters, keep up to this many of the original adapters.
setNumArtifactMode(long) OrientationSampleTransitionSummary
setNumArtifactModeFiltered(long) OrientationSampleTransitionSummary
setNumMismatches(double) RecalDatum
setNumNonRefPassingVariants(long) OrientationSampleTransitionSummary
setNumNotArtifactMode(long) OrientationSampleTransitionSummary
setNumObservations(long) RecalDatum
setNumSamplesPerLogEntry(int) GibbsSampler
Changes the number of samples per log entry.
setObq(double) OrientationSampleTransitionSummary
setOrCheckLane(int) ClusterData
Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckPf(boolean) ClusterData
Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckTile(int) ClusterData
Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckX(int) ClusterData
Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckY(int) ClusterData
Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOtherTranscripts(List<String>) GencodeFuncotation
setOtherTranscripts(List<String>) GencodeFuncotationBuilder
setOutput(File) SamFileTester
setOutputFile(File) OutputStreamSettings
Overwrites the outputFile with the process output.
setOutputFile(File, boolean) OutputStreamSettings
setOutputStream(OutputStream) SAMRecordSparkCodec
Sets the output stream that records will be written to.
setOutputStream(OutputStream, String) SAMRecordSparkCodec
Sets the output stream that records will be written to.
setOutputStream(OutputStream) ReadEndsForMarkDuplicatesCodec
setOutputStream(OutputStream) ReadEndsForMarkDuplicatesCodec
setOutputStream(OutputStream) RepresentativeReadIndexerCodec
setOverrideValuesInFuncotations(List<Funcotation>) DataSourceFuncotationFactory
setPaddedReferenceLoc(SimpleInterval) AssemblyResultSet
Changes the padded reference location.
setParent(int) PSPathogenReferenceTaxonProperties
setParent(int) PSTreeNode
setPedigreeFile(File) PedigreeAnnotation
Setter for pedigree file and founderIDs to be used by the GATKAnnotationPluginDescriptor to handle duplicated annotaiton
arguments between InbreedingCoeff and ExcessHet
setPerBaseOutput(File) TargetMetricsCollector.PerUnitTargetMetricCollector
Sets the (optional) File to write per-base coverage information to.
setPerTargetOutput(File) TargetMetricsCollector.PerUnitTargetMetricCollector
Sets the (optional) File to write per-target coverage information to.
setPf(boolean) ClusterData
setpLossofHet(double) FingerprintChecker
setPosition(String, int) GATKRead
Set the position of the read (the contig and the start position).
setPosition(Locatable) GATKRead
Set the position of the read using the position of an existing Locatable.
setPosition(String, int) SAMRecordToGATKReadAdapter
setPosition(Locatable) SAMRecordToGATKReadAdapter
setPositionInfo(AbstractIlluminaPositionFileReader.PositionInfo) CbclData
setPostReadFilterTransformer(ReadTransformer) MultiIntervalLocalReadShard
Reads in this shard will be transformed after filtering and before downsampling
setPredictedMateInformation(GATKRead) 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) MultiIntervalLocalReadShard
Reads in this shard will be transformed before filtering
setPrimaryAlignment(int) HitsForInsert
Set all alignments to not primary, except for the one specified by the argument.
setProgramRecord(SAMProgramRecord) AbstractAlignmentMerger
setProgramRecord(SAMProgramRecord) AbstractAlignmentMerger
setProgramsToRun(Collection<CollectMultipleMetrics.ProgramInterface>) CollectMultipleMetrics
Use this method when invoking CollectMultipleMetrics programmatically to run programs other than the ones
available via enum.
setProteinChange(String) GencodeFuncotation
setProteinChange(String) GencodeFuncotationBuilder
setProteinChangeEndPosition(Integer) SequenceComparison
setProteinChangeStartPosition(Integer) SequenceComparison
setPruneFactor(int) ReadThreadingAssembler
setQualities(byte[]) ReadData
setRank(String) PSPathogenReferenceTaxonProperties
setRank(String) PSTreeNode
setRankOf(int, String) PSTree
setRawIntensities(FourChannelIntensityData) ReadData
setRead(GATKRead) OverhangFixingManager.SplitRead
setReadFilter(ReadFilter) MultiIntervalLocalReadShard
Reads in this shard will be filtered using this filter before being returned.
setReadGroup(String) GATKRead
Set the ID of the read group this read belongs to, or null for none.
setReadGroup(short) ReadEnds
setReadGroup(short) Pair
setReadGroup(String) SAMRecordToGATKReadAdapter
setReadGroup(short) PhysicalLocationForMateCigar
setReadGroup(short) ReadEnds
setReadGroup(short) PhysicalLocation
setReadGroup(short) PhysicalLocationInt
setReadLength(int) ArtificialBAMBuilder
setReadsAsSupplemental(GATKRead, List<GATKRead>) 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) ReadData
setRecordLabel(String) ProgressMeter
Change the label used for records in logger messages.
setRecordsBetweenTimeChecks(long) ProgressMeter
Set the number of records we need to process before we check the current time
setRecoverDanglingBranches(boolean) ReadThreadingAssembler
setRedirectErrorStream(boolean) ProcessSettings
setRef(Allele, X) PerAlleleCollection
setRefAllele(String) GencodeFuncotation
setRefAllele(Allele) GencodeFuncotationBuilder
setReferenceAllele(String) SequenceComparison
setReferenceAminoAcidSequence(String) SequenceComparison
setReferenceBases(String) SequenceComparison
setReferenceCodingSequence(ReferenceSequence) SequenceComparison
setReferenceContext(String) GencodeFuncotation
setReferenceContext(String) GencodeFuncotationBuilder
setReferenceLength(long) PSPathogenTaxonScore
setReferenceSequence(File) SinglePassSamProgram
Set the reference File.
setReferenceWindow(Integer) SequenceComparison
setRegionForGenotyping(AssemblyRegion) AssemblyResultSet
Sets the region for genotyping.
setRemovePathsNotConnectedToRef(boolean) ReadThreadingAssembler
setResultState(boolean) SamRecordWithOrdinalAndSetDuplicateReadFlag
setResultState(boolean) SamRecordWithOrdinalAndSetDuplicateReadFlag
setSample(String) OrientationSampleTransitionSummary
setSampleContamination(Map<String, Double>) StandardCallerArgumentCollection
Set the sample contamination map using the provided map.
setSATag() SATagBuilder
Sets the stored SA tag information into the SA attribute field of the read encapsulated by the SATagBuilder
setScore(double) Haplotype
Set the score (an estimate of the support) of this haplotype.
setSecondaryVariantClassification(GencodeFuncotation.VariantClassification) GencodeFuncotation
setSecondaryVariantClassification(GencodeFuncotation.VariantClassification) GencodeFuncotationBuilder
setSentinel(V) 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.
setSize() PSKmerSet
setSize RepresentativeReadIndexer
SetSizeUtils org.broadinstitute.hellbender.tools.spark.utils
Set size utility
SetSizeUtils() SetSizeUtils
setSkipBlankLines(boolean) AbstractInputParser
setSkipNLoci(int) ArtificialBAMBuilder
setStart(int) GencodeFuncotation
setStart(int) GencodeFuncotationBuilder
setStart(GenomeLoc, int) 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) GencodeGtfExonFeature
setStop(GenomeLoc, int) 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) GencodeGtfExonFeature
setStrand(Strand) GencodeFuncotationBuilder
setStrand(Strand) SequenceComparison
setSupportedFuncotationFields(List<Path>) LocatableXsvFuncotationFactory
setTestVerbosity() BaseTest
setThreadingStartOnlyAtExistingVertex(boolean) ReadThreadingGraph
Changes the threading start location policy.
setThresholdForSelectingAdaptersToKeep(int) AdapterMarker
When this number of adapters have been matched, discard the least-frequently matching ones.
setTile(short) ReadEnds
setTile(short) Pair
setTile(int) ClusterData
setTile(short) PhysicalLocation
setTile(short) PhysicalLocationInt
setTiles(List<Integer>) ParameterizedFileUtil
setTilesForPerRunFile(List<Integer>) ParameterizedFileUtil
setTilesForPerRunFile(List<Integer>) PerTileOrPerRunFileUtil
setTo(int) CountSet
Set the set contents to a single integer value.
setTo(int...) CountSet
Set the content of this set to a collection of integers.
setToMarkQueueMinimumDistance(int) MarkQueue
Sets the minimum genomic distance such that we can be assured that all duplicates have been considered.
setTranscriptAlleleStart(Integer) SequenceComparison
setTranscriptCodingSequence(ReferenceSequence) SequenceComparison
setTranscriptExonNumber(Integer) GencodeFuncotation
setTranscriptExonNumber(int) GencodeFuncotationBuilder
setTranscriptLength(Integer) GencodeFuncotation
setTranscriptLength(Integer) GencodeFuncotationBuilder
setTranscriptPos(Integer) GencodeFuncotation
setTranscriptPos(Integer) GencodeFuncotationBuilder
Set the position (1-based, inclusive) relative to the start of the transcript of a the variant in the
GencodeFuncotation.
setTranscriptStrand(String) GencodeFuncotation
setTransientAttribute(Object, Object) SAMRecordToGATKReadAdapter
This is used to access the transient attribute store in the underlying SAMRecord.
setTraversalBounds(List<SimpleInterval>) ReadsDataSource
setTraversalBounds(TraversalParameters) ReadsDataSource
Restricts a traversal of this data source via
ReadsDataSource.iterator() to only return reads that overlap the given intervals,
and to unmapped reads if specified.
setTraversalBounds(List<SimpleInterval>, boolean) ReadsDataSource
Restricts a traversal of this data source via
ReadsDataSource.iterator() to only return reads that overlap the given intervals,
and to unmapped reads if specified.
setTreatGroupedDelimitersAsOne(boolean) AbstractInputParser
setTumorSeqAllele2(String) GencodeFuncotation
setTumorSeqAllele2(String) GencodeFuncotationBuilder
setUcscGenomeVersion(String) GencodeGtfFeature
setup(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>) 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>) MultiLevelReducibleCollector
Use an init method so that overloaded methods in subclasses can pass use parameters that are initialized in their constructor
setup(SAMFileHeader, File) CollectSequencingArtifactMetrics
setup(SAMFileHeader, File) CollectAlignmentSummaryMetrics
setup(SAMFileHeader, File) CollectBaseDistributionByCycle
setup(SAMFileHeader, File) CollectGcBiasMetrics
setup(SAMFileHeader, File) CollectInsertSizeMetrics
setup(SAMFileHeader, File) CollectQualityYieldMetrics
setup(SAMFileHeader, File) CollectRnaSeqMetrics
setup(SAMFileHeader, File) MeanQualityByCycle
setup(SAMFileHeader, File) QualityScoreDistribution
setup(SAMFileHeader, File) SinglePassSamProgram
Should be implemented by subclasses to do one-time initialization work.
setup(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>) MultiLevelCollector
Use an init method so that overloaded methods in subclasses can pass use parameters that are initialized in their constructor
setup(VCFHeader) CallingMetricAccumulator
setup(VCFHeader) GvcfMetricAccumulator
setupConfigAndExtractProgram(String[], List<String>, List<Class<? extends CommandLineProgram>>, String) Main
setupOpticalDuplicateFinder() AbstractOpticalDuplicateFinderCommandLineProgram
setupOpticalDuplicateFinder() AbstractOpticalDuplicateFinderCommandLineProgram
setUseOriginalQualities(boolean) QualityYieldMetrics
setValidated(boolean) BreakpointEvidence
setValidationStringency(ValidationStringency) IntegrationTestSpec
setValidationStringency(ValidationStringency) FingerprintChecker
setValue(Integer) KmerAndInterval
setValue(Integer) QNameAndInterval
setValue(Integer) KmerAndCount
setValue(V1) SVIntervalTree.Entry
setValue(T) GencodeGtfFeature.OptionalField
setValuesFromAlignment(SAMRecord, SAMRecord) AbstractAlignmentMerger
Sets the values from the alignment record on the unaligned BAM record.
setValuesFromAlignment(SAMRecord, SAMRecord, boolean) AbstractAlignmentMerger
Sets the values from the alignment record on the unaligned BAM record.
setVariantClassification(GencodeFuncotation.VariantClassification) GencodeFuncotation
setVariantClassification(GencodeFuncotation.VariantClassification) GencodeFuncotationBuilder
setVariantType(GencodeFuncotation.VariantType) GencodeFuncotation
setVariantType(GencodeFuncotation.VariantType) GencodeFuncotationBuilder
setVCFHeader(VCFHeader) VariantsSparkSink.SparkVCFOutputFormat
setVersion(String) GencodeFuncotation
setVersion(String) GencodeFuncotationBuilder
setWalkerType(String) GATKGSONWorkUnit
setWindow(int, int) 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) AbstractInputParser
setWriteHaplotypes(boolean) HaplotypeBAMWriter
Set the HaplotypeBAMWriter to write out the haplotypes as reads.
setX(int) ReadEnds
setX(int) Pair
setX(int) ClusterData
setX(int) PhysicalLocation
setX(int) PhysicalLocationInt
setX(int) PhysicalLocationShort
setY(int) ReadEnds
setY(int) Pair
setY(int) ClusterData
setY(int) PhysicalLocation
setY(int) PhysicalLocationInt
setY(int) PhysicalLocationShort
Sex org.broadinstitute.hellbender.utils.samples
ENUM of possible human sexes: male, female, or unknown
Sex picard.pedigree
Represents the sex of an individual.
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(JavaSparkContext, JavaRDD<L>, Class<L>, SAMSequenceDictionary, List<ShardBoundary>, int) SparkSharder
Create an RDD of
Shard from an RDD of coordinate sorted
Locatable without using a shuffle .
shard(JavaSparkContext, JavaRDD<L>, Class<L>, SAMSequenceDictionary, List<ShardBoundary>, int, boolean) SparkSharder
Create an RDD of
Shard from an RDD of coordinate sorted
Locatable, optionally using a shuffle.
ShardBoundary org.broadinstitute.hellbender.engine
Holds the bounds of a
Shard, both with and without padding
ShardBoundary(SimpleInterval, SimpleInterval) ShardBoundary
Create a new ShardBoundary from the given intervals
ShardBoundaryShard T > - Class in org.broadinstitute.hellbender.engine
ShardBoundaryShard(ShardBoundary, Iterable<T>) ShardBoundaryShard
SHARDED_OUTPUT_LONG_NAME GATKSparkTool
ShardedIntervalIterator org.broadinstitute.hellbender.utils.iterators
Iterator that will break up each input interval into shards.
ShardedIntervalIterator(Iterator<SimpleInterval>, int) ShardedIntervalIterator
shardedOutput GATKSparkTool
shardedPartsDir GATKSparkTool
shardIndex(int, int) IntervalUtils
number of the shard this offset is in.
shardingArgs HaplotypeCallerSpark
shardingArgs ReadsPipelineSpark
ShardingArgumentCollection() HaplotypeCallerSpark.ShardingArgumentCollection
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>) ShardToMultiIntervalShardAdapter
SharedSequenceMerger 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 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>) 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.
shiftedLogEvidenceProbability() HaplotypeProbabilities
Returns log (p(evidence)) + c assuming that the prior on haplotypes is given by
the internal haplotypeFrequencies
shiftedLogEvidenceProbabilityGivenOtherEvidence(HaplotypeProbabilities) HaplotypeProbabilities
returns the log-probability the evidence, using as priors the posteriors of another object
shiftedLogEvidenceProbabilityUsingGenotypeFrequencies(double[]) HaplotypeProbabilities
ShortVariantDiscoveryProgramGroup org.broadinstitute.hellbender.cmdline.programgroups
Tools that perform variant calling and genotyping for short variants (SNPs, SNVs and Indels)
ShortVariantDiscoveryProgramGroup() ShortVariantDiscoveryProgramGroup
shouldBeInLocations(ReadEndsForMateCigar) MarkQueue
Returns true if we should track this for optical duplicate detection, false otherwise
shouldErrorCorrectKmers() ReadThreadingAssembler
ShouldNeverReachHereException(String) GATKException.ShouldNeverReachHereException
ShouldNeverReachHereException(String, Throwable) GATKException.ShouldNeverReachHereException
ShouldNeverReachHereException(Throwable) GATKException.ShouldNeverReachHereException
showVerbose PileupSpark
In addition to the standard pileup output, adds 'verbose' output too.
showVerbose Pileup
In addition to the standard pileup output, adds 'verbose' output too.
shuffle AssemblyRegionWalkerSpark
shuffle IntervalWalkerSpark
shuffle LocusWalkerSpark
shuffle ReadWalkerSpark
shuffle VariantWalkerSpark
ShuffleJoinReadsWithRefBases org.broadinstitute.hellbender.engine.spark
RefBasesForReads queries the Google Genomics API for reference bases overlapping all of the reads.
ShuffleJoinReadsWithRefBases() ShuffleJoinReadsWithRefBases
ShuffleJoinReadsWithVariants org.broadinstitute.hellbender.engine.spark
PairReadsAndVariants takes two RDDs (GATKRead and Variant) and returns an RDD with a
(GATKRead,Iterable) for every read and all the variants that overlap.
ShuffleJoinReadsWithVariants() ShuffleJoinReadsWithVariants
shutdown() HaplotypeCallerEngine
Shutdown this HC engine, closing resources as appropriate
shutdown() Mutect2Engine
signalEndOfInput() Downsampler
Used to tell the downsampler that no more items will be submitted to it, and that it should
finalize any pending items.
signalEndOfInput() FractionalDownsampler
signalEndOfInput() LevelingDownsampler
signalEndOfInput() MutectDownsampler
signalEndOfInput() PassThroughDownsampler
signalEndOfInput() PositionalDownsampler
signalEndOfInput() ReservoirDownsampler
signalNoMoreReadsBefore(GATKRead) FractionalDownsampler
signalNoMoreReadsBefore(GATKRead) MutectDownsampler
signalNoMoreReadsBefore(GATKRead) PassThroughDownsampler
signalNoMoreReadsBefore(GATKRead) PositionalDownsampler
signalNoMoreReadsBefore(GATKRead) 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) ReservoirDownsampler
SILVERMANS_RULE_CONSTANT PosteriorSummaryUtils
SILVERMANS_RULE_EXPONENT PosteriorSummaryUtils
SimpleAnnotatedIntervalWriter org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
SimpleAnnotatedIntervalWriter(File) SimpleAnnotatedIntervalWriter
Initialize this writer to the given output file.
simpleBaseToBaseIndex(byte) BaseUtils
Converts a simple base to a base index
SimpleChimera org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
SimpleChimera(Kryo, Input) SimpleChimera
SimpleChimera(AlignmentInterval, AlignmentInterval, List<String>, String, String, SAMSequenceDictionary) SimpleChimera
Construct a new SimpleChimera from two alignment intervals.
SimpleChimera.Serializer org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
simpleComplement(byte) 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 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) SimpleCopyRatioCaller
SimpleCount org.broadinstitute.hellbender.tools.copynumber.formats.records
Represents a count at an interval.
SimpleCount(SimpleInterval, int) SimpleCount
SimpleCountCollection org.broadinstitute.hellbender.tools.copynumber.formats.collections
Simple data structure to pass and read/write a List of
SimpleCount objects.
SimpleCountCollection(SampleLocatableMetadata, List<SimpleCount>) SimpleCountCollection
SimpleGermlineTagger org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging
This utility class performs a simple tagging of germline segments in a tumor segments file.
SimpleInterval org.broadinstitute.hellbender.utils
Minimal immutable class representing a 1-based closed ended genomic interval
SimpleInterval does not allow null contig names.
SimpleInterval(String, int, int) SimpleInterval
Create a new immutable 1-based interval of the form [start, end]
SimpleInterval(Locatable) SimpleInterval
Create a new SimpleInterval from a Locatable
SimpleInterval(String) SimpleInterval
Makes an interval by parsing the string.
SimpleIntervalCollection org.broadinstitute.hellbender.tools.copynumber.formats.collections
SimpleIntervalCollection(File) SimpleIntervalCollection
SimpleIntervalCollection(LocatableMetadata, List<SimpleInterval>) SimpleIntervalCollection
SimpleKeyXsvFuncotationFactory 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) SimpleKeyXsvFuncotationFactory
SimpleKeyXsvFuncotationFactory(String, Path, String, String, int, SimpleKeyXsvFuncotationFactory.XsvDataKeyType, LinkedHashMap<String, String>) SimpleKeyXsvFuncotationFactory
SimpleKeyXsvFuncotationFactory(String, Path, String, String, int, SimpleKeyXsvFuncotationFactory.XsvDataKeyType, LinkedHashMap<String, String>, int) SimpleKeyXsvFuncotationFactory
SimpleKeyXsvFuncotationFactory(String, Path, String, String, int, SimpleKeyXsvFuncotationFactory.XsvDataKeyType, LinkedHashMap<String, String>, int, boolean) SimpleKeyXsvFuncotationFactory
SimpleKeyXsvFuncotationFactory.XsvDataKeyType org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv
SimpleLocatableMetadata org.broadinstitute.hellbender.tools.copynumber.formats.metadata
Metadata associated with a collection of locatables.
SimpleLocatableMetadata(SAMSequenceDictionary) SimpleLocatableMetadata
SimpleMarkDuplicatesWithMateCigar picard.sam.markduplicates
This is a simple tool to mark duplicates using the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator.
SimpleMarkDuplicatesWithMateCigar() SimpleMarkDuplicatesWithMateCigar
simpleMerge(Collection<VariantContext>, List<String>, GATKVariantContextUtils.FilteredRecordMergeType, GATKVariantContextUtils.GenotypeMergeType, boolean, boolean, String, boolean, boolean) GATKVariantContextUtils
Merges VariantContexts into a single hybrid.
simpleMerge(Collection<VariantContext>, List<String>, int, GATKVariantContextUtils.FilteredRecordMergeType, GATKVariantContextUtils.GenotypeMergeType, boolean, boolean, String, boolean, boolean) GATKVariantContextUtils
Merges VariantContexts into a single hybrid.
SimpleNovelAdjacencyAndChimericAlignmentEvidence org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
SimpleNovelAdjacencyAndChimericAlignmentEvidence.Serializer org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
SimpleNovelAdjacencyInterpreter 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() SimpleNovelAdjacencyInterpreter
SimplePosteriorSummary(double, double, double) ModeledSegment.SimplePosteriorSummary
SimplePosteriorSummary(List<Double>) ModeledSegment.SimplePosteriorSummary
SimpleRepeatMaskTransformer 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) SimpleRepeatMaskTransformer
simpleReverseComplement(byte[]) BaseUtils
Reverse complement a byte array of bases (that is, chars casted to bytes, *not* base indices in byte form)
SimpleSampleLocatableMetadata org.broadinstitute.hellbender.tools.copynumber.formats.metadata
Metadata associated with a collection of locatables associated with a single sample.
SimpleSampleLocatableMetadata(String, SAMSequenceDictionary) SimpleSampleLocatableMetadata
SimpleSampleMetadata org.broadinstitute.hellbender.tools.copynumber.formats.metadata
Metadata associated with a single sample.
SimpleSampleMetadata(String) SimpleSampleMetadata
SimpleSVD 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) SimpleSVD
SimpleSVType org.broadinstitute.hellbender.tools.spark.sv.discovery
SimpleSVType(String, Allele, int, Map<String, String>) SimpleSVType
SimpleSVType.Deletion org.broadinstitute.hellbender.tools.spark.sv.discovery
SimpleSVType.DuplicationInverted org.broadinstitute.hellbender.tools.spark.sv.discovery
SimpleSVType.DuplicationTandem org.broadinstitute.hellbender.tools.spark.sv.discovery
SimpleSVType.ImpreciseDeletion org.broadinstitute.hellbender.tools.spark.sv.discovery
SimpleSVType.Insertion org.broadinstitute.hellbender.tools.spark.sv.discovery
SimpleSVType.Inversion org.broadinstitute.hellbender.tools.spark.sv.discovery
SimpleSVType.TYPES org.broadinstitute.hellbender.tools.spark.sv.discovery
simplifyGraph() 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_END_ALIGNMENT_FULL_NAME BwaArgumentCollection
SINGLE_END_ALIGNMENT_SHORT_NAME BwaArgumentCollection
singleEndAlignment BwaArgumentCollection
Run single-end instead of paired-end alignment.
singleNewtonArgmaxUpdate(Function<Double, Double>, double, double, double, double, double) OptimizationUtils
One iteration of Newton's method for univariate optimization (i.e.
singleNewtonArgmaxUpdate(Function<Double, Double>, double, double, double) OptimizationUtils
SinglePassSamProgram 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() 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>) SingleSequenceReferenceAligner
SingleSequenceReferenceAligner(String, byte[], Function<? super T, List<byte[]>>, SingleSequenceReferenceAligner.TriFunction<? super T, List<List<BwaMemAlignment>>, List<String>, ? extends U>, Predicate<? super BwaMemAlignment>) SingleSequenceReferenceAligner
SingleSequenceReferenceAligner.TriFunction T ,U ,V ,W > - Interface in org.broadinstitute.hellbender.tools.spark.sv.utils
singletonIterator(T) SVUtils
singletonSampleList(String) SampleList
Creates a list with a single sample.
SingularValueDecomposer org.broadinstitute.hellbender.utils.svd
Perform singular value decomposition (and pseudoinverse calculation).
SITES_FILE_LONG_NAME ExomeStandardArgumentDefinitions
SITES_FILE_SHORT_NAME ExomeStandardArgumentDefinitions
SITES_ONLY_LONG_NAME StandardArgumentDefinitions
SIXTY_FOUR_MIB ParallelCopyGCSDirectoryIntoHDFSSpark
size() AlignmentContext
How many reads cover this locus?
size() AssemblyRegion
Get the number of reads currently in this region
size() AbstractRecordCollection
size() AnnotatedIntervalCollection
size() TableFuncotation
size() PairedStrandedIntervalTree
size() SVIntervalTree
Return the number of intervals in the tree.
size() HopscotchCollection
size() IntHistogram.CDF
size() LargeLongHopscotchSet
size() LongHopscotchSet
size() KBestHaplotypeFinder
size() ActivityProfile
How many profile results are in this profile?
size() SAMPileupFeature
Return the number of observed bases over the genomic location
size() XsvTableFeature
size() CountSet
size() IndexedSet
Returns number of elements in the set.
size() Dirichlet
size() 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() FractionalDownsampler
size() LevelingDownsampler
size() MutectDownsampler
size() PassThroughDownsampler
size() PositionalDownsampler
size() ReservoirDownsampler
size() GenomeLoc
How many BPs are covered by this locus?
size() GenomeLocSortedSet
return the size of the collection
size() IndexRange
Returns number indexes expanded by this range.
size() SeekableByteChannelPrefetcher
Returns the current size of entity to which this channel is connected.
size() ReadPileup
The number of elements in this pileup.
size() DiskBasedReadEndsForMarkDuplicatesMap
size() ReadEndsForMarkDuplicatesMap
size() CovariateKeyCache
Returns the size of this cache.
size() StandardCovariateList
Returns the size of the list of standard covariates.
size() SimpleInterval
size() XorWrapper
size() HaplotypeBlock
Returns the number of SNPs within the haplotype block.
size() DiskBasedReadEndsForMarkDuplicatesMap
size() MarkQueue
The number of records currently in this queue.
size() PhysicalLocationForMateCigarSet
The number of records in this set
size() ReadEndsForMarkDuplicatesMap
SIZE_AND_BASE_ORDER Haplotype
Compares two haplotypes first by their lengths and then by lexicographic order of their bases.
SIZE_OF ReadEndsForMarkDuplicates
SIZE_OF ReadEndsForMarkDuplicates
sizeBeforeLoc(GenomeLoc) GenomeLocSortedSet
Return the number of bps before loc in the sorted set
sizeInRam() DiskBasedReadEndsForMarkDuplicatesMap
sizeInRam() ReadEndsForMarkDuplicatesMap
sizeInRam() DiskBasedReadEndsForMarkDuplicatesMap
sizeInRam() ReadEndsForMarkDuplicatesMap
skimArray(T, boolean[]) 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) 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) Utils
Skims out positions of an array returning a shorter one with the remaning positions in the same order.
skip(int) ReadRecalibrationInfo
Should offset in this read be skipped (because it's covered by a known variation site?)
Skip ReadType
SKIP_CHROMS FindMendelianViolations
SKIP_FILTERS_LONG_NAME PSFilterArgumentCollection
SKIP_FILTERS_SHORT_NAME PSFilterArgumentCollection
SKIP_MATE_VALIDATION ValidateSamFile
SKIP_PRE_BWA_REPARTITION_LONG_NAME PSFilterArgumentCollection
SKIP_PRE_BWA_REPARTITION_SHORT_NAME PSFilterArgumentCollection
SKIP_PROMPT_LONG_NAME FixCallSetSampleOrdering
skipCommandLinePrompt FixCallSetSampleOrdering
skipEmptyFiles ParameterizedFileUtil
skipFamilyPriors CalculateGenotypePosteriors
Skip application of family-based priors.
skipFilters PSFilterArgumentCollection
skipPopulationPriors CalculateGenotypePosteriors
Skip application of population-based priors
skipPreBwaRepartition 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) FilterFileReader
skipRecords(int) LocsFileReader
skips ReadStructure
SliceSampler org.broadinstitute.hellbender.utils.mcmc
Implements slice sampling of a continuous, univariate, unnormalized probability density function,
which is assumed to be unimodal.
SliceSampler(RandomGenerator, Function<Double, Double>, double, double, double) SliceSampler
Creates a new sampler, given a random number generator, a continuous, univariate, unimodal, unnormalized
log probability density function, hard limits on the random variable, and a step width.
SliceSampler(RandomGenerator, Function<Double, Double>, double) SliceSampler
Creates a new sampler, given a random number generator, a continuous, univariate, unimodal, unnormalized
log probability density function, and a step width.
smallestPowerOfTwoGreaterThan(int) MathUtils
Returns the smallest power of 2 that exceeds or equals val
SMITH_WATERMAN_LONG_NAME AssemblyBasedCallerArgumentCollection
SmithWatermanAligner org.broadinstitute.hellbender.utils.smithwaterman
Interface and factory for Smith-Waterman aligners
SmithWatermanAligner.Implementation org.broadinstitute.hellbender.utils.smithwaterman
SmithWatermanAlignment org.broadinstitute.hellbender.utils.smithwaterman
smithWatermanImplementation AssemblyBasedCallerArgumentCollection
SmithWatermanIntelAligner org.broadinstitute.hellbender.utils.smithwaterman
SmithWatermanIntelAligner class that converts instance of
SWAlignerNativeBinding into a
SmithWatermanIntelAligner
This is optimized for Intel Architectures and can fail if Machine does not support AVX and will throw
UserException
SmithWatermanIntelAligner() SmithWatermanIntelAligner
Create a new SW pairwise aligner, which is implementation of smith waterman aligner that's takes advantage of intel hardware optimizations.
SmithWatermanJavaAligner 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 org.broadinstitute.hellbender.utils.smithwaterman
The state of a trace step through the matrix
SMOOTHING_CREDIBLE_INTERVAL_THRESHOLD_ALLELE_FRACTION_LONG_NAME ModelSegments
SMOOTHING_CREDIBLE_INTERVAL_THRESHOLD_COPY_RATIO_LONG_NAME ModelSegments
smoothSegments(int, int, double, double) MultidimensionalModeller
SNP FingerprintingDetailMetrics
The name of a representative SNP within the haplotype that was compared.
Snp 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>) Snp
SNP_ALLELES FingerprintingDetailMetrics
The possible alleles for the SNP.
SNP_COLUMN_NAME FalsePositiveRecord
SNP_FILE_LONG_NAME ExomeStandardArgumentDefinitions
SNP_FILE_SHORT_NAME ExomeStandardArgumentDefinitions
SNP_FPR_COLUMN_NAME FalsePositiveRecord
SNP_HETEROZYGOSITY HomoSapiensConstants
Standard heterozygous rate for SNP variation.
SNP_OUTPUT SplitVcfs
SNP_REFERENCE_BIAS CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The rate at which reference bases are observed at ref/alt heterozygous SNP sites.
snpCounter GenotypeConcordance
snpHeterozygosity GenotypeCalculationArgumentCollection
The expected heterozygosity value used to compute prior probability that a locus is non-reference.
snpHeterozygosity HaplotypeCallerGenotypingEngine
snpPadding AssemblyRegionTrimmerArgumentCollection
snps DbSnpBitSetUtil.DbSnpBitSets
snps DbSnpBitSetUtil.DbSnpBitSets
SNPSubstitutionType(byte, byte) BaseUtils
Returns the base substitution type of the 2 state SNP
softClipBothEndsByReferenceCoordinates(GATKRead, int, int) ReadClipper
softClipByReadCoordinates(GATKRead, int, int) ReadClipper
softClipByReferenceCoordinates(int, int) 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.
softClipToRegionIncludingClippedBases(GATKRead, int, int) ReadClipper
Soft clip the read to the variable region (from refStart to refStop) processing also the clipped bases
SOLID_NOCALL_STRATEGY RecalibrationArgumentCollection
SOLID_RECAL_MODE RecalibrationArgumentCollection
solve(int, UnivariateFunction, double, double) RobustBrentSolver
solve() SynchronizedUnivariateSolver
Solve the equations
SomaticGenotypingEngine org.broadinstitute.hellbender.tools.walkers.mutect
SomaticGenotypingEngine(SampleList, M2ArgumentCollection, String, String) SomaticGenotypingEngine
SomaticLikelihoodsEngine org.broadinstitute.hellbender.tools.walkers.mutect
Created by David Benjamin on 3/9/17.
SomaticLikelihoodsEngine() SomaticLikelihoodsEngine
SORT BedToIntervalList
SORT IntervalListToBed
SORT IntervalListTools
SORT_ORDER AddOrReplaceReadGroups
SORT_ORDER FastqToSam
SORT_ORDER FilterSamReads
SORT_ORDER FixMateInformation
SORT_ORDER MergeBamAlignment
SORT_ORDER MergeSamFiles
SORT_ORDER RevertOriginalBaseQualitiesAndAddMateCigar
SORT_ORDER RevertSam
SORT_ORDER SortSam
SORT_ORDER_SHORT_NAME StandardOptionDefinitions
sortAlleles(VariantContext, VCFHeader) VariantContextTestUtils
Method which reorders the AltAlleles of a VariantContext so that they are in alphabetical order.
sortAndMergeIntervals(GenomeLocParser, List<GenomeLoc>, IntervalMergingRule) IntervalUtils
Sorts and merges an interval list.
sortedIterator() ReadPileup
Iterator over sorted by read start PileupElements.
SORTING_COLLECTION_SIZE_RATIO MarkDuplicatesGATK
SORTING_COLLECTION_SIZE_RATIO MarkDuplicates
sortLocatablesBySequenceDictionary(Collection<T>, SAMSequenceDictionary) IntervalUtils
Sort by the contig then position as specified by the index order in the given sequence dictionary.
sortReadsAccordingToHeader(JavaRDD<GATKRead>, SAMFileHeader, int) SparkUtils
Do a total sort of an RDD of
GATKRead according to the sort order in the header.
SortSam picard.sam
Sorts a SAM or BAM file.
SortSam() SortSam
SortSamSpark org.broadinstitute.hellbender.tools.spark.pipelines
SortSamSpark() SortSamSpark
sortUsingElementsAsKeys(JavaRDD<T>, Comparator<T>, int) SparkUtils
Do a global sort of an RDD using the given comparator.
sortVariantContextsByPriority(Collection<VariantContext>, List<String>, GATKVariantContextUtils.GenotypeMergeType) GATKVariantContextUtils
sortVariantsByCoordinate(List<VariantContext>, SAMSequenceDictionary) SVVCFWriter
SortVcf 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() SortVcf
sourceContigName SimpleChimera
SPANNING_DELETION_SYMBOLIC_ALLELE_DEPRECATED GATKVCFConstants
SPANNING_DELETION_SYMBOLIC_ALLELE_NAME_DEPRECATED GATKVCFConstants
SPANNING_DELETIONS_KEY GATKVCFConstants
spanWith(Locatable) SimpleInterval
Returns a new SimpleInterval that represents the region between the endpoints of this and other.
spark_driver_extraJavaOptions() GATKConfig
spark_driver_maxResultSize() GATKConfig
spark_driver_userClassPathFirst() GATKConfig
spark_executor_extraJavaOptions() GATKConfig
spark_io_compression_codec() GATKConfig
spark_kryoserializer_buffer_max() GATKConfig
SPARK_PROGRAM_NAME_LONG_NAME SparkCommandLineProgram
SPARK_PROPERTY_NAME StandardArgumentDefinitions
spark_yarn_executor_memoryOverhead() GATKConfig
sparkArgs SparkCommandLineProgram
SparkBAMOutputFormat() ReadsSparkSink.SparkBAMOutputFormat
SparkCommandLineArgumentCollection org.broadinstitute.hellbender.engine.spark
Command line arguments needed for configuring a spark context
SparkCommandLineArgumentCollection() SparkCommandLineArgumentCollection
SparkCommandLineProgram org.broadinstitute.hellbender.engine.spark
SparkCommandLineProgram() SparkCommandLineProgram
SparkContextFactory org.broadinstitute.hellbender.engine.spark
Manages creation of the Spark context.
SparkConverter org.broadinstitute.hellbender.utils.spark
Class with helper methods to convert objects (mostly matrices) to/from Spark (particularly, in MLLib)
SparkCRAMOutputFormat() ReadsSparkSink.SparkCRAMOutputFormat
SparkHeaderlessBAMOutputFormat() ReadsSparkSink.SparkHeaderlessBAMOutputFormat
SparkHeaderlessCRAMOutputFormat() ReadsSparkSink.SparkHeaderlessCRAMOutputFormat
SparkHeaderlessSAMOutputFormat() ReadsSparkSink.SparkHeaderlessSAMOutputFormat
SparkHeaderlessVCFOutputFormat() VariantsSparkSink.SparkHeaderlessVCFOutputFormat
sparkReadAdapter(AlignmentRecord, SAMFileHeader) BDGAlignmentRecordToGATKReadAdapter
sparkReadAdapter(AlignmentRecord) BDGAlignmentRecordToGATKReadAdapter
SparkSAMOutputFormat() ReadsSparkSink.SparkSAMOutputFormat
SparkSharder org.broadinstitute.hellbender.engine.spark
Utility methods for sharding Locatable objects (such as reads) for given intervals, without using a shuffle.
SparkSharder() SparkSharder
SparkSingularValueDecomposer org.broadinstitute.hellbender.utils.svd
SVD using MLLib
SparkSingularValueDecomposer(JavaSparkContext) SparkSingularValueDecomposer
SparkTestUtils org.broadinstitute.hellbender.utils.test
SparkUtils org.broadinstitute.hellbender.utils.spark
Miscellaneous Spark-related utilities
sparkVariantAdapter(VariantContext) VariantContextVariantAdapter
SparkVCFOutputFormat() VariantsSparkSink.SparkVCFOutputFormat
specialArgumentsCollection CommandLineProgram
specialArgumentsCollection CommandLineProgram
SPECIES CreateSequenceDictionary
Splice(String, int, int) OverhangFixingManager.Splice
split(SimpleInterval) ContextShard
create a new shard, keeping only the variants that overlap
with the new interval.
split(SeqGraph, SeqVertex) CommonSuffixSplitter
Simple single-function interface to split and then update a graph
split() SharedVertexSequenceSplitter
Actually do the splitting up of the vertices
Must be called before calling updateGraph
split(int) GenomeLoc
Splits the contig into to regions: [start,split point) and [split point, end].
split(String, char) Utils
Splits a String using indexOf instead of regex to speed things up.
split(String, String) Utils
Splits a String using indexOf instead of regex to speed things up.
split(String, String[], String) Test
SPLIT_DELIM AS_RankSumTest
SPLIT_DELIM AS_RMSMappingQuality
SPLIT_DELIM AS_StrandBiasTest
SPLIT_READ_SUPPORT GATKSVVCFConstants
SPLIT_TO_N_FILES SplitSamByNumberOfReads
SPLIT_TO_N_READS SplitSamByNumberOfReads
splitAndTrimToIntervals(Set<SimpleInterval>) AssemblyRegion
Intersect this assembly region with the allowed intervals, returning a list of active regions
that only contain locations present in intervals
Note: modifications to the returned list have no effect on this region object.
splitAndUpdate(SeqVertex, SeqVertex) SharedVertexSequenceSplitter
Simple single-function interface to split and then update a graph
splitBySample(SAMFileHeader, String) ReadPileup
Splits the ReadPileup by sample
splitContextBySampleName(SAMFileHeader) AlignmentContext
splitContextBySampleName(String, SAMFileHeader) AlignmentContext
Splits the given AlignmentContext into a StratifiedAlignmentContext per sample, but referenced by sample name instead
of sample object.
splitContextBySampleName(ReadPileup, SAMFileHeader) AlignmentContext
spliterator() PathLineIterator
spliterator() TableReader
splitFactor RealignmentArgumentCollection
BWA-mem seed split factor
splitFixedIntervals(List<GenomeLoc>, int) IntervalUtils
Splits the genome locs up by size.
splitFixedWidth(String, List<Integer>) TextFormattingUtils
Parses a fixed width line of text.
splitGappedAlignment(AlignmentInterval, int, int) ContigAlignmentsModifier
Splits a gapped alignment into multiple alignment regions, based on input sensitivity: i.e.
SplitIntervals org.broadinstitute.hellbender.tools.walkers
This tool takes in intervals via the standard arguments of
IntervalArgumentCollection and splits them into interval files for scattering.
SplitIntervals() SplitIntervals
splitIntervalsToSubLists(List<GenomeLoc>, List<Integer>) IntervalUtils
Splits an interval list into multiple sublists.
splitIntoPrimitiveAlleles(VariantContext) GATKVariantContextUtils
Splits the alleles for the provided variant context into its primitive parts.
splitLocusIntervals(List<GenomeLoc>, int) IntervalUtils
splitNCigarRead(GATKRead, OverhangFixingManager, boolean, SAMFileHeader, boolean) 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 org.broadinstitute.hellbender.tools.walkers.rnaseq
Splits reads that contain Ns in their cigar string (e.g.
SplitNCigarReads() SplitNCigarReads
SplitRead(GATKRead, ReadMetadata, boolean) BreakpointEvidence.SplitRead
SplitRead(GATKRead) OverhangFixingManager.SplitRead
SplitReads org.broadinstitute.hellbender.tools
Outputs reads from a SAM/BAM/CRAM by read group, sample and library name
SplitReads() SplitReads
splitReadsBySample(SampleList, SAMFileHeader, Collection<GATKRead>) AssemblyBasedCallerUtils
splitReadsBySample(Collection<GATKRead>) Mutect2Engine
SplitSamByLibrary picard.sam
Command-line program to split a SAM or BAM file into separate files based on
library name.
SplitSamByLibrary() SplitSamByLibrary
SplitSamByNumberOfReads picard.sam
Splits the input queryname sorted or query-grouped SAM/BAM file and writes it into
multiple BAM files, each with an approximately equal number of reads.
SplitSamByNumberOfReads() SplitSamByNumberOfReads
SPLITTING_INDEX_GRANULARITY_LONG_NAME CreateHadoopBamSplittingIndex
SplitVcfs picard.vcf
Splits the input VCF file into two, one for indels and one for SNPs.
SplitVcfs() SplitVcfs
splitWhiteSpace(String) TextFormattingUtils
Parses a line of text by whitespace.
square(double) MathUtils
Calculate f(x) = x^2
STANDARD_CONFIDENCE_FOR_CALLING GenotypeCalculationArgumentCollection
The minimum phred-scaled confidence threshold at which variants should be called.
STANDARD_DEVIATION InsertSizeMetrics
Standard deviation of insert sizes over the "core" of the distribution.
STANDARD_DEVIATION InsertSizeMetrics
Standard deviation of insert sizes over the "core" of the distribution.
STANDARD_ENCODING GetSampleName
STANDARD_MUTECT_INFO_FIELDS GATKVCFConstants
STANDARD_NGS SmithWatermanAligner
StandardAnnotation org.broadinstitute.hellbender.tools.walkers.annotator
This is a marker interface used to indicate which annotations are "Standard".
StandardArgumentDefinitions 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 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() StandardCallerArgumentCollection
StandardCovariateList org.broadinstitute.hellbender.utils.recalibration.covariates
Represents the list of standard BQSR covariates.
StandardCovariateList(RecalibrationArgumentCollection, List<String>) StandardCovariateList
Creates a new list of standard BQSR covariates and initializes each covariate.
StandardCovariateList(RecalibrationArgumentCollection, SAMFileHeader) StandardCovariateList
Creates a new list of standard BQSR covariates and initializes each covariate.
standardDeviation(double, int, boolean) VariantDataManager
StandardHCAnnotation 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 CopyNumberStandardArgument
StandardMutectAnnotation org.broadinstitute.hellbender.tools.walkers.annotator
This is a marker interface used to indicate which annotations are "Standard" for Mutect2 only.
StandardOptionDefinitions 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() StandardOptionDefinitions
StandardValidationCollection() SequenceDictionaryValidationArgumentCollection.StandardValidationCollection
start() ProgressMeter
Start the progress meter and produce preliminary output such as column headings.
START ValidateBasicSomaticShortMutations
start ClippingOp
start GenomeLoc
start(RootDoc) GATKHelpDoclet
Create a doclet of the appropriate type and generate the FreeMarker templates properties.
start(String) BunnyLog
start(List<String>) StreamingPythonScriptExecutor
Start the Python process.
start(List<String>, boolean) StreamingPythonScriptExecutor
Start the Python process.
start() StreamingProcessController
Starts the remote process running based on the setting specified in the constructor.
start Gene.Transcript.Exon
start() Gene.Transcript
start Range
start(RootDoc) PicardHelpDoclet
Create a doclet of the appropriate type and generate the FreeMarker templates properties.
start() VariantAccumulatorExecutor.MultiThreadedChunkBased
start() VariantAccumulatorExecutor
Starts the work of the executor, returning immediately.
start() VcfFileSegment
START_COL_COMMENT AnnotatedIntervalCodec
START_END_SEPARATOR SimpleInterval
startAsynchronousBatchWrite(List<T>) AsynchronousStreamWriterService
Request that a batch of items be written to the stream on a background thread.
started() ProgressMeter
Returns whether the meter has been started.
startInAssembledContig AlignmentInterval
startingChr ArtificialReadQueryIterator
startPos ArtificialReadQueryIterator
startSequence(String) FastaReferenceWriter
Starts the input of the bases of a new sequence.
startSequence(String, int) FastaReferenceWriter
Starts the input of the bases of a new sequence.
startSequence(String, String) FastaReferenceWriter
Starts the input of the bases of a new sequence.
startSequence(String, String, int) FastaReferenceWriter
Starts the input of the bases of a new sequence.
startsOrEndsWithInsertionOrDeletion(Cigar) AlignmentUtils
Does cigar start or end with a deletion operation?
startTime PairHMM
state BAQ.BAQCalculationResult
state() ParameterizedModel
stateAlignedPosition(int) BAQ
decode the bit encoded state array values
stateIsIndel(int) BAQ
decode the bit encoded state array values
stateList ActivityProfile
STATIC_QUANTIZED_QUALS_LONG_NAME CompareBaseQualities
staticQuantizationQuals ApplyBQSRUniqueArgumentCollection
Static quantized quals are entirely separate from the quantize_qual option which uses dynamic binning.
staticQuantizationQuals CompareBaseQualities
Return value is 0 if the two files have identical base qualities and non-zero otherwise.
status SynchronizedUnivariateSolver.UnivariateSolverSummary
stddev() MathUtils.RunningAverage
stdDev(Collection<? extends Number>) MathUtils
Calculate the standard deviation of a collection of Number instances.
stdDev(double...) MathUtils
Calculate the standard deviation of a double array.
stddev(double[], int, int) MathUtil
Calculated the standard deviation of an array of doubles.
stddev(double[], int, int, double) MathUtil
Calculated the standard deviation of an array of doubles.
stdErrFuture ProcessControllerBase
stdOutFuture ProcessControllerBase
stepEnd(String) BunnyLog
stepForwardOnGenome() 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.
stop() ProgressMeter
Stop the progress meter and output summary statistics to the logger
stop ClippingOp
stop GenomeLoc
stop() VcfFileSegment
STOP_AFTER CollectMultipleMetrics
STOP_AFTER CollectOxoGMetrics
STOP_AFTER CollectWgsMetrics
STOP_AFTER CollectIndependentReplicateMetrics
STOP_AFTER SinglePassSamProgram
STOP_AFTER PositionBasedDownsampleSam
stopCluster(MiniDFSCluster) MiniClusterUtils
shut down the cluster
stopped() ProgressMeter
Returns whether the meter has been stopped.
stopSparkContext(JavaSparkContext) SparkContextFactory
Stop a JavaSparkContext, unless it is the test context.
STR_CONTRACTION_FILTER_NAME GATKVCFConstants
STR_PRESENT_KEY GATKVCFConstants
Strand org.broadinstitute.hellbender.tools.spark.sv.utils
Strand.Serializer org.broadinstitute.hellbender.tools.spark.sv.utils
STRAND_ARTIFACT_FILTER_NAME GATKVCFConstants
STRAND_BALANCE 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 GATKVCFConstants
STRAND_COUNT_BY_SAMPLE_KEY GATKVCFConstants
STRAND_ODDS_RATIO_KEY GATKVCFConstants
STRAND_SPECIFICITY CollectRnaSeqMetrics
StrandArtifact org.broadinstitute.hellbender.tools.walkers.annotator
StrandArtifact() StrandArtifact
StrandArtifact.ArtifactState org.broadinstitute.hellbender.tools.walkers.annotator
strandArtifactAlleleFractionThreshold M2FiltersArgumentCollection
strandArtifactPosteriorProbThreshold M2FiltersArgumentCollection
StrandBiasBySample org.broadinstitute.hellbender.tools.walkers.annotator
Number of forward and reverse reads that support REF and ALT alleles
StrandBiasBySample() StrandBiasBySample
StrandBiasTest org.broadinstitute.hellbender.tools.walkers.annotator
Class of tests to detect strand bias.
StrandBiasTest() StrandBiasTest
StrandedInterval org.broadinstitute.hellbender.tools.spark.sv.utils
Represents an interval and strand from the reference genome.
StrandedInterval(SVInterval, boolean) StrandedInterval
StrandedInterval(Kryo, Input) StrandedInterval
StrandedInterval.Serializer org.broadinstitute.hellbender.tools.spark.sv.utils
StrandOddsRatio org.broadinstitute.hellbender.tools.walkers.annotator
Strand bias estimated by the Symmetric Odds Ratio test
StrandOddsRatio() StrandOddsRatio
StrandSwitch org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
For symbolizing the change of strand from one alignment to the next
of an assembly contig.
STRANDSWITCHLESS_BND BreakEndVariantType.TransLocBND
STRATEGY DownsampleSam
stratify(AlignmentContext.ReadOrientation) AlignmentContext
Returns a potentially derived subcontext containing only forward, reverse, or in fact all reads
in alignment context context.
stream(CharSequence, int, int, SVKmer) SVDUSTFilteredKmerizer
stream(byte[], int, int, SVKmer) SVDUSTFilteredKmerizer
stream(CharSequence, int, int, SVKmer) SVKmerizer
stream(byte[], int, int, SVKmer) SVKmerizer
stream(byte[], int, SVKmer) SVKmerizer
stream() TableReader
Returns an stream on the reaming records in the source.
stream(Iterable<T>) Utils
stream(Iterator<T>) Utils
STREAM_BLOCK_TRANSFER_SIZE CapturedStreamOutput
StreamingProcessController org.broadinstitute.hellbender.utils.runtime
Facade to Runtime.exec() and java.lang.Process.
StreamingProcessController(ProcessSettings) StreamingProcessController
StreamingProcessController(ProcessSettings, String) StreamingProcessController
Create a controller using the specified settings.
StreamingProcessController(ProcessSettings, String, boolean) StreamingProcessController
Create a controller using the specified settings.
StreamingPythonScriptExecutor org.broadinstitute.hellbender.utils.python
Python executor used to interact with a keep-alive Python process.
StreamingPythonScriptExecutor(boolean) StreamingPythonScriptExecutor
The start method must be called to actually start the remote executable.
StreamingPythonScriptExecutor(PythonExecutorBase.PythonExecutableName, boolean) StreamingPythonScriptExecutor
The start method must be called to actually start the remote executable.
StreamLocation org.broadinstitute.hellbender.utils.runtime
Where to read/write a stream
StreamOutput org.broadinstitute.hellbender.utils.runtime
The content of stdout or stderr.
StreamOutput() StreamOutput
STRICT SplitVcfs
stringForCSV() RecalDatum
stringRep(ReadMetadata, int) 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) 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) BreakpointEvidence.TemplateSizeAnomaly
stringSeqsToString(String[], String) IlluminaUtil
stringSerializer AsynchronousStreamWriterService
Convenience function that can be provided to an AsynchronousStreamWriterService to serialize String objects.
STRIP_UNPAIRED_MATE_NUMBER FastqToSam
Deprecated.
StripMateNumberTransformer org.broadinstitute.hellbender.transformers
Removes /1 or /2 and any whitespace from the end of the read name if present
StripMateNumberTransformer() StripMateNumberTransformer
stripPLsAndAD(GenotypesContext) GATKVariantContextUtils
STRUCTURAL_VARIANT_SIZE_LOWER_BOUND StructuralVariationDiscoveryArgumentCollection
StructuralVariantDiscoveryProgramGroup org.broadinstitute.hellbender.cmdline.programgroups
Tools that detect structural variants
StructuralVariantDiscoveryProgramGroup() StructuralVariantDiscoveryProgramGroup
StructuralVariationDiscoveryArgumentCollection org.broadinstitute.hellbender.tools.spark.sv
StructuralVariationDiscoveryArgumentCollection() StructuralVariationDiscoveryArgumentCollection
StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection org.broadinstitute.hellbender.tools.spark.sv
StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection org.broadinstitute.hellbender.tools.spark.sv
StructuralVariationDiscoveryPipelineSpark org.broadinstitute.hellbender.tools.spark.sv
Runs the structural variation discovery workflow on a single sample
StructuralVariationDiscoveryPipelineSpark() StructuralVariationDiscoveryPipelineSpark
StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser org.broadinstitute.hellbender.tools.spark.sv
subComputeReadLikelihoodGivenHaplotypeLog10(byte[], byte[], byte[], byte[], byte[], byte[], int, boolean, int) Log10PairHMM
To be implemented by subclasses to do calculation for #computeReadLikelihoodGivenHaplotypeLog10
subComputeReadLikelihoodGivenHaplotypeLog10(byte[], byte[], byte[], byte[], byte[], byte[], int, boolean, int) LoglessPairHMM
To be implemented by subclasses to do calculation for #computeReadLikelihoodGivenHaplotypeLog10
subComputeReadLikelihoodGivenHaplotypeLog10(byte[], byte[], byte[], byte[], byte[], byte[], int, boolean, int) PairHMM
To be implemented by subclasses to do calculation for #computeReadLikelihoodGivenHaplotypeLog10
subdivideAndFillReads(String, int, int, ReadFilter) AddContextDataToReadSparkOptimized
Fill in reads that start in the given shard, and subshard the output to the requested size.
SubdivideAndFillReadsIterator(String, int, int, ReadFilter, ContextShard) AddContextDataToReadSparkOptimized.SubdivideAndFillReadsIterator
SUBDIVISION_MODE IntervalListTools
SUBDIVISION_MODE_lONG_NAME SplitIntervals
SUBDIVISION_MODE_SHORT_NAME SplitIntervals
subFinderLabels() AggregatedSubHaplotypeFinder
subKmer(int, int) Kmer
Create a derived shallow kmer that starts at newStart and has newLength bases
submit(T) Downsampler
Submit one item to the downsampler for consideration.
submit(Collection<T>) Downsampler
Submit a collection of items to the downsampler for consideration.
submit(GATKRead) FractionalDownsampler
submit(T) LevelingDownsampler
submit(Collection<T>) LevelingDownsampler
submit(GATKRead) MutectDownsampler
submit(GATKRead) PassThroughDownsampler
submit(GATKRead) PositionalDownsampler
submit(GATKRead) ReservoirDownsampler
subSequence(int, int) SVKmerizer.ASCIICharSequence
subsetAlleles(GenotypesContext, int, List<Allele>, List<Allele>, GenotypeAssignmentMethod, int) 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(VariantContext, List<Allele>) AlleleSubsettingUtils
subsetAlleles(GenotypesContext, List<Allele>, List<Allele>) 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.
SubsettedLikelihoodMatrix 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<A>, List<A>) SubsettedLikelihoodMatrix
subsettedPLIndices(int, List<Allele>, List<Allele>) 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>) 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) BaseGraph
Get a graph containing only the vertices within distance edges of target
subsetToRefOnly(VariantContext, int) GATKVariantContextUtils
Subset the samples in VC to reference only information with ref call alleles
Preserves DP if present
subsetToRefSource(int) BaseGraph
Get a subgraph of graph that contains only vertices within a given number of edges of the ref source vertex
subsetVCToMatchSnp(VariantContext, Snp) AlleleSubsettingUtils
Method to subset the alleles in the VariantContext to those in the input snp.
SUBSTITUTION ErrorSummaryMetrics
A single string representing the substition from REF_BASE to ALT_BASE for convenience.
SUBSTITUTION_RATE ErrorSummaryMetrics
The rate of the substitution in question.
Substructure(List<Integer>, List<Range>) 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) GenomeLoc
subtractRegions(GenomeLocSortedSet) GenomeLocSortedSet
successor(SVKmer.Base, int) SVKmer
successor(SVKmer.Base, int) 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) SVKmerShort
Returns a new SVKmerShort that's like this one, but with its leading base discarded and a new one added to the end.
SUFFICIENT_GOOD_REALIGNMENTS_LONG_NAME FilterAlignmentArtifacts
sum(IntToDoubleFunction) IndexRange
Sums the values of an int -> double function applied to this range
sum(double[][][]) MathUtils
Return sum of 3d array
sum(double[]) MathUtils
sum(int[]) MathUtils
sum(byte[]) MathUtils
sum(long[]) MathUtils
sum(long[], int, int) MathUtils
Returns the sum of the elements in the array starting with start and ending before stop.
sum(double[], int, int) MathUtils
Returns the sum of the elements in the array starting with start and ending before stop.
sum() Nucleotide.Counter
sum(double...) MathUtil.LogMath
Computes the sum of the provided log values.
sum(double[], double[]) MathUtil
calculates the sum of the arrays as a third array.
sum(double[]) MathUtil
Returns the sum of the elements in the array.
sum(long[], int, int) MathUtil
Returns the sum of the elements in the array starting with start and ending before stop.
SUM_GL_THRESH_NOCALL GATKVariantContextUtils
sumArrayFunction(int, int, MathUtils.IntToDoubleArrayFunction) MathUtils
sumLog10(double[]) MathUtils
Returns the sum of values whose log10s we have.
summary Concordance
SUMMARY GcBiasMetrics
SUMMARY_FILE_EXTENSION CollectRrbsMetrics
SUMMARY_FILE_SUFFIX FilterByOrientationBias
SUMMARY_LONG_NAME Concordance
SUMMARY_METRICS_FILE_EXTENSION GenotypeConcordance
SUMMARY_OUTPUT CollectGcBiasMetrics
SUMMARY_OUTPUT CheckFingerprint
SUMMARY_SHORT_NAME Concordance
summaryMetricsExtension CollectHiSeqXPfFailMetrics
sumOfBaseQualities(GATKRead) MarkDuplicatesScoringStrategy
Computes the sum of base qualities of the given read.
sumOfSquares(Collection<Integer>) MathUtils
Computes the sum of squares of the given collection of ints or 0.0 if the collection is empty.
sumOverAlleleIndicesAndCounts(IntToDoubleBiFunction) GenotypeAlleleCounts
supportedTypes() MultiTileParser
supportedTypes() PosParser
SUPPORTING_CALLSET_LONG_NAME GenotypeCalculationArgumentCollection
SUPPORTING_CALLSET_SHORT_NAME GenotypeCalculationArgumentCollection
SUPPORTING_CALLSETS_LONG_NAME CalculateGenotypePosteriors
SUPPORTING_CALLSETS_SHORT_NAME CalculateGenotypePosteriors
supportsMetricAccumulationLevel() CollectMultipleMetrics.ProgramInterface
supportsVariant(GATKRead, VariantContext, int) RealignmentEngine
supportVariants GenotypeCalculationArgumentCollection
Supporting external panel.
supportVariants CalculateGenotypePosteriors
Supporting external panels.
SvCigarUtils org.broadinstitute.hellbender.tools.spark.sv.utils
Various utility functions helping calling structural variants.
SvCigarUtils() SvCigarUtils
SVContext org.broadinstitute.hellbender.tools.spark.sv.utils
Variant context with additional method to mine the structural variant specific information from structural
variant records.
SVD org.broadinstitute.hellbender.utils.svd
Interface for SVD implementation.
SVDDenoisedCopyRatioResult org.broadinstitute.hellbender.tools.copynumber.denoising
SVDDenoisedCopyRatioResult(SampleLocatableMetadata, List<SimpleInterval>, RealMatrix, RealMatrix) SVDDenoisedCopyRatioResult
SVDDenoisingUtils org.broadinstitute.hellbender.tools.copynumber.denoising
Utility class for package-private methods for performing SVD-based denoising and related operations.
SVDFactory org.broadinstitute.hellbender.utils.svd
Entry point for creating an instance of SVD.
SVDFactory() SVDFactory
SvDiscoverFromLocalAssemblyContigAlignmentsSpark org.broadinstitute.hellbender.tools.spark.sv.discovery
(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints
SvDiscoverFromLocalAssemblyContigAlignmentsSpark() SvDiscoverFromLocalAssemblyContigAlignmentsSpark
SvDiscoverFromLocalAssemblyContigAlignmentsSpark.AssemblyContigsClassifiedByAlignmentSignatures org.broadinstitute.hellbender.tools.spark.sv.discovery
SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SAMFormattedContigAlignmentParser org.broadinstitute.hellbender.tools.spark.sv.discovery
SvDiscoveryInputMetaData org.broadinstitute.hellbender.tools.spark.sv.discovery
SvDiscoveryInputMetaData(JavaSparkContext, StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection, String, String, ReadMetadata, List<SVInterval>, PairedStrandedIntervalTree<EvidenceTargetLink>, Broadcast<SVIntervalTree<VariantContext>>, SAMFileHeader, ReferenceMultiSource, Logger) SvDiscoveryInputMetaData
SvDiscoveryInputMetaData.ReferenceData org.broadinstitute.hellbender.tools.spark.sv.discovery
SvDiscoveryInputMetaData.SampleSpecificData org.broadinstitute.hellbender.tools.spark.sv.discovery
SvDiscoveryUtils org.broadinstitute.hellbender.tools.spark.sv.discovery
SvDiscoveryUtils() SvDiscoveryUtils
SVDReadCountPanelOfNormals org.broadinstitute.hellbender.tools.copynumber.denoising
Interface for the panel of normals (PoN) for SVD-based coverage denoising.
SVDUSTFilteredKmerizer 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) SVDUSTFilteredKmerizer
SVDUSTFilteredKmerizer(CharSequence, int, int, SVKmer) SVDUSTFilteredKmerizer
SVFastqUtils org.broadinstitute.hellbender.tools.spark.sv.utils
Memory-economical utilities for producing a FASTQ file.
SVFastqUtils() SVFastqUtils
SVFastqUtils.FastqRead org.broadinstitute.hellbender.tools.spark.sv.utils
SVFastqUtils.FastqRead.Serializer org.broadinstitute.hellbender.tools.spark.sv.utils
SVFastqUtils.Mapping org.broadinstitute.hellbender.tools.spark.sv.utils
SVFileUtils org.broadinstitute.hellbender.tools.spark.sv.utils
SVFileUtils() SVFileUtils
SVInterval org.broadinstitute.hellbender.tools.spark.sv.utils
Naturally collating, simple interval.
SVInterval(int, int, int) SVInterval
SVInterval.Serializer org.broadinstitute.hellbender.tools.spark.sv.utils
SVIntervalTree V > - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
A Red-Black tree with intervals for keys.
SVIntervalTree() SVIntervalTree
SVIntervalTree.Entry V1 > - Interface in org.broadinstitute.hellbender.tools.spark.sv.utils
SVIntervalTree.FwdIterator org.broadinstitute.hellbender.tools.spark.sv.utils
SVIntervalTree.OverlapIterator org.broadinstitute.hellbender.tools.spark.sv.utils
SVIntervalTree.RevIterator org.broadinstitute.hellbender.tools.spark.sv.utils
SVIntervalTree.Serializer T > - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
SVIntervalTree.ValuesIterator V1 > - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
SVKmer org.broadinstitute.hellbender.tools.spark.sv.utils
SVKmer() SVKmer
SVKmer.Base org.broadinstitute.hellbender.tools.spark.sv.utils
SVKmerizer org.broadinstitute.hellbender.tools.spark.sv.utils
Iterator over successive Kmers from a sequence of characters.
SVKmerizer(byte[], int, SVKmer) SVKmerizer
SVKmerizer(byte[], int, int, SVKmer) SVKmerizer
SVKmerizer(CharSequence, int, SVKmer) SVKmerizer
SVKmerizer(CharSequence, int, int, SVKmer) SVKmerizer
SVKmerizer(int, CharSequence) SVKmerizer
SVKmerizer(int, int, CharSequence) SVKmerizer
SVKmerizer.ASCIICharSequence org.broadinstitute.hellbender.tools.spark.sv.utils
SVKmerLong org.broadinstitute.hellbender.tools.spark.sv.utils
An immutable SVKmerLong.
SVKmerLong() SVKmerLong
SVKmerLong(int) SVKmerLong
Makes an empty SVKmerLong.
SVKmerLong(SVKmerLong) SVKmerLong
SVKmerLong(SVKmer) SVKmerLong
SVKmerLong(Kryo, Input) SVKmerLong
SVKmerLong.Serializer org.broadinstitute.hellbender.tools.spark.sv.utils
SVKmerShort org.broadinstitute.hellbender.tools.spark.sv.utils
An immutable SVKmerShort.
SVKmerShort() SVKmerShort
Makes an empty SVKmerShort.
SVKmerShort(int) SVKmerShort
Makes an empty SVKmerShort.
SVKmerShort(SVKmerShort) SVKmerShort
SVKmerShort(long) SVKmerShort
SVKmerShort.Serializer org.broadinstitute.hellbender.tools.spark.sv.utils
svLen SvType
SVLEN GATKSVVCFConstants
SVLocation org.broadinstitute.hellbender.tools.spark.sv.utils
SVLocation(int, int) SVLocation
SVReadFilter org.broadinstitute.hellbender.tools.spark.sv.evidence
SVReadFilter(StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection) SVReadFilter
SVReferenceUtils org.broadinstitute.hellbender.tools.spark.sv.utils
SVReferenceUtils() SVReferenceUtils
SvType org.broadinstitute.hellbender.tools.spark.sv.discovery
Various types of structural variations
SvType(String, Allele, int, Map<String, String>) SvType
SVTYPE GATKSVVCFConstants
SVUtils org.broadinstitute.hellbender.tools.spark.sv.utils
Useful scraps of this and that.
SVUtils() SVUtils
SVUtils.IteratorFilter T > - Class in org.broadinstitute.hellbender.tools.spark.sv.utils
SVVCFReader org.broadinstitute.hellbender.tools.spark.sv.utils
SVVCFReader() SVVCFReader
SVVCFWriter org.broadinstitute.hellbender.tools.spark.sv.utils
A utility class that writes out variants to a VCF file.
SVVCFWriter() SVVCFWriter
swapAlleles(VariantContext, Allele, Allele) AlleleSubsettingUtils
Swaps one of the alleles in a VC (and its genotypes) with another.
SWAPPED_ALLELES 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>) LiftoverUtils
method to swap the reference and alt alleles of a bi-allelic, SNP
SWNativeAlignerWrapper org.broadinstitute.hellbender.utils.smithwaterman
SWNativeAlignerWrapper(SWAlignerNativeBinding) SWNativeAlignerWrapper
SYMB_ALT_ALLELE_DEL GATKSVVCFConstants
SYMB_ALT_ALLELE_DUP GATKSVVCFConstants
SYMB_ALT_ALLELE_INS GATKSVVCFConstants
SYMB_ALT_ALLELE_INV GATKSVVCFConstants
SYMB_ALT_ALLELE_INVDUP GATKSVVCFConstants
SYMBOLIC_ALLELE_DEFINITION_HEADER_TAG GATKVCFConstants
SYMBOLIC_UNASSEMBLED_EVENT_ALLELE EventMap
symmetricDirichlet(int, double) Dirichlet
Create a symmetric distribution Dir(a/K, a/K, a/K .
SynchronizedUnivariateSolver org.broadinstitute.hellbender.utils.solver
This class implements a synchronized univariate solver for solving multiple independent equations.
SynchronizedUnivariateSolver(Function<Map<Integer, Double>, Map<Integer, Double>>, Function<UnivariateSolverSpecifications, AbstractUnivariateSolver>, int) SynchronizedUnivariateSolver
Public constructor for invoking one of AbstractUnivariateSolver
SynchronizedUnivariateSolver.UnivariateSolverStatus org.broadinstitute.hellbender.utils.solver
SynchronizedUnivariateSolver.UnivariateSolverSummary org.broadinstitute.hellbender.utils.solver
Stores the summary of a univariate solver jobDescription
SYNTHETIC_PHASESET_PREFIX HaplotypeMap
SystemProperty org.broadinstitute.hellbender.utils.config
An annotation to denote Configuration options that should be injected into the Java System Properties.
VAExpression(String, List<FeatureInput<VariantContext>>) VariantAnnotatorEngine.VAExpression
VALID_ALIGNMENT_END ReadFilterLibrary
VALID_ALIGNMENT_START ReadFilterLibrary
ValidAlignmentEndReadFilter() ReadFilterLibrary.ValidAlignmentEndReadFilter
ValidAlignmentStartReadFilter() ReadFilterLibrary.ValidAlignmentStartReadFilter
validate() GermlineCallingArgumentCollection
validate() GermlineContigPloidyModelArgumentCollection
validate() GermlineDenoisingModelArgumentCollection
validate() HybridADVIArgumentCollection
validate(boolean, String) Utils
Check a condition that should always be true and throw an IllegalStateException if false.
validate(boolean, Supplier<String>) Utils
Check a condition that should always be true and throw an IllegalStateException if false.
VALIDATE_INDEX ValidateSamFile
VALIDATE_SAMPLE_MAP_LONG_NAME GenomicsDBImport
validateAllelesList() ReducibleAnnotationData
validateAndResolvePlugins() GATKAnnotationPluginDescriptor
Validate the list of arguments and reduce the list of annotations to those
actually seen on the command line.
validateAndResolvePlugins() 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) CopyNumberArgumentValidationUtils
Checks equality of the sequence dictionary and intervals contained in an
locatableCollection
against those contained in an
AnnotatedIntervalCollection represented by
annotatedIntervalsFile.
validateAnnotatedIntervalsSubset(File, AbstractLocatableCollection<?, ?>, Logger) CopyNumberArgumentValidationUtils
validateArg(boolean, String) Utils
validateArg(boolean, Supplier<String>) Utils
ValidateBasicSomaticShortMutations org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
ValidateBasicSomaticShortMutations() ValidateBasicSomaticShortMutations
validateCigar(List<CigarElement>) SvCigarUtils
Checks input list of cigar operations for:
empty input list;
there must be at least one alignment operation in the list;
deletion operation cannot neighbor clipping operations;
validateCountsAgainstScheme(GenotypeConcordanceScheme) GenotypeConcordanceCounts
Validates that there are no counts for NA states in the underlying scheme
validateCRAMDictionaryAgainstReference(SAMSequenceDictionary, SAMSequenceDictionary) SequenceDictionaryUtils
Tests for compatibility between a reference dictionary and a CRAM dictionary, using appropriate
validation settings.
validateDictionaries(String, SAMSequenceDictionary, String, SAMSequenceDictionary) SequenceDictionaryUtils
Tests for compatibility between two sequence dictionaries, using standard validation settings appropriate
for the GATK.
validateDictionaries(String, SAMSequenceDictionary, String, SAMSequenceDictionary, boolean, boolean) SequenceDictionaryUtils
Tests for compatibility between two sequence dictionaries.
validateEmitEmptyLociParameters() LocusWalker
The emit empty loci parameter comes with several pitfalls when used incorrectly.
validateExpectedSortOrder(SAMFileHeader.SortOrder, SAMFileHeader.SortOrder, boolean, String) ReadUtils
Validate that the expected input sort order is either "unsorted", or that it
matches the actualSortOrder.
validateGencodeGtfFeature(GencodeGtfFeature, int) GencodeGtfCodec
Validates a given
GencodeGtfFeature against a given version of the GENCODE GTF file spec.
validateGenomeLoc(String, int, int, int, boolean) 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.
validateIntervalArgumentCollection(IntervalArgumentCollection) CopyNumberArgumentValidationUtils
Validate that the interval-argument collection parameters minimally modify the input intervals.
validateIntervals(List<T>, SAMSequenceDictionary) CopyNumberArgumentValidationUtils
Validate that a list of locatables is valid and sorted according to a sequence dictionary and contains no duplicates or overlaps.
validateLocatableColumnName(String) XsvLocatableTableCodec
Throw an exception if the given column name cannot be used for one of the locatable columns.
validateNoOverlappingIntervals(List<T>) IntervalUtils
Throws Bad Input exception if any overlaps are detected within the list of locatables.
ValidateSamFile picard.sam
This tool reports on the validity of a SAM or BAM file relative to the SAM format
specification.
ValidateSamFile() ValidateSamFile
ValidateSamFile.Mode picard.sam
validateScheme() GenotypeConcordanceScheme
Check that all cells in the scheme exist.
validateSequenceDictionaries() GATKSparkTool
Validates standard tool inputs against each other.
validateSequenceDictionaries() ReadsPipelineSpark
ValidateVariants org.broadinstitute.hellbender.tools.walkers.variantutils
Validate a VCF file with a strict set of criteria
ValidateVariants() ValidateVariants
ValidateVariants.ValidationType org.broadinstitute.hellbender.tools.walkers.variantutils
VALIDATION_ALT_COVERAGE ValidateBasicSomaticShortMutations
VALIDATION_REF_COVERAGE ValidateBasicSomaticShortMutations
VALIDATION_STRINGENCY PicardCommandLineProgram
VALIDATION_STRINGENCY CommandLineProgram
validationCaseName ValidateBasicSomaticShortMutations
validationControlName ValidateBasicSomaticShortMutations
validIndex(int, int) Utils
Checks whether an index is within bounds considering a collection or array of a particular size
whose first position index is 0
value SVKmer.Base
value NestedIntegerArray.Leaf
VALUE_SEPARATOR Tranche
valueCounts CompressedDataList
valueOf(String) AlignmentContext.ReadOrientation
Returns the enum constant of this type with the specified name.
valueOf(String) JoinStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) MetricAccumulationLevel
Returns the enum constant of this type with the specified name.
valueOf(String) GermlineDenoisingModelArgumentCollection.CopyNumberPosteriorExpectationMode
Returns the enum constant of this type with the specified name.
valueOf(String) HybridADVIArgumentCollection.HybridADVIArgument
Returns the enum constant of this type with the specified name.
valueOf(String) DetermineGermlineContigPloidy.RunMode
Returns the enum constant of this type with the specified name.
valueOf(String) Metadata.Type
Returns the enum constant of this type with the specified name.
valueOf(String) CalledCopyRatioSegment.Call
Returns the enum constant of this type with the specified name.
valueOf(String) GermlineCNVCaller.RunMode
Returns the enum constant of this type with the specified name.
valueOf(String) AlleleFractionParameter
Returns the enum constant of this type with the specified name.
valueOf(String) CopyRatioParameter
Returns the enum constant of this type with the specified name.
valueOf(String) KernelSegmenter.ChangepointSortOrder
Returns the enum constant of this type with the specified name.
valueOf(String) OrientationBiasFilterSummaryTableColumn
Returns the enum constant of this type with the specified name.
valueOf(String) AminoAcid
Returns the enum constant of this type with the specified name.
valueOf(String) GencodeFuncotation.VariantClassification
Returns the enum constant of this type with the specified name.
valueOf(String) GencodeFuncotation.VariantType
Returns the enum constant of this type with the specified name.
valueOf(String) SimpleKeyXsvFuncotationFactory.XsvDataKeyType
Returns the enum constant of this type with the specified name.
valueOf(String) FuncotatorArgumentDefinitions.DataSourceType
Returns the enum constant of this type with the specified name.
valueOf(String) FuncotatorArgumentDefinitions.OutputFormatType
Returns the enum constant of this type with the specified name.
valueOf(String) TranscriptSelectionMode
Returns the enum constant of this type with the specified name.
valueOf(String) GatherVcfsCloud.GatherType
Returns the enum constant of this type with the specified name.
valueOf(String) CollectMultipleMetricsSpark.SparkCollectors
Returns the enum constant of this type with the specified name.
valueOf(String) AssemblyContigWithFineTunedAlignments.AlignmentSignatureBasicType
Returns the enum constant of this type with the specified name.
valueOf(String) AssemblyContigWithFineTunedAlignments.ReasonForAlignmentClassificationFailure
Returns the enum constant of this type with the specified name.
valueOf(String) ContigAlignmentsModifier.AlnModType.ModTypeString
Returns the enum constant of this type with the specified name.
valueOf(String) ContigAlignmentsModifier.AlnModType
Returns the enum constant of this type with the specified name.
valueOf(String) StrandSwitch
Returns the enum constant of this type with the specified name.
valueOf(String) SimpleSVType.TYPES
Returns the enum constant of this type with the specified name.
valueOf(String) TemplateFragmentOrdinal
Returns the enum constant of this type with the specified name.
valueOf(String) Strand
Returns the enum constant of this type with the specified name.
valueOf(String) SVKmer.Base
Returns the enum constant of this type with the specified name.
valueOf(String) StrandArtifact.ArtifactState
Returns the enum constant of this type with the specified name.
valueOf(String) ContaminationRecord.Level
Returns the enum constant of this type with the specified name.
valueOf(String) AFCalculatorImplementation
Returns the enum constant of this type with the specified name.
valueOf(String) GenotypeAssignmentMethod
Returns the enum constant of this type with the specified name.
valueOf(String) GenotypeLikelihoodsCalculationModel
Returns the enum constant of this type with the specified name.
valueOf(String) GenotypingOutputMode
Returns the enum constant of this type with the specified name.
valueOf(String) OutputMode
Returns the enum constant of this type with the specified name.
valueOf(String) AssemblyResult.Status
Returns the enum constant of this type with the specified name.
valueOf(String) PairHMMLikelihoodCalculationEngine.PCRErrorModel
Returns the enum constant of this type with the specified name.
valueOf(String) ReadLikelihoodCalculationEngine.Implementation
Returns the enum constant of this type with the specified name.
valueOf(String) ReferenceConfidenceMode
Returns the enum constant of this type with the specified name.
valueOf(String) CreateSomaticPanelOfNormals.DuplicateSampleStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) PerAlleleCollection.Type
Returns the enum constant of this type with the specified name.
valueOf(String) ASEReadCounter.CountPileupType
Returns the enum constant of this type with the specified name.
valueOf(String) ASEReadCounter.OUTPUT_FORMAT
Returns the enum constant of this type with the specified name.
valueOf(String) ConcordanceState
Returns the enum constant of this type with the specified name.
valueOf(String) ValidateVariants.ValidationType
Returns the enum constant of this type with the specified name.
valueOf(String) TensorType
Returns the enum constant of this type with the specified name.
valueOf(String) ActivityProfileState.Type
Returns the enum constant of this type with the specified name.
valueOf(String) Transition
Returns the enum constant of this type with the specified name.
valueOf(String) BAQ.CalculationMode
Returns the enum constant of this type with the specified name.
valueOf(String) BAQ.QualityMode
Returns the enum constant of this type with the specified name.
valueOf(String) BaseUtils.Base
Returns the enum constant of this type with the specified name.
valueOf(String) BaseUtils.BaseSubstitutionType
Returns the enum constant of this type with the specified name.
valueOf(String) ClippingRepresentation
Returns the enum constant of this type with the specified name.
valueOf(String) GencodeGtfFeature.AnnotationSource
Returns the enum constant of this type with the specified name.
valueOf(String) GencodeGtfFeature.FeatureTag
Returns the enum constant of this type with the specified name.
valueOf(String) GencodeGtfFeature.FeatureType
Returns the enum constant of this type with the specified name.
valueOf(String) GencodeGtfFeature.GeneTranscriptStatus
Returns the enum constant of this type with the specified name.
valueOf(String) GencodeGtfFeature.GeneTranscriptType
Returns the enum constant of this type with the specified name.
valueOf(String) GencodeGtfFeature.GenomicPhase
Returns the enum constant of this type with the specified name.
valueOf(String) GencodeGtfFeature.LocusLevel
Returns the enum constant of this type with the specified name.
valueOf(String) GencodeGtfFeature.RemapStatus
Returns the enum constant of this type with the specified name.
valueOf(String) GencodeGtfFeature.RemapTargetStatus
Returns the enum constant of this type with the specified name.
valueOf(String) GencodeGtfFeature.TranscriptSupportLevel
Returns the enum constant of this type with the specified name.
valueOf(String) DownsampleType
Returns the enum constant of this type with the specified name.
valueOf(String) GenomeLocParser.ValidationLevel
Returns the enum constant of this type with the specified name.
valueOf(String) DiploidGenotype
Returns the enum constant of this type with the specified name.
valueOf(String) HaplotypeBAMWriter.WriterType
Returns the enum constant of this type with the specified name.
valueOf(String) IlluminaAdapterPair
Returns the enum constant of this type with the specified name.
valueOf(String) IntervalMergingRule
Returns the enum constant of this type with the specified name.
valueOf(String) IntervalSetRule
Returns the enum constant of this type with the specified name.
valueOf(String) IntervalUtils.IntervalBreakpointType
Returns the enum constant of this type with the specified name.
valueOf(String) MannWhitneyU.TestType
Returns the enum constant of this type with the specified name.
valueOf(String) Decile
Returns the enum constant of this type with the specified name.
valueOf(String) ParameterizedModel.UpdateMethod
Returns the enum constant of this type with the specified name.
valueOf(String) ParameterTableColumn
Returns the enum constant of this type with the specified name.
valueOf(String) NGSPlatform
Returns the enum constant of this type with the specified name.
valueOf(String) Nucleotide
Returns the enum constant of this type with the specified name.
valueOf(byte) Nucleotide
Returns the nucleotide that corresponds to a particular byte typed base code.
valueOf(String) PairHMM.Implementation
Returns the enum constant of this type with the specified name.
valueOf(String) VectorLoglessPairHMM.Implementation
Returns the enum constant of this type with the specified name.
valueOf(String) PythonExecutorBase.PythonExecutableName
Returns the enum constant of this type with the specified name.
valueOf(String) RScriptLibrary
Returns the enum constant of this type with the specified name.
valueOf(String) MarkDuplicatesScoringStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) MarkDuplicatesSparkRecord.Type
Returns the enum constant of this type with the specified name.
valueOf(String) HitsForInsert.NumPrimaryAlignmentState
Returns the enum constant of this type with the specified name.
valueOf(String) ReadsWriteFormat
Returns the enum constant of this type with the specified name.
valueOf(String) ReadUtils.ClippingTail
Returns the enum constant of this type with the specified name.
valueOf(String) EventType
Returns the enum constant of this type with the specified name.
valueOf(String) GATKReportColumnFormat.Alignment
Returns the enum constant of this type with the specified name.
valueOf(String) GATKReportDataType
Returns the enum constant of this type with the specified name.
valueOf(String) GATKReportTable.Sorting
Returns the enum constant of this type with the specified name.
valueOf(String) GATKReportTable.TableDataHeaderFields
Returns the enum constant of this type with the specified name.
valueOf(String) GATKReportTable.TableNameHeaderFields
Returns the enum constant of this type with the specified name.
valueOf(String) GATKReportVersion
Returns the enum constant of this type with the specified name.
valueOf(String) ProcessControllerBase.ProcessStream
Returns the enum constant of this type with the specified name.
valueOf(String) StreamLocation
Returns the enum constant of this type with the specified name.
valueOf(String) Affection
Returns the enum constant of this type with the specified name.
valueOf(String) PedigreeValidationType
Returns the enum constant of this type with the specified name.
valueOf(String) PedReader.Field
Returns the enum constant of this type with the specified name.
valueOf(String) PedReader.MissingPedField
Returns the enum constant of this type with the specified name.
valueOf(String) Sex
Returns the enum constant of this type with the specified name.
valueOf(String) SequenceDictionaryUtils.SequenceDictionaryCompatibility
Returns the enum constant of this type with the specified name.
valueOf(String) SequencerFlowClass
Returns the enum constant of this type with the specified name.
valueOf(String) SmithWatermanAligner.Implementation
Returns the enum constant of this type with the specified name.
valueOf(String) SmithWatermanJavaAligner.State
Returns the enum constant of this type with the specified name.
valueOf(String) SynchronizedUnivariateSolver.UnivariateSolverStatus
Returns the enum constant of this type with the specified name.
valueOf(String) Trilean
Returns the enum constant of this type with the specified name.
valueOf(String) DbSnpVariantType
Returns the enum constant of this type with the specified name.
valueOf(String) GATKVariantContextUtils.FilteredRecordMergeType
Returns the enum constant of this type with the specified name.
valueOf(String) GATKVariantContextUtils.GenotypeMergeType
Returns the enum constant of this type with the specified name.
valueOf(String) GATKVCFIndexType
Returns the enum constant of this type with the specified name.
valueOf(String) AlignmentSummaryMetrics.Category
Returns the enum constant of this type with the specified name.
valueOf(String) Transition.Base
Returns the enum constant of this type with the specified name.
valueOf(String) Transition
Returns the enum constant of this type with the specified name.
valueOf(String) CollectMultipleMetrics.Program
Returns the enum constant of this type with the specified name.
valueOf(String) CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
Returns the enum constant of this type with the specified name.
valueOf(String) RnaSeqMetricsCollector.StrandSpecificity
Returns the enum constant of this type with the specified name.
valueOf(String) MetricAccumulationLevel
Returns the enum constant of this type with the specified name.
valueOf(String) LocusFunction
Returns the enum constant of this type with the specified name.
valueOf(String) RefFlatReader.RefFlatColumns
Returns the enum constant of this type with the specified name.
valueOf(String) CrosscheckMetric.DataType
Returns the enum constant of this type with the specified name.
valueOf(String) CrosscheckMetric.FingerprintResult
Returns the enum constant of this type with the specified name.
valueOf(String) DiploidGenotype
Returns the enum constant of this type with the specified name.
valueOf(String) DiploidHaplotype
Returns the enum constant of this type with the specified name.
valueOf(String) HaplotypeProbabilities.Genotype
Returns the enum constant of this type with the specified name.
valueOf(String) IlluminaBasecallsToFastq.ReadNameFormat
Returns the enum constant of this type with the specified name.
valueOf(String) IlluminaDataType
Returns the enum constant of this type with the specified name.
valueOf(String) IlluminaFileUtil.SupportedIlluminaFormat
Returns the enum constant of this type with the specified name.
valueOf(String) IlluminaMetricsCode
Returns the enum constant of this type with the specified name.
valueOf(String) IntensityChannel
Returns the enum constant of this type with the specified name.
valueOf(String) TileMetricsOutReader.TileMetricsVersion
Returns the enum constant of this type with the specified name.
valueOf(String) ReadType
Returns the enum constant of this type with the specified name.
valueOf(String) TileTemplateRead
Returns the enum constant of this type with the specified name.
valueOf(String) CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
Returns the enum constant of this type with the specified name.
valueOf(String) PathHelper.PathProviders
Returns the enum constant of this type with the specified name.
valueOf(String) Sex
Returns the enum constant of this type with the specified name.
valueOf(String) AbstractAlignmentMerger.UnmappingReadStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) FilterSamReads.Filter
Returns the enum constant of this type with the specified name.
valueOf(String) MarkDuplicates.DuplicateTaggingPolicy
Returns the enum constant of this type with the specified name.
valueOf(String) MarkDuplicates.DuplicateType
Returns the enum constant of this type with the specified name.
valueOf(String) RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
Returns the enum constant of this type with the specified name.
valueOf(String) RevertSam.FileType
Returns the enum constant of this type with the specified name.
valueOf(String) ValidateSamFile.Mode
Returns the enum constant of this type with the specified name.
valueOf(String) ViewSam.AlignmentStatus
Returns the enum constant of this type with the specified name.
valueOf(String) ViewSam.PfStatus
Returns the enum constant of this type with the specified name.
valueOf(String) BaitDesigner.DesignStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) IlluminaUtil.IlluminaAdapterPair
Returns the enum constant of this type with the specified name.
valueOf(String) IntervalListScatterer.Mode
Returns the enum constant of this type with the specified name.
valueOf(String) IntervalListTools.Action
Returns the enum constant of this type with the specified name.
valueOf(String) VariantType
Returns the enum constant of this type with the specified name.
valueOf(String) GenotypeConcordanceStateCodes
Returns the enum constant of this type with the specified name.
valueOf(String) GenotypeConcordanceStates.CallState
Returns the enum constant of this type with the specified name.
valueOf(String) GenotypeConcordanceStates.ContingencyState
Returns the enum constant of this type with the specified name.
valueOf(String) GenotypeConcordanceStates.TruthState
Returns the enum constant of this type with the specified name.
values() AlignmentContext.ReadOrientation
Returns an array containing the constants of this enum type, in
the order they are declared.
values() JoinStrategy
Returns an array containing the constants of this enum type, in
the order they are declared.
values() MetricAccumulationLevel
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GermlineDenoisingModelArgumentCollection.CopyNumberPosteriorExpectationMode
Returns an array containing the constants of this enum type, in
the order they are declared.
values() HybridADVIArgumentCollection.HybridADVIArgument
Returns an array containing the constants of this enum type, in
the order they are declared.
values() DetermineGermlineContigPloidy.RunMode
Returns an array containing the constants of this enum type, in
the order they are declared.
values() Metadata.Type
Returns an array containing the constants of this enum type, in
the order they are declared.
values() CalledCopyRatioSegment.Call
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GermlineCNVCaller.RunMode
Returns an array containing the constants of this enum type, in
the order they are declared.
values() AlleleFractionParameter
Returns an array containing the constants of this enum type, in
the order they are declared.
values() CopyRatioParameter
Returns an array containing the constants of this enum type, in
the order they are declared.
values() KernelSegmenter.ChangepointSortOrder
Returns an array containing the constants of this enum type, in
the order they are declared.
values() OrientationBiasFilterSummaryTableColumn
Returns an array containing the constants of this enum type, in
the order they are declared.
values() AminoAcid
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GencodeFuncotation.VariantClassification
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GencodeFuncotation.VariantType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() TableFuncotation
values() SimpleKeyXsvFuncotationFactory.XsvDataKeyType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() FuncotatorArgumentDefinitions.DataSourceType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() FuncotatorArgumentDefinitions.OutputFormatType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() TranscriptSelectionMode
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GatherVcfsCloud.GatherType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() CollectMultipleMetricsSpark.SparkCollectors
Returns an array containing the constants of this enum type, in
the order they are declared.
values() AssemblyContigWithFineTunedAlignments.AlignmentSignatureBasicType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() AssemblyContigWithFineTunedAlignments.ReasonForAlignmentClassificationFailure
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ContigAlignmentsModifier.AlnModType.ModTypeString
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ContigAlignmentsModifier.AlnModType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() StrandSwitch
Returns an array containing the constants of this enum type, in
the order they are declared.
values() SimpleSVType.TYPES
Returns an array containing the constants of this enum type, in
the order they are declared.
values() TemplateFragmentOrdinal
Returns an array containing the constants of this enum type, in
the order they are declared.
values() Strand
Returns an array containing the constants of this enum type, in
the order they are declared.
values() SVKmer.Base
Returns an array containing the constants of this enum type, in
the order they are declared.
values() StrandArtifact.ArtifactState
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ContaminationRecord.Level
Returns an array containing the constants of this enum type, in
the order they are declared.
values() AFCalculatorImplementation
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GenotypeAssignmentMethod
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GenotypeLikelihoodsCalculationModel
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GenotypingOutputMode
Returns an array containing the constants of this enum type, in
the order they are declared.
values() OutputMode
Returns an array containing the constants of this enum type, in
the order they are declared.
values() AssemblyResult.Status
Returns an array containing the constants of this enum type, in
the order they are declared.
values() PairHMMLikelihoodCalculationEngine.PCRErrorModel
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ReadLikelihoodCalculationEngine.Implementation
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ReferenceConfidenceMode
Returns an array containing the constants of this enum type, in
the order they are declared.
values() CreateSomaticPanelOfNormals.DuplicateSampleStrategy
Returns an array containing the constants of this enum type, in
the order they are declared.
values() PerAlleleCollection.Type
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ASEReadCounter.CountPileupType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ASEReadCounter.OUTPUT_FORMAT
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ConcordanceState
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ValidateVariants.ValidationType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() TensorType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ActivityProfileState.Type
Returns an array containing the constants of this enum type, in
the order they are declared.
values() Transition
Returns an array containing the constants of this enum type, in
the order they are declared.
values() BAQ.CalculationMode
Returns an array containing the constants of this enum type, in
the order they are declared.
values() BAQ.QualityMode
Returns an array containing the constants of this enum type, in
the order they are declared.
values() BaseUtils.Base
Returns an array containing the constants of this enum type, in
the order they are declared.
values() BaseUtils.BaseSubstitutionType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ClippingRepresentation
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GencodeGtfFeature.AnnotationSource
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GencodeGtfFeature.FeatureTag
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GencodeGtfFeature.FeatureType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GencodeGtfFeature.GeneTranscriptStatus
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GencodeGtfFeature.GeneTranscriptType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GencodeGtfFeature.GenomicPhase
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GencodeGtfFeature.LocusLevel
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GencodeGtfFeature.RemapStatus
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GencodeGtfFeature.RemapTargetStatus
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GencodeGtfFeature.TranscriptSupportLevel
Returns an array containing the constants of this enum type, in
the order they are declared.
values() DownsampleType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GenomeLocParser.ValidationLevel
Returns an array containing the constants of this enum type, in
the order they are declared.
values() DiploidGenotype
Returns an array containing the constants of this enum type, in
the order they are declared.
values() HaplotypeBAMWriter.WriterType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IlluminaAdapterPair
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IntervalMergingRule
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IntervalSetRule
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IntervalUtils.IntervalBreakpointType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() MannWhitneyU.TestType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() Decile
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ParameterizedModel.UpdateMethod
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ParameterizedState
Returns a List of the
Parameter objects that are held internally as values of the parameter map.
values() ParameterTableColumn
Returns an array containing the constants of this enum type, in
the order they are declared.
values() NGSPlatform
Returns an array containing the constants of this enum type, in
the order they are declared.
values() Nucleotide
Returns an array containing the constants of this enum type, in
the order they are declared.
values() PairHMM.Implementation
Returns an array containing the constants of this enum type, in
the order they are declared.
values() VectorLoglessPairHMM.Implementation
Returns an array containing the constants of this enum type, in
the order they are declared.
values() PythonExecutorBase.PythonExecutableName
Returns an array containing the constants of this enum type, in
the order they are declared.
values() RScriptLibrary
Returns an array containing the constants of this enum type, in
the order they are declared.
values() MarkDuplicatesScoringStrategy
Returns an array containing the constants of this enum type, in
the order they are declared.
values() MarkDuplicatesSparkRecord.Type
Returns an array containing the constants of this enum type, in
the order they are declared.
values() HitsForInsert.NumPrimaryAlignmentState
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ReadsWriteFormat
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ReadUtils.ClippingTail
Returns an array containing the constants of this enum type, in
the order they are declared.
values() EventType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GATKReportColumnFormat.Alignment
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GATKReportDataType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GATKReportTable.Sorting
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GATKReportTable.TableDataHeaderFields
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GATKReportTable.TableNameHeaderFields
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GATKReportVersion
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ProcessControllerBase.ProcessStream
Returns an array containing the constants of this enum type, in
the order they are declared.
values() StreamLocation
Returns an array containing the constants of this enum type, in
the order they are declared.
values() Affection
Returns an array containing the constants of this enum type, in
the order they are declared.
values() PedigreeValidationType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() PedReader.Field
Returns an array containing the constants of this enum type, in
the order they are declared.
values() PedReader.MissingPedField
Returns an array containing the constants of this enum type, in
the order they are declared.
values() Sex
Returns an array containing the constants of this enum type, in
the order they are declared.
values() SequenceDictionaryUtils.SequenceDictionaryCompatibility
Returns an array containing the constants of this enum type, in
the order they are declared.
values() SequencerFlowClass
Returns an array containing the constants of this enum type, in
the order they are declared.
values() SmithWatermanAligner.Implementation
Returns an array containing the constants of this enum type, in
the order they are declared.
values() SmithWatermanJavaAligner.State
Returns an array containing the constants of this enum type, in
the order they are declared.
values() SynchronizedUnivariateSolver.UnivariateSolverStatus
Returns an array containing the constants of this enum type, in
the order they are declared.
values() Trilean
Returns an array containing the constants of this enum type, in
the order they are declared.
values() DbSnpVariantType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GATKVariantContextUtils.AlleleMapper
values() GATKVariantContextUtils.FilteredRecordMergeType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GATKVariantContextUtils.GenotypeMergeType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GATKVCFIndexType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() AlignmentSummaryMetrics.Category
Returns an array containing the constants of this enum type, in
the order they are declared.
values() Transition.Base
Returns an array containing the constants of this enum type, in
the order they are declared.
values() Transition
Returns an array containing the constants of this enum type, in
the order they are declared.
values() CollectMultipleMetrics.Program
Returns an array containing the constants of this enum type, in
the order they are declared.
values() CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
Returns an array containing the constants of this enum type, in
the order they are declared.
values() RnaSeqMetricsCollector.StrandSpecificity
Returns an array containing the constants of this enum type, in
the order they are declared.
values() MetricAccumulationLevel
Returns an array containing the constants of this enum type, in
the order they are declared.
values() LocusFunction
Returns an array containing the constants of this enum type, in
the order they are declared.
values() RefFlatReader.RefFlatColumns
Returns an array containing the constants of this enum type, in
the order they are declared.
values() CrosscheckMetric.DataType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() CrosscheckMetric.FingerprintResult
Returns an array containing the constants of this enum type, in
the order they are declared.
values() DiploidGenotype
Returns an array containing the constants of this enum type, in
the order they are declared.
values() DiploidHaplotype
Returns an array containing the constants of this enum type, in
the order they are declared.
values() HaplotypeProbabilities.Genotype
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IlluminaBasecallsToFastq.ReadNameFormat
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IlluminaDataType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IlluminaFileUtil.SupportedIlluminaFormat
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IlluminaMetricsCode
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IntensityChannel
Returns an array containing the constants of this enum type, in
the order they are declared.
values() TileMetricsOutReader.TileMetricsVersion
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ReadType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() TileTemplateRead
Returns an array containing the constants of this enum type, in
the order they are declared.
values() CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
Returns an array containing the constants of this enum type, in
the order they are declared.
values() PathHelper.PathProviders
Returns an array containing the constants of this enum type, in
the order they are declared.
values() Sex
Returns an array containing the constants of this enum type, in
the order they are declared.
values() AbstractAlignmentMerger.UnmappingReadStrategy
Returns an array containing the constants of this enum type, in
the order they are declared.
values() FilterSamReads.Filter
Returns an array containing the constants of this enum type, in
the order they are declared.
values() MarkDuplicates.DuplicateTaggingPolicy
Returns an array containing the constants of this enum type, in
the order they are declared.
values() MarkDuplicates.DuplicateType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
Returns an array containing the constants of this enum type, in
the order they are declared.
values() RevertSam.FileType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ValidateSamFile.Mode
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ViewSam.AlignmentStatus
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ViewSam.PfStatus
Returns an array containing the constants of this enum type, in
the order they are declared.
values() BaitDesigner.DesignStrategy
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IlluminaUtil.IlluminaAdapterPair
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IntervalListScatterer.Mode
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IntervalListTools.Action
Returns an array containing the constants of this enum type, in
the order they are declared.
values() VariantType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GenotypeConcordanceStateCodes
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GenotypeConcordanceStates.CallState
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GenotypeConcordanceStates.ContingencyState
Returns an array containing the constants of this enum type, in
the order they are declared.
values() GenotypeConcordanceStates.TruthState
Returns an array containing the constants of this enum type, in
the order they are declared.
valuesBySampleIndex ReadLikelihoods
Indexed per sample, allele and finally read (within sample).
ValuesIterator(Iterator<SVIntervalTree.Entry<V1>>) SVIntervalTree.ValuesIterator
var() MathUtils.RunningAverage
VAR_PPV GenotypeConcordanceSummaryMetrics
The ppv (positive predictive value) for all (heterozygous and homozygous) variants (PPV is the TP / (TP + FP))
VAR_SENSITIVITY GenotypeConcordanceSummaryMetrics
The sensitivity for all (heterozygous and homozygous) variants (Sensitivity is TP / (TP + FN))
VAR_SPECIFICITY GenotypeConcordanceSummaryMetrics
The specificity for all (heterozygous and homozygous) variants (Specificity is TN / (FP + TN))
VARIANT_LONG_NAME StandardArgumentDefinitions
VARIANT_SHARDSIZE VariantShard
VARIANT_SHORT_NAME StandardArgumentDefinitions
VARIANT_TYPE GenotypeConcordanceContingencyMetrics
The type of the event (i.e.
VARIANT_TYPE GenotypeConcordanceDetailMetrics
The type of the event (i.e.
VARIANT_TYPE GenotypeConcordanceSummaryMetrics
The type of the event (i.e.
VARIANT_TYPE_KEY GATKVCFConstants
VariantAccumulatorExecutor ACCUMULATOR extends VariantProcessor.Accumulator <RESULT >,RESULT > - Interface in picard.vcf.processor
VariantAccumulatorExecutor.MultiThreadedChunkBased A extends VariantProcessor.Accumulator <R >,R > - Class in picard.vcf.processor
VariantAnnotation org.broadinstitute.hellbender.tools.walkers.annotator
Superclass of all variant annotations.
VariantAnnotation() VariantAnnotation
VariantAnnotator org.broadinstitute.hellbender.tools.walkers.annotator
Annotate variant calls with context information
VariantAnnotator() VariantAnnotator
VariantAnnotatorEngine org.broadinstitute.hellbender.tools.walkers.annotator
The class responsible for computing annotations for variants.
VariantAnnotatorEngine(Collection<Annotation>, FeatureInput<VariantContext>, List<FeatureInput<VariantContext>>, boolean) VariantAnnotatorEngine
Creates an annotation engine from a list of selected annotations output from command line parsing
VariantAnnotatorEngine.VAExpression org.broadinstitute.hellbender.tools.walkers.annotator
A container object for storing the objects necessary for carrying over expression annotations.
VariantCallContext org.broadinstitute.hellbender.tools.walkers.genotyper
Useful helper class to communicate the results of calculateGenotype to framework
VariantCallingDetailMetrics() CollectVariantCallingMetrics.VariantCallingDetailMetrics
VariantCallingSummaryMetrics() CollectVariantCallingMetrics.VariantCallingSummaryMetrics
VariantContextTestUtils org.broadinstitute.hellbender.utils.test
VariantContextVariantAdapter org.broadinstitute.hellbender.utils.variant
VariantContextVariantAdapter wraps the existing htsjdk VariantContext class so it can be
used with the
GATKVariant API.
VariantContextVariantAdapter(VariantContext) VariantContextVariantAdapter
VariantDataManager org.broadinstitute.hellbender.tools.walkers.vqsr
VariantDataManager(List<String>, VariantRecalibratorArgumentCollection) VariantDataManager
VariantEvaluationProgramGroup picard.cmdline.programgroups
Tools that evaluate and refine variant calls, e.g.
VariantEvaluationProgramGroup() VariantEvaluationProgramGroup
variantFiles OptionalVariantInputArgumentCollection
variantFiles RequiredVariantInputArgumentCollection
VariantFilter org.broadinstitute.hellbender.engine.filters
VariantFilter picard.vcf.filter
Interface for classes that can generate filters for VariantContexts.
VariantFilteringProgramGroup picard.cmdline.programgroups
Tools that filter variants
VariantFilteringProgramGroup() VariantFilteringProgramGroup
VariantFilterLibrary org.broadinstitute.hellbender.engine.filters
Collects common variant filters.
VariantFilterLibrary() VariantFilterLibrary
VariantFiltration org.broadinstitute.hellbender.tools.walkers.filters
Filter variant calls based on INFO and/or FORMAT annotations
VariantFiltration() VariantFiltration
variantId SvType
VariantIDsVariantFilter org.broadinstitute.hellbender.engine.filters
Keep only variants with any of these IDs.
VariantIDsVariantFilter(Set<String>) VariantIDsVariantFilter
VariantIteratorProducer picard.vcf.processor
A mechanism for iterating over CloseableIterator of VariantContexts in in some fashion, given VCF files and optionally
an interval list.
VariantIteratorProducer() VariantIteratorProducer
VariantManipulationProgramGroup picard.cmdline.programgroups
Tools that manipulate variant call format (VCF) data
VariantManipulationProgramGroup() VariantManipulationProgramGroup
VariantOverlapAnnotator 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>) VariantOverlapAnnotator
Create a new VariantOverlapAnnotator
VariantOverlapAnnotator(FeatureInput<VariantContext>, Map<FeatureInput<VariantContext>, String>) 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
VariantProcessor.Builder A extends VariantProcessor.Accumulator <R >,R > - Class in picard.vcf.processor
VariantProcessor.ResultMerger RESULT > - Interface in picard.vcf.processor
VariantRecalibrator org.broadinstitute.hellbender.tools.walkers.vqsr
Build a recalibration model to score variant quality for filtering purposes
VariantRecalibrator() VariantRecalibrator
VariantRecalibratorEngine org.broadinstitute.hellbender.tools.walkers.vqsr
VariantRecalibratorEngine(VariantRecalibratorArgumentCollection) VariantRecalibratorEngine
variants ContextShard
variantsAreEqual(GATKVariant, GATKVariant) VariantUtils
VariantShard org.broadinstitute.hellbender.engine
VariantShard is section of the genome that's used for sharding work for pairing things with
variants.
VariantShard(int, String) VariantShard
variantShardPadding VariantWalkerSpark
variantShardSize VariantWalkerSpark
variantSource TrainingSet
variantsOverlapping(SimpleInterval) ContextShard
Returns the variants that overlap the query interval, in start-position order.
VariantsSource org.broadinstitute.hellbender.engine.datasources
VariantsSource loads variants from a local file (GCS Bucket to come).
VariantsSource() VariantsSource
VariantsSparkSink org.broadinstitute.hellbender.engine.spark.datasources
VariantsSparkSink writes variants to a VCF file in parallel using Hadoop-BAM.
VariantsSparkSink() VariantsSparkSink
VariantsSparkSink.GvcfKeyIgnoringVCFRecordWriter K > - Class in org.broadinstitute.hellbender.engine.spark.datasources
VariantsSparkSink.SparkHeaderlessVCFOutputFormat org.broadinstitute.hellbender.engine.spark.datasources
VariantsSparkSink.SparkVCFOutputFormat org.broadinstitute.hellbender.engine.spark.datasources
VariantsSparkSource org.broadinstitute.hellbender.engine.spark.datasources
VariantsSparkSource loads Variants from files serially (using FeatureDataSource) or in parallel
using Hadoop-BAM.
VariantsSparkSource(JavaSparkContext) VariantsSparkSource
VariantsToTable org.broadinstitute.hellbender.tools.walkers.variantutils
Extract fields from a VCF file to a tab-delimited table
VariantsToTable() VariantsToTable
VariantType picard.util
Enum to hold the possible types of dbSnps.
VariantTypesVariantFilter org.broadinstitute.hellbender.engine.filters
Keep only variants with any of these variant types.
VariantTypesVariantFilter(Set<VariantContext.Type>) VariantTypesVariantFilter
VariantUtils org.broadinstitute.hellbender.utils.variant
VariantUtils contains utility methods for the Variant interface.
VariantUtils() VariantUtils
VariantWalker 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() VariantWalker
VariantWalkerBase org.broadinstitute.hellbender.engine
Base class for variant 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.
VariantWalkerBase() VariantWalkerBase
VariantWalkerContext org.broadinstitute.hellbender.engine.spark
VariantWalkerContext(VariantContext, ReadsContext, ReferenceContext, FeatureContext) VariantWalkerContext
VariantWalkerSpark org.broadinstitute.hellbender.engine.spark
VariantWalkerSpark() VariantWalkerSpark
VCF CollectIndependentReplicateMetrics
vcf() VcfFileSegment
VCF_BUFFER_SIZE_ARG_NAME GenomicsDBImport
VCF_DIR FindMendelianViolations
VCF_FILE_EXTENSION VcfUtils
VCF_INITIALIZER_THREADS_LONG_NAME GenomicsDBImport
VcfFileSegment picard.vcf.processor
Describes a segment of a particular VCF file.
VcfFileSegment() VcfFileSegment
VcfFileSegmentGenerator picard.vcf.processor
VcfFileSegmentGenerator() VcfFileSegmentGenerator
VcfFormatConverter picard.vcf
Converts an ASCII VCF file to a binary BCF or vice versa.
VcfFormatConverter() VcfFormatConverter
VcfFuncotationFactory org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf
A class to create annotations from VCF feature sources.
VcfFuncotationFactory(String, String, Path) VcfFuncotationFactory
VcfFuncotationFactory(String, String, Path, LinkedHashMap<String, String>) VcfFuncotationFactory
vcfHeader VariantsSparkSink.SparkVCFOutputFormat
VcfOutputRenderer org.broadinstitute.hellbender.tools.funcotator.vcfOutput
A Funcotator output renderer for writing to VCF files.
VcfOutputRenderer(VariantContextWriter, VCFHeader, List<DataSourceFuncotationFactory>) VcfOutputRenderer
VcfOutputRenderer(VariantContextWriter, List<DataSourceFuncotationFactory>, VCFHeader, LinkedHashMap<String, String>, LinkedHashMap<String, String>) VcfOutputRenderer
VcfOutputRenderer(VariantContextWriter, List<DataSourceFuncotationFactory>, VCFHeader, LinkedHashMap<String, String>, LinkedHashMap<String, String>, Set<VCFHeaderLine>) VcfOutputRenderer
VcfToIntervalList picard.vcf
Converts a VCF or BCF file to a Picard Interval List.
VcfToIntervalList() VcfToIntervalList
VcfUtils org.broadinstitute.hellbender.utils.variant
Utils for dealing with VCF files.
VcfUtils picard.vcf
Created by farjoun on 4/1/17.
VcfUtils() VcfUtils
vectorDiff(int[], int[]) MathUtils
Compute Z=X-Y for two numeric vectors X and Y
VectorLoglessPairHMM org.broadinstitute.hellbender.utils.pairhmm
Class for performing the pair HMM for local alignment using AVX instructions contained in a native shared library.
VectorLoglessPairHMM(VectorLoglessPairHMM.Implementation, PairHMMNativeArguments) VectorLoglessPairHMM
Create a VectorLoglessPairHMM
VectorLoglessPairHMM.Implementation org.broadinstitute.hellbender.utils.pairhmm
Type for implementation of VectorLoglessPairHMM
VERBOSITY CommandLineProgram
VERBOSITY CommandLineProgram
VERBOSITY_NAME StandardArgumentDefinitions
verify(List<Integer>, int[]) MultiTileBclFileUtil
verify(List<Integer>, int[]) MultiTileFileUtil
expectedCycles are not checked in this implementation.
verify(List<Integer>, int[]) 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[]) PerTileFileUtil
verify(List<Integer>, int[]) PerTileOrPerRunFileUtil
verify(List<Integer>, int[]) PerTilePerCycleFileUtil
verify(List<Integer>) TileIndex
verifyData(List<Integer>, int[]) MultiTileParser
verifyData(List<Integer>, int[]) PerTileParser
verifyDivisibilityWithRefShard() ReadsPreprocessingPipelineTestData
version DataSourceFuncotationFactory
VERSION Funcotator
VERSION MafOutputRenderer
version FilterFileReader
Version number found in the FilterFile, this should equal 3
ViewSam picard.sam
Prints a SAM or BAM file to the screen.
ViewSam() ViewSam
ViewSam.AlignmentStatus picard.sam
ViewSam.PfStatus picard.sam
ViterbiAlgorithm org.broadinstitute.hellbender.utils.hmm
Implements the Viterbi Algorithm.
ViterbiAlgorithm() ViterbiAlgorithm
VQS_LOD_KEY GATKVCFConstants
VQSLOD_CUTOFF ApplyVQSR
VQSLODTranche org.broadinstitute.hellbender.tools.walkers.vqsr
VQSLODTranche(double, int, double, int, double, int, int, VariantRecalibratorArgumentCollection.Mode, String) VQSLODTranche