A_FOLLOWED_BY_INSERTION_BASE PileupElement
AA_CALL InfiniumGTCFile
AB_CALL InfiniumGTCFile
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 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 picard.sam.markduplicates.util
Little class used to package up a header and an iterable/iterator.
AbstractOpticalDuplicateFinderCommandLineProgram picard.sam.markduplicates.util
Abstract class that holds parameters and methods common to classes that optical duplicate detection.
AbstractOpticalDuplicateFinderCommandLineProgram() AbstractOpticalDuplicateFinderCommandLineProgram
AbstractReadThreadingGraph org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
AbstractReadThreadingGraph(int, boolean, byte, int) AbstractReadThreadingGraph
Create a new ReadThreadingAssembler using kmerSize for matching
AbstractReadThreadingGraph.MyEdgeFactory org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
Edge factory that encapsulates the numPruningSamples assembly parameter
AbstractReadThreadingGraph.TraversalDirection org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
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.
AC_ADJUSTED_KEY GATKVCFConstants
accept(int, int, int) SVInterval.SVIntervalConstructorArgsValidator
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)
ACCEPTS_ALL SVInterval.SVIntervalConstructorArgsValidator
accessibleTruthSites Tranche
accessionToTaxId PSTaxonomyDatabase
accumulate(VariantContext) CallingMetricAccumulator
Incorporates the provided variant's data into the metric analysis.
accumulate(VariantContext) GvcfMetricAccumulator
accumulate(VariantContext) VariantProcessor.Accumulator
accumulateData(VariantContext, ReferenceContext) Mutect2FilteringEngine
accumulateDataForLearning(VariantContext, ErrorProbabilities, Mutect2FilteringEngine) FilteredHaplotypeFilter
accumulateDataForLearning(VariantContext, ErrorProbabilities, Mutect2FilteringEngine) Mutect2VariantFilter
accumulateDataForLearning(VariantContext, ErrorProbabilities, Mutect2FilteringEngine) StrandArtifactFilter
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 AssemblyRegionArgumentCollection
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
ActivityProfileStateIterator org.broadinstitute.hellbender.engine
ActivityProfileStateIterator(MultiIntervalShard<GATKRead>, SAMFileHeader, ReferenceDataSource, FeatureManager, AssemblyRegionEvaluator, boolean) ActivityProfileStateIterator
Constructs an AssemblyRegionIterator over a provided read shard
ActivityProfileStateRange org.broadinstitute.hellbender.utils.activityprofile
ActivityProfileStateRange(MultiIntervalShard<?>, Iterator<ActivityProfileState>) ActivityProfileStateRange
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
AdaptiveChainPruner V extends BaseVertex ,E extends BaseEdge > - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
AdaptiveChainPruner(double, double, int) AdaptiveChainPruner
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(AnnotatedInterval) AnnotatedIntervalWriter
Write one region to the file.
add(AnnotatedInterval) SimpleAnnotatedIntervalWriter
Write one region to the file.
add(GATKRead) FlagStat.FlagStatus
add(String, List<Funcotation>) FuncotationMap
Add the given funcotations to the given transcript ID.
add(String, Funcotation) FuncotationMap
Add the given funcotation to the given transcript ID.
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(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(char) Nucleotide.Counter
add(int, double, double, double, double, double, double, int) SynchronizedUnivariateSolver
Add a solver jobDescription
add(int, double, double, double, double, double, int) SynchronizedUnivariateSolver
add(int, Genotype) GVCFBlock
add(int, int, Genotype) GVCFBlock
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(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.
addAll(char...) Nucleotide.Counter
Increase by one the count for a nucleotide for each
occurrence of such in the input char array base codes.
addAll(CharSequence) Nucleotide.Counter
Increase by one the count for a nucleotide for each
occurrence of such in the input CharSequence.
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.
addArgs(Object...) RScriptExecutor
Adds args to the end of the Rscript command line.
addArtifactProbability(double) ThresholdCalculator
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.
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) BaseCalculator
the function by which new loci are "shown" to the calculator
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) BaseErrorAggregation
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) BaseErrorCalculator
the function by which new loci are "shown" to the calculator
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) IndelErrorCalculator
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) OverlappingReadsErrorCalculator
The function by which new loci are "shown" to the calculator
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) SimpleErrorCalculator
The function by which new loci are "shown" to the calculator
addBaseQHistogram(MetricsFile<WgsMetrics, Integer>) AbstractWgsMetricsCollector
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
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
addEvidence(Map<String, List<EVIDENCE>>, double) AlleleLikelihoods
Add more evidence to the collection.
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
FeatureInputs after initialization that were not
specified as command-line arguments.
addFilterToGenotype(String, String) OrientationBiasUtils
Create an updated genotype string when trying to add a filter value.
addFirstOfPairOrFragment(SAMRecord) HitsForInsert
addGenotypeData(ReferenceConfidenceResult, GenotypeBuilder) ReferenceConfidenceModel
addGenotypeData(ReferenceConfidenceResult, GenotypeBuilder) SomaticReferenceConfidenceModel
addHaplotype(HaplotypeBlock) HaplotypeMap
Adds a HaplotypeBlock to the map and updates all the relevant caches/indices.
addHomRefSite(VariantContext, Genotype) GVCFBlockCombiner
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
addInfoFieldAnnotations(VariantContext, VariantContextBuilder, boolean) AlleleSubsettingUtils
Add the VCF INFO field annotations for the used alleles when subsetting
addJunctionTree(JunctionTreeLinkedDeBruinGraph.ThreadingTree) JTBestHaplotype
Add a junction tree (corresponding to the current vertex for traversal, note that if a tree has already been visited by this path then it is ignored)
addKmer(Kmer, int) 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
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) AlleleLikelihoods
Add alleles that are missing in the evidence-likelihoods collection giving all evidence 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) AlleleLikelihoods
Adds the non-reference allele to the evidence-likelihood collection setting each evidence likelihood to the second
best found (or best one if only one allele has likelihood).
addNonRefSymbolicAllele(VariantContext) ReferenceConfidenceUtils
AddOATag picard.sam
AddOATag() AddOATag
addObservation(GATKRead) KSWindowFinder
addObservation(int) IntHistogram
addObservations(int, long) IntHistogram
addObservations(IntHistogram) IntHistogram
addOp(ClippingOp) ReadClipper
Add clipping operation to the read.
AddOriginalAlignmentTags org.broadinstitute.hellbender.tools
AddOriginalAlignmentTags() AddOriginalAlignmentTags
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
addOutputSAMProgramRecord GATKTool
addOutputVCFCommandLine GATKTool
addOutputVCFCommandLine GATKSparkTool
addParameterSampler(V2, ParameterSampler<U, V2, S2, T2>, Class<U>) ParameterizedModel.GibbsBuilder
addPileup(ReadPileup) AllelePileupCounter
addPrefetcher(int, SeekableByteChannel) SeekableByteChannelPrefetcher
Wraps the provided SeekableByteChannel within a SeekableByteChannelPrefetcher, using the provided buffer size
addRangesToHeader(VCFHeader) GVCFBlockCombiner
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
addReadsToKmers(Collection<GATKRead>) ReadErrorCorrector
Top-level entry point that adds a collection of reads to our kmer list.
addReferenceFilesForSpark(JavaSparkContext, String) GATKSparkTool
Register the reference file (and associated dictionary and index) to be downloaded to every node using Spark's
copying mechanism (SparkContext#addFile()).
addRegion(GenomeLoc) GenomeLocSortedSet
Adds a GenomeLoc to the collection, merging it if it overlaps another region.
ADDRESS_A_ID_HEADER_NAME IlluminaManifest
ADDRESS_B_ID_HEADER_NAME IlluminaManifest
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
addSamplesFromSampleNames(Collection<String>) SampleDBBuilder
Integrates the collection of sample names with the samples already present
addScoreNormalized(double) PSPathogenTaxonScore
addScript(Resource) RScriptExecutor
addScript(File) RScriptExecutor
addSecondOfPair(SAMRecord) HitsForInsert
addSelenocysteine(GencodeGtfSelenocysteineFeature) GencodeGtfTranscriptFeature
addSelfScore(double) PSPathogenTaxonScore
addSequence(byte[], boolean) AbstractReadThreadingGraph
Add the all bases in sequence to the graph
addSequence(String, byte[], boolean) AbstractReadThreadingGraph
Add all bases in sequence to this graph
addSequence(String, byte[], int, boolean) AbstractReadThreadingGraph
Add all bases in sequence to this graph
addSingletonToCount(LibraryIdGenerator) AbstractMarkDuplicatesCommandLineProgram
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
Add two double arrays, modifying the first
addToArrayInPlace(int[], int[]) MathUtils
Add two int arrays, modifying the first
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<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) AbstractWgsMetricsCollector
Adds collected metrics and depth histogram to file
addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) WgsMetricsProcessor
Adds result metric's data to input file
addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) WgsMetricsProcessorImpl
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.
addToReference(SimpleInterval, byte) FastaReferenceMaker
addTotalReads(int) PSPathogenTaxonScore
addTrailingSlashIfNecessary(String) CopyNumberArgumentValidationUtils
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
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
addVCFsForSpark(JavaSparkContext, List<String>) GATKSparkTool
Register the VCF file (and associated index) to be downloaded to every node using Spark's copying mechanism
(SparkContext#addFile()).
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
ADENINE Nucleotide
adjustQualsOfOverlappingPairedFragments(Pair<GATKRead, GATKRead>, boolean, OptionalInt, OptionalInt) FragmentUtils
Fix two overlapping reads from the same fragment by adjusting base qualities, if possible
Looks at the bases and alignment, and tries its best to create adjusted base qualities so that the observations
are not treated independently.
advance() AbstractInputParser
advanceBlock(GATKRead) KSWindowFinder
advanceFile() BasicInputParser
advancePosition(SimpleInterval) FastaReferenceMaker
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, Map<Allele, Double>) AFCalculationResult
Create a results object capability of storing results for calls with up to maxAltAlleles
afDataSource FilterFuncotations
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)
AFPriorProvider org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
Class that produces allele-frequency priors.
AFPriorProvider() AFPriorProvider
AFScale VariantEval
afterExecute(Runnable, Throwable) ThreadPoolExecutorWithExceptions
afterFile AnalyzeCovariates
File containing the recalibration tables from the second pass.
afterFirstPass() TwoPassVariantWalker
Process the data collected during the first pass.
afterFirstPass() ExampleTwoPassVariantWalker
afterFirstPass() FilterFuncotations
afterFirstPass() ArHetvarFilter
afterFirstPass() TwoPassFuncotationFilter
afterFirstPass() CNNScoreVariants
afterFirstPass() FilterVariantTranches
afterNthPass(int) MultiplePassVariantWalker
Process the data collected during the first pass.
afterNthPass(int) TwoPassVariantWalker
afterNthPass(int) FilterMutectCalls
afterPipeline(JavaSparkContext) SparkCommandLineProgram
Extend this method to run code after the pipeline returns.
afTolerance GenotypeGVCFs
Margin of error in allele fraction to consider a somatic variant homoplasmic, i.e.
aggregate(List<Integer>) BaseQuality
aggregate(List<Integer>) FragmentLength
aggregate(List<Integer>) MappingQuality
aggregate(List<Integer>) PerAlleleAnnotation
aggregate(List<Integer>) ReadPosition
aliases() InsertSizeDistributionShape
AliasProvider org.broadinstitute.hellbender.tools.funcotator
Class for managing aliases and querying
Funcotation to determine fields.
AliasProvider(LinkedHashMap<String, List<String>>) AliasProvider
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_REGION_TAG AssemblyBasedCallerUtils
ALIGNMENT_SCORE_DIFFERENCE_KEY GATKVCFConstants
ALIGNMENT_STATUS ViewSam
ALIGNMENT_TO_BEST_HAPLOTYPE_SW_PARAMETERS CigarUtils
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_KMERS F1R2FilterConstants
ALL_SITES_LONG_NAME GenotypeGVCFs
ALL_SITES_SHORT_NAME GenotypeGVCFs
ALL_TRANSCRIPT_DELIMITER VcfOutputRenderer
The delimiter to use when separating the information regarding a transcript.
allAlleles GenotypeConcordance.Alleles
allele AlleleLikelihoods.BestAllele
Null if there is no possible match (no allele?).
ALLELE_A InfiniumVcfFields
ALLELE_A_PROBE_SEQ_HEADER_NAME IlluminaManifest
ALLELE_B InfiniumVcfFields
ALLELE_B_PROBE_SEQ_HEADER_NAME IlluminaManifest
ALLELE_BALANCE_HET_KEY GATKVCFConstants
ALLELE_BALANCE_HOM_KEY GATKVCFConstants
ALLELE_BALANCE_KEY GATKVCFConstants
ALLELE_EXTENSION HaplotypeCallerGenotypingEngine
ALLELE_FRACTION CollectWgsMetrics
ALLELE_FRACTION CollectTargetedMetrics
ALLELE_FRACTION TheoreticalSensitivityMetrics
The allele fraction which theoretical sensitivity is calculated for.
ALLELE_FRACTION_DELTA_LONG_NAME CombineGVCFs
ALLELE_FRACTION_FILTER_NAME GATKVCFConstants
ALLELE_FRACTION_KEY GATKVCFConstants
ALLELE_FRACTION_LEGACY_SEGMENTS_FILE_SUFFIX ModelSegments
ALLELE_FRACTION_MODEL_PARAMETER_FILE_SUFFIX ModelSegments
ALLELE_FREQUENCY_DATA_SOURCE_NAME FuncotatorArgumentDefinitions
ALLELE_SPECIFIC_ANNOTATION_PREFIX GATKVCFConstants
ALLELE_SPECIFIC_PREFIX GATKVCFConstants
ALLELE_SPECIFIC_PRINT_DELIM AnnotationUtils
ALLELE_SPECIFIC_REDUCED_DELIM AnnotationUtils
ALLELE_SPECIFIC_SPLIT_REGEX AnnotationUtils
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.
AlleleCount org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
Stratifies the eval RODs by the allele count of the alternate allele
Looks first at the MLEAC value in the INFO field, and uses that value if present.
AlleleCount() AlleleCount
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.
AlleleFraction org.broadinstitute.hellbender.tools.walkers.annotator
Variant allele fraction for each sample.
AlleleFraction() AlleleFraction
AlleleFractionCluster org.broadinstitute.hellbender.tools.walkers.mutect.clustering
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.
AlleleFrequency org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
Stratifies the eval RODs by the allele frequency of the alternate allele
Either uses a constant 0.005 frequency grid, and projects the AF INFO field value or logit scale from -30 to 30.
AlleleFrequency() AlleleFrequency
AlleleFrequency.StratifyingScale org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
AlleleFrequencyCalculator org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
AlleleFrequencyCalculator(double, double, double, int) AlleleFrequencyCalculator
alleleFrequencyCalculator GenotypingEngine
AlleleFrequencyExacUtils org.broadinstitute.hellbender.tools.funcotator.filtrationRules
Allele frequency calculations for the Exac dataset
AlleleFrequencyExacUtils() AlleleFrequencyExacUtils
AlleleFrequencyQC org.broadinstitute.hellbender.tools.walkers.varianteval
This tool uses VariantEval to bin variants in Thousand Genomes by allele frequency.
AlleleFrequencyQC() AlleleFrequencyQC
AlleleFrequencyQCMetric org.broadinstitute.hellbender.metrics.analysis
AlleleFrequencyQCMetric() AlleleFrequencyQCMetric
AlleleFrequencyUtils org.broadinstitute.hellbender.tools.funcotator.filtrationRules
Allele frequency utilities that are dataset-agnostic
AlleleFrequencyUtils() AlleleFrequencyUtils
alleleIndexAt(int) GenotypeAlleleCounts
Returns the index of the allele from its rank in the genotype.
AlleleLikelihoodMatrixMapper A extends htsjdk.variant.variantcontext.Allele> - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
Creates
LikelihoodMatrix mappers to be used when working with a subset of the original alleles.
AlleleLikelihoodMatrixMapper(AlleleListPermutation<A>) AlleleLikelihoodMatrixMapper
Constructs a new mapper given an allele-list permutation.
AlleleLikelihoods EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele> - Class in org.broadinstitute.hellbender.utils.genotyper
Evidence-likelihoods container implementation based on integer indexed arrays.
AlleleLikelihoods(SampleList, AlleleList<A>, Map<String, List<EVIDENCE>>) AlleleLikelihoods
Constructs a new evidence-likelihood collection.
AlleleLikelihoods.BestAllele org.broadinstitute.hellbender.utils.genotyper
Contains information about the best allele for a unit of evidence.
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 AssemblyBasedCallerArgumentCollection
alleles() SubsettedLikelihoodMatrix
alleles AlleleLikelihoods
Allele list
alleles() AlleleLikelihoods
Returns the samples in this evidence-likelihood collection.
alleles() LikelihoodMatrix
List of alleles in the matrix sorted by their index in the collection.
Alleles(OrderedSet<String>, String, String, String, String) GenotypeConcordance.Alleles
AlleleSpecificAnnotation org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
This is a marker interface used to indicate which annotations are allele-specific.
AlleleSpecificAnnotationData T > - Class in org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
A class to encapsulate the raw data for allele-specific classes compatible with the ReducibleAnnotation interface
AlleleSpecificAnnotationData(List<Allele>, String) AlleleSpecificAnnotationData
allelesToIndex(int...) GenotypeLikelihoodCalculator
Give a list of alleles, returns the likelihood array index.
allelesToStringList(List<Allele>) LiftoverUtils
This is a utility method that will convert a list of alleles into a list of base strings.
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_INCOMPLETE_DICT_CONCORDANCE ReorderSam
ALLOW_MISSING_FIELDS_IN_HEADER LiftoverVcf
ALLOW_MISSING_UMIS UmiAwareMarkDuplicatesWithMateCigar
ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS PositionBasedDownsampleSam
ALLOW_MULTIPLE_SORT_ORDERS_IN_INPUT_ARG MarkDuplicatesSpark
AllowAllReadsReadFilter() ReadFilterLibrary.AllowAllReadsReadFilter
AllowAllVariantsVariantFilter() VariantFilterLibrary.AllowAllVariantsVariantFilter
allowedShortFragmentOverhang StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
allowedVariance AlleleFrequencyQC
allowMultipleSortOrders MarkDuplicatesSpark
allowNonUniqueKmersInRef ReadThreadingAssemblerArgumentCollection
By default, the program does not allow processing of reference sections that contain non-unique kmers.
allowOlderRawKeyValues RMSMappingQuality
allVisitedAlignmentsEqual() SamComparisonMetric
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
alreadyBuilt AbstractReadThreadingGraph
ALSO_IGNORE_DUPLICATES CollectGcBiasMetrics
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_FRACTIONS_FOR_SEGMENTATION ContaminationSegmenter
ALT_HIST_EXTENSION F1R2CountsCollector
ALT_NAMES CreateSequenceDictionary
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.
ALT_TABLE_EXTENSION F1R2CountsCollector
altAllele SvType
altHaplotypeSequence BreakpointsInference
AltSiteRecord org.broadinstitute.hellbender.tools.walkers.readorientation
Created by tsato on 10/11/17.
AltSiteRecord(String, int, int, int, int, Nucleotide) AltSiteRecord
AltSiteRecord.AltSiteRecordTableWriter org.broadinstitute.hellbender.tools.walkers.readorientation
Writer
AltSiteRecordTableWriter(Path, String) AltSiteRecord.AltSiteRecordTableWriter
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
AMINO Nucleotide
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 org.broadinstitute.hellbender.tools.walkers.varianteval.util
ANALYSIS_DIR BamToBfq
ANALYSIS_VERSION CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The version number of the analysis run
ANALYSIS_VERSION_NUMBER GtcToVcf
ANALYSIS_VERSION_NUMBER InfiniumVcfFields
AnalysisModuleScanner org.broadinstitute.hellbender.tools.walkers.varianteval.util
AnalysisModuleScanner(Class<?>) AnalysisModuleScanner
create a report scanner from the passed in class
AnalysisModuleScanner(Object) AnalysisModuleScanner
create a report scanner from the passed in class
AnalyzeCovariates org.broadinstitute.hellbender.tools.walkers.bqsr
Evaluate and compare base quality score recalibration tables
AnalyzeCovariates() AnalyzeCovariates
AnalyzeSaturationMutagenesis org.broadinstitute.hellbender.tools
Process reads from a saturation mutagenesis experiment.
AnalyzeSaturationMutagenesis() AnalyzeSaturationMutagenesis
AnalyzeSaturationMutagenesis.ReportTypeCounts org.broadinstitute.hellbender.tools
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(SVInterval.SVIntervalConstructorArgsValidator) SVInterval.SVIntervalConstructorArgsValidator
andThen(ReadTransformer) ReadTransformer
andThen(VariantTransformer) VariantTransformer
annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>) AlleleFraction
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) AS_InbreedingCoeff
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) AS_QualByDepth
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) AS_RankSumTest
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) AS_RMSMappingQuality
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) BaseQualityHistogram
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) ChromosomeCounts
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) CountNs
Calculate annotations for each allele based on given VariantContext and likelihoods for a given genotype's sample
and add the annotations to the GenotypeBuilder.
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) Coverage
annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>) DepthPerAlleleBySample
annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>) DepthPerSampleHC
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) ExcessHet
annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>) GenotypeAnnotation
Computes the annotation for the given genotype and the likelihoods per read.
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) GenotypeSummaries
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) InbreedingCoeff
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) InfoFieldAnnotation
Computes the annotation for the given variant and the likelihoods per read.
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) MappingQualityZero
annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>) OrientationBiasReadCounts
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) OriginalAlignment
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, 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, AlleleLikelihoods<GATKRead, Allele>) PossibleDeNovo
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) QualByDepth
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) RankSumTest
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) ReferenceBases
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) RMSMappingQuality
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) SampleList
annotate(ReferenceContext, VariantContext, Genotype, GenotypeBuilder, AlleleLikelihoods<GATKRead, Allele>) StrandBiasBySample
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) StrandBiasTest
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) TandemRepeat
annotate(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, 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_ACTIVE_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, ReferenceMultiSparkSource, StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsSparkArgumentCollection, Logger) AnnotatedVariantProducer
annotateContext(VariantContext, FeatureContext, ReferenceContext, AlleleLikelihoods<GATKRead, Allele>, Predicate<VariantAnnotation>) VariantAnnotatorEngine
Annotates the given variant context - adds all annotations that satisfy the predicate.
ANNOTATED_INTERVAL_DEFAULT_CONFIG_RESOURCE AnnotatedIntervalCodec
ANNOTATED_INTERVALS_FILE_LONG_NAME CopyNumberStandardArgument
ANNOTATED_VCF_LONG_NAME ValidateBasicSomaticShortMutations
AnnotatedInterval org.broadinstitute.hellbender.tools.copynumber.formats.records
Represents an interval with a set of annotations.
AnnotatedInterval(SimpleInterval, AnnotationMap) 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.utils.codecs
AnnotatedIntervalCodec() AnnotatedIntervalCodec
Use the default config for tribble.
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
AnnotatedIntervalToSegmentVariantContextConverter org.broadinstitute.hellbender.tools.funcotator
Converts an annotated interval representing a segment to a variant context.
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
annotatedVcf ValidateBasicSomaticShortMutations
AnnotateIntervals org.broadinstitute.hellbender.tools.copynumber
Annotates intervals with GC content, and optionally, mappability and segmental-duplication 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, AlleleLikelihoods<GATKRead, Allele>) AS_QualByDepth
Note: There is no raw annotation for AS_QualByDepth and thus this method does nothing.
annotateRawData(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, 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, AlleleLikelihoods<GATKRead, Allele>) AS_RMSMappingQuality
annotateRawData(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) AS_StrandBiasTest
Uses the likelihoods map to generate a 2x2 strand contingency table by counting the total read support for each
allele in either the forward or reverse direction.
annotateRawData(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) ReducibleAnnotation
Generate the raw data necessary to calculate the annotation.
annotateRawData(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) ExcessHet
Generate the raw data necessary to calculate the annotation.
annotateRawData(ReferenceContext, VariantContext, AlleleLikelihoods<GATKRead, Allele>) RMSMappingQuality
Generate the raw data necessary to calculate the annotation.
annotateReadLikelihoodsWithRegions(AlleleLikelihoods<GATKRead, Haplotype>, Locatable) AssemblyBasedCallerUtils
Annotates reads in AlleleLikelihoods with alignment region (the ref region spanned by the haplotype the read is aligned to) and
callable region (the ref region over which a caller is using these AlleleLikelihoods to call variants)
annotateReadLikelihoodsWithSupportedAlleles(VariantContext, AlleleLikelihoods<GATKRead, Allele>) AssemblyBasedCallerUtils
For the given variant, reads are annotated with which alleles they support, if any.
annotateReadLikelihoodsWithSupportedAlleles(VariantContext, AlleleLikelihoods<U, Allele>, Function<U, Collection<GATKRead>>) AssemblyBasedCallerUtils
For the given variant, reads are annotated with which alleles they support, if any.
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) OrientationBiasReadCounts
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
annotateWithLikelihoods(VariantContext, Genotype, Set<Allele>, AlleleLikelihoods<GATKRead, Allele>) DepthPerAlleleBySample
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_LONG_NAME FuncotatorArgumentDefinitions
Do not give this a static default value or the integration tests will get hosed.
ANNOTATION_GROUP_LONG_NAME StandardArgumentDefinitions
ANNOTATION_GROUP_SHORT_NAME StandardArgumentDefinitions
ANNOTATION_LONG_NAME StandardArgumentDefinitions
ANNOTATION_OVERRIDES_LONG_NAME FuncotatorArgumentDefinitions
Do not give this a static default value or the integration tests will get hosed.
annotation_packages() GATKConfig
ANNOTATION_SHORT_NAME StandardArgumentDefinitions
annotationEngine GenotypingEngine
annotationEngine SomaticGenotypingEngine
AnnotationException picard.annotation
Exception thrown when loading gene annotations.
AnnotationException(String) AnnotationException
AnnotationException(String, Throwable) AnnotationException
AnnotationKey T > - Class in org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation
Represents a key for a named, typed annotation.
AnnotationKey(String, Class<T>, Function<T, Boolean>) AnnotationKey
annotationKeys VariantDataManager
AnnotationMap org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation
Represents an immutable ordered collection of named, typed annotations for an interval.
AnnotationMap(List<Pair<AnnotationKey<?>, Object>>) AnnotationMap
annotationOrder VariantRecalibrator
annotationOverrideMap DataSourceFuncotationFactory
Map of ANNOTATION_NAME -> OVERRIDE_VALUE.
ANNOTATIONS CopyNumberAnnotations
This defines the canonical order of these annotations.
ANNOTATIONS_TO_EXCLUDE_LONG_NAME StandardArgumentDefinitions
ANNOTATIONS_TO_EXCLUDE_SHORT_NAME StandardArgumentDefinitions
ANNOTATIONS_TO_MATCH MergeAnnotatedRegionsByAnnotation
annotationSource GencodeGtfFeatureBaseData
Keyword identifying the source of this feature.
AnnotationUtils org.broadinstitute.hellbender.tools.walkers.annotator
annotatorEngine ReferenceConfidenceVariantContextMerger
anonymousOptionalFields GencodeGtfFeatureBaseData
Additional optional GTF fields.
ANY Nucleotide
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
appendPathToDir(String, String) IOUtils
Appends path to the given parent dir.
appendSATagString(StringBuilder) AlignmentInterval
Appends the SA string representation of this interval into a builder.
apply(AbstractConcordanceWalker.TruthVersusEval, ReadsContext, ReferenceContext) AbstractConcordanceWalker
apply(AssemblyRegion, ReferenceContext, FeatureContext) AssemblyRegionWalker
Process an individual AssemblyRegion.
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(GATKRead, ReferenceContext, FeatureContext) MultiplePassReadWalker
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) MultiplePassVariantWalker
Make final to hide it from subclasses
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) MultiVariantWalker
Process an individual variant.
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, List<ReadsContext>) MultiVariantWalkerGroupedOnStart
This method must be implemented by tool authors.
apply(List<VariantContext>, List<ReadsContext>) MultiVariantWalkerGroupedOnStart
apply(GATKRead, ReferenceContext, FeatureContext) ReadWalker
Process an individual read (with optional contextual information).
apply(ReferenceContext, ReadsContext, FeatureContext) ReferenceWalker
Process an individual reference locus (with optional contextual information).
apply(GATKRead) ReferenceWindowFunctions.FixedWindowFunction
apply(Locatable, List<VariantContext>, ReadsContext, ReferenceContext, FeatureContext) VariantLocusWalker
Process by locus, with all variants overlapping the current locus, or by individual variant when in by-variants
traversal mode.
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) VariantWalker
Process an individual variant.
apply(GATKRead, ReferenceContext, FeatureContext) AddOriginalAlignmentTags
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(ReferenceContext, ReadsContext, FeatureContext) ExampleReferenceWalker
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(AnnotatedInterval, ReadsContext, ReferenceContext, FeatureContext) FuncotateSegments
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, Iterable<GATKVariant>>, SAMFileHeader, String, RecalibrationArgumentCollection) BaseRecalibratorSparkFn
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, List<ReadsContext>) CombineGVCFs
apply(AlignmentContext, ReferenceContext, FeatureContext) GetPileupSummaries
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) CountVariants
apply(ReferenceContext, ReadsContext, FeatureContext) CountBasesInReference
apply(ReferenceContext, ReadsContext, FeatureContext) FastaAlternateReferenceMaker
apply(ReferenceContext, ReadsContext, FeatureContext) FastaReferenceMaker
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) VariantFiltration
apply(Locatable, List<VariantContext>, ReadsContext, ReferenceContext, FeatureContext) GenotypeGVCFs
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) GnarlyGenotyper
apply(AssemblyRegion, ReferenceContext, FeatureContext) HaplotypeCaller
apply(AlignmentContext, ReferenceContext, FeatureContext) MethylationTypeCaller
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) CreateSomaticPanelOfNormals
apply(AssemblyRegion, ReferenceContext, FeatureContext) Mutect2
apply(AlignmentContext, ReferenceContext, FeatureContext) CheckPileup
apply(AlignmentContext, ReferenceContext, FeatureContext) Pileup
apply(AlignmentContext, ReferenceContext, FeatureContext) CollectF1R2Counts
apply(List<VariantContext>, ReferenceContext, List<ReadsContext>) 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(AbstractConcordanceWalker.TruthVersusEval, ReadsContext, ReferenceContext) EvaluateInfoFieldConcordance
apply(AbstractConcordanceWalker.TruthVersusEval, ReadsContext, ReferenceContext) MergeMutect2CallsWithMC3
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) RemoveNearbyIndels
apply(ReferenceContext, ReadsContext, FeatureContext, VariantContext, VariantContext) EvaluationContext
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) VariantEval
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) CalculateGenotypePosteriors
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) LeftAlignAndTrimVariants
Left aligns variants in repetitive regions.
apply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) ReblockGVCF
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) 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) PalindromeArtifactClipReadTransformer
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
applyFiltersAndAccumulateOutputStats(VariantContext, ReferenceContext) Mutect2FilteringEngine
Create a filtered variant and record statistics for the final pass of
FilterMutectCalls
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.
AR_INFO_VALUE AutosomalRecessiveConstants
ARE_EQUAL SamComparisonMetric
Whether or not to consider the two input files equal.
areAlignmentsEqual() SamComparison
Returns true if the alignments are equal, false otherwise.
areAnyGencodeFuncotation(List<Funcotation>) FuncotatorUtils
areEqual() SamComparison
areEqual() SamComparison
areHeadersEqual() SamComparison
Returns true if the headers are equal, false otherwise.
areHistogramsEmpty() CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
areVariantsAtSameLocusConcordant(VariantContext, VariantContext) AbstractConcordanceWalker
areVariantsAtSameLocusConcordant(VariantContext, VariantContext) Concordance
areVariantsAtSameLocusConcordant(VariantContext, VariantContext) EvaluateInfoFieldConcordance
areVariantsAtSameLocusConcordant(VariantContext, VariantContext) MergeMutect2CallsWithMC3
argmax(Function<Double, Double>, double, double, double) OptimizationUtils
ARGUMENT_COLUMN_NAME RecalUtils
ARGUMENT_REPORT_TABLE_TITLE RecalUtils
ARGUMENT_VALUE_COLUMN_NAME RecalUtils
ArHetvarFilter org.broadinstitute.hellbender.tools.funcotator.filtrationRules
ArHetvarFilter(FilterFuncotations.Reference, String[]) ArHetvarFilter
ArHomvarFilter org.broadinstitute.hellbender.tools.funcotator.filtrationRules
ArHomvarFilter(FilterFuncotations.Reference) ArHomvarFilter
ARRAY_DIM StrandBiasTest
ARRAY_SIZE StrandBiasTest
ARRAY_TYPE InfiniumVcfFields
arrayListCollector(int) SVUtils
Provides a stream collector that will collect items into an array list with a given initial capacity.
arrayMax(int[]) MathUtils
arrayMax(double[]) MathUtils
arrayMin(int[]) MathUtils
ArraysControlCodesSummaryMetrics() CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
ArraysControlInfo picard.arrays.illumina
A simple class to store names and counts for the the Control Information fields that are stored in an Illumina GTC file.
ArraysControlInfo(String, String, int, int) ArraysControlInfo
ArraysVariantCallingDetailMetrics() CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
ArraysVariantCallingSummaryMetrics() CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
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.
ARTIFACT_PRIOR_EXTENSION LearnReadOrientationModel
ARTIFACT_PRIOR_TABLE_NAME M2FiltersArgumentCollection
ARTIFACT_PRIOR_TABLE_SHORT_NAME M2FiltersArgumentCollection
ArtifactPrior org.broadinstitute.hellbender.tools.walkers.readorientation
Container for the artifact prior probabilities for the read orientation model
ArtifactPrior(String, double[], int, int) ArtifactPrior
ArtifactPrior.ArtifactPriorTableReader org.broadinstitute.hellbender.tools.walkers.readorientation
ArtifactPrior.ArtifactPriorTableWriter org.broadinstitute.hellbender.tools.walkers.readorientation
ArtifactPriorCollection org.broadinstitute.hellbender.tools.walkers.readorientation
ArtifactPriorCollection(String) ArtifactPriorCollection
ArtifactPriorTableReader(Path) ArtifactPrior.ArtifactPriorTableReader
ArtifactPriorTableWriter(Path, String) ArtifactPrior.ArtifactPriorTableWriter
ArtifactState org.broadinstitute.hellbender.tools.walkers.readorientation
This enum encapsulates the domain of the discrete latent random variable z
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_ALT_ALLELE_DEPTH_KEY GATKVCFConstants
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_QUAL_APPROX_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_VARIANT_DEPTH_KEY GATKVCFConstants
AS_VQS_LOD_KEY GATKVCFConstants
AS_Warning ReferenceConfidenceVariantContextMerger
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, boolean) 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_ALIGNMENT_MQ_FILTER_DEFAULT StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsSparkArgumentCollection
ASSEMBLY_BASED_VARIANT_ALN_LENGTH_FILTER_KEY GATKSVVCFConstants
ASSEMBLY_BASED_VARIANT_MQ_FILTER_KEY GATKSVVCFConstants
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
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.DiscoverVariantsFromContigAlignmentsSparkArgumentCollection
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
assemblyRegionArgs AssemblyRegionWalkerSpark
assemblyRegionArgs ReadsPipelineSpark
AssemblyRegionArgumentCollection org.broadinstitute.hellbender.engine.spark
AssemblyRegionArgumentCollection() AssemblyRegionArgumentCollection
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() HaplotypeCallerSpark
assemblyRegionEvaluator() HaplotypeCaller
assemblyRegionEvaluator() Mutect2
assemblyRegionEvaluatorSupplierBroadcast(JavaSparkContext) AssemblyRegionWalkerSpark
Tools that use an evaluator that is expensive to create, and/or that is not compatible with Spark broadcast, can
override this method to return a broadcast of a supplier of the evaluator.
assemblyRegionEvaluatorSupplierBroadcast(JavaSparkContext) HaplotypeCallerSpark
AssemblyRegionFromActivityProfileStateIterator org.broadinstitute.hellbender.engine
AssemblyRegionFromActivityProfileStateIterator(Iterator<ActivityProfileState>, SAMFileHeader, int, int, int, double, int) AssemblyRegionFromActivityProfileStateIterator
Constructs an AssemblyRegionIterator over a provided read shard
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 AssemblyRegionArgumentCollection
AssemblyRegionReadShardArgumentCollection org.broadinstitute.hellbender.engine.spark
AssemblyRegionReadShardArgumentCollection() AssemblyRegionReadShardArgumentCollection
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.
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, AbstractReadThreadingGraph) 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.
assemblyStateOutput HaplotypeCallerArgumentCollection
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.
assertConfigFilePropertiesAreValid(Properties, Path) FuncotatorArgumentDefinitions.DataSourceType
assertConfigPropertiesContainsKey(String, Properties, Path) DataSourceUtils
Asserts that the given key is contained in the given configProperties.
assertFileIsReadable(Path) IOUtils
assertIntegerPropertiesField(Properties, String, Path) DataSourceUtils
Asserts that the given field is contained in the given props and is an integer value.
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.
assertPathsAreReadable(String...) IOUtils
assertProperFileStructure(File) BclReader
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.
asSetOfSamples() SampleList
Returns a Set unmodifiable view of the sample-list
assignGenotypeLikelihoods(List<Haplotype>, AlleleLikelihoods<GATKRead, Haplotype>, Map<String, List<GATKRead>>, byte[], SimpleInterval, SimpleInterval, FeatureContext, List<VariantContext>, boolean, int, SAMFileHeader, boolean) 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 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
AsynchronousStreamWriter T > - Class in org.broadinstitute.hellbender.utils.runtime
A service that can be used to write to a stream using a thread background thread and an executor service.
AsynchronousStreamWriter(ExecutorService, OutputStream, Function<T, ByteArrayOutputStream>) AsynchronousStreamWriter
AsyncIterator T > - Class in picard.util
Wrapper around a CloseableIterator that reads in a separate thread, for cases in which that might be
efficient.
AsyncIterator(CloseableIterator<T>, int, String) AsyncIterator
AT_DROPOUT PanelMetricsBase
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_ALLELES LiftoverVcf
Attribute used to store the position of the failed variant on the target contig prior to finding out that alleles do not match.
ATTEMPTED_LOCUS 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
ATTRIBUTE_TO_CLEAR_LONG_NAME RevertSamSpark
attributeMap ReducibleAnnotationData
ATTRIBUTES_TO_REMOVE MergeBamAlignment
ATTRIBUTES_TO_RETAIN MergeBamAlignment
ATTRIBUTES_TO_REVERSE MergeBamAlignment
ATTRIBUTES_TO_REVERSE_COMPLEMENT MergeBamAlignment
attributesToClear RevertSamSpark
attributeToList(Object) GATKProtectedVariantContextUtils
AUTOCALL_CALL_RATE CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The overall autocall call rate
AUTOCALL_DATE CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The date this sample was autocalled
AUTOCALL_DATE InfiniumVcfFields
AUTOCALL_GENDER CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The sex, as determined by Autocall
AUTOCALL_GENDER InfiniumVcfFields
AUTOCALL_PF CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
Whether the sample passes QC based on call rate threshold
AUTOCALL_VERSION CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The version of autocall used for calling this sample
AUTOCALL_VERSION InfiniumVcfFields
AutoCloseableCollection org.broadinstitute.hellbender.utils.collections
An AutoCloseable collection that will automatically close all of its elements.
AutoCloseableCollection(Collection<? extends AutoCloseable>) AutoCloseableCollection
AUTOSOMAL_RECESSIVE_GENES AutosomalRecessiveConstants
AUTOSOMAL_REF_COPY_NUMBER_LONG_NAME PostprocessGermlineCNVCalls
AutosomalRecessiveConstants org.broadinstitute.hellbender.tools.funcotator.filtrationRules
AutosomalRecessiveConstants() AutosomalRecessiveConstants
AVG_INTERVAL_DP_BY_SAMPLE_KEY GATKVCFConstants
AVG_INTERVAL_DP_KEY GATKVCFConstants
avgAvgDiffs ThetaVariantEvaluator
avgHet ThetaVariantEvaluator
avgVarAF VariantAFEvaluator
awaitCompletion() VariantAccumulatorExecutor
Blocks until the work is complete.
awaitCompletion() VariantAccumulatorExecutor.MultiThreadedChunkBased
awaitThreadPoolTermination(String, ThreadPoolExecutor, Duration) ThreadPoolExecutorUtil
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) CachingIndexedFastaSequenceFile
Open the given indexed fasta sequence file.
CachingIndexedFastaSequenceFile(Path, boolean) CachingIndexedFastaSequenceFile
Open the given indexed fasta sequence file.
CachingIndexedFastaSequenceFile(Path, long, boolean, boolean) 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, boolean) ReferenceConfidenceModel
Calculate the genotype likelihoods for the sample in pileup for being hom-ref contrasted with being ref vs.
calcGenotypeLikelihoodsOfRefVsAny(int, ReadPileup, byte, byte, MathUtils.RunningAverage, boolean) SomaticReferenceConfidenceModel
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(VariantContext) AlleleFrequencyCalculator
calculate(VariantContext, int) AlleleFrequencyCalculator
Compute the probability of the alleles segregating given the genotype likelihoods of the samples in vc
CALCULATE_BY CalculateFingerprintMetrics
CALCULATE_TUMOR_AWARE_RESULTS CrosscheckFingerprints
calculateAllGcs(byte[], int, int) GcBiasUtils
calculateAnnotationFromGTfield(GenotypesContext) AS_StrandBiasTest
calculateAnnotationFromGTfield(GenotypesContext) FisherStrand
calculateAnnotationFromGTfield(GenotypesContext) StrandBiasTest
calculateAnnotationFromGTfield(GenotypesContext) StrandOddsRatio
calculateAnnotationFromLikelihoods(AlleleLikelihoods<GATKRead, Allele>, VariantContext) AS_FisherStrand
calculateAnnotationFromLikelihoods(AlleleLikelihoods<GATKRead, Allele>, VariantContext) AS_StrandOddsRatio
calculateAnnotationFromLikelihoods(AlleleLikelihoods<GATKRead, Allele>, VariantContext) FisherStrand
calculateAnnotationFromLikelihoods(AlleleLikelihoods<GATKRead, Allele>, VariantContext) StrandBiasTest
calculateAnnotationFromLikelihoods(AlleleLikelihoods<GATKRead, Allele>, VariantContext) StrandOddsRatio
calculateArtifactProbabilities(VariantContext, Mutect2FilteringEngine) StrandArtifactFilter
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.
calculateChecksumFromMessageDigest() NioFileCopierWithProgressMeter
calculateChecksumOnInputStream(InputStream) NioFileCopierWithProgressMeter.ChecksumCalculator
calculateCigar(byte[], SmithWatermanAligner) Path
Calculate the cigar elements for this path against the reference sequence
calculateCigar(byte[], byte[], SmithWatermanAligner, SWOverhangStrategy) 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
calculateContaminationFromHoms(List<PileupSummary>) ContaminationModel
Calculate the contamination in a tumor sample using the hom alt and hom ref sites inferred from this model, which
could be derived from the tumor itself or a matched normal.
calculateDerivedFields() ErrorSummaryMetrics
calculateDerivedFields() MergeableMetricBase
Placeholder method that will calculate the derived fields from the other ones.
calculateDerivedFields() IndependentReplicateMetric
calculateDerivedFields() WgsMetrics
calculateDerivedFields() CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
calculateDerivedFields() CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
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() BaseErrorMetric
calculateDerivedFields() IndelErrorMetric
calculateDerivedFields() OverlappingErrorMetric
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.
calculateEH(VariantContext, GenotypeCounts, int) ExcessHet
calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) ContaminationFilter
calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) FilteredHaplotypeFilter
calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) GermlineFilter
calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) HardFilter
calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) Mutect2VariantFilter
calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) NormalArtifactFilter
calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) PolymeraseSlippageFilter
calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) ReadOrientationFilter
calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) StrandArtifactFilter
calculateErrorProbability(VariantContext, Mutect2FilteringEngine, ReferenceContext) TumorEvidenceFilter
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.
CalculateFingerprintMetrics picard.fingerprint
Calculates various metrics on a sample fingerprint, indicating whether the fingerprint satisfies the assumptions we have.
CalculateFingerprintMetrics() CalculateFingerprintMetrics
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, List<VariantContext>) GenotypingEngine
Main entry function to calculate genotypes of a given VC with corresponding GL's that is shared across genotypers (namely UG and HC).
calculateGenotypes(VariantContext, GenotypeLikelihoodsCalculationModel) GenotypingEngine
calculateGLsForThisEvent(AlleleLikelihoods<GATKRead, 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.
calculateNumReadsSupportingAllele(ReadPileup, Allele, Allele, int) PowerCalculationUtils
Get a count of the number of reads supporting an allele in a given pileup.
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, AlleleLikelihoods<GATKRead, Allele>, ReducibleAnnotationData) AS_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, AlleleLikelihoods<GATKRead, Haplotype>, PloidyModel, List<VariantContext>) ReferenceConfidenceModel
calculateRefConfidence(Haplotype, Collection<Haplotype>, SimpleInterval, AssemblyRegion, AlleleLikelihoods<GATKRead, 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
calculateSensitivities(int, Histogram<Integer>, Histogram<Integer>, List<Double>) TheoreticalSensitivity
This is a utility function to calculate the metrics specific to running
theoretical sensitivity over several different allele fractions.
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
calculateThresholdBasedOnFalseDiscoveryRate(List<Double>, double) ThresholdCalculator
Compute the filtering threshold that ensures that the false positive rate among the resulting pass variants
will not exceed the requested false positive rate
calculateTwoSidedU(double[], double[]) 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_RATE CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The overall call rate
CALL_RATE_PF_THRESHOLD CollectArraysVariantCallingMetrics
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
CALLABLE_DEPTH_LONG_NAME M2ArgumentCollection
CALLABLE_REGION_TAG AssemblyBasedCallerUtils
CALLABLE_SITES_NAME Mutect2Engine
callableDepth M2ArgumentCollection
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 org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Carries the result of a call to #assignGenotypeLikelihoods
CalledHaplotypes(List<VariantContext>, Set<Haplotype>) CalledHaplotypes
CalledLegacySegment org.broadinstitute.hellbender.tools.copynumber.formats.records
CalledLegacySegment(String, SimpleInterval, int, double, CalledCopyRatioSegment.Call) CalledLegacySegment
CalledLegacySegmentCollection org.broadinstitute.hellbender.tools.copynumber.formats.collections
Represents a CBS-style segmentation to enable IGV-compatible plotting.
CalledLegacySegmentCollection(SampleLocatableMetadata, List<CalledLegacySegment>) CalledLegacySegmentCollection
CalledLegacySegmentCollection(File) CalledLegacySegmentCollection
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, ReferenceMultiSparkSource, 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(AlleleLikelihoods<GATKRead, Haplotype>, AssemblyResultSet, ReferenceContext, SimpleInterval, FeatureContext, List<VariantContext>, SAMFileHeader, boolean, boolean) SomaticGenotypingEngine
Main entry point of class - given a particular set of haplotypes, samples and reference context, compute
genotype likelihoods and assemble into a list of variant contexts and genomic events ready for calling
The list of samples we're working with is obtained from the readLikelihoods
callRegion(Locatable, List<VariantContext>, ReferenceContext, FeatureContext, ReferenceConfidenceVariantContextMerger, boolean, double, double) GenotypeGVCFsEngine
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
callState GenotypeConcordanceStates.TruthAndCallStates
callVariantsWithHaplotypeCallerAndWriteOutput(JavaSparkContext, JavaRDD<GATKRead>, SAMFileHeader, SAMSequenceDictionary, String, List<ShardBoundary>, HaplotypeCallerArgumentCollection, AssemblyRegionReadShardArgumentCollection, AssemblyRegionArgumentCollection, boolean, String, Collection<Annotation>, Logger, boolean, boolean) 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
canDecodeFileChecks(String) XsvLocatableTableCodec
Checks the content of the given config file to see if it can be decoded.
canDecodeFileChecks(String, String) XsvLocatableTableCodec
Checks the content of the given config file and backing data file to see if they can be decoded.
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 ReadThreadingAssemblerArgumentCollection
captureAssemblyFailureBAM ReadThreadingAssemblerArgumentCollection
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
Casava18ReadNameEncoder picard.fastq
A read name encoder conforming to the standard described by Illumina Casava 1.8.
Casava18ReadNameEncoder(String, String, String) Casava18ReadNameEncoder
CASE_DETERMINE_PLOIDY_AND_DEPTH_PYTHON_SCRIPT DetermineGermlineContigPloidy
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
CATEGORY CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
Grouping categories for controls.
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
CDF(float[], long) IntHistogram.CDF
CDF_PREFIX ReadMetadata
CENTERS_KEY MergeMutect2CallsWithMC3
CF1R2Args CollectF1R2Counts
CHAIN LiftOverIntervalList
CHAIN LiftoverVcf
ChainPruner V extends BaseVertex ,E extends BaseEdge > - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
ChainPruner() ChainPruner
chainsToRemove(List<Path<V, E>>) AdaptiveChainPruner
chainsToRemove(List<Path<V, E>>) ChainPruner
chainsToRemove(List<Path<V, E>>) LowWeightChainPruner
changeCallToGQ0HomRef(VariantContext, Map<String, Object>) ReblockGVCF
Note that this modifies attrMap as a side effect
changeEvidence(Map<EVIDENCE, EVIDENCE>) AlleleLikelihoods
changeTraversalModeToByVariant() VariantLocusWalker
Traverse by variant instead of by grouped by locus.
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 --is-host-aligned was not set to true (or vice versa).
checkCigarAndConvertTerminalInsertionToSoftClip(Cigar) SvCigarUtils
Checks the input CIGAR for assumption that operator 'D' is not immediately adjacent to clipping operators.
checkCommand(String[]) ProcessSettings
checkError() GVCFWriter
checkFilter(Set<Map.Entry<String, String>>, VariantContext) FuncotationFilter
Check all of this filter's rules against a set of Funcotations.
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.
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.
checksum NioFileCopierWithProgressMeter
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
CHI_SQ_VALUE AlleleFrequencyQCMetric
CHI_SQUARED_PVALUE FingerprintMetrics
The Chi-squared pvalue of the observed counts vector relative to the expected counts, (3x2 table)
CHIMERA_KB_MIN CollectJumpingLibraryMetrics
ChimeraUtil picard.analysis
ChimeraUtil() ChimeraUtil
CHIMERIC_ALIGNMENTS_HIGHMQ_THRESHOLD StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsSparkArgumentCollection
CHIMERIC_ORIGINAL_ALIGNMENT_FILTER_NAME GATKVCFConstants
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.
ChimericOriginalAlignmentFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
ChimericOriginalAlignmentFilter(double) ChimericOriginalAlignmentFilter
CHIP_TYPE CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The chip type name
CHIP_WELL_BARCODE CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The chip well barcode of the Illumina array being assayed
CHIP_WELL_BARCODE InfiniumVcfFields
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)
TODO: This method cannot recognize equivalent alleles (See https://github.com/broadinstitute/gatk/issues/5061)
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.
CHROMOSOME_HEADER_NAME IlluminaManifest
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?
CigarOperatorsInReadStratifier(CigarOperator) ReadBaseStratification.CigarOperatorsInReadStratifier
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
cleanOverlappingReadPairs(List<GATKRead>, SampleList, SAMFileHeader, boolean, OptionalInt, OptionalInt) AssemblyBasedCallerUtils
Modify base qualities when paired reads overlap to account for the possibility of PCR error.
CleanSam picard.sam
CleanSam() CleanSam
cleanUpCigar(Cigar) AlignmentUtils
Clean up the incoming cigar
Removes elements with zero size
Clips away beginning deletion operators
cleanUpHighQualityVariant(VariantContext, VariantContext) ReblockGVCF
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() FilteringOutputStats
clear() ThresholdCalculator
clear() StratificationManager
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
clearAccumulatedData() FilteredHaplotypeFilter
clearAccumulatedData() Mutect2VariantFilter
clearAccumulatedData() StrandArtifactFilter
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
clearTransientAttribute(String) GATKRead
Clear an individual transient attribute on the read.
clearTransientAttribute(String) SAMRecordToGATKReadAdapter
CLINSIG_INFO_KEY FilterFuncotationsConstants
Key for the INFO field added to all variants by
FilterFuncotations,
indicating the clinical significance (if any) of the Funcotations on that variant.
CLINSIG_INFO_KEY_DESCRIPTION FilterFuncotationsConstants
Description for
"CLINSIG" to include in VCF headers.
CLINSIG_INFO_NOT_SIGNIFICANT FilterFuncotationsConstants
Value to assign to
"CLINSIG" for variants that have no
clinically-significant Funcotations.
CLINSIG_INFO_VALUE ClinVarFilter
Value to include in the
"CLINSIG"
INFO annotation of variants matching this rule.
CLINSIG_INFO_VALUE LmmFilter
Value to include in the
"CLINSIG"
INFO annotation of variants matching this rule.
CLINSIG_INFO_VALUE LofFilter
Value to include in the
"CLINSIG"
INFO annotation of variants matching this rule.
ClinVarFilter org.broadinstitute.hellbender.tools.funcotator.filtrationRules
FuncotationFilter matching variants which:
Occur on a gene in the American College of Medical Genomics (ACMG)'s list of clinically-significant variants
Have been labeled by ClinVar as pathogenic or likely pathogenic
Have a max MAF of 5% across sub-populations of ExAC or gnomAD
ClinVarFilter(FilterFuncotations.AlleleFrequencyDataSource) ClinVarFilter
Build a new ClinVar filter using the ExAC or gnomAD datasoure
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() TestingReadThreadingGraph
clone() BaseGraph
clone() SeqGraph
clone() ReadThreadingGraph
clone() MathUtils.RunningAverage
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() CompositeOutputRenderer
close() DataSourceFuncotationFactory
close() CosmicFuncotationFactory
close() GencodeFuncotationFactory
close() VcfFuncotationFactory
close() FuncotatorEngine
Shutdown the engine.
close() GeneListOutputRenderer
Since we have to wait until all segments are processed, the output renderer will do nothing until closed.
close() MafOutputRenderer
close() OutputRenderer
close() SimpleTsvOutputRenderer
close() VcfOutputRenderer
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() AutoCloseableCollection
close() CachingIndexedFastaSequenceFile
Close the backing ReferenceSequenceFile
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() AbstractAlignmentMerger
close() MultiHitAlignedReadIterator
close() SAMFileGATKReadWriter
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() XReadLines
close() SimpleXSVWriter
close() TableReader
close() TableWriter
close() GVCFWriter
Close this GVCF writer.
close() IlluminaAdpcFileWriter
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.
closeAndArchiveFiles() F1R2CountsCollector
CloseAtEndIterator E > - Class in org.broadinstitute.hellbender.utils.iterators
An Iterator that automatically closes a resource when the end of the iteration is
reached.
CloseAtEndIterator(Iterator<E>, AutoCloseable) CloseAtEndIterator
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() AddOriginalAlignmentTags
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() FilterFuncotations
closeTool() FuncotateSegments
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() FastaReferenceMaker
closeTool() VariantFiltration
closeTool() GenotypeGVCFs
closeTool() GnarlyGenotyper
closeTool() HaplotypeCaller
closeTool() MethylationTypeCaller
closeTool() CreateSomaticPanelOfNormals
closeTool() FilterMutectCalls
closeTool() Mutect2
closeTool() CheckPileup
closeTool() Pileup
closeTool() CollectF1R2Counts
closeTool() FilterAlignmentArtifacts
closeTool() RevertBaseQualityScores
closeTool() ASEReadCounter
closeTool() SplitNCigarReads
closeTool() UnmarkDuplicates
closeTool() AnnotateVcfWithBamDepth
closeTool() AnnotateVcfWithExpectedAlleleFraction
closeTool() ValidateBasicSomaticShortMutations
closeTool() MergeMutect2CallsWithMC3
closeTool() RemoveNearbyIndels
closeTool() CalculateGenotypePosteriors
closeTool() LeftAlignAndTrimVariants
Close out the new variants file.
closeTool() ReblockGVCF
closeTool() SelectVariants
Close out the new variants file.
closeTool() UpdateVCFSequenceDictionary
Close out the new variants file.
closeTool() ApplyVQSR
closeTool() CNNScoreVariants
closeTool() FilterVariantTranches
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_FILE GtcToVcf
CLUSTER_FILE InfiniumVcfFields
CLUSTER_FILE_NAME CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The name of the cluster file used
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.PopulateBarcode, boolean) ClusterDataToSamConverter
Constructor
CLUSTERED_EVENTS_FILTER_NAME GATKVCFConstants
CLUSTERED_SNP_FILTER_NAME VariantFiltration
ClusteredCrosscheckMetric picard.fingerprint
ClusteredCrosscheckMetric() ClusteredCrosscheckMetric
ClusteredCrosscheckMetric(CrosscheckMetric) ClusteredCrosscheckMetric
ClusteredEventsFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
ClusteredEventsFilter(int) ClusteredEventsFilter
clusteringMetadata() SomaticClusteringModel
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.DiscoverVariantsFromContigAlignmentsSparkArgumentCollection
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
CODON_LENGTH AminoAcid
The length of a codon in bases.
COHORT_DENOISING_CALLING_PYTHON_SCRIPT GermlineCNVCaller
COHORT_DETERMINE_PLOIDY_AND_DEPTH_PYTHON_SCRIPT DetermineGermlineContigPloidy
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
CollectAllelicCountsSpark org.broadinstitute.hellbender.tools.copynumber
CollectAllelicCountsSpark() CollectAllelicCountsSpark
CollectArraysVariantCallingMetrics picard.arrays
Collects summary and per-sample metrics about variant calls in a VCF file.
CollectArraysVariantCallingMetrics() CollectArraysVariantCallingMetrics
CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics picard.arrays
CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics picard.arrays
CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics picard.arrays
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
CollectF1R2Counts org.broadinstitute.hellbender.tools.walkers.readorientation
At each genomic locus, count the number of F1R2/F2R1 alt reads.
CollectF1R2Counts() CollectF1R2Counts
CollectF1R2CountsArgumentCollection org.broadinstitute.hellbender.tools.walkers.readorientation
CollectF1R2CountsArgumentCollection() CollectF1R2CountsArgumentCollection
collectFromCollector(AllelicCountCollector) AllelicCountCollector
Reminder that any additional information used through this method will not be able to enforce the minBaseQuality.
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
CollectionStratifier(Collection<ReadBaseStratification.RecordAndOffsetStratifier<?>>) ReadBaseStratification.CollectionStratifier
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
CollectReadCounts.Format org.broadinstitute.hellbender.tools.copynumber
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
CollectSamErrorMetrics picard.sam.SamErrorMetric
Program to collect error metrics on bases stratified in various ways.
CollectSamErrorMetrics() CollectSamErrorMetrics
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.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
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
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(AllelicCountCollector, AllelicCountCollector, SampleLocatableMetadata) AllelicCountCollector
TODO: Docs and input parameter checking
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(VariantEvaluator) VariantEvaluator
Evaluation modules that override this function to indicate that they support
combining the results of two independent collections of eval data into
a single meaningful result.
combine(V, V) StratificationManager.Combiner
take two values of type V and return a combined value of type V
combine(EvaluationContext) EvaluationContext
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
COMBINE_VARIANTS_DISTANCE MultiVariantWalkerGroupedOnStart
combineAdjacentCigarElements(Cigar) CigarUtils
Combines equal adjacent elements of a Cigar object
combineAltDepthOneHistogramWithRC(List<Histogram<Integer>>, List<Histogram<Integer>>, int) LearnReadOrientationModel
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) according to their primary raw key
Mutates annotationMap by removing the annotations that were combined
Additionally, will combine other annotations by parsing them as numbers and reducing them
down to the
combineAttributeMap(ReducibleAnnotationData<Histogram>, ReducibleAnnotationData<Histogram>) AS_RankSumTest
combineAttributeMap(ReducibleAnnotationData<Double>, ReducibleAnnotationData<Double>) AS_RMSMappingQuality
combineAttributeMap(ReducibleAnnotationData<List<Integer>>, ReducibleAnnotationData<List<Integer>>) AS_StrandBiasTest
CombineGVCFs org.broadinstitute.hellbender.tools.walkers
Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file
CombineGVCFs() CombineGVCFs
COMBINER EvaluationContext
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<?>>) ExcessHet
Combine raw data, typically during the merging of raw data contained in multiple gVCFs as in CombineGVCFs and the
preliminary merge for GenotypeGVCFs
combineRawData(List<Allele>, List<ReducibleAnnotationData<?>>) RMSMappingQuality
combineRefHistogramWithRC(String, Histogram<Integer>, Histogram<Integer>, int) LearnReadOrientationModel
CombineSegmentBreakpoints org.broadinstitute.hellbender.tools.copynumber.utils
CombineSegmentBreakpoints() CombineSegmentBreakpoints
combineStates(List<Object>, List<Object>) StratificationManager
combineStrats(K, K, StratificationManager.Combiner<V>, Map<Object, Object>) StratificationManager
Remaps the stratifications from one stratification set to another, combining
the values in V according to the combiner function.
combineTables(NestedIntegerArray<RecalDatum>, NestedIntegerArray<RecalDatum>) 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
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 AddCommentsToBam
COMMENT FastqToSam
COMMENT AbstractMarkDuplicatesCommandLineProgram
COMMENT MergeSamFiles
COMMENT IntervalListTools
COMMENT_DELIMITER TableCodec
COMMENT_PREFIX CopyNumberFormatsUtils
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(TransientFieldPhysicalLocation, TransientFieldPhysicalLocation) MarkDuplicatesSparkUtils.TransientFieldPhysicalLocationComparator
compare(PileupSummary, PileupSummary) PileupSummary.PileupSummaryComparator
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(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
CompareIntervalLists org.broadinstitute.hellbender.tools
CompareIntervalLists() CompareIntervalLists
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(VariantEvaluator) VariantEvaluator
compareTo(VariantStratifier) VariantStratifier
compareTo(SortableJexlVCMatchExp) SortableJexlVCMatchExp
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(Pair<X, Y>) Pair
compareTo(PrimaryAlignmentKey) PrimaryAlignmentKey
compareTo(GenotypeConcordanceStates.TruthAndCallStates) GenotypeConcordanceStates.TruthAndCallStates
CompareVariantContextToLocus(SAMSequenceDictionary, VariantContext, Locus) CollectSamErrorMetrics
Compares a VariantContext to a Locus providing information regarding possible overlap, or relative location
COMPARISON_LONG_NAME StandardArgumentDefinitions
COMPARISON_SHORT_NAME StandardArgumentDefinitions
CompFeatureInput org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
Required stratification grouping output by each comp
CompFeatureInput() CompFeatureInput
CompFiltered ValidationReport
complement() Transition
Return the complementary transition.
complement() Nucleotide
Returns the complement nucleotide code for this one.
complement(byte, boolean) Nucleotide
Returns the complement for a base code.
complement(byte) Nucleotide
Returns the complement for a base code.
complement() Transition
Return the complementary transition.
COMPLEX_CHIMERA_VCF_FILE_NAME SvDiscoverFromLocalAssemblyContigAlignmentsSpark
ComplexityPartitioner org.broadinstitute.hellbender.tools.spark.sv.utils
A Spark Partitioner that puts tasks with greater complexities into earlier partitions.
ComplexityPartitioner(int[]) ComplexityPartitioner
CompMonoEvalFiltered ValidationReport
CompMonoEvalMono ValidationReport
CompMonoEvalNoCall ValidationReport
CompMonoEvalPoly ValidationReport
compose(ReadTransformer) ReadTransformer
compose(VariantTransformer) VariantTransformer
composeAlleleFrequencyPriorProvider(int, double, List<Double>) GenotypingEngine
Function that fills vector with allele frequency priors.
composeCallAttributes(VariantContext, List<Integer>, AFCalculationResult, List<Allele>, GenotypesContext) GenotypingEngine
composeHaplotypeBasedOnReference(int, int, ReferenceMultiSparkSource) SVContext
Composes the haplotype that corresponds to an allele based on the reference sequence.
composeLine(AltSiteRecord, DataLine) AltSiteRecord.AltSiteRecordTableWriter
composeLine(ArtifactPrior, DataLine) ArtifactPrior.ArtifactPriorTableWriter
composeLine(ConcordanceSummaryRecord, DataLine) ConcordanceSummaryRecord.Writer
composeLine(InfoConcordanceRecord, DataLine) InfoConcordanceRecord.InfoConcordanceWriter
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
CompositeOutputRenderer org.broadinstitute.hellbender.tools.funcotator.compositeoutput
Class to make multiple funcotator output at the same time.
CompositeOutputRenderer(List<OutputRenderer>, String) CompositeOutputRenderer
CompOverlap org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
The Broad Institute
SOFTWARE COPYRIGHT NOTICE AGREEMENT
This software and its documentation are copyright 2009 by the
Broad Institute/Massachusetts Institute of Technology.
CompOverlap() CompOverlap
CompPolyEvalFiltered ValidationReport
CompPolyEvalMono ValidationReport
CompPolyEvalNoCall ValidationReport
CompPolyEvalPoly ValidationReport
compRate CompOverlap
compRate() CompOverlap
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.
compsProvided VariantEval
The variant file(s) to compare against.
compute(int) DigammaCache
compute(int) IntToDoubleFunctionCache
compute(int) Log10Cache
compute(int) Log10FactorialCache
COMPUTE_SLOD UnifiedArgumentCollection
Note that calculating the SLOD increases the runtime by an appreciable amount.
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<GATKRead, 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<GATKRead, 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.
computeLogPenaltyScore(int, int) KBestHaplotype
computeMaxAcceptableAlleleCount(int, int) GenotypeLikelihoodCalculators
Compute the maximally acceptable allele count (ref allele included) given the maximally acceptable genotype count.
computeQScore(long) ErrorMetric
compute a qscore given the number of errors and the total number of bases.
computeQScore(long, long) ErrorMetric
compute a qscore given the number of errors and the total number of bases.
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.
computeResponsibilities(Nucleotide, Nucleotide, int, int, int, double[], boolean) LearnReadOrientationModelEngine
Return normalized probabilities
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
concordanceRate() CompOverlap
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
concordantRate CompOverlap
concordantRate MetricsCollection
CONCRETE_TYPES ValidateVariants.ValidationType
Unmodifiable set of concrete validation types.
confidence AlleleLikelihoods.BestAllele
Confidence that the evidence actually was generated under that likelihood.
CONFIDENCE_REGION_LONG_NAME AbstractConcordanceWalker
CONFIDENCE_REGION_SHORT_NAME AbstractConcordanceWalker
CONFIG_FILE_EXTENSION 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_IS_B37_DATA_SOURCE DataSourceUtils
CONFIG_FILE_FIELD_NAME_LOOKAHEAD_CACHE_BP DataSourceUtils
CONFIG_FILE_FIELD_NAME_NAME DataSourceUtils
CONFIG_FILE_FIELD_NAME_NCBI_BUILD_VERSION 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_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.
CONFIG_RESOURCE GeneListOutputRenderer
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
consensusStratifier ReadBaseStratification
Stratify by tags used during duplex and single index consensus calling.
ConsensusStratifier() ReadBaseStratification.ConsensusStratifier
CONSOLIDATE_ARG_NAME GenomicsDBImport
consolidateCigar(Cigar) AlignmentUtils
Need a well-formed, consolidated Cigar string so that the left aligning code works properly.
constantsAreInitialized PairHMM
constructLibraryIndex(SAMFileHeader) MarkDuplicatesSparkUtils
Method which generates a map of the libraries found tagged in readgroups from the header so they can be serialized as indexes to save space
constructStaticQuantizedMapping(List<Integer>, boolean) BQSRReadTransformer
Constructs an array that maps particular quantized values to a rounded value in staticQuantizedQuals
Rounding is done in probability space.
consume(GATKRead, ReferenceContext, FeatureContext) MultiplePassReadWalker.GATKReadConsumer
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
consumeFinalizedItems() PushPullTransformer
Return (and *remove*) all items that have survived transformation and are waiting to be retrieved.
consumeFinalizedItems() GVCFBlockCombiner
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(SVInterval) SVInterval
contains(Object) HopscotchCollection
contains(long) LargeLongHopscotchSet
contains(long) LongBloomFilter
contains(long) LongHopscotchSet
contains(long, int) LongHopscotchSet
contains(Locatable) GencodeGtfFeature
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(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
containsKey(Set<Map.Entry<String, String>>, String) FuncotationFilter
Does the set of funcotations contain the key supplied
containsKey(List<Object>) StratificationManager
containsKey(Object) StratificationManager
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
containsValue(Object) StratificationManager
containsVertex(V) Path
Does this path contain the given vertex?
contamination HaplotypeProbabilitiesFromContaminatorSequence
CONTAMINATION IdentifyContaminant
CONTAMINATION_ESTIMATE_LONG_NAME M2FiltersArgumentCollection
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_QUAL_KEY GATKVCFConstants
CONTAMINATION_TABLE_LONG_NAME M2FiltersArgumentCollection
Input files and values to use if inputs are missing
contaminationDownsampling(Map<String, Double>) AlleleLikelihoods
Downsamples reads based on contamination fractions making sure that all alleles are affected proportionally.
contaminationEstimate M2FiltersArgumentCollection
ContaminationFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
ContaminationFilter(List<File>, double) ContaminationFilter
ContaminationModel org.broadinstitute.hellbender.tools.walkers.contamination
This is the probabilistic contamination model that we use to distinguish homs from hets
The model is similar to that of ContEst, in that it assumes that each contaminant read is independently drawn from
the population.
ContaminationModel(List<PileupSummary>) ContaminationModel
ContaminationRecord org.broadinstitute.hellbender.tools.walkers.contamination
Created by David Benjamin on 2/13/17.
ContaminationRecord(String, double, double) ContaminationRecord
ContaminationSegmenter org.broadinstitute.hellbender.tools.walkers.contamination
contaminationTables 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
Contig org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
Stratifies the evaluation by each contig in the reference sequence
Contig() Contig
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
ContigChimericAlignmentIterativeInterpreter org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
This class scans the chimeric alignments of input
AlignedContig,
filters out the alignments that offers weak evidence for a breakpoint and,
makes interpretation based on the
SimpleChimera extracted.
ContigChimericAlignmentIterativeInterpreter() ContigChimericAlignmentIterativeInterpreter
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).
CONTROL CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
Various control intensities that are present on the infinium chips.
CONTROL_INFO ArraysControlInfo
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(AnnotatedInterval, ReferenceContext) AnnotatedIntervalToSegmentVariantContextConverter
Convert a segment (as annotated interval) to a VariantContext.
convert(Method, String) CustomBooleanConverter
convert(GATKRead, SAMFileHeader) GATKReadToBDGAlignmentRecordConverter
convert(GATKRead, SAMFileHeader, SequenceDictionary, ReadGroupDictionary) GATKReadToBDGAlignmentRecordConverter
convert(SAMRecord, SequenceDictionary, ReadGroupDictionary) GATKReadToBDGAlignmentRecordConverter
convert(File, File, File, Boolean) SamFormatConverter
Convert a file from one of sam/bam/cram format to another based on the extension of output.
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_BASE_COVERAGE_KEY GATKVCFConstants
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.
convertHG19ContigToB37Contig(String) FuncotatorUtils
Converts a given HG19 style contig name to the equivalent in B37.
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
convertLODtoInt(double, int) SomaticGVCFBlockCombiner
convertLODtoInt(double) SomaticGVCFWriter
convertMetric(TargetMetrics) HsMetricCollector
convertMetric(TargetMetrics) TargetedPcrMetricsCollector
convertMetric(TargetMetrics) TargetMetricsCollector
convertPicardStyleToPosixStyle(String[]) CommandLineSyntaxTranslater
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_NEUTRAL_ALLELE AnnotatedIntervalToSegmentVariantContextConverter
COPY_NEUTRAL_ALLELE_STRING AnnotatedIntervalToSegmentVariantContextConverter
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_LEGACY_SEGMENTS_FILE_SUFFIX ModelSegments
COPY_RATIO_MODEL_PARAMETER_FILE_SUFFIX ModelSegments
COPY_RATIO_SEGMENTS_FOR_CALLER_FILE_SUFFIX ModelSegments
COPY_SPEED_HISTORY_SIZE NioFileCopierWithProgressMeter
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 evidence for a given allele into an array from a particular offset.
copyBuffer NioFileCopierWithProgressMeter
copyComplete NioFileCopierWithProgressMeter
copyFile(String, String) BucketUtils
Copies a file.
copyFromBaseClass(T, S) ReflectionUtil
CopyNumberAnnotations org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation
CopyNumberAnnotations() CopyNumberAnnotations
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
CORRECT_OVERLAPPING_BASE_QUALITIES_LONG_NAME HaplotypeCallerArgumentCollection
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
CosmicFuncotationFactory(Path, LinkedHashMap<String, String>, String, boolean) CosmicFuncotationFactory
CouldNotCreateOutputFile(File, String, Exception) UserException.CouldNotCreateOutputFile
CouldNotCreateOutputFile(File, String) UserException.CouldNotCreateOutputFile
CouldNotCreateOutputFile(String, String) UserException.CouldNotCreateOutputFile
CouldNotCreateOutputFile(String, String, Exception) UserException.CouldNotCreateOutputFile
CouldNotCreateOutputFile(File, Exception) UserException.CouldNotCreateOutputFile
CouldNotCreateOutputFile(String, Exception) UserException.CouldNotCreateOutputFile
CouldNotIndexFile(Path, 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_FIELD_NAMES CustomMafFuncotationCreator
COUNT_OUTPUT IntervalListTools
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
CountBasesInReference org.broadinstitute.hellbender.tools.walkers.fasta
CountBasesInReference() CountBasesInReference
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
Counts the number of mendelian violations in the provided sample DB.
CountingAdapterFilter picard.filter
Counting filter that discards reads are unaligned or aligned with MQ==0 and whose 5' ends look like adapter
Sequence
CountingAdapterFilter() CountingAdapterFilter
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.
CountNs org.broadinstitute.hellbender.tools.walkers.annotator
Apply a read-based annotation that reports the number of Ns seen at a given site.
CountNs() CountNs
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
countRefBasesBasedOnUnclippedAlignment(GATKRead, int, int) CigarUtils
Compute the number of reference bases between the start (inclusive) and end (exclusive) cigar elements.
countRefBasesIncludingSoftClips(GATKRead, int, int) CigarUtils
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.
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
CountVariants org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
CountVariants() CountVariants
CountVariantsSpark org.broadinstitute.hellbender.tools.spark.pipelines
CountVariantsSpark() CountVariantsSpark
Covariate org.broadinstitute.hellbender.utils.recalibration.covariates
The Covariate interface.
COVARIATE ErrorMetric
The value of the covariate define the bases included in this metric
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 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 org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
CpG is a stratification module for VariantEval that divides the input data by within/not within a CpG site
CpG() CpG
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_EVENT_KEY 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(Locatable, Allele, String) LocatableFuncotationCreator
Create a funcotation with only the locatable inforamtion (CONTIG, START, and END) from a locatable.
create(List<String>, List<String>, Allele, String, FuncotationMetadata) TableFuncotation
Create a TableFuncotation with given name value pairs.
create(LinkedHashSet<String>, List<String>, Allele, String, FuncotationMetadata) TableFuncotation
Convenience method to create a table funcotation from a LinkedHashSet, which preserves order.
create(LinkedHashMap<String, String>, Allele, String, FuncotationMetadata) TableFuncotation
create(XsvTableFeature, Allele, String, FuncotationMetadata) TableFuncotation
create(FuncotationMap) FuncotationMap
Copy creation.
create(List<VCFInfoHeaderLine>) VcfFuncotationMetadata
create(int, int, String, String) ProteinChangeInfo
Create a
ProteinChangeInfo object containing given information about a protein change.
create(Allele, Allele, int, int, String, Strand, boolean) ProteinChangeInfo
Create a
ProteinChangeInfo object which will represent the change in the protein sequence
which would be caused by a variant.
create(String) StrandCorrectedAllele
create(String, Strand) StrandCorrectedAllele
create(String, boolean) StrandCorrectedAllele
create(String, boolean, Strand) StrandCorrectedAllele
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(Path, Path) NioFileCopierWithProgressMeter
create(Path, Path, boolean) NioFileCopierWithProgressMeter
create(Path, Path, boolean, NioFileCopierWithProgressMeter.Verbosity) NioFileCopierWithProgressMeter
create(List<GATKRead>) Fragment
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_BAM_SPLITTING_INDEX_LONG_NAME GATKSparkTool
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(VariantContext, int, List<Haplotype>) AssemblyBasedCallerUtils
Returns a mapping from Allele in the mergedVC, which represents all of the alleles being genotyped at loc,
to a list of Haplotypes that support that allele.
createAlleleMapping(Allele, 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.
createAlleleToFuncotationMapFromFuncotationVcfAttribute(String[], VariantContext, String, String) FuncotatorUtils
Create a mapping for a single variant.
createAndAvoidFailure(List<GATKRead>) Fragment
createAndSetHeader(int) ArtificialBAMBuilder
createAnnotationEngine() ReblockGVCF
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.
createArtificialSamHeaderWithPrograms(int, int, int, int) ArtificialReadUtils
Creates an artificial SAM header, matching the parameters, chromosomes which will be labeled chr1, chr2, etc
It also adds program records.
createArtificialSamHeaderWithReadGroup(SAMReadGroupRecord) ArtificialReadUtils
Creates an artificial SAM header with standard test parameters and a Read Group
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
createAsAllTableFuncotationsFromVcf(String, String[], String, Allele, String) FuncotationMap
Create a FuncotationMap where all Funcotations will be TableFuncotations.
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.
createColumnNameToAliasesMap(Path) SimpleTsvOutputRenderer
Create key value pairs where the key is the output column name and the value is a list of possible field names, in order of priority.
createColumnNameToFieldNameMap(FuncotationMap, String) AliasProvider
Create a mapping that links the fields of this alias provider to the funcotation fields in the given
FuncotationMap.
createCommonSAMWriter(File, File, SAMFileHeader, boolean, boolean, boolean) ReadUtils
Create a common SAMFileWriter for use with GATK tools.
createCommonSAMWriter(Path, Path, 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, Path, SAMFileHeader, boolean, OpenOption...) ReadUtils
Create a common SAMFileWriter from a factory for use with GATK tools.
createCustomMafCountFields(VariantContext, List<TumorNormalPair>) CustomMafFuncotationCreator
createCustomMafDbSnpFields(List<Funcotation>) CustomMafFuncotationCreator
Creates a list of funcotations for each input dbSNP funcotation.
createDataFIFO() StreamingProcessController
Create a temporary FIFO suitable for sending output to the remote process.
createDataSourceFuncotationFactoriesForDataSources(Map<Path, Properties>, LinkedHashMap<String, String>, TranscriptSelectionMode, Set<String>, GATKTool, int, FlankSettings, boolean) 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
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, SAMFileHeader, AssemblyRegion) AssemblyBasedCallerUtils
createEdge(MultiDeBruijnVertex, MultiDeBruijnVertex) AbstractReadThreadingGraph.MyEdgeFactory
createEmpty() FuncotationMap
createEmptyHistogram() LibraryStatistics
createEmptyHistogram() IntHistogram.CDF
createEvaluationContext(Set<Class<? extends VariantEvaluator>>) VariantEval
Create the EvaluationContext (new instance) for the provided set of VariantEvaluators.
createExportConfiguration(String, String, String, String, GenomicsDBOptions) GenomicsDBUtils
createExportConfiguration(String, String, String, String) GenomicsDBUtils
createFeatureContextForTesting(Map<FeatureInput<? extends Feature>, Class<? extends Feature>>, String, SimpleInterval, int, int, int, Path) FeatureContext
Convenience method to create a new instance for test methods.
createFifoFile(Path) IOUtils
Create a Unix FIFO file with the given path string.
createFifoFile(Path, boolean) IOUtils
Create a Unix FIFO file with the given path string.
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
createFromFile(Path, LinkedHashMap<String, String>, LinkedHashMap<String, String>, Set<String>, Path, String, boolean) SimpleTsvOutputRenderer
createFromGencodeFuncotations(List<GencodeFuncotation>) FuncotationMap
This method checks for transcript duplications in the list of GencodeFuncotations.
createFromResource(Path, LinkedHashMap<String, String>, LinkedHashMap<String, String>, Set<String>, Path, String, boolean) SimpleTsvOutputRenderer
Use when loading the config file from the jar.
createFuncotationFromLinkedHashMap(LinkedHashMap<String, String>, Allele, String) OutputRenderer
Utility for output renderers.
createFuncotationMapForVariant(VariantContext, ReferenceContext, FeatureContext) FuncotatorEngine
createFuncotations(VariantContext, ReferenceContext, FeatureContext) DataSourceFuncotationFactory
Creates a
List of
Funcotation for the given
variant,
referenceContext, and
featureContext.
createFuncotations(VariantContext, ReferenceContext, FeatureContext, List<GencodeFuncotation>) DataSourceFuncotationFactory
Creates a
List of
Funcotation for the given
variant,
referenceContext,
featureContext, and
gencodeFuncotations.
createFuncotations(VariantContext, FuncotationMetadata, String) FuncotatorUtils
Create funcotations (one for each alt allele) corresponding to the given variant context.
createFuncotationsOnSegment(VariantContext, ReferenceContext, List<Feature>) DataSourceFuncotationFactory
Sublclasses that support annotating segments should override this method to create funcotations for segments.
createFuncotationsOnSegment(VariantContext, ReferenceContext, List<Feature>) GencodeFuncotationFactory
Create Funcotations for a given segment variant context.
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
Attempts to treat the given features as
GencodeGtfFeature objects in order to
create funcotations for the given variant and reference.
createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>, List<GencodeFuncotation>) GencodeFuncotationFactory
Creates a
List of
Funcotation for the given
variant,
referenceContext,
featureContext, and
gencodeFuncotations.
createFuncotationsOnVariant(VariantContext, ReferenceContext, List<Feature>) VcfFuncotationFactory
Creates a
List of
Funcotation for the given
variant,
referenceContext, and
featureContext.
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.
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.
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
createIntronicCDnaString(int, List<? extends Locatable>, String, String) FuncotatorUtils
Create a cDNA string for an intronic variant.
createLibraryStatistics(long) ReadMetadata.LibraryRawStatistics
createLikelihoodCalculationEngine(LikelihoodEngineArgumentCollection) AssemblyBasedCallerUtils
Instantiates the appropriate likelihood calculation engine.
createLinkedHashMapFromLists(List<T>, List<U>) FuncotatorUtils
Create a linked hash map from two lists with corresponding values.
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
createNoTranscriptInfo(List<Funcotation>) FuncotationMap
createOptimalCoverageAlignmentSetsForContigs(JavaRDD<GATKRead>, SAMFileHeader, Set<String>, Double, Logger) AssemblyContigAlignmentsConfigPicker
Filters input alignments of single-ended long reads, e.g.
createOutputBamIndex GATKTool
createOutputBamIndex GATKSparkTool
createOutputBamIndex() GATKConfig
createOutputBamMD5 GATKTool
createOutputBamSplittingIndex GATKSparkTool
createOutputVariantIndex GATKTool
createOutputVariantIndex GATKSparkTool
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.
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
createReadThreadingAssembler() M2ArgumentCollection
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) MinorAlleleFractionRecord.MinorAlleleFractionTableReader
createRecord(DataLine) ArtifactPrior.ArtifactPriorTableReader
createRecord(DataLine) ConcordanceSummaryRecord.Reader
createRecord(DataLine) InfoConcordanceRecord.InfoConcordanceReader
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
createReferenceSnippet(Allele, Allele, ReferenceContext, Strand, int) FuncotatorUtils
Get the bases around the given ref allele in the correct direction of the strand for this variant.
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
createShard(Iterable<T>) ShardBoundary
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
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.
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.
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.
createTempPath(String, String) IOUtils
Creates a temp path that will be deleted on exit.
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)
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 vcfOutput's extension, using the best available sequence dictionary for
this tool, and default index, leniency and md5 generation settings.
createVCFWriter(Path) GATKTool
Creates a VariantContextWriter whose outputFile type is determined by
vcfOutput's extension, using the best available sequence dictionary for
this tool, and default index, leniency and md5 generation settings.
createVCFWriter(Path, SAMSequenceDictionary, boolean, Options...) 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
CreateVerifyIDIntensityContaminationMetricsFile picard.arrays
A simple program to create a standard picard metrics file
from the output of VerifyIDIntensity
CreateVerifyIDIntensityContaminationMetricsFile() CreateVerifyIDIntensityContaminationMetricsFile
createWithUnknownAttributes(List<String>) FuncotationMetadataUtils
createWorkUnit(DocumentedFeature, ClassDoc, Class<?>) GATKHelpDoclet
createWorkUnit(DocumentedFeature, ClassDoc, Class<?>) PicardHelpDoclet
CROSS_ENTROPY_LOD FingerprintMetrics
The categorical cross entropy of the counts of genotypes relative to expected (big is bad)
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
currentReadBaseStratifier ReadBaseStratification
Stratifies bases into the current (uppercase) base as it was read from the sequencer (i.e.
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() RevertSamSpark
Enforce that output ordering is queryname when sanitization is turned on since it requires a queryname sort.
customCommandLineValidation() CNNScoreVariants
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() CollectArraysVariantCallingMetrics
customCommandLineValidation() GtcToVcf
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() CollectSamErrorMetrics
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
CustomMafFuncotationCreator org.broadinstitute.hellbender.tools.funcotator.mafOutput
Produces custom MAF fields (e.g.
CustomMafFuncotationCreator() CustomMafFuncotationCreator
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_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
CYTOSINE Nucleotide
F ReadEnds
F1R2_KEY GATKVCFConstants
F1R2_TAR_GZ_NAME M2ArgumentCollection
f1r2Args M2ArgumentCollection
F1R2CountsCollector org.broadinstitute.hellbender.tools.walkers.readorientation
F1R2CountsCollector(CollectF1R2CountsArgumentCollection, SAMFileHeader, File, Collection<String>) F1R2CountsCollector
F1R2FilterConstants org.broadinstitute.hellbender.tools.walkers.readorientation
Created by tsato on 3/14/18.
F1R2FilterConstants() F1R2FilterConstants
F1R2FilterUtils org.broadinstitute.hellbender.tools.walkers.readorientation
F1R2FilterUtils() F1R2FilterUtils
f1r2TarGz M2ArgumentCollection
F2R1_KEY GATKVCFConstants
F_SCORE_BETA_LONG_NAME M2FiltersArgumentCollection
FAIL_REF InfiniumVcfFields
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
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
FALSE_DISCOVERY_RATE_LONG_NAME M2FiltersArgumentCollection
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 org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
Stratifies the eval RODs by each family in the eval ROD, as described by the pedigree.
Family() Family
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
FastaAlternateReferenceMaker org.broadinstitute.hellbender.tools.walkers.fasta
Generate an alternative reference sequence over the specified interval
FastaAlternateReferenceMaker() FastaAlternateReferenceMaker
FastaReferenceMaker org.broadinstitute.hellbender.tools.walkers.fasta
Create a subset of a FASTA reference sequence
FastaReferenceMaker() FastaReferenceMaker
fastBernoulliEntropy(double) MathUtils
Computes the entropy -p*ln(p) - (1-p)*ln(1-p) of a Bernoulli distribution with success probability p
using an extremely fast Pade approximation that is very accurate for all values of 0 <= p <= 1.
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.
FDR ValidationReport
FDR_METADATA_TAG FilterStats
fdrToTiTv(double, double) TrancheManager
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_LONG_NAME StandardArgumentDefinitions
FEATURE_QUERY_LOOKAHEAD AnnotateIntervals
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.
FeatureContext(FeatureContext, SimpleInterval) FeatureContext
Creates a new FeatureContext given a FeatureContext 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.
FeatureDataSource(FeatureInput<T>, int, Class<? extends Feature>, int, int, GenomicsDBOptions) FeatureDataSource
Creates a FeatureDataSource backed by the provided FeatureInput.
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, GenomicsDBOptions) 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.
featurePath IndexFeatureFile
features GATKTool
Our source of Feature data (null if no source of Features was provided)
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
FIELD_DELIMITER VcfOutputRenderer
The delimiter for each field within the VCF Funcotation field.
FieldName_Annotation_Transcript MafOutputRendererConstants
FieldName_BAM_File MafOutputRendererConstants
FieldName_CCLE_ONCOMAP_overlapping_mutations MafOutputRendererConstants
FieldName_CCLE_ONCOMAP_total_mutations_in_gene MafOutputRendererConstants
FieldName_cDNA_Change MafOutputRendererConstants
FieldName_Center MafOutputRendererConstants
FieldName_CGC_Mutation_Type MafOutputRendererConstants
FieldName_CGC_Other_Diseases MafOutputRendererConstants
FieldName_CGC_Translocation_Partner MafOutputRendererConstants
FieldName_CGC_Tumor_Types_Germline MafOutputRendererConstants
FieldName_CGC_Tumor_Types_Somatic MafOutputRendererConstants
FieldName_Chromosome MafOutputRendererConstants
FieldName_Codon_Change MafOutputRendererConstants
FieldName_COSMIC_fusion_genes MafOutputRendererConstants
FieldName_COSMIC_overlapping_mutations MafOutputRendererConstants
FieldName_COSMIC_tissue_types_affected MafOutputRendererConstants
FieldName_COSMIC_total_alterations_in_gene MafOutputRendererConstants
FieldName_dbSNP_RS MafOutputRendererConstants
FieldName_dbSNP_Val_Status MafOutputRendererConstants
FieldName_Description MafOutputRendererConstants
FieldName_DNARepairGenes_Activity_linked_to_OMIM MafOutputRendererConstants
FieldName_DrugBank MafOutputRendererConstants
FieldName_End_Position MafOutputRendererConstants
FieldName_Entrez_Gene_Id MafOutputRendererConstants
FieldName_FamilialCancerDatabase_Syndromes MafOutputRendererConstants
FieldName_gc_content MafOutputRendererConstants
FieldName_Genome_Change MafOutputRendererConstants
FieldName_GO_Biological_Process MafOutputRendererConstants
FieldName_GO_Cellular_Component MafOutputRendererConstants
FieldName_GO_Molecular_Function MafOutputRendererConstants
FieldName_Hugo_Symbol MafOutputRendererConstants
FieldName_Match_Norm_Seq_Allele1 MafOutputRendererConstants
FieldName_Match_Norm_Seq_Allele2 MafOutputRendererConstants
FieldName_Match_Norm_Validation_Allele1 MafOutputRendererConstants
FieldName_Match_Norm_Validation_Allele2 MafOutputRendererConstants
FieldName_Matched_Norm_Sample_Barcode MafOutputRendererConstants
FieldName_Matched_Norm_Sample_UUID MafOutputRendererConstants
FieldName_Mutation_Status MafOutputRendererConstants
FieldName_MUTSIG_Published_Results MafOutputRendererConstants
FieldName_n_alt_count MafOutputRendererConstants
FieldName_n_ref_count MafOutputRendererConstants
FieldName_NCBI_Build MafOutputRendererConstants
FieldName_OREGANNO_ID MafOutputRendererConstants
FieldName_OREGANNO_Values MafOutputRendererConstants
FieldName_Other_Transcripts MafOutputRendererConstants
FieldName_Protein_Change MafOutputRendererConstants
FieldName_ref_context MafOutputRendererConstants
FieldName_Reference_Allele MafOutputRendererConstants
FieldName_Refseq_mRNA_Id MafOutputRendererConstants
FieldName_Refseq_prot_Id MafOutputRendererConstants
FieldName_Score MafOutputRendererConstants
FieldName_Sequence_Source MafOutputRendererConstants
FieldName_Sequencer MafOutputRendererConstants
FieldName_Sequencing_Phase MafOutputRendererConstants
FieldName_Start_Position MafOutputRendererConstants
FieldName_Strand MafOutputRendererConstants
FieldName_SwissProt_acc_Id MafOutputRendererConstants
FieldName_SwissProt_entry_Id MafOutputRendererConstants
FieldName_t_alt_count MafOutputRendererConstants
FieldName_t_ref_count MafOutputRendererConstants
FieldName_TCGAscape_Amplification_Peaks MafOutputRendererConstants
FieldName_TCGAscape_Deletion_Peaks MafOutputRendererConstants
FieldName_Transcript_Exon MafOutputRendererConstants
FieldName_Transcript_Position MafOutputRendererConstants
FieldName_Transcript_Strand MafOutputRendererConstants
FieldName_tumor_f MafOutputRendererConstants
FieldName_Tumor_Sample_Barcode MafOutputRendererConstants
FieldName_Tumor_Sample_UUID MafOutputRendererConstants
FieldName_Tumor_Seq_Allele1 MafOutputRendererConstants
FieldName_Tumor_Seq_Allele2 MafOutputRendererConstants
FieldName_Tumor_Validation_Allele1 MafOutputRendererConstants
FieldName_Tumor_Validation_Allele2 MafOutputRendererConstants
FieldName_Tumorscape_Amplification_Peaks MafOutputRendererConstants
FieldName_Tumorscape_Deletion_Peaks MafOutputRendererConstants
FieldName_UniProt_AApos MafOutputRendererConstants
FieldName_UniProt_Experimental_Info MafOutputRendererConstants
FieldName_UniProt_Natural_Variations MafOutputRendererConstants
FieldName_UniProt_Region MafOutputRendererConstants
FieldName_UniProt_Site MafOutputRendererConstants
FieldName_Validation_Method MafOutputRendererConstants
FieldName_Validation_Status MafOutputRendererConstants
FieldName_Variant_Classification MafOutputRendererConstants
FieldName_Variant_Type MafOutputRendererConstants
FieldName_Verification_Status MafOutputRendererConstants
fieldsToTake VariantsToTable
Any standard VCF column (CHROM, ID, QUAL) or any annotation name in the INFO field (e.g., -F AC) to include in
the output table.
FifoBuffer 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 CreateVerifyIDIntensityContaminationMetricsFile
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
fileToPath(File) IOUtils
Convert File to Path, returning null if input was null.
fileToTile(String) NewIlluminaDataProvider
fileToTile(String) ParameterizedFileUtil
Returns only lane and tile information as PerTileFt's do not have End information.
fill(String) SimpleXSVWriter.LineBuilder
Fills in every empty column of the pending line with the provided value
FILL_POOLS BaitDesigner
fillIdx KSWindowFinder
fillQualsFromLikelihood(VariantContext, AlleleLikelihoods<GATKRead, Allele>, List<Double>, List<Double>, int) RankSumTest
fillWithRandomBases(byte[], int, int) BaseUtils
Fill an array section with random bases.
Filter org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
Stratifies by the FILTER status (PASS, FAIL) of the eval records
Filter() Filter
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_REV_COMP LiftoverVcf
Filter name to use when a target cannot be lifted over.
FILTER_DELIMITER FilterFuncotationsConstants
Delimiting string to place between values in the
"CLINSIG" INFO field
when Funcotations for a variant match multiple filters.
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.
filterAndWriteMergedVCF(String, List<VariantContext>, SvDiscoveryInputMetaData) SvDiscoverFromLocalAssemblyContigAlignmentsSpark
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
filterCollectionByExpressions(Collection<String>, Collection<String>, boolean) Utils
Given a collection of strings and a collection of regular expressions, generates the set of strings that match
any expression
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
FilteredHaplotypeFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
FilteredHaplotypeFilter(double) FilteredHaplotypeFilter
filteredTrueNegative(VariantContext) AbstractConcordanceWalker.TruthVersusEval
filteredTrueNegativesAndFalseNegativesVcf Concordance
filterExpressions VariantFiltration
VariantFiltration accepts any number of JEXL expressions (so you can have two named filters by using
--filter-name One --filter-expression "X < 1" --filter-name Two --filter-expression "X > 2").
FilterFileFaker 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
FilterFuncotations org.broadinstitute.hellbender.tools.funcotator
Filter variants based on clinically-significant Funcotations.
FilterFuncotations() FilterFuncotations
FilterFuncotations.AlleleFrequencyDataSource org.broadinstitute.hellbender.tools.funcotator
The allele frequency data source that was used when Funcotating the input VCF.
FilterFuncotations.Reference org.broadinstitute.hellbender.tools.funcotator
The version of the Human Genome reference which was used when Funcotating the input VCF.
FilterFuncotationsConstants org.broadinstitute.hellbender.tools.funcotator
FilterFuncotationsConstants() FilterFuncotationsConstants
FilterFuncotationsUtils org.broadinstitute.hellbender.tools.funcotator
FilterFuncotationsUtils() FilterFuncotationsUtils
FILTERING_STATS_EXTENSION FilterMutectCalls
FILTERING_STATS_LONG_NAME FilterMutectCalls
FILTERING_STATUS_VCF_KEY FilterMutectCalls
FilteringOutputStats org.broadinstitute.hellbender.tools.walkers.mutect.filtering
Helper class used on the final pass of
FilterMutectCalls to record total expected true positives, false positives,
and false negatives, as well as false positives and false negatives attributable to each filter
FilteringOutputStats(List<Mutect2VariantFilter>) FilteringOutputStats
FilterIntervals org.broadinstitute.hellbender.tools.copynumber
FilterIntervals() FilterIntervals
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.filtering
Filter variants in a Mutect2 VCF callset.
FilterMutectCalls() FilterMutectCalls
filterName() BaseQualityFilter
filterName() ChimericOriginalAlignmentFilter
filterName() ClusteredEventsFilter
filterName() ContaminationFilter
filterName() DuplicatedAltReadFilter
filterName() FilteredHaplotypeFilter
filterName() FragmentLengthFilter
filterName() GermlineFilter
filterName() MappingQualityFilter
filterName() MinAlleleFractionFilter
filterName() MultiallelicFilter
filterName() Mutect2VariantFilter
filterName() NormalArtifactFilter
filterName() NRatioFilter
filterName() PanelOfNormalsFilter
filterName() PolymeraseSlippageFilter
filterName() PolymorphicNuMTFilter
filterName() ReadOrientationFilter
filterName() ReadPositionFilter
filterName() StrandArtifactFilter
filterName() StrictStrandBiasFilter
filterName() TumorEvidenceFilter
filterNames VariantFiltration
This name is put in the FILTER field for variants that get filtered.
filterOut(SAMRecord) CountingFilter
filterOut(SAMRecord, SAMRecord) CountingFilter
filterPoorlyModeledEvidence(ToDoubleFunction<EVIDENCE>) AlleleLikelihoods
Removes those read that the best possible likelihood given any allele is just too low.
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
FilterStats org.broadinstitute.hellbender.tools.walkers.mutect.filtering
FilterStats(String, double, double, double, double) FilterStats
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.
filterToMaxNumberOfAltAllelesBasedOnScores(int, List<Allele>, double[]) AlleleSubsettingUtils
filterToOnlyOverlappingEvidence(SimpleInterval) AlleleLikelihoods
Removes evidence that does not overlap certain genomic location.
FilterType org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
Stratifies by the FILTER type(s) for each line, with PASS used for passing
FilterType() FilterType
FilterVariantTranches org.broadinstitute.hellbender.tools.walkers.vqsr
Apply tranche filtering to VCF based on scores from an annotation in 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.
finalizeAnnotations(VariantContext, VariantContext) VariantAnnotatorEngine
Finalize reducible annotations (those that use raw data in gVCFs)
finalizeData() BaseRecalibrationEngine
Finalize, if appropriate, all derived data in recalibrationTables.
finalizeEvaluation() CompOverlap
finalizeEvaluation() CountVariants
finalizeEvaluation() IndelLengthHistogram
finalizeEvaluation() IndelSummary
finalizeEvaluation() MultiallelicSummary
finalizeEvaluation() ThetaVariantEvaluator
finalizeEvaluation() TiTvVariantEvaluator
finalizeEvaluation() ValidationReport
finalizeEvaluation() VariantAFEvaluator
finalizeEvaluation() VariantEvaluator
finalizeEvaluation() VariantSummary
finalizeGenotype(VariantContext) GnarlyGenotyperEngine
finalizeGenotype(VariantContext, VariantContextBuilder) GnarlyGenotyperEngine
Calculates final annotation value for VC and calls genotypes, if necessary
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) ExcessHet
Calculate the final annotation value from the raw data which was generated by either annotateRawData or calculateRawData
finalizeRawData(VariantContext, VariantContext) RMSMappingQuality
finalizeRawGVCFVarDPValues(String, int) AS_QualByDepth
finalizeRawMQ(VariantContext) RMSMappingQuality
finalizeRecalibrationTables(RecalibrationTables) BaseRecalibrationEngine
Finalize, if appropriate, all derived data in recalibrationTables.
finalizeRegion(AssemblyRegion, boolean, boolean, byte, SAMFileHeader, SampleList, boolean) 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.
FindAssemblyRegionsSpark org.broadinstitute.hellbender.engine.spark
Find assembly regions from reads in a distributed Spark setting.
FindAssemblyRegionsSpark() FindAssemblyRegionsSpark
FindBadGenomicKmersSpark org.broadinstitute.hellbender.tools.spark.sv.evidence
Identifies sequences that occur at high frequency in a reference
FindBadGenomicKmersSpark() FindBadGenomicKmersSpark
findBestHaplotypes(int) GraphBasedKBestHaplotypeFinder
Implement Dijkstra's algorithm as described in https://en.wikipedia.org/wiki/K_shortest_path_routing
findBestHaplotypes(int) JunctionTreeKBestHaplotypeFinder
The primary engine for finding haplotypes based on junction trees.
findBestHaplotypes(int) KBestHaplotypeFinder
findBestHaplotypes() KBestHaplotypeFinder
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.
findJointAlignments(List<List<BwaMemAlignment>>, int) RealignmentEngine
Find all common alignments of a set of unitigs.
findKmer(Kmer) KmerSearchableGraph
Returns the vertex that represents or contains the last base of a given kmer.
findKmer(Kmer) AbstractReadThreadingGraph
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.
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
findSegments(List<PileupSummary>) ContaminationSegmenter
Partition the genome into segments of allelic copy number state using kernel segmentation of likely hets.
findStart(AbstractReadThreadingGraph.SequenceForKmers) AbstractReadThreadingGraph
Find vertex and its position in seqForKmers where we should start assembling seqForKmers
findStartForJunctionThreading(AbstractReadThreadingGraph.SequenceForKmers) JunctionTreeLinkedDeBruinGraph
Find vertex and its position in seqForKmers where we should start assembling seqForKmers
findTile(int) TileIndex
findTileMetricsFiles(File, int, boolean) TileMetricsUtil
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
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_GENDER InfiniumVcfFields
FINGERPRINT_GENOTYPES_VCF_FILE GtcToVcf
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
FingerprintMetrics picard.fingerprint
Class for holding metrics on a single fingerprint.
FingerprintMetrics() FingerprintMetrics
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
firstAlignmentIsTooShort(AlignmentInterval, AlignmentInterval, Integer) ContigChimericAlignmentIterativeInterpreter
firstBase(int) SVKmer
firstBase(int) SVKmerLong
firstBase(int) SVKmerShort
firstIntervalFile CompareIntervalLists
FirstOfPairReadFilter() ReadFilterLibrary.FirstOfPairReadFilter
firstPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) TwoPassVariantWalker
firstPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) ExampleTwoPassVariantWalker
firstPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) FilterFuncotations
firstPassApply(VariantContext) ArHetvarFilter
firstPassApply(VariantContext) TwoPassFuncotationFilter
firstPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) CNNScoreVariants
firstPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) FilterVariantTranches
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
FIVE_PRIME_FLANK_SIZE_DEFAULT_VALUE FuncotatorArgumentDefinitions
FIVE_PRIME_FLANK_SIZE_NAME FuncotatorArgumentDefinitions
fivePrimeFlankSize FlankSettings
fivePrimeFlankSize FuncotatorVariantArgumentCollection
FixCallSetSampleOrdering org.broadinstitute.hellbender.tools
FixCallSetSampleOrdering() FixCallSetSampleOrdering
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
FlankSettings org.broadinstitute.hellbender.tools.funcotator
Simple struct container class for the 5'/3' flank settings.
FlankSettings(int, int) FlankSettings
FLAT_BETA BetaDistributionShape
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.
floatToByteArray(float) InfiniumDataFile
Utility method to convert a float to a byte array
floorBlocks HaplotypeCallerArgumentCollection
Output the band lower bound for each GQ block instead of the min GQ -- for better compression
FLOWCELL_BARCODE BamToBfq
FLOWCELL_BARCODE IlluminaBasecallsToFastq
flowCellTileStratifier ReadBaseStratification
Stratifies base into their read's tile which is parsed from the read-name.
FlowCellTileStratifier() ReadBaseStratification.FlowCellTileStratifier
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 ValidationReport
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 PanelMetricsBase
The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to
the mean coverage level in those targets.
FOLD_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(CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics, Collection<CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics>) CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
foldInto(T, Collection<T>) CollectVariantCallingMetrics.VariantCallingSummaryMetrics
FORCE_ACTIVE_REGIONS_LONG_NAME AssemblyRegionWalker
FORCE_B37_TO_HG19_REFERENCE_CONTIG_CONVERSION FuncotatorArgumentDefinitions
FORCE_CALL_ALLELES_LONG_NAME AssemblyBasedCallerArgumentCollection
FORCE_CALL_FILTERED_ALLELES_LONG_NAME AssemblyBasedCallerArgumentCollection
FORCE_CALL_FILTERED_ALLELES_SHORT_NAME AssemblyBasedCallerArgumentCollection
FORCE_GC IlluminaBasecallsToFastq
FORCE_GC IlluminaBasecallsToSam
FORCE_PLATFORM RecalibrationArgumentCollection
forceActive AssemblyRegionWalker
forceCallFiltered AssemblyBasedCallerArgumentCollection
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
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
forEachAbsentAlleleIndex(IntConsumer, int) GenotypeAlleleCounts
Perform an action for every allele index not represented in this genotype.
forEachAlleleIndexAndCount(IntBiConsumer) GenotypeAlleleCounts
forEachRead(MultiplePassReadWalker.GATKReadConsumer) MultiplePassReadWalker
Provides a single traversal over all input reads.
forEachRemaining(Consumer<? super E>) CloseAtEndIterator
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.
formatFloatForVcf(float) GtcToVcf
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
formatMillisecondsTime(long) NioFileCopierWithProgressMeter
formattedPercent(long, long) Utils
Convenience function that formats a percentage as a %.2f string
formattedRatio(long, long) Utils
Convenience function that formats a ratio as a %.2f string
formattedValue(double) StrandOddsRatio
formatTimeRemainingAsTimestamp NioFileCopierWithProgressMeter
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 ValidationReport
FP_COUNT GenotypeConcordanceContingencyMetrics
The FP (false positive) count across all variants
FP_FN GenotypeConcordanceScheme
FP_GENDER CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The sex, as reported for the fingerprinted sample
FP_ONLY GenotypeConcordanceScheme
FP_TN GenotypeConcordanceScheme
FP_TN_FN GenotypeConcordanceScheme
FR ReadEnds
FRACTION PositionBasedDownsampleSam
FRACTION_INFO_FIELD CreateSomaticPanelOfNormals
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
All available evidence coming from a single biological fragment.
Fragment(GATKRead) Fragment
Fragment(Pair<GATKRead, GATKRead>) Fragment
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, Map<String, Byte>) Fragment
FRAGMENT_NUMBER_SEPARATOR_CHR SVFastqUtils
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
FragmentLengthFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
FragmentLengthFilter(double) FragmentLengthFilter
FragmentLengthReadFilter org.broadinstitute.hellbender.engine.filters
Keep only read pairs (0x1) with absolute insert length less than or equal to the specified maximum,
and/or greater than or equal to the specified minimum.
FragmentLengthReadFilter() FragmentLengthReadFilter
FRAGMENTS JumpingLibraryMetrics
The number of fragments in the SAM file
FragmentUtils org.broadinstitute.hellbender.utils.fragments
frameshift_rate_for_coding_indels IndelSummary
freeDistance() SingleBarcodeDistanceMetric
+++lifted from Commons Lang Text +++
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
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
fromMeanAndStdDeviation(double, double) InsertSizeDistributionShape
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
fromReadMetadataFile(String) InsertSizeDistributionShape
fromSerializationFile(String) InsertSizeDistributionShape
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
fromString(String) Sex
Decodes the Sex from a String.
fromTextFile(String) InsertSizeDistributionShape
fScoreBeta M2FiltersArgumentCollection
fullString() ArraysControlInfo
FuncotateSegments org.broadinstitute.hellbender.tools.funcotator
Perform functional annotation on a segment file (tsv).
FuncotateSegments() FuncotateSegments
Funcotation org.broadinstitute.hellbender.tools.funcotator
Abstract class representing a
Funcotator annotation.
FuncotationFilter org.broadinstitute.hellbender.tools.funcotator.filtrationRules
FuncotationMap org.broadinstitute.hellbender.tools.funcotator
A linked map of transcript IDs to funcotations.
FuncotationMetadata org.broadinstitute.hellbender.tools.funcotator.metadata
Represents metadata information for fields in in a Funcotation.
FuncotationMetadataUtils org.broadinstitute.hellbender.tools.funcotator.metadata
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.
FuncotatorConstants org.broadinstitute.hellbender.tools.funcotator
FuncotatorConstants() FuncotatorConstants
FuncotatorDataSourceDownloader org.broadinstitute.hellbender.tools.funcotator
FuncotatorDataSourceDownloader() FuncotatorDataSourceDownloader
FuncotatorEngine org.broadinstitute.hellbender.tools.funcotator
Class that performs functional annotation of variants.
FuncotatorEngine(BaseFuncotatorArgumentCollection, SAMSequenceDictionary, FuncotationMetadata, List<DataSourceFuncotationFactory>) FuncotatorEngine
Create a
FuncotatorEngine using the given
metadata and
funcotationFactories representing
the kinds of
Funcotations to be created and the data sources from which they should be created,
respectively.
FuncotatorSegmentArgumentCollection org.broadinstitute.hellbender.tools.funcotator
FuncotatorSegmentArgumentCollection() FuncotatorSegmentArgumentCollection
FuncotatorUtils org.broadinstitute.hellbender.tools.funcotator
FuncotatorUtils.Genus org.broadinstitute.hellbender.tools.funcotator
A type to keep track of different specific genuses.
FuncotatorUtils.TranscriptCodingSequenceException org.broadinstitute.hellbender.tools.funcotator
Class representing exceptions that arise when trying to create a coding sequence for a variant:
FuncotatorVariantArgumentCollection org.broadinstitute.hellbender.tools.funcotator
FuncotatorVariantArgumentCollection() FuncotatorVariantArgumentCollection
FunctionalClass org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
Stratifies by nonsense, missense, silent, and all annotations in the input ROD, from the INFO field annotation.
FunctionalClass() FunctionalClass
FunctionalClass.FunctionalType org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
fvalue(int) EvidenceFeatures
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
GAP_CHARACTER AlignmentUtils
gapLen(SVInterval) SVInterval
GAPPED_ALIGNMENT_BREAK_DEFAULT_SENSITIVITY StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsSparkArgumentCollection
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.
GatherPileupSummaries org.broadinstitute.hellbender.tools.walkers.contamination
GatherPileupSummaries() GatherPileupSummaries
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
GATKPathSpecifier org.broadinstitute.hellbender.engine
GATK tool command line arguments that are input or output resources.
GATKPathSpecifier(String) GATKPathSpecifier
The raw value for this specifier as provided by the user.
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
GATKSparkTool.ReadInputMergingPolicy org.broadinstitute.hellbender.engine.spark
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 CopyNumberAnnotations
GC_CONTENT_KEY GATKVCFConstants
GC_CURVE_STANDARD_DEVIATION_LONG_NAME GermlineDenoisingModelArgumentCollection
GC_DROPOUT PanelMetricsBase
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.
GC_SCORE InfiniumVcfFields
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
gcContentStratifier ReadBaseStratification
A stratifier that uses GC (of the read) to stratify.
GCContentStratifier() ReadBaseStratification.GCContentStratifier
gcpHMM LikelihoodEngineArgumentCollection
GCS_PREFIX BucketUtils
GCS_SCHEME BucketUtils
gcsMaxRetries() GATKConfig
gcsProjectForRequesterPays() 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.
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
GencodeFuncotationBuilder(GencodeFuncotation) GencodeFuncotationBuilder
GencodeFuncotationFactory org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode
GencodeFuncotationFactory(Path, String, String, TranscriptSelectionMode, Set<String>, LinkedHashMap<String, String>, FeatureInput<? extends Feature>, String) GencodeFuncotationFactory
GencodeFuncotationFactory(Path, String, String, TranscriptSelectionMode, Set<String>, LinkedHashMap<String, String>, FeatureInput<? extends Feature>, FlankSettings, String) GencodeFuncotationFactory
GencodeFuncotationFactory(Path, String, String, TranscriptSelectionMode, Set<String>, LinkedHashMap<String, String>, FeatureInput<? extends Feature>, FlankSettings, boolean, String, boolean) 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.
GENDER_CONCORDANCE_PF CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
Whether or not the three sexs agree
GENDER_GTC GtcToVcf
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
GeneListOutputRenderer org.broadinstitute.hellbender.tools.funcotator.genelistoutput
This class can
- only work on segments.
GeneListOutputRenderer(Path, LinkedHashMap<String, String>, LinkedHashMap<String, String>, Set<String>, String) GeneListOutputRenderer
geneName GencodeGtfFeatureBaseData
generateAD(int[], int[]) ReferenceConfidenceVariantContextMerger
Generates a new AD array by adding zeros for missing alleles given the set of indexes of the Genotype's current
alleles from the original AD.
generateAdditionalWriters(List<SAMReadGroupRecord>, FastqWriterFactory) SamToFastq
generateAdditionalWriters(List<SAMReadGroupRecord>, FastqWriterFactory) SamToFastqWithTags
generateAF(double[], int[]) ReferenceConfidenceVariantContextMerger
Generates a new AF (allele fraction) array
generateAnnotationValueVector(VCFHeaderLineCount, List<?>, int[]) ReferenceConfidenceVariantContextMerger
Generates a new annotation value array by adding zeros for missing alleles given the set of indexes of the Genotype's current
alleles from the original annotation value array.
generateCsv(File, Map<String, RecalibrationReport>) 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
generateJunctionTrees() JunctionTreeLinkedDeBruinGraph
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, double, int, Histogram<Integer>, int) CollectRawWgsMetrics
generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, 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, double, int, Histogram<Integer>, int) CollectWgsMetricsWithNonZeroCoverage
generatingAccumulatorsBy(VariantProcessor.AccumulatorGenerator<A, R>) VariantProcessor.Builder
GENES_SUFFIX GencodeFuncotationFactory
Used when generating the genes field name for segment funcotations.
geneStatus GencodeGtfFeatureBaseData
geneType GencodeGtfFeatureBaseData
GENOME_ASSEMBLY CreateSequenceDictionary
GENOME_BUILD_HEADER_NAME IlluminaManifest
GENOME_SIZE PanelMetricsBase
The number of bases in the reference genome used for alignment.
GENOME_TERRITORY 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 IOUtils
Schemes starting with gendb could be GenomicsDB paths
genomicPhase GencodeGtfFeatureBaseData
Frame/phase of this feature.
genomicPosition GencodeGtfFeatureBaseData
Location of this feature on the genome.
GenomicsDBBCFCodec org.broadinstitute.hellbender.engine
GenomicsD uses htslib to generate BCF v2.2 streams that are specially modified for consumption
by GATK.
GenomicsDBBCFCodec() GenomicsDBBCFCodec
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
genomicsDBOptions VariantWalkerBase
GenomicsDBOptions org.broadinstitute.hellbender.tools.genomicsdb
Encapsulates the GenomicsDB-specific options relevant to the FeatureDataSource
GenomicsDBOptions() GenomicsDBOptions
GenomicsDBOptions(Path) GenomicsDBOptions
GenomicsDBOptions(Path, boolean, int) GenomicsDBOptions
GenomicsDBUtils org.broadinstitute.hellbender.tools.genomicsdb
Utility class containing various methods for working with GenomicsDB
Contains code to modify the GenomicsDB import input using the Protobuf API
References:
GenomicsDB Protobuf structs: https://github.com/GenomicsDB/GenomicsDB/blob/master/src/resources/genomicsdb_vid_mapping.proto
Protobuf generated Java code guide:
https://developers.google.com/protocol-buffers/docs/javatutorial#the-protocol-buffer-api
https://developers.google.com/protocol-buffers/docs/reference/java-generated
GenomicsDBUtils() GenomicsDBUtils
genomicStrand GencodeGtfFeatureBaseData
Which strand this feature is on.
genotype InfiniumGTCRecord
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 CalculateFingerprintMetrics
GENOTYPE_LOD_THRESHOLD CheckFingerprint
GENOTYPE_PON_SITES_LONG_NAME M2ArgumentCollection
GENOTYPE_PRIOR_KEY GATKVCFConstants
GENOTYPE_QUALITY_BY_ALLELE_BALANCE GATKVCFConstants
GENOTYPE_QUALITY_BY_ALT_CONFIDENCE 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
genotypeArgs ReblockGVCF
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.
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.
GenotypeFilterSummary org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
Created by bimber on 5/17/2017.
GenotypeFilterSummary() GenotypeFilterSummary
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
GenotypeGVCFsEngine org.broadinstitute.hellbender.tools.walkers
Engine class to allow for other classes to replicate the behavior of GenotypeGVCFs.
GenotypeGVCFsEngine(VariantAnnotatorEngine, GenotypeCalculationArgumentCollection, boolean, VCFHeader) GenotypeGVCFsEngine
Create and initialize a new GenotypeGVCFsEngine given a collection of GenotypeGVCF arguments and a VCF header
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<EVIDENCE, 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
genotypeScore InfiniumGTCRecord
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
GenotypingArraysProgramGroup picard.cmdline.programgroups
Miscellaneous tools, e.g.
GenotypingArraysProgramGroup() GenotypingArraysProgramGroup
GenotypingData A extends htsjdk.variant.variantcontext.Allele> - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
Encapsulates the data use to make the genotype calls.
GenotypingData(PloidyModel, AlleleLikelihoods<GATKRead, A>) 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, boolean) GenotypingEngine
Construct a new genotyper engine, on a specific subset of samples.
GenotypingLikelihoods A extends htsjdk.variant.variantcontext.Allele> - Class in org.broadinstitute.hellbender.tools.walkers.genotyper
Genotyping Likelihoods collection.
GERMLINE_ARG_LONG_NAME FuncotatorDataSourceDownloader
GERMLINE_QUAL_KEY 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
GermlineFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
GermlineFilter(List<File>) GermlineFilter
germlineProbability(double, double, double, double, double) GermlineFilter
germlineResource CreateSomaticPanelOfNormals
A resource, such as gnomAD, containing population allele frequencies of common and rare variants.
germlineResource M2ArgumentCollection
A resource, such as gnomAD, containing population allele frequencies of common and rare variants.
get(String) TableFuncotation
get(String) FuncotationMap
Get all funcotations for the given transcript.
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) ArtifactPriorCollection
get(String, Nucleotide, ReadOrientation) DepthOneHistograms
get(int) StratificationManager
get(List<Object>) StratificationManager
get(Object) StratificationManager
get(String) TableFeature
Gets the value associated with the key.
get(String) XsvTableFeature
get(int) XsvTableFeature
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 unit of evidence given a haplotype.
get(Double) Histogram
Return the count of items in the bin corresponding to the provided value
get(int) IntToDoubleFunctionCache
Get the value of the function, expanding the cache as necessary.
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
getAaCalls() InfiniumGTCFile
getAaEndPos() ProteinChangeInfo
getAaStartPos() ProteinChangeInfo
getAbbreviation() ConcordanceState
getAbCalls() InfiniumGTCFile
getAbsoluteAccuracy() UnivariateSolverSpecifications
getAbsolutePathWithGenomicsDBURIScheme(GATKPathSpecifier) IOUtils
Get the GenomicsDB equivalent absolute URL for a given path
getAbsolutePathWithoutFileProtocol(Path) IOUtils
Gets the absolute Path name with the URI marker, handling the special case of the default file system by removing
the file:// prefix.
getAccessionLength(String) PSPathogenReferenceTaxonProperties
getAccessions() PSPathogenReferenceTaxonProperties
getAccumulatedOutput() StreamingPythonScriptExecutor
getAccurateKmerCoverage(int) ReadMetadata
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(BaseVertex, boolean) 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
getAddressAId() IlluminaManifestRecord
getAddressBId() IlluminaManifestRecord
getAffection() Sample
getAFScale() VariantEval
getAfterLastAlignedBaseOffset(GATKRead) ReadUtils
Returns the offset (0-based) after the last base in the record that is aligned against the reference.
getAlignedAlternateAllele() 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(StrandCorrectedReferenceBases, int, Allele, Allele, int, int, Strand, Locatable) 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.
getAllele(int) GenotypingData
getAllele(int) GenotypingLikelihoods
getAllele(int) SubsettedLikelihoodMatrix
getAllele(int) AlleleLikelihoods
Returns the allele given its index.
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.
getAllele1() DiploidGenotype
getAllele1() Snp
getAllele2() DiploidGenotype
getAllele2() Snp
getAlleleA() Build37ExtendedIlluminaManifestRecord
getAlleleAProbeSeq() IlluminaManifestRecord
getAlleleB() Build37ExtendedIlluminaManifestRecord
getAlleleBProbeSeq() IlluminaManifestRecord
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).
getAlleleDepths(GenotypesContext) AS_QualByDepth
getAlleleFrequency() PileupSummary
getAlleleLengthListOfString(String) AnnotationUtils
Handles all the Java and htsjdk parsing shenanigans
getAlleles(String) FuncotationMap
Get all the alleles in all of the funcotations for a given transcript ID.
getAlleles() AlleleSpecificAnnotationData
getAlleles() ReducibleAnnotationData
Note: parent class ReducibleAnnotationData is non-allele specific and stores all values with the no-call allele
getAlleles() Snp
getAllelesConsistentWithGivenAlleles(List<VariantContext>, VariantContext) AssemblyBasedCallerUtils
getAlleleStart() SequenceComparison
getAlleleString() Snp
getAllelesUsedInGenotyping() AFCalculationResult
Get the list of alleles actually used in genotyping, which may be smaller than the actual list of alleles requested
getAllelicCounts() AllelicCountCollector
Get the allelic counts gathered so far.
getAllFamilyName() VariantEval
getAllFeatures() GencodeGtfExonFeature
getAllFeatures() GencodeGtfGeneFeature
getAllFeatures() GencodeGtfTranscriptFeature
getAllFilterLines() GATKVCFHeaderLines
getAllFormatLines() GATKVCFHeaderLines
getAllInfoLines() GATKVCFHeaderLines
getAllIntervals() SVFastqUtils.Mapping
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.
getAllPossibleHeaderNames() Build37ExtendedIlluminaManifest
getAllPossibleHeaderNames() IlluminaManifest
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() ReferenceFileSparkSource
getAllSampleName() VariantEval
getAllSequenceDictionaries() FeatureManager
Returns the sequence dictionaries associated with all feature sources.
getAllSnps() HaplotypeMap
Returns an unmodifiable collection of all SNPs in all Haplotype blocks.
getAllStates() Stratifier
getAllStates() VariantStratifier
getAllTiles() CbclReader
getAllValues() TableFeature
Gets all the values in order.
getAllValues() NestedIntegerArray
getAllVariantHeaders() FeatureManager
This method finds and returns all of the variant headers from the feature sources.
getAlpha() BetaDistributionShape
getAlt(Allele) PerAlleleCollection
getAltAaSeq() ProteinChangeInfo
getAltAllele() GencodeFuncotation
getAltAllele() TableFuncotation
getAltAllele() Funcotation
getAltAllele() SvType
getAltAllele() AltSiteRecord
getAltAlleleOfArtifact() ArtifactState
getAltAlleles() PerAlleleCollection
getAltCount() PileupSummary
getAltCount() Datum
getAltCount() AltSiteRecord
getAltDepth1Resonsibilities(int) LearnReadOrientationModelEngine
getAlternate() BasicValidationResult
getAlternateAllele() SequenceComparison
getAlternateAlleleFraction() AllelicCount
getAlternateSequence(StrandCorrectedReferenceBases, int, Allele, Allele, Strand) FuncotatorUtils
Get the full alternate sequence given a reference coding sequence, and two alleles.
getAltF1R2() AltSiteRecord
getAltForwardCountFromFlattenedContingencyTable(int[]) StrandBiasBySample
getAltFraction() PileupSummary
getAltHaplotypeSequence() NovelAdjacencyAndAltHaplotype
getAltHaplotypeSequence() SimpleNovelAdjacencyAndChimericAlignmentEvidence
getAltHistogramsFromExtractedTar(File) F1R2CountsCollector
getAltNucleotide() AllelicCount
getAltReadCount() AllelicCount
getAltResonsibilities(int) LearnReadOrientationModelEngine
getAltReverseCountFromFlattenedContingencyTable(int[]) StrandBiasBySample
getAltTablesFromExtractedTar(File) F1R2CountsCollector
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
getAnalysis() AnalysisModuleScanner
getAndValidateConfigFileContentsOnPath(Path, boolean) 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
getAnnotationMap() AnnotatedInterval
getAnnotations() AnnotatedInterval
Returns a copy of the annotations as a map.
getAnnotations() AnnotatedIntervalCollection
getAnnotations() AnnotatedIntervalHeader
getAnnotationSource() GencodeGtfFeature
getAnnotationTranscript() GencodeFuncotation
getAnnotationValue(String) AnnotatedInterval
getAnnotationValueOrDefault(String, String) AnnotatedInterval
getAnonymousOptionalFields() GencodeGtfFeature
getApplicableNextEdgesBasedOnJunctionTrees(List<E>, Set<E>, int) JTBestHaplotype
This method is the primary logic of deciding how to traverse junction paths and with what score.
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.
getArguments() Funcotator
getArtifactMode() OrientationSampleTransitionSummary
getArtifactModeComplement() OrientationSampleTransitionSummary
getArtifactProb() Datum
getArtifactProbability() StrandArtifactFilter.EStep
getArtificialReadsBasedOnSATag(SAMFileHeader) SATagBuilder
Returns a list of artificial GATKReads corresponding to the reads described by the SA tag in read.
getAsRealMatrix(LikelihoodMatrix<EVIDENCE, Allele>) SomaticGenotypingEngine
getAssayFormat() IlluminaManifest
getAssayHeaderNames() IlluminaManifest
getAssayHeaderNameToIndex() IlluminaManifest
getAssembledIntervals() SvDiscoveryInputMetaData.SampleSpecificData
getAssembledIntervals() FindBreakpointEvidenceSpark.AssembledEvidenceResults
getAssembly() AlignedAssemblyOrExcuse
getAssemblyId() AlignedAssemblyOrExcuse
getAssemblyRegion() AssemblyRegionWalkerContext
getAssemblyRegionArgumentCollection() AssemblyRegionWalkerSpark
getAssemblyRegionArgumentCollection() ExampleAssemblyRegionWalkerSpark
getAssemblyRegionArgumentCollection() HaplotypeCallerSpark
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.
getAssemblyRegionsFast(JavaSparkContext, JavaRDD<GATKRead>, SAMFileHeader, SAMSequenceDictionary, String, FeatureManager, List<ShardBoundary>, Broadcast<Supplier<AssemblyRegionEvaluator>>, AssemblyRegionReadShardArgumentCollection, AssemblyRegionArgumentCollection, boolean, boolean) FindAssemblyRegionsSpark
Get an RDD of assembly regions for the given reads and intervals using the fast algorithm (looks for
assembly regions in each read shard in parallel).
getAssemblyRegionsStrict(JavaSparkContext, JavaRDD<GATKRead>, SAMFileHeader, SAMSequenceDictionary, String, FeatureManager, List<ShardBoundary>, Broadcast<Supplier<AssemblyRegionEvaluator>>, AssemblyRegionReadShardArgumentCollection, AssemblyRegionArgumentCollection, boolean, boolean) FindAssemblyRegionsSpark
Get an RDD of assembly regions for the given reads and intervals using the strict algorithm (looks for
assembly regions in each contig in parallel).
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
getAsynchronousStreamWriter(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(VariantContext, String) GATKProtectedVariantContextUtils
Composes the double array from a genotype annotation.
getAttributeAsDoubleArray(Genotype, String, Supplier<double[]>, double) GATKProtectedVariantContextUtils
Composes the double array from a genotype annotation.
getAttributeAsDoubleList(VariantContext, String, double) Mutect2Engine
getAttributeAsInt(Genotype, String, int) GATKProtectedVariantContextUtils
Returns an attribute as an integer.
getAttributeAsIntArray(VariantContext, String, Supplier<int[]>, int) GATKProtectedVariantContextUtils
Composes the int array from an INFO annotation.
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
getAttributeAsLong(VariantContext, String, Long) GATKProtectedVariantContextUtils
Get Long attribute from a variant context.
getAttributeAsLongList(VariantContext, String, Long) GATKProtectedVariantContextUtils
Composes the Long List from a variant context.
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
getAttributeAsStringList(VariantContext, String) SVUtils
todo: this should be fixed in a new major version of htsjdk
this exist because for whatever reason,
VC.getAttributeAsStringList() sometimes returns a giant single string, while using
VC.getAttributeAsString() gives back an array.....
getAttributeAsStringStream(VariantContext, String) SVUtils
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.
getAutoCallDate() InfiniumGTCFile
getAutoCallVersion() InfiniumGTCFile
getAvailableTiles() IlluminaDataProviderFactory
Return the list of tiles available for this flowcell and lane.
getAvgReadLen() ReadMetadata
getB37Chr() Build37ExtendedIlluminaManifestRecord
getB37Pos() Build37ExtendedIlluminaManifestRecord
getBadMappings() 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
getBaseCalls() InfiniumGTCFile
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(GATKRead, VariantContext) BaseQuality
getBaseQuality() SAMPileupElement
Get the quality
getBaseQuality(int) GATKRead
getBaseQuality(int) SAMRecordToGATKReadAdapter
getBaseQualityCount() GATKRead
getBaseQualityCount() SAMRecordToGATKReadAdapter
getBaseQualityHistogram() TargetMetricsCollector
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() StrandCorrectedReferenceBases
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
getBasesAndBaseQualitiesAlignedOneToOne(GATKRead) AlignmentUtils
Returns the "IGV View" of all the bases and base qualities in a read aligned to the reference according to the cigar, dropping any bases
that might be in the read but aren't in the reference.
getBasesCoveringRefInterval(int, int, byte[], int, Cigar) 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, ReferenceContext, Strand, int) 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
getBaseString(Strand) StrandCorrectedReferenceBases
getBaseString() StrandCorrectedReferenceBases
getBasicInformation() SvType
getBbCalls() InfiniumGTCFile
getBciFile() BclIndexReader
getBeadSetId() IlluminaManifestRecord
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
getBestAvailableSequenceDictionary() UpdateVCFSequenceDictionary
getBeta() BetaDistributionShape
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
getCachedPath() PathSpecifier
getCacheHits() CachingIndexedFastaSequenceFile
getCacheMisses() CachingIndexedFastaSequenceFile
getCacheSize() CachingIndexedFastaSequenceFile
getCall() CalledCopyRatioSegment
getCall() CalledLegacySegment
getCallableRegion() AssemblyRegionTrimmer.Result
Returns the trimmed variant containing region
getCalledHaplotypes() CalledHaplotypes
Get the set of haplotypes that we actually called (i.e., underlying one of the VCs in getCalls().
getCallIntegerCopyNumberState() IntegerCopyNumberSegment
getCallRate() InfiniumGTCFile
getCalls() CalledHaplotypes
Get the list of calls made at this location
getCanonicalChromosomes(String, SAMSequenceDictionary) SVUtils
Canonical chromosomes are defined, for homo sapiens, as chromosomes 1-22, chromosome X and Y.
getCanonicalChromosomesBroadcast() SvDiscoveryInputMetaData.ReferenceData
getCanonicalPath(File) CopyNumberArgumentValidationUtils
getCanonicalPath(String) CopyNumberArgumentValidationUtils
getCapacity() CircularByteBuffer
Returns the total capacity of the buffer (empty+filled).
getCategory() ArraysControlInfo
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.
getChannel(IntensityChannel) FourChannelIntensityData
getChannels() TensorType
getChecksum() NioFileCopierWithProgressMeterResults
getChecksumAlgorithm() NioFileCopierWithProgressMeterResults
Get the checksum algorithm used to calculate the checksum of the downloaded file.
getChild() Trio
getChildID() Trio
getChildren() PSTreeNode
getChildrenNodes() JunctionTreeLinkedDeBruinGraph.ThreadingNode
getChildrenOf(int) PSTree
getChr() SAMPileupFeature
Deprecated.
getChr() IlluminaManifestRecord
getChrom() Snp
getChromosome() GencodeFuncotation
getChromosomeName() GencodeGtfFeature
getChromosomes() InfiniumNormalizationManifest
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.
getCigarModifiedOffset(PileupElement) ReferenceConfidenceModel
Calculate the index of the current pileup position against the reference-aligned read
This offset should be representative of the "IGV view" for the read where insertions are collapsed and deletions
are padded so that we can easily count the mismatches against the reference
getCigarOperator() 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.
getClosestExonIndex(int, List<? extends Locatable>) FuncotatorUtils
Get the index of the exon that is closest to the given start position of a variant.
getCloudStorageConfiguration(int, String) 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].
getClusterFile() InfiniumGTCFile
getCnvCallsBroadcast() SvDiscoveryInputMetaData.SampleSpecificData
getCode() AminoAcid
getCode() GenotypeConcordanceStates.CallState
getCode() GenotypeConcordanceStates.TruthState
getCodecForFile(Path) FeatureManager
Utility method that determines the correct codec to use to read Features from the provided file.
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(int, String, String, Strand, Integer, Integer, Integer) FuncotatorUtils
Get the coding sequence change string from the given variant information.
getCodonChange() GencodeFuncotation
getCodonChangeString(SequenceComparison, Locatable) 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
getCommandLineParser(Object) 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.
getCompAFStratifier() VariantEval
getComparator() AbstractLocatableCollection
getComparator(Set<String>) TranscriptSelectionMode
getComparisonOrder() CompOverlap
getComparisonOrder() CountVariants
getComparisonOrder() GenotypeFilterSummary
getComparisonOrder() IndelLengthHistogram
getComparisonOrder() IndelSummary
getComparisonOrder() MendelianViolationEvaluator
getComparisonOrder() MetricsCollection
getComparisonOrder() MultiallelicSummary
getComparisonOrder() PrintMissingComp
getComparisonOrder() ThetaVariantEvaluator
getComparisonOrder() TiTvVariantEvaluator
getComparisonOrder() ValidationReport
getComparisonOrder() VariantAFEvaluator
getComparisonOrder() VariantEvaluator
getComparisonOrder() VariantSummary
getComplement(byte) BaseUtils
getComplication() NovelAdjacencyAndAltHaplotype
getCompressedBlockSize() BaseBclReader.TileData
getComps() VariantEval
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() ReferenceContext
getContig() ReferenceShard
getContig() Shard
getContig() ShardBoundary
getContig() VariantShard
getContig() AlleleFractionSegment
getContig() AllelicCount
getContig() AnnotatedInterval
getContig() CopyRatio
getContig() CopyRatioSegment
getContig() IntegerCopyNumberSegment
getContig() IntervalCopyNumberGenotypingData
getContig() LegacySegment
getContig() LinearCopyRatio
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() ActivityProfileStateRange
getContig() GencodeGtfFeature
getContig() SAMPileupFeature
getContig() TableFeature
getContig() XsvTableFeature
getContig() GenomeLoc
getContig() AlignmentStateMachine
Get the contig of the underlying read
getContig() Fragment
getContig() SAMRecordToGATKReadAdapter
getContig() SimpleInterval
getContig() MinimalVariant
getContig() VariantContextVariantAdapter
getContig() GVCFBlock
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() VariantEval
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(AlleleLikelihoods<GATKRead, Allele>, VariantContext, int) StrandBiasTest
Allocate and fill a 2x2 strand contingency table.
getContingencyTable(AlleleLikelihoods<GATKRead, Allele>, VariantContext, int, Collection<String>) StrandBiasTest
Allocate and fill a 2x2 strand contingency table.
getControl() ArraysControlInfo
getCopyNumber() IntegerCopyNumberState
getCopyNumberPosterior(IntegerCopyNumberState) CopyNumberPosteriorDistribution
Get the probability for a given copy number state
getCopyNumberPosteriorDistribution() IntervalCopyNumberGenotypingData
getCorrectReferenceContext(VariantContext, ReferenceContext) FuncotatorEngine
Gets the correct
ReferenceContext for the
variant being processed based on if the B37->HG19 conversion is required.
getCount(AnalyzeSaturationMutagenesis.ReportType) AnalyzeSaturationMutagenesis.ReportTypeCounts
getCount() SimpleCount
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
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() AnalysisModuleScanner
getData() VariantDataManager
getDataSourceInfoString() OutputRenderer
getDataSourceName() GencodeFuncotation
getDataSourceName() TableFuncotation
getDataSourceName() Funcotation
getDataSourceName() XsvTableFeature
getDataType() GATKReportColumn
getDateFromVcfOtherHeaderLine(VCFHeader, String, SimpleDateFormat) InfiniumVcfFields
getDateManufactured() IlluminaManifest
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
getDecisionEdgesTakenSinceLastJunctionTreeEvidence() JTBestHaplotype
Return an accounting of how many edge decision (where there is a choice) have consecutively been based on the raw graph weights
(as opposed to being based on junction tree evidence).
getDefaultAlleleFrequency() 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.
getDefaultMaxMnpDistance() AssemblyBasedCallerArgumentCollection
getDefaultMaxMnpDistance() HaplotypeCallerArgumentCollection
getDefaultMaxMnpDistance() M2ArgumentCollection
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() CollectAllelicCountsSpark
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() CountReadsSpark
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() RevertSamSpark
getDefaultReadFilters() DiscoverVariantsFromContigAlignmentsSAMSpark
getDefaultReadFilters() CpxVariantReInterpreterSpark
getDefaultReadFilters() SvDiscoverFromLocalAssemblyContigAlignmentsSpark
getDefaultReadFilters() MarkDuplicatesSpark
getDefaultReadFilters() CompareDuplicatesSpark
getDefaultReadFilters() VariantAnnotator
getDefaultReadFilters() BaseRecalibrator
getDefaultReadFilters() GetPileupSummaries
getDefaultReadFilters() HaplotypeCaller
getDefaultReadFilters() Mutect2
getDefaultReadFilters() CheckPileup
getDefaultReadFilters() Pileup
getDefaultReadFilters() CollectF1R2Counts
getDefaultReadFilters() FilterAlignmentArtifacts
getDefaultReadFilters() RevertBaseQualityScores
getDefaultReadFilters() ASEReadCounter
getDefaultReadFilters() SplitNCigarReads
getDefaultReadFilters() UnmarkDuplicates
getDefaultReadFilters() ValidateBasicSomaticShortMutations
getDefaultReadFilters() CNNScoreVariants
getDefaultToolVCFHeaderLines() GATKTool
getDefaultToolVCFHeaderLines() GATKSparkTool
getDefaultToolVCFHeaderLines() SvDiscoveryInputMetaData
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
getDefaultVariantAnnotationGroups() ReblockGVCF
getDefaultVariantAnnotations() GATKTool
Returns the default list of
Annotations that are used for this tool.
getDefaultVariantAnnotations() GATKSparkTool
getDefaultVariantTransformer() FuncotatorEngine
getDefaultVCFHeaderLines(String, String, String, String, String) GATKVariantContextUtils
A method that constructs a mutable set of VCF header lines containing the tool name, version, date and command line,
and return to the requesting tool.
getDelegatee() ProgressReportingDelegatingCodec
getDeletionsKeySet() ReadCovariates
getDeletionsKeySet(int) ReadCovariates
getDenoisedCopyRatios() SVDDenoisedCopyRatioResult
getDensity() TileMetricsOutReader
getDeprecatedRawKeyName() RMSMappingQuality
getDepth(GenotypesContext, AlleleLikelihoods<GATKRead, Allele>) QualByDepth
getDepth() AltSiteRecord
getDepthHistogram() CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
getDepthHistogram() TargetMetricsCollector
getDepths() TargetMetricsCollector.Coverage
Gets the coverage depths as an array of ints.
getDescendentScore() PSPathogenTaxonScore
getDescription() CopyNumberProgramGroup
getDescription() CoverageAnalysisProgramGroup
getDescription() ExampleProgramGroup
getDescription() MetagenomicsProgramGroup
getDescription() MethylationProgramGroup
getDescription() ShortVariantDiscoveryProgramGroup
getDescription() StructuralVariantDiscoveryProgramGroup
getDescription() TestProgramGroup
getDescription() SVFastqUtils.FastqRead
getDescription() BaseQuality
getDescription() FragmentLength
getDescription() MappingQuality
getDescription() PerAlleleAnnotation
getDescription() ReadPosition
getDescription() BaseCallingProgramGroup
getDescription() DiagnosticsAndQCProgramGroup
getDescription() GenotypingArraysProgramGroup
getDescription() IntervalsManipulationProgramGroup
getDescription() OtherProgramGroup
getDescription() ReadDataManipulationProgramGroup
getDescription() ReferenceProgramGroup
getDescription() Testing
getDescription() VariantEvaluationProgramGroup
getDescription() VariantFilteringProgramGroup
getDescription() VariantManipulationProgramGroup
getDescriptions() AlleleFraction
getDescriptions() BaseQualityHistogram
getDescriptions() ChromosomeCounts
getDescriptions() CountNs
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() OrientationBiasReadCounts
getDescriptions() OriginalAlignment
getDescriptions() PerAlleleAnnotation
getDescriptions() ReferenceBases
getDescriptions() RMSMappingQuality
getDescriptions() StrandBiasBySample
getDescriptions() UniqueAltReadCount
getDescriptorFileName() IlluminaManifest
getDescriptorLengths() ReadStructure.Substructure
getDest() NioFileCopierWithProgressMeter
getDestination() NioFileCopierWithProgressMeterResults
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
getDisplayMessage() ProcessControllerAckResult
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.
getDistanceBetweenNovelAdjacencies() NovelAdjacencyAndAltHaplotype
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
getDrivingFeatureFile() FuncotateSegments
getDrivingVariantCacheLookAheadBases() VariantWalkerBase
When performing a query on the driving variants input(s), the number of additional bases beyond the end
of the query for which overlapping variants should be pre-fetched and cached.
getDrivingVariantPaths() MultiVariantInputArgumentCollection.DefaultMultiVariantInputArgumentCollection
getDrivingVariantPaths() MultiVariantInputArgumentCollection
getDrivingVariantsFeatureInput() VariantLocusWalker
Returns the feature input for the driving variants file.
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.
getDuplicateCountHist() LibraryIdGenerator
getDuplicatedItems(Collection<T>) Utils
Gets duplicated items in the collection.
getDuplicateMarkingsDiffer() SamComparison
getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator, SAMRecordDuplicateComparator) SimpleMarkDuplicatesWithMateCigar
getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator, SAMRecordDuplicateComparator) UmiAwareMarkDuplicatesWithMateCigar
getDupSeqOrientationsOnCtg() BreakpointComplications.SmallDuplicationBreakpointComplications
getDupSeqRepeatNumOnCtg() BreakpointComplications.SmallDuplicationBreakpointComplications
getDupSeqRepeatNumOnRef() BreakpointComplications.SmallDuplicationBreakpointComplications
getDupSeqRepeatUnitRefSpan() BreakpointComplications.InvertedDuplicationBreakpointComplications
getDupSeqRepeatUnitRefSpan() BreakpointComplications.SmallDuplicationBreakpointComplications
getDx() InfiniumGTCFile
getEdges() Path
Get the edges of this path in order.
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
getEffectiveCounts() LearnReadOrientationModelEngine
getEffectiveCounts(ArtifactState) LearnReadOrientationModelEngine
getEigensampleVectors() HDF5SVDReadCountPanelOfNormals
getEigensampleVectors() SVDReadCountPanelOfNormals
Returns a modifiable copy of an array containing the orthnonormal matrix of eigensample vectors.
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, AlleleLikelihoods<GATKRead, Allele>.BestAllele) LikelihoodRankSumTest
getElementForRead(GATKRead, int) LikelihoodRankSumTest
getElementForRead(GATKRead, int) MappingQualityRankSumTest
getElementForRead(GATKRead, int, AlleleLikelihoods<GATKRead, 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
getEmissionLogOdds() M2ArgumentCollection
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
getEmptyBins(int) F1R2FilterConstants
getEnableAllAnnotations() DefaultGATKVariantAnnotationArgumentCollection
getEnableAllAnnotations() GATKAnnotationArgumentCollection
Returns true if all annotations are enabled; false otherwise.
getEncapsulatedSamRecord() SAMRecordToGATKReadAdapter
getEnd() AbstractConcordanceWalker.TruthVersusEval
getEnd() AlignmentContext
getEnd() AssemblyRegion
getEnd() ReferenceContext
getEnd() Shard
getEnd() ShardBoundary
getEnd() AlleleFractionSegment
getEnd() AllelicCount
getEnd() AnnotatedInterval
getEnd() CopyRatio
getEnd() CopyRatioSegment
getEnd() IntegerCopyNumberSegment
getEnd() IntervalCopyNumberGenotypingData
getEnd() LegacySegment
getEnd() LinearCopyRatio
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() Fragment
getEnd() SAMRecordToGATKReadAdapter
getEnd() SimpleInterval
getEnd() MinimalVariant
getEnd() VariantContextVariantAdapter
getEnd() GVCFBlock
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
getEquivalentFormatHeaderLine(String) GATKVCFHeaderLines
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.
getErrorProbability() ErrorProbabilities
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
getEvalKey() InfoConcordanceRecord
getEvals() VariantEval
getEvaluationClasses() EvaluationContext
Returns a set of VariantEvaluator classes to be used
getEvaluationContexts(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) VariantEval
Given specific eval and comp VCs and the sample name, return an iterable
over all of the applicable state keys.
getEvaluationData() VariantDataManager
getEvaluationInstances() EvaluationContext
Return a list of instances of each VariantEvaluator (see getEvaluationClasses).
getEventMap() Haplotype
getEvidence(int) SubsettedLikelihoodMatrix
getEvidence(int) LikelihoodMatrix
Returns the allele given its index.
getEvidenceCount() JunctionTreeLinkedDeBruinGraph.ThreadingNode
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
getExpClusters() IlluminaManifestRecord
getExpectedChecksum() NioFileCopierWithProgressMeterResults
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
getExtendedManifestVersion() Build37ExtendedIlluminaManifest
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
getExtraGraphFileLines() BaseGraph
getExtraGraphFileLines() JunctionTreeLinkedDeBruinGraph
getF1R2(Genotype) OrientationBiasUtils
getF1R2StateForAlt(Nucleotide) ArtifactState
getF2R1(Genotype) OrientationBiasUtils
getF2R1StateForAlt(Nucleotide) ArtifactState
getFalseDiscoveryRate() FilterStats
getFalseNegativeCount() FilterStats
getFalseNegativeCount() FilterAnalysisRecord
getFalseNegativeRate() FilterStats
getFalseNegatives() ConcordanceSummaryRecord
getFalsePositiveCount() FilterStats
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
getFamilyCalledCount() MendelianViolation
getFamilyID() Sample
getFamilyId() PedFile.PedTrio
getFamilyIDs() SampleDB
Returns a sorted set of the family IDs in all samples
getFamilyLowQualsCount() MendelianViolation
getFamilyNamesForEvaluation() VariantEval
getFamilyNamesForStratification() VariantEval
getFamilyNoCallCount() MendelianViolation
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>, Locatable) 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
getFieldNames(String) FuncotationMap
Get all field names found in the funcotations for the given transcript ID.
getFieldNameToListIndexInProtobufVidMappingObject(GenomicsDBVidMapProto.VidMappingPB) GenomicsDBUtils
In vidMapPB, fields is a list of GenomicsDBVidMapProto.GenomicsDBFieldInfo objects
Each GenomicsDBFieldInfo object contains information about a specific field in the GenomicsDB store
We iterate over the list and create a field name to list index map
getFieldOrDefault(String, String) Funcotation
getFields() AliasProvider
Get the fields that have aliases.
getFields() DelimitedTextFileWithHeaderIterator.Row
getFields() TabbedTextFileWithHeaderParser.Row
getFieldValue(String, String, Allele) FuncotationMap
getFile() AbstractIlluminaPositionFileReader
getFile() TileIndex
getFileExtension() CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
getFileExtension() CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
getFileExtension() CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
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
getFilterName() FuncotationFilter
getFilterName() FilterStats
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) Fingerprint
getFingerprintMetrics(Fingerprint) CalculateFingerprintMetrics
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
getFirstSnp() HaplotypeBlock
Gets the arbitrarily first SNP in the haplotype.
getFirstStart() ReadMetadata.PartitionBounds
getFirstVertex() Path
Get the first vertex in this path
getFlag() Build37ExtendedIlluminaManifestRecord
getFlatPrior(Nucleotide) LearnReadOrientationModelEngine
getFloatIterator(int, File) MMapBackedIteratorFactory
getForceSort() SamAlignmentMerger
getForceSort() SamAlignmentMerger
getFormat() AlleleCount
getFormat() IndelSize
getFormat() VariantStratifier
getFormat() GATKReportColumn
getFormatLine(String) GATKSVVCFHeaderLines
getFormatLine(String) GATKVCFHeaderLines
getFormatLines() GATKSVVCFHeaderLines
getForwardAltCount() StrandArtifactFilter.EStep
getForwardArtifactResponsibility() StrandArtifactFilter.EStep
getForwardBases() ReferenceContext
Get the bases in this context, from the beginning of the interval to the end of the window.
getForwardCount() StrandArtifactFilter.EStep
getForwardStrand() BreakpointEvidence.ReadEvidence
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(ReferenceSequenceFile) AssemblyRegion
See #getActiveRegionReference but using the span including regions not the extended span
getFullReference(ReferenceSequenceFile, int) AssemblyRegion
See #getActiveRegionReference but using the span including regions not the extended span
getFullReferenceWithPadding() AssemblyResultSet
Returns the current full reference with padding.
getFunctionValueAccuracy() UnivariateSolverSpecifications
getG() FourChannelIntensityData
getGA4GHEnd() SimpleInterval
getGA4GHStart() SimpleInterval
getGapExtensionProb() BAQ
getGapOpenProb() BAQ
getGATKConfig() ConfigFactory
Quick way to get the GATK configuration.
getGatkReadJavaRDD(TraversalParameters, ReadsSparkSource, String) GATKSparkTool
getGcContent() GencodeFuncotation
getGcContent() SequenceComparison
getGencodeVersion() FilterFuncotations.Reference
getGender() InfiniumGTCFile
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
getGenomeBuild() IlluminaManifestRecord
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
getGenomicsDBAbsolutePath(GATKPathSpecifier) IOUtils
Gets the absolute Path for a GenomicsDB path
getGenomicsDBFeatureReader(GATKPathSpecifier, File, GenomicsDBOptions) FeatureDataSource
getGenomicsDBOptions() GATKTool
Get the GenomicsDB read settings for the current tool
getGenomicsDBOptions() VariantWalkerBase
getGenomicsDBOptions() GnarlyGenotyper
getGenomicsDBPath(GATKPathSpecifier) IOUtils
If path is prefaced with gendb:// or gendb.CloudURIScheme:// , this method returns an absolute path acceptable
by GenomicsDB by stripping off gendb:// for files or gendb. for Cloud URIs respectively .
getGenomicsDBPath(String) IOUtils
If path is prefaced with gendb:// or gendb.CloudURIScheme:// , this method returns an absolute path acceptable
by GenomicsDB by stripping off gendb:// for files or gendb. for Cloud URIs respectively .
getGenomicStartLocation() GencodeGtfFeature
getGenomicStrand() GencodeGtfFeature
getGenotype(String, InfiniumGTCRecord, IlluminaManifestRecord, Allele, Allele) GtcToVcf
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
getGraph() Path
Get the graph of this path
getGreen() ArraysControlInfo
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() FingerprintChecker
getHeader() HaplotypeMap
getHeader() AbstractAlignmentMerger
getHeaderBroadcast() SvDiscoveryInputMetaData.SampleSpecificData
getHeaderContents() IlluminaManifest
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() VariantLocusWalker
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() RevertSamSpark.FileType
getHelpDoc() TensorType
getHelpDoc() DistanceMetric
getHelpDoc() FilterSamReads.Filter
getHelpDoc() RevertSam.FileType
getHelpDoc() IntervalListScatterMode
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
getHetPercent() InfiniumGTCFile
getHets() GenotypeCounts
getHgGenomeBuild() IlluminaManifestRecord
getHighQualityDepthHistogram() AbstractWgsMetricsCollector
getHistogram(long[], String, String) AbstractWgsMetricsCollector
getHistograms() DepthOneHistograms
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.
getIdentifier() InfiniumDataFile
getIlmnId() IlluminaManifestRecord
getIlmnStrand() IlluminaManifestRecord
getImagingDate() InfiniumGTCFile
getImagingUser() InfiniumGTCFile
getIncompatibleEvaluators() AlleleCount
getIncompatibleEvaluators() Family
getIncompatibleEvaluators() Sample
getIncompatibleEvaluators() VariantStratifier
The way for a stratifier to specify that it's incompatible with specific evaluations.
getIndelAdjustedAlleleChangeStartPosition(VariantContext) FuncotatorUtils
Get the start position of the difference between the reference and alternate alleles in the given VariantContext.
getIndelAdjustedAlleleChangeStartPosition(VariantContext, Allele) FuncotatorUtils
Get the start position of the difference between the reference and alternate alleles in the given VariantContext.
getIndelCounter() GenotypeConcordance
getIndelElement(SamLocusIterator.RecordAndOffset) ReadBaseStratification
getIndelFalsePositiveRate() FalsePositiveRecord
getIndelFalsePositives() FalsePositiveRecord
getIndelLength() Datum
getIndentString(int) CountingReadFilter
getIndentString(int) CountingVariantFilter
getIndex(SVInterval) SVIntervalTree
Find the rank of the specified interval.
getIndex() MarkDuplicatesSparkUtils.IndexPair
getIndex() UnivariateSolverJobDescription
getIndex() IlluminaManifestRecord
getIndexForColumn(String) SimpleXSVWriter
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
getInheritance() MendelianViolation
getInitialGuess() UnivariateSolverJobDescription
getInitialLogOdds() M2ArgumentCollection
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() GATKPathSpecifier
getInputStream() PathSpecifier
getInputStream() PathURI
Get a InputStream for this URI if a provider is for the URI's scheme is available.
getInputStream() ReadEndsForMarkDuplicatesCodec
getInputStream() RepresentativeReadIndexerCodec
getInsertedSequence() SVContext
Returns the inserted sequence.
getInsertedSequenceForwardStrandRep() BreakpointComplications
getInsertionMappings() AssemblyContigWithFineTunedAlignments
getInsertionsKeySet() ReadCovariates
getInsertionsKeySet(int) ReadCovariates
getInstance() RMSMappingQuality
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
getIntegerFromVcfOtherHeaderLine(VCFHeader, String) InfiniumVcfFields
getIntegerIterator(int, File) MMapBackedIteratorFactory
getIntensityOnly() IlluminaManifestRecord
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() LegacySegment
getInterval() LinearCopyRatio
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
getIntervalForFatInsertion() NovelAdjacencyAndAltHaplotype
Return the interval being replaced, anchored 1 bp from left,
i.e.
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.
getJexlExpressions() VariantEval
getJunctionTreeForNode(MultiDeBruijnVertex) JunctionTreeLinkedDeBruinGraph
getKernel() BandPassActivityProfile
Get the kernel of this band pass filter.
getKey() KmerAndInterval
getKey() QNameAndInterval
getKey() KmerAndCount
getKey(List<Object>) StratificationManager
getKey() KV
getKeyForFragment(int, boolean, int, byte) ReadsKey
getKeyForPair(SAMFileHeader, GATKRead, GATKRead, Map<String, Byte>) ReadsKey
getKeyNames() AlleleFraction
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() BaseQualityHistogram
getKeyNames() BaseQualityRankSumTest
getKeyNames() ChromosomeCounts
getKeyNames() ClippingRankSumTest
getKeyNames() CountNs
getKeyNames() Coverage
getKeyNames() DepthPerAlleleBySample
getKeyNames() DepthPerSampleHC
getKeyNames() ExcessHet
getKeyNames() FisherStrand
getKeyNames() GenotypeSummaries
getKeyNames() InbreedingCoeff
getKeyNames() LikelihoodRankSumTest
getKeyNames() MappingQualityRankSumTest
getKeyNames() MappingQualityZero
getKeyNames() OrientationBiasReadCounts
getKeyNames() OriginalAlignment
getKeyNames() PerAlleleAnnotation
getKeyNames() PossibleDeNovo
getKeyNames() QualByDepth
getKeyNames() ReadPosRankSumTest
getKeyNames() ReferenceBases
getKeyNames() RMSMappingQuality
getKeyNames() SampleList
getKeyNames() StrandBiasBySample
getKeyNames() StrandOddsRatio
getKeyNames() TandemRepeat
getKeyNames() UniqueAltReadCount
getKeyNames() VariantAnnotation
Return the keys
getKeys() AnnotationMap
getKeys(List<List<Object>>) StratificationManager
getKeySet(int, EventType) ReadCovariates
Get the keys for all covariates at read position for error model
getKeySet(EventType) ReadCovariates
getKingdomTaxonId() PSPathogenTaxonScore
getKmerAround(int, int) ReferenceContext
Get a kmer around a position in reference without altering the internal state of the object
The position must lie within the window
Returns null when, at the ends of a contig, we cannot expand the window to the requested size
getKmerCount(Kmer) 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
getKmerVertex(Kmer, boolean) AbstractReadThreadingGraph
Get the unique vertex for kmer, or null if not possible.
getKnownCNVsFile() VariantEval
getKnowns() VariantEval
getKnownTypes() SvType
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
getLastEdge() Path
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
getLeft() Pair
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
getLengthForDupTandemExpansion() NovelAdjacencyAndAltHaplotype
the new copies' length + inserted sequence length for simple expansion
for complex expansion: the difference between affected reference region's size and the alt haplotype's length
throws UnsupportedOperationException otherwise
getLengthOf(int) 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
getLibrary(GATKRead, SAMFileHeader) ReadUtils
Returns the library associated with the provided read's read group.
getLibraryForRead(GATKRead, SAMFileHeader, String) MarkDuplicatesSparkUtils
Returns the library associated with the provided read's read group.
getLibraryId(SAMRecord) LibraryIdGenerator
Get the library ID for the given SAM record.
getLibraryId() TransientFieldPhysicalLocation
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
getLine() Build37ExtendedIlluminaManifestRecord
getLine() IlluminaManifestRecord
getLinearCopyRatio() LinearCopyRatio
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.
getLociCount() IlluminaManifest
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
getLog10PosteriorOfAlleleAbsent(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.
getLog2CopyRatioSimplePosteriorSummary() ModeledSegment
getLog2CopyRatioValue() CopyRatio
getLog2CopyRatioValues() CopyRatioCollection
getLog_of_base() MathUtil.LogMath
getLogger() VariantEval
getLogIndelPrior() M2FiltersArgumentCollection
getLogLikelihoodArray() PairHMM
Return the results of the computeLogLikelihoods function
getLogLikelihoods() HaplotypeProbabilities
getLogLikelihoods() HaplotypeProbabilitiesFromContaminatorSequence
getLogPriorOfSomaticVariant(VariantContext, int) SomaticClusteringModel
getLogPriorOfVariantVersusArtifact() SomaticClusteringModel
getLogRDev() InfiniumGTCFile
getLogSnvPrior() M2FiltersArgumentCollection
getLogSomaticPrior(VariantContext, int) Mutect2FilteringEngine
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
getMainSourceFileAsFeatureInput() DataSourceFuncotationFactory
getMajorGenomeBuild() IlluminaManifestRecord
getManifest(Class<?>) RuntimeUtils
getManifestFile() IlluminaManifest
getManifestFileHeaderNames() IlluminaManifest
getManifestFileParser() IlluminaManifest
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() SamComparison
getMappingsMatch() SamComparison
getMappingsMatch() SamComparison
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(ReferenceFileSparkSource, 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
getMatchesOrDefault(Set<Map.Entry<String, String>>, Predicate<Map.Entry<String, String>>, String) FuncotationFilter
Given a set of extracted funcotations, return a Stream of values whose entry matches the supplied predicate
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.
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
getMaxAlternateAlleles() GenomicsDBOptions
getMaxEvaluations() UnivariateSolverJobDescription
getMaximumKmerSize() AssemblyResultSet
Returns the maximum kmerSize available.
getMaximumTrackedValue() IntHistogram
getMaxMedianFragmentSize() ReadMetadata
getMaxMinorAlleleFreq(Set<Map.Entry<String, String>>) AlleleFrequencyExacUtils
Calculate the max MAF across all ExAC sub-populations from the given Funcotations.
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
getMayBeNullGoodMappingToNonCanonicalChromosome() AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings
getMean() InfoConcordanceRecord
getMeanBaseQuality() LibraryStatistics
getMeanBaseQuality() ReadMetadata
getMeanLog2CopyRatio() CopyRatioSegment
getMeanLog2CopyRatio() MultidimensionalSegment
getMeanVector() VariantDataManager
getMedian() LibraryStatistics
getMedianDP() GVCFBlock
Get the median DP observed within this band
If there are an even number of DPs recorded in this band the median is the mean of the two middle values
getMedianPartitionSpan() 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
getMendelianViolationQualThreshold() VariantEval
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.
getMergedReinterpretedCalls() SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants
getMessage(Throwable) UserException
getMessage(int) RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
getMetadata() AbstractRecordCollection
getMetadata() GencodeFuncotation
getMetadata() TableFuncotation
getMetadata() Funcotation
getMetadata() TableReader
getMetadataType() AbstractLocatableCollection
getMetadataType() AbstractSampleLocatableCollection
getMetadataType() AbstractSampleRecordCollection
getMetric() BaseCalculator
Returns the metric generated by the observed loci
getMetric() IndelErrorCalculator
Returns the metric generated by the observed loci
getMetric() OverlappingReadsErrorCalculator
Returns the metric generated by the observed loci
getMetric() SimpleErrorCalculator
Returns the metric generated by the observed loci
getMetricCode() TileMetricsOutReader.IlluminaLaneTileCode
getMetricCode() TileMetricsOutReader.IlluminaTileMetrics
getMetrics(CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) AbstractWgsMetricsCollector
Creates CollectWgsMetrics.WgsMetrics - the object holding the result of CollectWgsMetrics
getMetrics() ExtractIlluminaBarcodes.PerTileBarcodeExtractor
getMetrics() BaseErrorAggregation
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
getMiddleBase(String) F1R2FilterUtils
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
getMinDP() GVCFBlock
Get the min DP observed within this band
getMinEvidenceMapQ() SVReadFilter
getMinEvidenceMatchLength() SVReadFilter
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
getMinPhaseQuality() VariantEval
getMinSingleEndMatchBases() AdapterMarker
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() SamComparison
getMissingRight() SamComparison
getMissingRight() SamComparison
getMitochondrialAminoAcidByCodon(String) FuncotatorUtils
Returns the
AminoAcid corresponding to the given three-letter Mitochondrial
rawCodon.
getMitochondrialAminoAcidByCodon(String, boolean, FuncotatorUtils.Genus) FuncotatorUtils
Returns the
AminoAcid corresponding to the given three-letter Mitochondrial
rawCodon.
getMixingFraction() MixingFraction
getModeledSegments() MultidimensionalModeller
getModuleClass() AnalysisModuleScanner
getMoltenAnnotation() AnalysisModuleScanner
getMoltenField() AnalysisModuleScanner
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
getMultiVariantInputArgumentCollection() MultiVariantWalker
Return an argument collection that provides the driving variants.
getMultiVariantInputArgumentCollection() VariantEval
getName() CopyNumberProgramGroup
getName() CoverageAnalysisProgramGroup
getName() ExampleProgramGroup
getName() MetagenomicsProgramGroup
getName() MethylationProgramGroup
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() AnnotationKey
getName() AminoAcid
getName() DataSourceFuncotationFactory
getName() CosmicFuncotationFactory
getName() GencodeFuncotationFactory
getName() VcfFuncotationFactory
getName() LocatableXsvFuncotationFactory
getName() SimpleKeyXsvFuncotationFactory
getName() PSPathogenReferenceTaxonProperties
getName() PSTreeNode
getName() SvDiscoverFromLocalAssemblyContigAlignmentsSpark.StructuralVariantFilter
getName() SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SVAlignmentLengthFilter
getName() SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SVMappingQualityFilter
getName() SVFastqUtils.FastqRead
getName() MendelianViolationEvaluator
getName() PrintMissingComp
getName() VariantStratifier
getName() TrancheManager.SelectionMetric
getName() GencodeGtfFeature.OptionalField
getName() GATKDocWorkUnit
getName() AdapterPair
getName() IlluminaAdapterPair
getName() Parameter
getName() GATKRead
getName() MarkDuplicatesSparkRecord
getName() SAMRecordToGATKReadAdapter
getName() QualQuantizer.QualInterval
getName() IlluminaManifestRecord
getName() BaseCallingProgramGroup
getName() DiagnosticsAndQCProgramGroup
getName() GenotypingArraysProgramGroup
getName() IntervalsManipulationProgramGroup
getName() OtherProgramGroup
getName() ReadDataManipulationProgramGroup
getName() ReferenceProgramGroup
getName() Testing
getName() VariantEvaluationProgramGroup
getName() VariantFilteringProgramGroup
getName() VariantManipulationProgramGroup
getName() Snp
getName() AdapterPair
getName() IlluminaUtil.IlluminaAdapterPair
getNameForInput(FeatureInput<VariantContext>) VariantEval
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.
getNegativeACKMessage() ProcessControllerAckResult
getNegativeMAD() LibraryStatistics
getNewLineBuilder() SimpleXSVWriter
Builds a new LineBuilder and writes out the previous line if it exists.
getNextKmerVertexForChainExtension(Kmer, boolean, MultiDeBruijnVertex) AbstractReadThreadingGraph
getNextKmerVertexForChainExtension(Kmer, boolean, MultiDeBruijnVertex) JunctionTreeLinkedDeBruinGraph
getNextKmerVertexForChainExtension(Kmer, boolean, MultiDeBruijnVertex) ReadThreadingGraph
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
getNMiddleBases(String, int) ReferenceBases
getNObservations(int) IntHistogram
getNodeIDs() PSTree
getNodes() GraphUtils.Graph
getNoise() ReadData
getNoMatchMetric() ExtractIlluminaBarcodes.PerTileBarcodeExtractor
getNonArtifactStates() ArtifactState
getNonLogValue(double) MathUtil.LogMath
Returns the decimal representation of the provided log values.
getNonOpticalDuplicateCountHist() LibraryIdGenerator
getNonOverlappingAltAlleleBaseString(Allele, Allele, boolean) FuncotatorUtils
Get the string of bases that are different from the given alleles.
getNonSequencingErrorProb() Datum
getNonSomaticProbability() ErrorProbabilities
getNormal() TumorNormalPair
getNovelAdjacencyReferenceLocations() SimpleNovelAdjacencyAndChimericAlignmentEvidence
getNPartitions() ReadMetadata
getnProcessedLoci() VariantEval
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.
getNumAltExamples() ArtifactPrior
getNumAltSupportingReadsInNormal() BasicValidationResult
getNumArtifactMode() OrientationSampleTransitionSummary
getNumArtifactModeFiltered() OrientationSampleTransitionSummary
getNumAssays() IlluminaManifest
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
getNumberOfSamplesForEvaluation() VariantEval
getNumberOfSnps() InfiniumGTCFile
getNumCalls() InfiniumGTCFile
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
getNumExamples() ArtifactPrior
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
getNumIntensityOnly() InfiniumGTCFile
getNumMismatches() RecalDatum
getNumNoCalls() InfiniumGTCFile
getNumNonRefPassingVariants() OrientationSampleTransitionSummary
getNumNotArtifactMode() OrientationSampleTransitionSummary
getNumObservations() RecalDatum
getNumOfTies() MannWhitneyU.RankedData
getNumPoints() AlleleFractionSegment
getNumPoints() CopyRatioSegment
getNumPoints() IntegerCopyNumberSegment
getNumPointsAlleleFraction() ModeledSegment
getNumPointsAlleleFraction() MultidimensionalSegment
getNumPointsCopyRatio() ModeledSegment
getNumPointsCopyRatio() MultidimensionalSegment
getNumProbes() LegacySegment
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
getNumUniqueContexts() ArtifactPriorCollection
getOAContig(GATKRead) AddOriginalAlignmentTags
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.
getOffset() InfiniumFileTOC
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.
getOffsetX() InfiniumTransformation
getOffsetY() InfiniumTransformation
getOps() ReadClipper
Check the list of operations set up for this read.
getOpticalDupesByLibraryId() MarkDuplicatesWithMateCigarIterator
getOpticalDuplicateCountHist() LibraryIdGenerator
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
getOptionalIntegerFromVcfOtherHeaderLine(VCFHeader, String) InfiniumVcfFields
getOptionalValueFromVcfOtherHeaderLine(VCFHeader, String) InfiniumVcfFields
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, ReferenceMultiSparkSource) BreakEndVariantType.InterChromosomeBreakend
getOrderedMates(NovelAdjacencyAndAltHaplotype, ReferenceMultiSparkSource) BreakEndVariantType.IntraChromosomalStrandSwitch33BreakEnd
getOrderedMates(NovelAdjacencyAndAltHaplotype, ReferenceMultiSparkSource) BreakEndVariantType.IntraChromosomalStrandSwitch55BreakEnd
getOrderedMates(NovelAdjacencyAndAltHaplotype, ReferenceMultiSparkSource) BreakEndVariantType.IntraChromosomeRefOrderSwap
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
getOtherOrientation(ReadOrientation) ReadOrientation
getOtherTranscripts() GencodeFuncotation
getOutputCycles() OutputMapping
getOutputDescriptors() OutputMapping
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() GATKPathSpecifier
Open a path for writing regardless of whether it's on GCS, HDFS or local disk.
getOutputStream() PathSpecifier
getOutputStream() PathURI
Get an OutputStream for this URI if a provider is for the URI's scheme.
getOutputStream() ReadEndsForMarkDuplicatesCodec
getOutputStream() RepresentativeReadIndexerCodec
getOutputString() CalledCopyRatioSegment.Call
getOverlapDetector() AbstractLocatableCollection
getOverlapNames() VariantOverlapAnnotator
Get the collection of names of overlap sets ued by this annotator.
getOverlapping(GenomeLoc) GenomeLocSortedSet
Return a list of intervals overlapping loc
getOverlappingEvents(int) EventMap
Returns any events in the map that overlap loc, including spanning deletions and events that start at loc.
getOverlappingExonPositions(Allele, Allele, String, int, int, Strand, List<? extends Locatable>) 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
getOverlappingVariantContext(Locatable, Collection<VariantContext>) GATKVariantContextUtils
Return the rightmost variant context in maybeOverlapping that overlaps curPos
getOverlappingVariants() ReadContextData
getP() MannWhitneyU.Result
getP05Green() InfiniumGTCFile
getP05Red() InfiniumGTCFile
getP10GC() InfiniumGTCFile
getP50GC() InfiniumGTCFile
getP50Green() InfiniumGTCFile
getP50Red() InfiniumGTCFile
getP95Green() InfiniumGTCFile
getP95Red() InfiniumGTCFile
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, TraversalParameters, long, boolean) 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.
getPathToDataFile(String) XsvLocatableTableCodec
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
getPi(ArtifactState) ArtifactPrior
getPi() ArtifactPrior
getPileup(Locatable, Iterable<GATKRead>) GATKProtectedVariantContextUtils
Get the pileup of reads covering a locus.
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.
getPileupsOverReference(SAMFileHeader, SimpleInterval, AlleleLikelihoods<GATKRead, Haplotype>, SampleList) AssemblyBasedCallerUtils
Get a list of pileups that span the entire active region span, in order, one for each position
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
getPloidy() IlluminaManifestRecord
getPloidy() InfiniumGTCFile
getPloidyModel() HaplotypeCallerGenotypingEngine
Returns the ploidy-model used by this genotyping engine.
getPloidyType() InfiniumGTCFile
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.
getPluginDescriptors() VariantEval
getPmtGreen() InfiniumGTCFile
getPmtRed() InfiniumGTCFile
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.
getPopulationLikelihood() MatchResults
getPos() Snp
getPosition() AlignmentContext
getPosition() SVLocation
getPosition() IlluminaManifestRecord
getPositionInfo() CbclData
getPositions() InfiniumNormalizationManifest
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
getPrimaryRawKey() AS_BaseQualityRankSumTest
Get the string that's used to combine data for this annotation
getPrimaryRawKey() AS_MappingQualityRankSumTest
Get the string that's used to combine data for this annotation
getPrimaryRawKey() AS_QualByDepth
getPrimaryRawKey() AS_ReadPosRankSumTest
Get the string that's used to combine data for this annotation
getPrimaryRawKey() AS_RMSMappingQuality
getPrimaryRawKey() AS_StrandBiasTest
getPrimaryRawKey() ReducibleAnnotation
Get the string that's used to combine data for this annotation
getPrimaryRawKey() RMSMappingQuality
getPrintableId() Fingerprint
getPriorProbablities() HaplotypeProbabilities
getProbabilitiesAsArray() ActivityProfile
Get the probabilities of the states as a single linear array of doubles
getProbabilitiesByFilter() ErrorProbabilities
getProbeIntervals() CollectHsMetrics
getProbeIntervals() CollectTargetedMetrics
getProbeIntervals() CollectTargetedPcrMetrics
getProbeSetName() CollectHsMetrics
getProbeSetName() CollectTargetedMetrics
getProbeSetName() CollectTargetedPcrMetrics
getProcess() StreamingPythonScriptExecutor
Get the Process object associated with this executor.
getProcess() ProcessControllerBase
getProcessOutput() StreamingProcessController
Wait for *any* output from the process (to stdout or stderr), by draining the stream(s) until no more
output is available.
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() ReferenceWalker
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.
getProteinChangeInfo() SequenceComparison
getProteinChangePosition(Integer) FuncotatorUtils
Get the Protein change start position (1-based, inclusive) given the aligned position of the coding sequence.
getProtobufVidMappingFromJsonFile(String) GenomicsDBUtils
Parse the vid json and create an in-memory Protobuf structure representing the
information in the JSON file
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
getRawControlXIntensities() InfiniumGTCFile
getRawControlXIntensity(int) InfiniumGTCFile
getRawControlYIntensities() InfiniumGTCFile
getRawControlYIntensity(int) InfiniumGTCFile
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
getRawInputString() PathSpecifier
Return the raw input string provided to the constructor.
getRawInputString() PathURI
Return the raw input string that was provided to the constructor.
getRawIntensities() ReadData
getRawKeyName() ExcessHet
getRawKeyNames() ReducibleAnnotation
Get all the raw key names for this annotation
getRCContext() ArtifactPrior
getRead() ReadWalkerContext
getRead() ReadClipper
The original read.
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(GATKRead, int, boolean) ReadUtils
Returns the read coordinate corresponding to the requested reference coordinate.
getReadCoordinateForReferenceCoordinate(int, Cigar, int, ReadUtils.ClippingTail, boolean) ReadUtils
Returns the read coordinate corresponding to the requested reference coordinate for a given alignmentStart/Cigar combination.
getReadCoordinateForReferenceCoordinateUpToEndOfRead(GATKRead, int, ReadUtils.ClippingTail) ReadUtils
getReadCoordinateForReferenceCoordinateUpToEndOfRead(GATKRead, int, ReadUtils.ClippingTail, boolean) ReadUtils
getReadCount() BreakpointEvidence.TemplateSizeAnomaly
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() BreakpointEvidence.ReadEvidence
getReadGroup() GATKRead
getReadGroup() TransientFieldPhysicalLocation
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
getReadInputMergingPolicy() GATKSparkTool
getReadInputMergingPolicy() MarkDuplicatesSpark
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() Fragment
getReadsContext() IntervalWalkerContext
getReadsContext() VariantWalkerContext
getReadSourceHeaderMap() GATKSparkTool
Returns a map of read input to header.
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
getReadThreadingAssemblerArgumentCollection() AssemblyBasedCallerArgumentCollection
getReadThreadingAssemblerArgumentCollection() HaplotypeCallerArgumentCollection
getReadThreadingAssemblerArgumentCollection() M2ArgumentCollection
getReadThreadingJunctionTrees(boolean) JunctionTreeLinkedDeBruinGraph
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.
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(int) InfiniumGTCFile
getRecord() ReadEndsForMateCigar
getRecordReadName() ReadEndsForMateCigar
getRecords() AbstractRecordCollection
getRecords() AnnotatedIntervalCollection
getRed() ArraysControlInfo
getRef() PerAlleleCollection
getRef() SAMPileupFeature
Returns the reference basse
getRef() GVCFBlock
getRefAaSeq() ProteinChangeInfo
getRefAllele() GencodeFuncotation
getRefAllele() AlleleSpecificAnnotationData
Get the reference allele for this allele-specific data.
getRefAllele() PerAlleleCollection
getRefAllele() Build37ExtendedIlluminaManifestRecord
getRefCount() PileupSummary
getRefCount() AltSiteRecord
getReference() GATKSparkTool
getReference() GenomicsDBOptions
getReference() BasicValidationResult
getReference() ArtificialBAMBuilder
getReferenceAllele() SequenceComparison
getReferenceBases(SimpleInterval) ReferenceFileSparkSource
getReferenceBases(SimpleInterval) ReferenceHadoopSparkSource
getReferenceBases(SimpleInterval) ReferenceMultiSparkSource
Return reference bases for the given interval.
getReferenceBases(SimpleInterval) ReferenceSparkSource
getReferenceBases(SimpleInterval) ReferenceTwoBitSparkSource
Gets the reference bases spanning the requested interval.
getReferenceBases() SequenceComparison
getReferenceBasesRDD(JavaSparkContext, int, ReferenceMultiSparkSource, 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
getReferenceBytes(MultiDeBruijnVertex, MultiDeBruijnVertex, boolean, boolean) JunctionTreeLinkedDeBruinGraph
Walk along the reference path in the graph and pull out the corresponding bases
NOTE: this attempts to generate the longest sequence of refernce bases in the event that fromVertex or toVertex are non-unique
getReferenceContext() AssemblyRegionWalkerContext
getReferenceContext() IntervalWalkerContext
getReferenceContext() LocusWalkerContext
getReferenceContext() ReadWalkerContext
getReferenceContext() VariantWalkerContext
getReferenceContext() GencodeFuncotation
getReferenceContext() AltSiteRecord
getReferenceContext() ArtifactPrior
getReferenceData() SvDiscoveryInputMetaData
getReferenceDictionary() GATKTool
Returns the reference sequence dictionary if there is a reference (hasReference() == true), otherwise null.
getReferenceFasta() FingerprintChecker
getReferenceFile() CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
getReferenceFile() CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
getReferenceFile() OptionalReferenceArgumentCollection
getReferenceFile() ReferenceArgumentCollection
getReferenceFile() RequiredReferenceArgumentCollection
getReferenceFile() CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
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
getReferencePath(MultiDeBruijnVertex, AbstractReadThreadingGraph.TraversalDirection, Optional<MultiSampleEdge>) AbstractReadThreadingGraph
Finds the path in the graph from this vertex to the reference sink, including this vertex
getReferencePath(MultiDeBruijnVertex, AbstractReadThreadingGraph.TraversalDirection, Optional<MultiSampleEdge>) JunctionTreeLinkedDeBruinGraph
Finds the path in the graph from this vertex to the reference sink, including this vertex
getReferenceSequence() SAMRecordAndReference
getReferenceSequence() SAMRecordAndReference
getReferenceSequenceDictionary(SAMSequenceDictionary) ReferenceFileSparkSource
getReferenceSequenceDictionary(SAMSequenceDictionary) ReferenceHadoopSparkSource
getReferenceSequenceDictionary(SAMSequenceDictionary) ReferenceMultiSparkSource
Return a sequence dictionary for the reference.
getReferenceSequenceDictionary(SAMSequenceDictionary) ReferenceSparkSource
getReferenceSequenceDictionary(SAMSequenceDictionary) ReferenceTwoBitSparkSource
getReferenceSequenceDictionary() GATKSparkTool
getReferenceSequenceDictionaryBroadcast() SvDiscoveryInputMetaData.ReferenceData
getReferenceSinkVertex() BaseGraph
getReferenceSinkVertex() JunctionTreeLinkedDeBruinGraph
NOTE: we override the old behavior here to allow for looping/nonunique references to be handled properly
getReferenceSourceVertex() BaseGraph
getReferenceSourceVertex() JunctionTreeLinkedDeBruinGraph
NOTE: we override the old behavior here to allow for looping/nonunique references to be handled properly
getReferenceWindow(SimpleInterval) ReferenceWalker
Determine the window to use when creating the ReferenceContext in apply.
getReferenceWindow(SimpleInterval) ExampleReferenceWalker
getReferenceWindowForRead(GATKRead, int) BAQ
Given a read, get an interval representing the span of reference bases required by BAQ for that read
getReferenceWindowFunction() ReferenceMultiSparkSource
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
getRefF1R2() AltSiteRecord
getRefFrequency() PileupSummary
getRefHistogramsFromExtractedTar(File) F1R2CountsCollector
getRefNucleotide() AllelicCount
getRefReadCount() AllelicCount
getRefResonsibilities(int) LearnReadOrientationModelEngine
getRefs() GenotypeCounts
getRefStrand() IlluminaManifestRecord
getRefToRefArtifacts(Nucleotide) ArtifactState
getRegionForGenotyping() AssemblyResultSet
Returns the current region for genotyping.
getReInterpretMultiSegmentsCalls() SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants
getReInterpretZeroOrOneSegmentCalls() SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants
getRelativeAccuracy() UnivariateSolverSpecifications
getRelativeClass() Resource
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) AlleleCount
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) AlleleFrequency
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) CompFeatureInput
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) Contig
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) CpG
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) Degeneracy
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) EvalFeatureInput
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) Family
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) Filter
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) FilterType
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) FunctionalClass
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) IndelSize
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) IntervalStratification
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) JexlExpression
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) Novelty
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) OneBPIndel
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) Sample
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) SnpEffPositionModifier
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) TandemRepeat
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) VariantStratifier
getRelevantStates(ReferenceContext, ReadsContext, FeatureContext, VariantContext, String, VariantContext, String, String, String) VariantType
getRemainingDuration(long, double) NioFileCopierWithProgressMeter
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
getReserved1() InfiniumTransformation
getReserved2() InfiniumTransformation
getReserved3() InfiniumTransformation
getReserved4() InfiniumTransformation
getReserved5() InfiniumTransformation
getReserved6() InfiniumTransformation
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
getResultState() ActivityProfileState
getResultValue() ActivityProfileState
getRevCompState() ArtifactState
getReverseAltCount() StrandArtifactFilter.EStep
getReverseArtifactResponsibility() StrandArtifactFilter.EStep
getReverseComplement() ArtifactPrior
getReverseComplementOfRecord() AltSiteRecord
Contract: only call this method on an
AltSiteRecord whose reference context is *not* in the
getReverseCount() StrandArtifactFilter.EStep
getReverseOutputFieldNameMap() MafOutputRenderer
No field ordering is preserved in the output of this method.
getReverseValueToListMap(Map<T, List<U>>) Utils
Take a map of a value to a list and reverse it.
getRight() PairedStrandedIntervals
getRight() Pair
getRightClipPoint(byte[]) BaseQualityClipReadTransformer
Returns right clip point or -1 if no clip
getRoot() StratificationManager
getRootNode() JunctionTreeLinkedDeBruinGraph.ThreadingTree
getRow(int) GATKReportTable
Get entire row from the given row index in the table
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.
getRsId() Build37ExtendedIlluminaManifestRecord
getRunFile(File, Pattern) ParameterizedFileUtil
getRunning() ProcessControllerBase
getRunningMetric(int) TrancheManager.SelectionMetric
getRunningMetric(int) TrancheManager.TruthSensitivityMetric
getSamFileHeader() AnnotatedIntervalCollection
Can return null
getSamFileHeader() AnnotatedIntervalHeader
Can be null
getSamFileHeader() CollectWgsMetrics
This method should only be called after this.getSamReader() is called.
getSAMFlagsForRead(GATKRead) ReadUtils
Construct a set of SAM bitwise flags from a GATKRead
getSample() OrientationSampleTransitionSummary
getSample() ContaminationRecord
getSample(int) GenotypingData
getSample(int) GenotypingLikelihoods
getSample(int) HeterogeneousPloidyModel
getSample(int) HomogeneousPloidyModel
getSample() ArtifactPriorCollection
getSample() MixingFraction
getSample(int) AlleleLikelihoods
Returns sample name given its index.
getSample(int) IndexedSampleList
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
getSampleDB() VariantEval
getSampleId() SvDiscoveryInputMetaData.SampleSpecificData
getSampleId(SAMFileHeader) SVUtils
getSampleLikelihood() MatchResults
getSampleName() SampleLocatableMetadata
getSampleName() SampleMetadata
getSampleName() SimpleSampleLocatableMetadata
getSampleName() SimpleSampleMetadata
getSampleName() CoveragePerContig
getSampleName() LegacySegment
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.
getSampleName() InfiniumGTCFile
getSampleNamesForEvaluation() VariantEval
getSampleNamesForStratification() VariantEval
getSamplePlate() InfiniumGTCFile
getSamplePloidy() VariantEval
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
getSampleWell() InfiniumGTCFile
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
getSamRecordComparator(SAMFileHeader.SortOrder) SVUtils
Given sortOrder, provide appropriate comparator.
getSamRecordIndex() ReadEndsForMateCigar
A number of convenience functions
getSAMString() GATKRead
Get a string representation of this read in SAM string format, terminated with '\n'.
getSAMString() SAMRecordToGATKReadAdapter
getSAtagForGoodMappingToNonCanonicalChromosome() AssemblyContigWithFineTunedAlignments
getScaleX() InfiniumTransformation
getScaleY() InfiniumTransformation
getScannerName() InfiniumGTCFile
getScannerVersion() InfiniumGTCFile
getScheme() PathURI
Return the scheme for this PathURI.
getScheme(boolean) GenotypeConcordanceSchemeFactory
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.
getSecondaryRawKeys() AS_BaseQualityRankSumTest
Get additional raw key strings that are not the primary key
getSecondaryRawKeys() AS_MappingQualityRankSumTest
Get additional raw key strings that are not the primary key
getSecondaryRawKeys() AS_QualByDepth
getSecondaryRawKeys() AS_ReadPosRankSumTest
Get additional raw key strings that are not the primary key
getSecondaryRawKeys() AS_RMSMappingQuality
Get additional raw key strings that are not the primary key
getSecondaryRawKeys() AS_StrandBiasTest
Get additional raw key strings that are not the primary key
getSecondaryRawKeys() ReducibleAnnotation
Get additional raw key strings that are not the primary key
getSecondaryRawKeys() RMSMappingQuality
Get additional raw key strings that are not the primary key
getSecondaryVariantClassification() GencodeFuncotation
getSecondOfPair(int) HitsForInsert
getSecondsInAssembly() AlignedAssemblyOrExcuse
getSegment() MinorAlleleFractionRecord
getSegmentEndExonOverlap() SegmentExonOverlaps
getSegmentMean() LegacySegment
getSegmentStartExonOverlap() SegmentExonOverlaps
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.
getSentrixBarcode() InfiniumGTCFile
getSeqGraph() AssemblyResult
getSequence() BaseVertex
Get the sequence of bases contained in this vertex
Do not modify these bytes in any way!
getSequence(String) CachingIndexedFastaSequenceFile
Retrieves the complete sequence described by this contig.
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() CachingIndexedFastaSequenceFile
Returns the sequence dictionary associated with this reference file
getSequenceDictionary() GenomeLocParser
Return the master sequence dictionary used within this GenomeLocParser
getSequenceDictionaryForDrivingVariants() MultiVariantWalker
getSequenceDictionaryForDrivingVariants() VariantLocusWalker
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
getSexConcordance(String, String, String) CollectArraysVariantCallingMetrics
getShardBoundary() ShardBoundaryShard
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.
getShear() InfiniumTransformation
getSigma() BandPassActivityProfile
Get the Gaussian kernel sigma value
getSimpleName() VariantEvaluator
getSingleBarcodeDistanceQuery(int, int) BarcodeEditDistanceQuery
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
NOTE: We return a LinkedHashSet here in order to preserve the determinism in the output order of VertexSet(),
which is deterministic in output due to the underlying sets all being LinkedHashSets.
getSize() NioFileCopierWithProgressMeterResults
getSize() GVCFBlock
getSizeOf() ReadEndsForMarkDuplicates
getSizeOf() ReadEndsForMarkDuplicatesWithBarcodes
getSizeOnRead() AlignmentInterval
getSkipNLoci() ArtificialBAMBuilder
getSnp() IlluminaManifestRecord
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.
getSnpManifest() InfiniumGTCFile
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, ...].
getSomaticClusteringModel() Mutect2FilteringEngine
getSortedSampleSet(Map<String, VCFHeader>, GATKVariantContextUtils.GenotypeMergeType) VcfUtils
getSource() ChannelAsSeekableStream
getSource() NioFileCopierWithProgressMeter
getSource() NioFileCopierWithProgressMeterResults
getSource() TableReader
Returns the reader source name.
getSource() IlluminaManifestRecord
getSource() Fingerprint
getSourceContig() AssemblyContigWithFineTunedAlignments
getSources() BaseGraph
Get the set of source vertices of this graph
NOTE: We return a LinkedHashSet here in order to preserve the determinism in the output order of VertexSet(),
which is deterministic in output due to the underlying sets all being LinkedHashSets.
getSourceSeq() IlluminaManifestRecord
getSourceStrand() IlluminaManifestRecord
getSourceVersion() IlluminaManifestRecord
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.
getSpanningIntervals(List<? extends Locatable>, SAMSequenceDictionary) IntervalUtils
Get a single interval per contig that includes all of the specified intervals
(This is used to improve GenomicsDB performance for exomes)
getSpanningIterator(Iterator<Tuple2<K, V>>) SparkUtils
An iterator that groups values having the same key into iterable collections.
getSparkContext(String, Map<String, String>, String) SparkContextFactory
Get a JavaSparkContext.
getSparkMaster() SparkCommandLineArgumentCollection
getSparkProperties() SparkCommandLineArgumentCollection
getSparkVerbosity(Log.LogLevel) SparkCommandLineArgumentCollection
Returns the Spark log level for the argument set.
getSpecies() IlluminaManifestRecord
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() VariantLocusWalker
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() ReferenceContext
getStart() Shard
getStart() ShardBoundary
getStart() AlleleFractionSegment
getStart() AllelicCount
getStart() AnnotatedInterval
getStart() CopyRatio
getStart() CopyRatioSegment
getStart() IntegerCopyNumberSegment
getStart() IntervalCopyNumberGenotypingData
getStart() LegacySegment
getStart() LinearCopyRatio
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() Fragment
getStart() SAMRecordToGATKReadAdapter
getStart() SimpleInterval
Gets the 1-based start position of the interval on the contig.
getStart() MinimalVariant
getStart() VariantContextVariantAdapter
getStart() GVCFBlock
getStartCodon() GencodeGtfExonFeature
getStartColumn() XsvLocatableTableCodec
getStartColumnName() AnnotatedIntervalHeader
getStartingVC() GVCFBlock
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
getStates() ArtifactState
getStatesForKey(int) StratificationManager
getStatistic() MutectStats
getStatistics() SeekableByteChannelPrefetcher
getStatus() AssemblyResult
getStd() InfoConcordanceRecord
getStderr() ProcessOutput
getStderrSettings() ProcessSettings
getStdinSettings() ProcessSettings
getStdout() ProcessOutput
getStdoutSettings() ProcessSettings
getStop() GenomeLoc
getStopCodon() GencodeGtfExonFeature
getStopLocation() GenomeLoc
getStopPosition() Haplotype
getStrand() SequenceComparison
getStrand() StrandCorrectedAllele
getStrand() StrandCorrectedReferenceBases
getStrand() StrandedInterval
getStrandCorrectedAllele(Allele, Strand) FuncotatorUtils
Get the strand-corrected (reverse complemented) Allele for the given Allele and Strand.
getStrandCounts(Genotype) StrandBiasTest
getStrandCountsFromLikelihoodMap(VariantContext, AlleleLikelihoods<GATKRead, 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
getStratifiers() StratificationManager
getStratsAndStatesForKey(int) StratificationManager
getStratsAndStatesStringForKey(int) StratificationManager
getStreamLocations() InputStreamSettings
getStreamLocations() OutputStreamSettings
getStructuralVariantLength() SVContext
Returns the absolute structural variant length as recorded in the SVLEN annotation.
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.
getSubsetOfVariantContext(VariantContext, String) VariantEvalUtils
Subset a VariantContext to a single sample
getSubsetOfVariantContext(VariantContext, Set<String>) VariantEvalUtils
Subset a VariantContext to a set of samples
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
getSuffix() BaseCalculator
The suffix that pertains to the implementation of aggregation
getSuffix() BaseErrorAggregation
getSuffix() IndelErrorCalculator
The suffix that pertains to the implementation of aggregation
getSuffix() OverlappingReadsErrorCalculator
The suffix that pertains to the implementation of aggregation
getSuffix() ReadBaseStratification.BinnedReadCycleStratifier
getSuffix() ReadBaseStratification.CigarOperatorsInReadStratifier
getSuffix() ReadBaseStratification.CollectionStratifier
getSuffix() ReadBaseStratification.ConsensusStratifier
getSuffix() ReadBaseStratification.FlowCellTileStratifier
getSuffix() ReadBaseStratification.GCContentStratifier
getSuffix() ReadBaseStratification.IndelLengthStratifier
getSuffix() ReadBaseStratification.IndelsInReadStratifier
getSuffix() ReadBaseStratification.LongShortHomopolymerStratifier
getSuffix() ReadBaseStratification.MismatchesInReadStratifier
getSuffix() ReadBaseStratification.NsInReadStratifier
getSuffix() ReadBaseStratification.PairStratifier
getSuffix() ReadBaseStratification.RecordAndOffsetStratifier
getSuffix() SimpleErrorCalculator
The suffix that pertains to the implementation of aggregation
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
getSupportedFuncotationFieldsForSegments() DataSourceFuncotationFactory
getSupportedFuncotationFieldsForSegments() GencodeFuncotationFactory
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
getTableDescription() GATKReportTable
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
getTag() GATKPathSpecifier
getTagAttributes() GATKPathSpecifier
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
getTechnicalArtifactProbability() ErrorProbabilities
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
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
getTheta() InfiniumTransformation
getThreadingGraph() AssemblyResult
getThreadLocal() ProcessController
Returns a thread local ProcessController.
getThreshold() Mutect2FilteringEngine
Maximum probability that a potential variant is not a true somatic mutation.
getThreshold() ThresholdCalculator
getThreshold(double) TrancheManager.SelectionMetric
getThreshold(double) TrancheManager.TruthSensitivityMetric
getThresholdForSelectingAdaptersToKeep() AdapterMarker
getTies() MannWhitneyU.TestStatistic
getTile() TransientFieldPhysicalLocation
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
getToolkitName(Class<?>) RuntimeUtils
getToolkitShortName() CommandLineProgram
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
envirogetnment.
getToolVersion() OutputRenderer
getToPathFailureReason() PathSpecifier
getToPathFailureReason() PathURI
Return a string message describing why this URI cannot be converted to a java.nio.file.Path
(#isPath() returns false).
getTopGenomicSeq() IlluminaManifestRecord
getTotal() TargetMetricsCollector.Coverage
getTotalBaseQuality() ReadMetadata.LibraryRawStatistics
getTotalCount() PileupSummary
getTotalCount() Datum
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.
getTranscriptEndPos() GencodeFuncotation
getTranscriptExonNumber() GencodeFuncotation
getTranscriptFuncotations(FuncotationMap) FilterFuncotationsUtils
Munge a FuncotationMap into a stream of sets of pairs of funcotation name / funcotation value.
getTranscriptId() GencodeGtfFeature
getTranscriptIdWithoutVersionNumber(String) FuncotatorUtils
Removes the transcript ID version number from the given transcript ID (if it exists).
getTranscriptLength() GencodeFuncotation
getTranscriptList() FuncotationMap
Get the list of transcripts, in order.
getTranscriptName() GencodeGtfFeature
getTranscripts() GencodeGtfGeneFeature
getTranscriptStartPos() GencodeFuncotation
getTranscriptStatus() GencodeGtfFeature
getTranscriptStrand() GencodeFuncotation
getTranscriptType() GencodeGtfFeature
getTransformedReadStream(ReadFilter) GATKTool
Returns a stream over the reads, which are:
1.
getTransformedVariantStream(CountingVariantFilter) VariantWalkerBase
Returns a stream over the variants, which are:
1.
getTransformedVariantStream(Spliterator<VariantContext>, VariantTransformer, CountingVariantFilter, VariantTransformer) VariantWalkerBase
Returns a stream over the variants returned by source, which are:
1.
getTransientAttribute(Object) GATKRead
This is used to access a transient attribute store provided by the underlying implementation.
getTransientAttribute(Object) SAMRecordToGATKReadAdapter
This is used to access the transient attribute store in the underlying SAMRecord.
getTraversalIntervals() GATKTool
Returns the list of intervals to iterate, either limited to the user-supplied intervals or the entire reference genome if none were specified.
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() PedigreeAnnotation
Computes the trios from the provided pedigree file
getTrios(boolean) SampleDB
Returns all the trios present in the sample database.
getTrios() SampleDB
Returns all the trios present in the db.
getTrueKey() InfoConcordanceRecord
getTrueNegativeCount() FilterAnalysisRecord
getTruePositives() ConcordanceSummaryRecord
getTrueU() MannWhitneyU.TestStatistic
getTruth() AbstractConcordanceWalker.TruthVersusEval
getTruthHeader() AbstractConcordanceWalker
getTruthIfPresentElseEval() AbstractConcordanceWalker.TruthVersusEval
getTruthSensitivity() Tranche
getTumor() TumorNormalPair
getTumorLogOdds() Datum
getTumorLogOdds(VariantContext) Mutect2FilteringEngine
Get the (Natural) log odds of variants from the log-10 odds in a VariantContext object
getTumorSeqAllele2() GencodeFuncotation
getType() AnnotationKey
getType() DataSourceFuncotationFactory
getType() CosmicFuncotationFactory
getType() GencodeFuncotationFactory
getType() VcfFuncotationFactory
getType() LocatableXsvFuncotationFactory
getType() SimpleKeyXsvFuncotationFactory
getType() EmptyFragment
getType() Fragment
getType() MarkDuplicatesSparkRecord
getType() Pair
getType() Passthrough
getTypeInferredFromSimpleChimera() NovelAdjacencyAndAltHaplotype
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
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() SamComparison
getUnmappedLeft() SamComparison
getUnmappedLeft() SamComparison
getUnmappedRight() SamComparison
getUnmappedRight() SamComparison
getUnpairedReads() PSPairedUnpairedSplitterSpark
getUpdatedGenotypes(VariantContext, Genotype, Genotype, Genotype, ArrayList<Genotype>) FamilyLikelihoods
Applies the trio genotype combination to the given trio.
getUpdateMethod() ParameterizedModel
getUpper() PosteriorSummary
getURI() PathSpecifier
getURI() PathURI
Get a java.net.URI object for this PathURI.
getURIString() PathSpecifier
getURIString() PathURI
Returns the string from which this PathURI was originally created.
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(AnnotationKey<T>) AnnotationMap
getValue(int) EvidenceFeatures
getValue() KmerAndInterval
getValue() QNameAndInterval
getValue() KmerAndCount
getValue() SVIntervalTree.Entry
getValue() MarkDuplicatesSparkUtils.IndexPair
getValue() MutectStats
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
getValueFromVcfOtherHeaderLine(VCFHeader, String) InfiniumVcfFields
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>, Locatable) 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() EvidenceFeatures
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
getVarFamilyCalledCount() MendelianViolation
getVarianceVector() VariantDataManager
getVariant() VariantWalkerContext
getVariantChromosome() SvType
getVariantClassification() GencodeFuncotation
getVariantContexts() EventMap
Get the variant contexts in order of start position in this event map
getVariantContextsFromActiveHaplotypes(int, List<Haplotype>, boolean) AssemblyBasedCallerUtils
Returns the list of events discovered in assembled haplotypes that are active at this location.
getVariantContextsFromGivenAlleles(int, List<VariantContext>, boolean) AssemblyBasedCallerUtils
Returns the list of given alleles active at this location.
getVariantEvaluators() EvaluationContext
Returns a sorted set of VariantEvaluators
getVariantEvalWalker() VariantStratifier
getVariants(JavaSparkContext) VariantWalkerSpark
Loads variants and the corresponding reads, reference and features into a JavaRDD for the intervals specified.
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.
getVariantStart() SvType
getVariantStop() SvType
getVariantType() GencodeFuncotation
getVariantType() ConcordanceSummaryRecord
getVariantType() InfoConcordanceRecord
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
getVerbosity() NioFileCopierWithProgressMeter
getVersion() CommandLineProgram
getVersion() HDF5SVDReadCountPanelOfNormals
getVersion() SVDReadCountPanelOfNormals
Returns the PoN version.
getVersion() DataSourceFuncotationFactory
getVersion() GATKReport
getVersion(Class<?>) RuntimeUtils
getVersion() InfiniumTransformation
getVersion() CommandLineProgram
getVertices() Path
Get the list of vertices in this path in order defined by the edges of the path
getViolationsCount() MendelianViolation
getWalker() VariantEvaluator
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.
getWrapped() UniqueIDWrapper
getWriter(File) ConcordanceSummaryRecord
getWriter(Path) InfoConcordanceRecord
Get a table writer
getX() TransientFieldPhysicalLocation
getX() ClusterData
getX() PhysicalLocation
getX() PhysicalLocationInt
getXCoordinate() CbclData
getY() TransientFieldPhysicalLocation
getY() ClusterData
getY() PhysicalLocation
getY() PhysicalLocationInt
getYCoordinate() CbclData
getZ() MannWhitneyU.Result
getZeroBasedTileNumber() TileIndex.TileIndexRecord
getZeroInitializedEnumMap(Class<T>) SVUtils
getZishScore(int) LibraryStatistics
getZishScore(String, int) ReadMetadata
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
GnarlyGenotyper org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper
Perform "quick and dirty" joint genotyping on one or more samples pre-called with HaplotypeCaller
GnarlyGenotyper() GnarlyGenotyper
GnarlyGenotyperEngine org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper
Guts of the GnarlyGenotyper
GnarlyGenotyperEngine(boolean, int, boolean, boolean) GnarlyGenotyperEngine
gold_standard_matching_rate IndelSummary
goldStandard VariantEval
Some analyses want to count overlap not with dbSNP (which is in general very open) but
actually want to itemize their overlap specifically with a set of gold standard sites
such as HapMap, OMNI, or the gold standard indels.
GOOD_CIGAR ReadFilterLibrary
GoodAndBadMappings(List<AlignmentInterval>) AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings
GoodAndBadMappings(List<AlignmentInterval>, List<AlignmentInterval>, AlignmentInterval) AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings
GoodAndBadMappings(List<AlignmentInterval>, List<AlignmentInterval>) AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings
GoodCigarReadFilter() ReadFilterLibrary.GoodCigarReadFilter
goodNonCanonicalMappingSATag SimpleChimera
GQ_BAND_LONG_NAME HaplotypeCallerArgumentCollection
GQ_BAND_SHORT_NAME HaplotypeCallerArgumentCollection
GQ_MEAN_KEY GATKVCFConstants
GQ_STDEV_KEY GATKVCFConstants
grabCount() KmerAndCount
granularity CreateHadoopBamSplittingIndex
graph KBestHaplotypeFinder
Graph() GraphUtils.Graph
GraphBasedKBestHaplotypeFinder V extends BaseVertex ,E extends BaseEdge > - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
Efficient algorithm to obtain the list of best haplotypes given the
instance.
GraphBasedKBestHaplotypeFinder(BaseGraph<V, E>, Set<V>, Set<V>) GraphBasedKBestHaplotypeFinder
Constructs a new best haplotypes finder.
GraphBasedKBestHaplotypeFinder(BaseGraph<V, E>, V, V) GraphBasedKBestHaplotypeFinder
Constructor for the special case of a single source and sink
GraphBasedKBestHaplotypeFinder(BaseGraph<V, E>) GraphBasedKBestHaplotypeFinder
Constructor for the default case of all sources and sinks
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
GREEN CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
The green intensity value for the control.
groupEvidence(Function<EVIDENCE, U>, Function<List<EVIDENCE>, NEW_EVIDENCE_TYPE>) AlleleLikelihoods
Group evidence into lists of evidence -- for example group by read name to force read pairs to support a single haplotype.
groupIntervalsByContig(List<SimpleInterval>) IntervalUtils
Accepts a sorted List of intervals, and returns a List of Lists of intervals grouped by contig,
one List per contig.
GTA InfiniumVcfFields
GtcToVcf picard.arrays
Class to convert a GTC file and a BPM file to a VCF file.
GtcToVcf() GtcToVcf
GTZ InfiniumVcfFields
GUANINE Nucleotide
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_BLOCK GVCFWriter
GVCF_FILE_EXTENSION IndexFeatureFile
GVCF_INPUT CollectVariantCallingMetrics
GVCF_VALIDATE ValidateVariants
GVCFBlock org.broadinstitute.hellbender.utils.variant.writers
GVCFBlock(VariantContext, int, int) GVCFBlock
GVCFBlockCombiner org.broadinstitute.hellbender.utils.variant.writers
Combines variants into GVCF blocks.
GVCFBlockCombiner(List<Number>, int, boolean) GVCFBlockCombiner
GVCFBlockCombiningIterator org.broadinstitute.hellbender.utils.variant.writers
Turns an iterator of VariantContext into one which combines GVCF blocks.
GVCFBlockCombiningIterator(Iterator<VariantContext>, List<Number>, int) GVCFBlockCombiningIterator
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.
GVCFGQBands M2ArgumentCollection
When Mutect2 is run in reference confidence mode with banding compression enabled (-ERC GVCF), homozygous-reference
sites are compressed into bands of similar tumor LOD (TLOD) that are emitted as a single VCF record.
GVCFGQBands ReblockGVCF
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
Merges blocks based on GQ
GVCFWriter(VariantContextWriter, List<Number>, int, boolean) GVCFWriter
Create a new GVCF writer
Should be a non-empty list of boundaries.
GVCFWriter(VariantContextWriter, List<Number>, int) GVCFWriter
ID VerifyIDIntensityContaminationMetrics
The ID of this entry
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() VariantTransformer
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
identityFunction() Utils
Returns a function that always returns its input argument.
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
IGC InfiniumVcfFields
IGNORE ValidateSamFile
IGNORE_FILTER_STATUS GenotypeConcordance
IGNORE_ITR_ARTIFACTS_LONG_NAME M2ArgumentCollection
IGNORE_LANE_INFO UnifiedArgumentCollection
IGNORE_MISSING_MATES FixMateInformation
IGNORE_READ_GROUPS CheckFingerprint
IGNORE_SAFETY_CHECKS_LONG_NAME GatherVcfsCloud
IGNORE_SEQUENCE CollectMultipleMetrics
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
ignoreAC0Sites() VariantEval
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
ILLUMINA_BUILD InfiniumVcfFields
ILLUMINA_CHR InfiniumVcfFields
ILLUMINA_FLAGGED_BAD_CHR IlluminaManifestRecord
ILLUMINA_ID_HEADER_NAME IlluminaManifest
ILLUMINA_NORMALIZATION_MANIFEST GtcToVcf
ILLUMINA_POS InfiniumVcfFields
ILLUMINA_STRAND InfiniumVcfFields
ILLUMINA_STRAND_HEADER_NAME IlluminaManifest
IlluminaAdapterPair org.broadinstitute.hellbender.utils.illumina
Describes adapters used on each pair of strands
IlluminaAdpcFileWriter picard.arrays.illumina
A class to encompass writing an Illumina adpc.bin file.
IlluminaAdpcFileWriter(File) IlluminaAdpcFileWriter
IlluminaAdpcFileWriter.Record picard.arrays.illumina
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
IlluminaGenotype picard.arrays.illumina
IlluminaLaneMetrics picard.illumina
Embodies characteristics that describe a lane.
IlluminaLaneMetrics() IlluminaLaneMetrics
IlluminaLaneMetricsCollector() CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
IlluminaLaneTileCode(int, int, int) TileMetricsOutReader.IlluminaLaneTileCode
IlluminaManifest picard.arrays.illumina
A class to represent an Illumina Manifest file.
IlluminaManifest(File) IlluminaManifest
IlluminaManifest(File, int) IlluminaManifest
IlluminaManifestRecord picard.arrays.illumina
A class to represent a record (line) from an Illumina Manifest [Assay] entry
IlluminaManifestRecord.IlluminaStrand picard.arrays.illumina
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
IMAGING_DATE CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The date that this sample was imaged
IMAGING_DATE InfiniumVcfFields
IMPRECISE GATKSVVCFConstants
ImpreciseDeletion(EvidenceTargetLink, int, ReadMetadata, ReferenceMultiSparkSource) SimpleSVType.ImpreciseDeletion
ImpreciseVariantDetector org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
ImpreciseVariantDetector() ImpreciseVariantDetector
impreciseVariantEvidenceThreshold StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsSparkArgumentCollection
IMPUTE_ZEROS_LONG_NAME CreateReadCountPanelOfNormals
in ReadEndsForMarkDuplicatesCodec
in RepresentativeReadIndexerCodec
IN_PON_KEY 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
INCLUDE_BARCODE_QUALITY IlluminaBasecallsToSam
INCLUDE_BC_IN_RG_TAG IlluminaBasecallsToSam
INCLUDE_BQ_HISTOGRAM CollectWgsMetrics
INCLUDE_DUPLICATES CollectSequencingArtifactMetrics
INCLUDE_DUPLICATES CollectInsertSizeMetrics
INCLUDE_FILTERED IntervalListTools
INCLUDE_FILTERED VcfToIntervalList
INCLUDE_FILTERED_SHORT_NAME VcfToIntervalList
INCLUDE_INDELS CollectTargetedMetrics
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
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() HaplotypeCallerSpark
includeReadsWithDeletionsInIsActivePileups() HaplotypeCaller
includeReadsWithDeletionsInIsActivePileups() Mutect2
includeRefAllele() BaseQuality
includeRefAllele() FragmentLength
includeRefAllele() MappingQuality
includeRefAllele() PerAlleleAnnotation
includes(Nucleotide) Nucleotide
Checks whether this nucleotide code encloses all possible nucleotides for another code.
includes(byte) Nucleotide
Checks whether this nucleotide code encloses all possible nucleotides for another code.
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
NOTE: We return a LinkedHashSet here in order to preserve the determinism in the output order of VertexSet(),
which is deterministic in output due to the underlying sets all being LinkedHashSets.
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 according to the canonical ordering of PLs.
increment(String, Nucleotide, ReadOrientation, int) DepthOneHistograms
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
INCREMENTAL_WORKSPACE_ARG_LONG_NAME GenomicsDBImport
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_het_to_hom_ratio IndelSummary
INDEL_HETEROZYGOSITY HomoSapiensConstants
Standard heterozygous rate for INDEL variation.
INDEL_INFORMATIVE_BASES_CACHE_ATTRIBUTE_NAME ReferenceConfidenceModel
indel_novelty_rate IndelSummary
INDEL_OUTPUT SplitVcfs
INDEL_START_QUAL Mutect2Engine
INDEL_START_TOLERANCE_LONG_NAME FilterAlignmentArtifacts
indelCounter GenotypeConcordance
IndelDPPerSample VariantSummary
IndelErrorCalculator picard.sam.SamErrorMetric
A calculator that estimates the error rate of the bases it observes for indels only.
IndelErrorCalculator() IndelErrorCalculator
IndelErrorMetric picard.sam.SamErrorMetric
Metric to be used for InDel errors
IndelErrorMetric(String, long, long, long, long, long) IndelErrorMetric
IndelErrorMetric() IndelErrorMetric
indelHeterozygosity GenotypeCalculationArgumentCollection
This argument informs the prior probability of having an indel at a site.
indelHeterozygosity HaplotypeCallerGenotypingEngine
indelLength(VariantContext, int) SomaticClusteringModel
IndelLengthHistogram org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
Simple utility for histogramming indel lengths
Based on code from chartl
IndelLengthHistogram() IndelLengthHistogram
indelLengthStratifier ReadBaseStratification
Stratifies into the number of bases in an insertion
IndelLengthStratifier() ReadBaseStratification.IndelLengthStratifier
indelNoveltyRate MultiallelicSummary
IndelNoveltyRate VariantSummary
indelPadding ReadThreadingAssemblerArgumentCollection
Include at least this many bases around an event for calling it
indelRate CountVariants
indelRatePerBp CountVariants
indelRatio MetricsCollection
indelRatioLociBased MetricsCollection
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.
indelsInReadStratifier ReadBaseStratification
Stratify by Indels in the read cigars.
IndelsInReadStratifier() ReadBaseStratification.IndelsInReadStratifier
IndelSize org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
Stratifies the eval RODs by the indel size
Indel sizes are stratified from sizes -100 to +100.
IndelSize() IndelSize
indelSizeToEliminateInRefModel HaplotypeCallerArgumentCollection
This parameter determines the maximum size of an indel considered as potentially segregating in the
reference model.
IndelSummary org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
IndelSummary() IndelSummary
indelToMatch PairHMMModel
Position in the transition probability array for the Indel-to-Match transition.
INDEPENDENT_MATES_LONG_NAME M2ArgumentCollection
independentMates M2ArgumentCollection
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 an 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) AlleleLikelihoods
Returns the index of an allele within the likelihood collection.
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.
indexOfEvidence(EVIDENCE) SubsettedLikelihoodMatrix
indexOfEvidence(EVIDENCE) LikelihoodMatrix
Queries the index of a unit of evidence in the matrix.
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.
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) AlleleLikelihoods
Returns the index of a sample within the likelihood collection.
indexOfSample(String) IndexedSampleList
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
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
inferSimpleTypeFromNovelAdjacency(NovelAdjacencyAndAltHaplotype, ReferenceMultiSparkSource) ContigChimericAlignmentIterativeInterpreter
InfiniumDataFile picard.arrays.illumina
A class to provide methods for accessing Illumina Infinium Data Files.
InfiniumEGTFile picard.arrays.illumina
A class to parse the contents of an Illumina Infinium cluster (EGT) file
A cluster file contains information about the clustering information used in mapping red / green intensity information
to genotype calls
InfiniumEGTFile(File) InfiniumEGTFile
InfiniumFileTOC picard.arrays.illumina
A class to encapsulate the table of contents for an Illumina Infinium Data Files.
InfiniumFileTOC() InfiniumFileTOC
InfiniumGTCFile picard.arrays.illumina
A class to parse the contents of an Illumina Infinium genotype (GTC) file
A GTC file is the output of Illumina's genotype calling software (either Autocall or Autoconvert) and
contains genotype calls, confidence scores, basecalls and raw intensities for all calls made on the chip.
InfiniumGTCFile(DataInputStream, InfiniumNormalizationManifest) InfiniumGTCFile
Creates an InfiniumGTCFile object and parses the given input stream.
InfiniumGTCRecord picard.arrays.illumina
InfiniumGTCRecord(String) InfiniumGTCRecord
InfiniumNormalizationManifest picard.arrays.illumina
A class to parse the contents of an Illumina Infinium Normalization Manifest file
An Illumina Infinium Normalization Manifest file contains a subset of the information contained in the Illumina
Manifest file in addition to the normalization ID which is needed for normalizating intensities in GtcToVcf
InfiniumNormalizationManifest(File) InfiniumNormalizationManifest
InfiniumTransformation picard.arrays.illumina
InfiniumTransformation() InfiniumTransformation
InfiniumVcfFields picard.arrays.illumina
A class to store fields that are specific to a VCF generated from an Illumina GTC file.
InfiniumVcfFields() InfiniumVcfFields
InfiniumVcfFields.GENOTYPE_VALUES picard.arrays.illumina
INFO FingerprintMetrics
Additional information about the fingerprint
InfoConcordanceReader(Path) InfoConcordanceRecord.InfoConcordanceReader
InfoConcordanceRecord org.broadinstitute.hellbender.tools.walkers.validation
Keeps track of concordance between two info fields.
InfoConcordanceRecord(VariantContext.Type, String, String, double, double) InfoConcordanceRecord
Record keeps track of concordance between values from INFO-field keys of a VCF.
InfoConcordanceRecord.InfoConcordanceReader org.broadinstitute.hellbender.tools.walkers.validation
Table reading class for InfoConcordanceRecords
InfoConcordanceRecord.InfoConcordanceWriter org.broadinstitute.hellbender.tools.walkers.validation
Table writing class for InfoConcordanceRecords
InfoFieldAnnotation org.broadinstitute.hellbender.tools.walkers.annotator
Annotations relevant to the INFO field of the variant file (ie annotations for sites).
InfoFieldAnnotation() InfoFieldAnnotation
INIT_ARD_REL_UNEXPLAINED_VARIANCE_LONG_NAME GermlineDenoisingModelArgumentCollection
INITIAL_MAF_THRESHOLD ContaminationModel
INITIAL_TEMPERATURE_LONG_NAME HybridADVIArgumentCollection
INITIAL_THRESHOLD_LONG_NAME M2FiltersArgumentCollection
INITIAL_TUMOR_LOG_10_ODDS_LONG_NAME M2ArgumentCollection
INITIAL_TUMOR_LOG_10_ODDS_SHORT_NAME M2ArgumentCollection
initialErrorRateForPruning ReadThreadingAssemblerArgumentCollection
Initial base error rate guess for the probabilistic adaptive pruning model.
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(ReadThreadingAssemblerArgumentCollection, SAMSequenceDictionary, boolean) AssemblyRegionTrimmer
Initializes the trimmer.
initialize(ReferenceSequenceFile) OverhangFixingManager.Splice
initialize(VariantEval) MendelianViolationEvaluator
initialize(VariantEval) VariantEvaluator
initialize(VariantEval) VariantSummary
initialize() AlleleCount
initialize() AlleleFrequency
initialize() CompFeatureInput
initialize() Contig
initialize() CpG
initialize() Degeneracy
initialize() EvalFeatureInput
initialize() Family
initialize() Filter
initialize() FilterType
initialize() FunctionalClass
initialize() IndelSize
initialize() IntervalStratification
initialize() JexlExpression
initialize() Novelty
initialize() OneBPIndel
initialize() Sample
initialize() SnpEffPositionModifier
initialize() TandemRepeat
initialize() VariantStratifier
initialize() VariantType
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() PathProvider
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() VariantLocusWalker
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.
initializeDrivingVariants() VariantEval
initializeEvaluationObjects(boolean, List<String>) VariantEvalUtils
Initialize required, standard and user-specified evaluation objects
initializeIntervals() GenomicsDBImport
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().
initializeStratificationObjects(boolean, List<String>) VariantEvalUtils
Initialize required, standard and user-specified stratification objects
initialLogPriorOfVariantVersusArtifact M2FiltersArgumentCollection
initialPosteriorThreshold M2FiltersArgumentCollection
initiateCopy() NioFileCopierWithProgressMeter
initiateScheme() GA4GHScheme
initiateScheme() GA4GHSchemeWithMissingAsHomRef
initiateScheme() GenotypeConcordanceScheme
initStreamWriter(Function<T, ByteArrayOutputStream>) StreamingPythonScriptExecutor
Obtain a stream writer that serializes and writes batches of items of type T on a background thread.
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 CollectJumpingLibraryMetrics
INPUT CollectMultipleMetrics
INPUT CollectOxoGMetrics
INPUT CollectRrbsMetrics
INPUT CollectWgsMetrics
INPUT CollectTargetedMetrics
INPUT CollectIndependentReplicateMetrics
INPUT SinglePassSamProgram
INPUT CollectArraysVariantCallingMetrics
INPUT CreateVerifyIDIntensityContaminationMetricsFile
INPUT GtcToVcf
INPUT BamToBfq
INPUT CalculateFingerprintMetrics
INPUT CheckFingerprint
INPUT ClusterCrosscheckMetrics
INPUT CrosscheckFingerprints
INPUT IdentifyContaminant
INPUT CollectIlluminaBasecallingMetrics
INPUT MarkIlluminaAdapters
INPUT NonNFastaSize
INPUT NormalizeFasta
INPUT AddCommentsToBam
INPUT AddOATag
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 CollectSamErrorMetrics
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 MakeVcfSampleNameMap
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 DetermineGermlineContigPloidy
INPUT_MODEL_INTERVAL_FILE GermlineCNVCaller
INPUT_SAMPLE_FILE_MAP CrosscheckFingerprints
INPUT_SAMPLE_MAP CrosscheckFingerprints
INPUT_SHORT_NAME StandardArgumentDefinitions
INPUT_SHORT_NAME StandardOptionDefinitions
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(String, int, int, String, Allele, Allele, int, Map<String, Object>) SimpleSVType.Insertion
Insertion(NovelAdjacencyAndAltHaplotype, ReferenceMultiSparkSource) SimpleSVType.Insertion
insertion_to_deletion_ratio IndelSummary
insertion_to_deletion_ratio_for_large_indels IndelSummary
insertionDeletionRatio CountVariants
insertionMappings SimpleChimera
INSERTIONS_DEFAULT_QUALITY RecalibrationArgumentCollection
A default base qualities to use as a prior (reported quality) in the insertion covariate model.
INSERTIONS_Q IndelErrorMetric
The (phred) rate of insertions.
insertionsInReadStratifier ReadBaseStratification
Stratify by Insertions in the read cigars.
insertionToInsertion PairHMMModel
Position in the transition probability array for the Insertion-to-Insertion transition.
insertLengthStratifier ReadBaseStratification
Stratifies into the read-pairs estimated insert-length, as long as it isn't larger than 10x the length of the read
InsertSizeDistribution org.broadinstitute.hellbender.tools.spark.sv
Holds the information characterizing and insert size distribution.
InsertSizeDistribution(String) InsertSizeDistribution
InsertSizeDistributionShape org.broadinstitute.hellbender.tools.spark.sv
Supported insert size distributions shapes.
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, 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.TransientFieldPhysicalLocationComparator
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(DoubleUnaryOperator, double, double, int) IntegrationUtils
integrate2d(ToDoubleBiFunction<Double, Double>, double, double, int, double, double, int) IntegrationUtils
IntegrationUtils org.broadinstitute.hellbender.utils
Created by tsato on 5/1/17.
IntegrationUtils() IntegrationUtils
INTENSITY_ONLY_HEADER_NAME IlluminaManifest
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.
InterChromosomeBreakend(String, int, String, Allele, Allele, Map<String, Object>, boolean) BreakEndVariantType.InterChromosomeBreakend
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(Nucleotide) Nucleotide
Returns the nucleotide code that include all and only the nucleotides that are
included by this another code.
intersect(byte, byte) Nucleotide
Checks whether two nucleotides intersect given their byte encodings.
intersect(Locatable) SimpleInterval
Returns the intersection of the two intervals.
INTERSECT_INTERVALS GenotypeConcordance
interval ShardBoundary
INTERVAL_CONTIG_NAMES_SUB_PATH HDF5Utils
INTERVAL_EXCLUSION_PADDING_LONG_NAME IntervalArgumentCollection
INTERVAL_FILE_EXTENSION_FULL_NAME SplitIntervals
INTERVAL_FILE_EXTENSIONS IntervalUtils
Recognized extensions for interval files
INTERVAL_GC_CONTENT_KEY GATKVCFConstants
INTERVAL_ITERATOR CollectSamErrorMetrics
INTERVAL_LIST ExtractSequences
INTERVAL_LIST AddOATag
INTERVAL_LIST FilterSamReads
INTERVAL_LIST ViewSam
INTERVAL_LIST_FILE_NAME GermlineCNVNamingConstants
INTERVAL_LIST_LONG_NAME GenomicsDBImport
INTERVAL_LIST_SIZE_WARNING_THRESHOLD GenomicsDBImport
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 DetermineGermlineContigPloidy
intervalArgumentCollection FilterIntervals
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
IntervalListScatter picard.util.IntervalList
IntervalListScatter(IntervalListScatterer, IntervalList, int) IntervalListScatter
IntervalListScatterer picard.util.IntervalList
An interface for a class that scatters IntervalLists.
IntervalListScattererByBaseCount picard.util.IntervalList
a Baseclass for scatterers that scatter by uniqued base count.
IntervalListScattererByBaseCount() IntervalListScattererByBaseCount
IntervalListScattererByIntervalCount picard.util.IntervalList
Scatters IntervalList by interval count so that resulting IntervalList's have the same number of intervals in them.
IntervalListScattererByIntervalCount() IntervalListScattererByIntervalCount
IntervalListScattererWithoutSubdivision picard.util.IntervalList
A BaseCount Scatterer that avoid breaking-up intervals.
IntervalListScattererWithoutSubdivision() IntervalListScattererWithoutSubdivision
IntervalListScattererWithoutSubdivisionWithOverflow picard.util.IntervalList
IntervalListScattererWithoutSubdivisionWithOverflow() IntervalListScattererWithoutSubdivisionWithOverflow
IntervalListScattererWithSubdivision picard.util.IntervalList
An IntervalListScatterer that attempts to place the same number of (uniquified) bases in each output interval list.
IntervalListScattererWithSubdivision() IntervalListScattererWithSubdivision
IntervalListScatterMode picard.util.IntervalList
An enum to control the creation of the various IntervalListScatter objects
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
IntervalOverlapReadFilter org.broadinstitute.hellbender.engine.filters
A simple read filter that allows for the user to specify intervals at the filtering stage.
IntervalOverlapReadFilter() IntervalOverlapReadFilter
Default constructor.
IntervalOverlapReadFilter(List<String>) IntervalOverlapReadFilter
Constructor with provided 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 WgsMetrics
The intervals over which this metric was computed.
INTERVALS NonNFastaSize
INTERVALS MergeSamFiles
INTERVALS CollectSamErrorMetrics
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
intervalsFile VariantEval
File containing tribble-readable features for the IntervalStratificiation
intervalSize(List<GenomeLoc>) IntervalUtils
IntervalsManipulationProgramGroup picard.cmdline.programgroups
Tools that process genomic intervals in various formats.
IntervalsManipulationProgramGroup() IntervalsManipulationProgramGroup
intervalsSpecified() IntervalArgumentCollection
Have any intervals been specified for inclusion or exclusion
IntervalStratification org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
Stratifies the variants by whether they overlap an interval in the set provided on the command line.
IntervalStratification() IntervalStratification
intervalStrings OptionalIntervalArgumentCollection
intervalStrings RequiredIntervalArgumentCollection
intervalStrings IntervalOverlapReadFilter
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
intervalWeight(Interval) IntervalListScatterer
A method that defines the "weight" of an interval list for the purpose of scattering.
intervalWeight(Interval) IntervalListScattererByBaseCount
intervalWeight(Interval) IntervalListScattererByIntervalCount
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
IntraChromosomalStrandSwitch33BreakEnd(String, int, String, Allele, Allele, Map<String, Object>, boolean) BreakEndVariantType.IntraChromosomalStrandSwitch33BreakEnd
IntraChromosomalStrandSwitch55BreakEnd(String, int, String, Allele, Allele, Map<String, Object>, boolean) BreakEndVariantType.IntraChromosomalStrandSwitch55BreakEnd
IntraChromosomeRefOrderSwap(String, int, String, Allele, Allele, Map<String, Object>, boolean) BreakEndVariantType.IntraChromosomeRefOrderSwap
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.
IntToDoubleFunctionCache org.broadinstitute.hellbender.utils
A helper class to maintain a cache of an int to double function defined on n = 0, 1, 2.
IntToDoubleFunctionCache() IntToDoubleFunctionCache
INV33 GATKSVVCFConstants
INV55 GATKSVVCFConstants
INV_LOG_2 MathUtils
INV_LOG_2 ParamUtils
INVALID Nucleotide
INVALID_ELEMENT_FROM_READ RankSumTest
INVALID_TABLE_NAME_REGEX GATKReportTable
REGEX that matches any table with an invalid name
INVALIDATE_PREVIOUS_FILTERS_LONG_NAME StandardArgumentDefinitions
inverseRate(long, long) VariantEvaluator
Inversion(String, int, int, String, Allele, Allele, int, Map<String, Object>) SimpleSVType.Inversion
Inversion(NovelAdjacencyAndAltHaplotype, int, ReferenceMultiSparkSource) SimpleSVType.Inversion
INVERT IntervalListTools
INVERT_GT_LONG_NAME VariantFiltration
INVERT_LONG_NAME VariantFiltration
INVERT_SOFT_CLIP_RATIO_FILTER ReadFilterArgumentDefinitions
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_HOST_ALIGNED_LONG_NAME PSFilterArgumentCollection
IS_HOST_ALIGNED_SHORT_NAME PSFilterArgumentCollection
IS_NOVASEQ CollectIlluminaLaneMetrics
IS_ORIENTATION_BIAS_ARTIFACT_MODE OrientationBiasFilterConstants
IS_ORIENTATION_BIAS_CUT OrientationBiasFilterConstants
IS_ORIENTATION_BIAS_RC_ARTIFACT_MODE OrientationBiasFilterConstants
IS_SINGLETON_KEY VariantEval
IS_ZCALLED CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
Whether the sample was zcalled
isAbleToValidateGenotype(Genotype, Allele) BasicSomaticShortMutationValidator
isAbove(NioFileCopierWithProgressMeter.Verbosity) NioFileCopierWithProgressMeter.Verbosity
isAcceptableFeatureType(Class<? extends Feature>) FeatureWalker
Returns whether the given class of features is acceptable for this walker.
isAcceptableFeatureType(Class<? extends Feature>) ExampleFeatureWalker
isAcceptableFeatureType(Class<? extends Feature>) FuncotateSegments
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() ReadlessAssemblyRegion
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
isAdapter(SAMRecord) AdapterUtility
Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns
true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
isAdapterSequence(byte[], boolean) AdapterUtility
Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns
true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
isAdapterSequence(byte[]) 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?
isAlleleSpecific(InfoFieldAnnotation) AnnotationUtils
Helper function to determine if an annotation is allele-specific
isAllRegularBases(byte[]) BaseUtils
isAltAfterAssembly(PileupElement, byte) ReferenceConfidenceModel
isAltBeforeAssembly(PileupElement, byte) ReferenceConfidenceModel
isAmbiguous() Nucleotide
Checks whether the nucleotide refer to an ambiguous base.
isAmbiguous() IlluminaManifestRecord
isAntiTraining TrainingSet
isAppendFile() OutputStreamSettings
isArtifact(VariantContext, Mutect2FilteringEngine) BaseQualityFilter
isArtifact(VariantContext, Mutect2FilteringEngine) ChimericOriginalAlignmentFilter
isArtifact(VariantContext, Mutect2FilteringEngine) ClusteredEventsFilter
isArtifact(VariantContext, Mutect2FilteringEngine) DuplicatedAltReadFilter
isArtifact(VariantContext, Mutect2FilteringEngine) FragmentLengthFilter
isArtifact(VariantContext, Mutect2FilteringEngine) HardFilter
isArtifact(VariantContext, Mutect2FilteringEngine) MappingQualityFilter
isArtifact(VariantContext, Mutect2FilteringEngine) MinAlleleFractionFilter
isArtifact(VariantContext, Mutect2FilteringEngine) MultiallelicFilter
isArtifact(VariantContext, Mutect2FilteringEngine) NRatioFilter
isArtifact(VariantContext, Mutect2FilteringEngine) PanelOfNormalsFilter
isArtifact(VariantContext, Mutect2FilteringEngine) PolymorphicNuMTFilter
isArtifact(VariantContext, Mutect2FilteringEngine) ReadPositionFilter
isArtifact(VariantContext, Mutect2FilteringEngine) StrictStrandBiasFilter
isAvailable PathProvider
isBad() Build37ExtendedIlluminaManifestRecord
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
isBufferTruncated() CapturedStreamOutput
isBufferTruncated() StreamOutput
Returns true if the buffer was truncated.
isCandidateForFatInsertion() NovelAdjacencyAndAltHaplotype
For replacement, one could have a case where the sequence being replaced (i.e.
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(GATKPathSpecifier) BucketUtils
Return true if this GATKPathSpecifier represents a gcs URI.
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() ReferenceMultiSparkSource
Returns whether this reference source can be used with Spark broadcast.
isCompatibleWithSparkBroadcast() ReferenceSparkSource
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.
isConsensus TrainingSet
isContaminant(HitsForInsert) AbstractAlignmentMerger
isContaminant(HitsForInsert) SamAlignmentMerger
Criteria for contaminant reads:
1.
isContiguous(VariantContext) GVCFBlock
isCopyComplete() NioFileCopierWithProgressMeter
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
isDestFileValid() NioFileCopierWithProgressMeterResults
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 if the genotype is a 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
isDupContraction() BreakpointComplications.SmallDuplicationBreakpointComplications
isDupe() Build37ExtendedIlluminaManifestRecord
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() StratificationManager
isEmpty() ActivityProfile
Is this profile empty? (ie., does it contain no ActivityProfileStates?)
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
isF1R2(GATKRead) ReadUtils
isF2R1(GATKRead) ReadUtils
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.
isGencodeFuncotation(Funcotation) FuncotatorUtils
isGenomicsDBPath(GATKPathSpecifier) IOUtils
Check if a given GATKPathSpecifier represents a GenomicsDB URI.
isGenomicsDBPath(String) IOUtils
Check if a given path represents GenomicsDB URI.
isGenotypeInTransition(Genotype, Transition) OrientationBiasUtils
Complement of the artifact mode is NOT considered.
isGenotypeInTransitionsWithComplement(Genotype, Collection<Transition>) OrientationBiasUtils
isGenotypeInTransitionWithComplement(Genotype, Transition) OrientationBiasUtils
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.
isHDF5File(Path) IOUtils
Given a Path, determine if it is an HDF5 file without requiring that we're on a platform that supports
HDF5 (let the caller decide if a return value of false is fatal).
isHeaderLine(String[]) TableReader
Determines whether a line is a repetition of the header.
isHeterozygous() DiploidGenotype
isHigherPriorityThan(SnpEffUtil.EffectFunctionalClass) SnpEffUtil.EffectFunctionalClass
isHomogeneous() HeterogeneousPloidyModel
isHomogeneous() HomogeneousPloidyModel
isHomogeneous() PloidyModel
Checks whether the ploidy is homogeneous across all samples.
isHomomozygous() 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
isIndel() IlluminaManifestRecord
isIndelAlignedTooFarLeft(Cigar, int) AlignmentUtils
Check if cigar aligns indel too far left
isIndelBetweenCodons(int, int, String, Strand) FuncotatorUtils
Checks to see whether a given indel location occurs on a codon boundary.
isIndexed() CachingIndexedFastaSequenceFile
isInformative() AlleleLikelihoods.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
isKeepValid() AbstractAlignmentMerger.UnmappingReadStrategy
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?
isLegacyPicardStyle(String[]) CommandLineSyntaxTranslater
isLinearChainStart(SeqVertex) SeqGraph
Is source vertex potentially a start of a linear chain of vertices?
We are a start of a zip chain if our out degree is 1 and either the
the vertex has no incoming connections or 2 or more (we must start a chain) or
we have exactly one incoming vertex and that one has out-degree > 1 (i.e., source's incoming
vertex couldn't be a start itself
isLowQualityGraph() AbstractReadThreadingGraph
isLowQualityGraph() JunctionTreeLinkedDeBruinGraph
isLowQualityGraph() 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.
isNaturalLog AlleleLikelihoods
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
isNormal(Genotype) Mutect2FilteringEngine
isNotFailure() AlignedAssemblyOrExcuse
isOpen() SeekableByteChannelPrefetcher
Tells whether or not this channel is open.
isOpticalDuplicate ReadEnds
A *transient* flag marking this read end as being an optical duplicate.
isOutOfNoiseFloor() BasicValidationResult
isOverwriteExisting() NioFileCopierWithProgressMeter
isPaired() GATKRead
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'.
isPath() PathSpecifier
isPath() PathURI
Return true if this {code PathURI} can be resolved to an java.nio Path.
isPerformDownsampling() LIBSDownsamplingInfo
isPf() CbclData
isPf() ClusterData
isPhasing(IlluminaMetricsCode) IlluminaMetricsCode
isPopulateOaTag() 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
isPositiveAck() ProcessControllerAckResult
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
isProperlyPolymorphic(VariantContext) GATKVariantContextUtils
Determines whether the provided VariantContext has real alternate alleles.
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
isReciprocalOverlap(SimpleInterval, SimpleInterval, double) IntervalUtils
Determine whether the two intervals specified overlap each other by at least the threshold proportion specified.
isRecoverDanglingBranches() ReadThreadingAssembler
isRedirectErrorStream() ProcessSettings
isRef() BaseEdge
Does this edge indicate a path through the reference graph?
isReference() KBestHaplotype
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
isSegmentVariantContext(VariantContext) FuncotatorUtils
Determine whether a given variant context represents a segment.
isSequenceDictionaryFromIndex(SAMSequenceDictionary) IndexUtils
isSequenceDictionaryUsingB37Reference(SAMSequenceDictionary) FuncotatorUtils
Returns if the given SAMSequenceDictionary is for the B37 Human Genome Reference.
isSilent() NioFileCopierWithProgressMeter
isSink(V) BaseGraph
isSkipBlankLines() AbstractInputParser
isSnp() GATKVariant
isSnp() MinimalVariant
isSnp() VariantContextVariantAdapter
isSnp() IlluminaManifestRecord
isSoloTranscript() Gene.Transcript
isSource(V) BaseGraph
isSpanningDeletion(Allele) GATKVCFConstants
isSpanningDeletionOnly(VariantContext) GATKVariantContextUtils
isSpecialFile(File) IOUtils
Returns true if the file is a special file.
isStandard() Nucleotide
Checks whether the nucleotide refers to a concrete (rather than ambiguous) base.
isStop() AminoAcid
isSubsettingToSpecificSamples() VariantEval
isSubTypeOf(SnpEffUtil.EffectType, SnpEffUtil.EffectType) SnpEffUtil
isSupplementaryAlignment() GATKRead
isSupplementaryAlignment() SAMRecordToGATKReadAdapter
isSupportConnected() BetaBinomialDistribution
isSupportingSegmentFuncotation() DataSourceFuncotationFactory
isSupportingSegmentFuncotation() GencodeFuncotationFactory
isSymbolicEnd() JunctionTreeLinkedDeBruinGraph.ThreadingNode
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
isThreadingStart(Kmer, boolean) AbstractReadThreadingGraph
Checks whether a kmer can be the threading start based on the current threading start location policy.
isThreadingStart(Kmer, boolean) JunctionTreeLinkedDeBruinGraph
Checks whether a kmer can be the threading start based on the current threading start location policy.
isThreadingStart(Kmer, boolean) ReadThreadingGraph
Checks whether a kmer can be the threading start based on the current threading start location policy.
isTraining TrainingSet
isTransition(byte, byte) BaseUtils
isTransition(VariantContext) GATKVariantContextUtils
If this is a BiAllelic SNP, is it a transition?
isTreatGroupedDelimitersAsOne() AbstractInputParser
isTruth TrainingSet
isTumor(Genotype) Mutect2FilteringEngine
isTwoBit(String) ReferenceTwoBitSparkSource
isUnmapped() AlignedContig
isUnmapped(GenomeLoc) GenomeLoc
isUnmapped() GenomeLoc
Return true if this GenomeLoc represents the UNMAPPED location
isUnmapped() GATKRead
isUnmapped() SAMRecordToGATKReadAdapter
isUnmappedGenomeLocString(String) GenomeLocParser
isUnmixedMnpIgnoringNonRef(VariantContext) GATKVariantContextUtils
Returns true if the context represents a MNP.
isUnplaced() GATKRead
Does the read have a position assigned to it for sorting purposes.
isUnplaced() SAMRecordToGATKReadAdapter
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) OrientationBiasReadCounts
isUsableRead(GATKRead, int) RankSumTest
Can the read be used in comparative tests between ref / alt bases?
isUsableRead(GATKRead, int) ReadPosRankSumTest
isValid() Nucleotide
Whether this nucleotide code is valid or not.
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.
isValidLog10Probability(double) MathUtils
isValidLog10ProbabilityVector(double[], int, boolean) MathUtils
Check that the log10 prob vector vector is well formed
isValidProbability(double) MathUtils
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
Tests whether there is a mendelian violation between the supplied samples.
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).
iterateOnGenotypes(VariantContext, List<Allele>, Map<Allele, Integer>, int[], boolean, boolean, int[]) GnarlyGenotyperEngine
Remove the NON_REF allele from the genotypes, updating PLs, ADs, and GT calls
iterator() FeatureDataSource
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() 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() IndexedSet
iterator() CompressedDataList
iterator() GenomeLocSortedSet
get an iterator over this collection
iterator() PushToPullIterator
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() 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() IlluminaManifest
iterator() BaseIlluminaDataProvider
iterator() ReadStructure.Substructure
iterator() TileIndex
iterator AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
iterator() AbstractInputParser
iterator() IntervalListScatter
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
M2_CENTER_NAME MergeMutect2CallsWithMC3
M2_FILTERS_HEADER_LINE MergeMutect2CallsWithMC3
M2_FILTERS_KEY MergeMutect2CallsWithMC3
M2ArgumentCollection org.broadinstitute.hellbender.tools.walkers.mutect
M2ArgumentCollection() M2ArgumentCollection
M2FiltersArgumentCollection org.broadinstitute.hellbender.tools.walkers.mutect.filtering
M2FiltersArgumentCollection() M2FiltersArgumentCollection
MACHINE_NAME IlluminaBasecallsToFastq
MAD_COVERAGE WgsMetrics
The median absolute deviation of coverage of the genome after all filters are applied.
MAF_DBSNP_VAL_STATUS_DELIMITER CustomMafFuncotationCreator
MAF_DBSNP_VAL_STATUS_FIELD CustomMafFuncotationCreator
MAF_STEP_SIZE ContaminationModel
MAF_TO_SWITCH_TO_HOM_REF ContaminationModel
MAF_TO_SWITCH_TO_UNSCRUPULOUS_HOM_REF ContaminationModel
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>, String, Set<String>, String) MafOutputRenderer
MafOutputRendererConstants org.broadinstitute.hellbender.tools.funcotator.mafOutput
MafOutputRendererConstants() MafOutputRendererConstants
mafTransform(String, String, String) MafOutputRenderer
Transforms a given value to the equivalent MAF-valid value based on the given key.
mafTransformInvert(String, String, String) MafOutputRenderer
Transforms a given value from a MAF-valid value to a general-purpose value based on the given key.
MAGIC_STRING ReadMetadata.Serializer
Placed at the beginning of each standalone serialization of the meta-data
identifies file that most likely are valid serializations.
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[]) PicardCommandLine
Override this if you want to include different java packages to search for classes that extend CommandLineProgram.
main(String[]) DuplicationMetrics
main(String[]) Test
mainEntry(String[]) Main
mainSourceFileAsFeatureInput DataSourceFuncotationFactory
The backing data store as a FeatureInput to leverage tribble querying.
make() IntervalListScatterMode
Create the scatterer
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, int, AlleleLikelihoods<GATKRead, Allele>, VariantContext, VariantAnnotatorEngine) 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.
makeCalculator(GenotypeCalculationArgumentCollection) AlleleFrequencyCalculator
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
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
makeEvalVariantFilter() EvaluateInfoFieldConcordance
makeEvalVariantFilter() MergeMutect2CallsWithMC3
makeExceptionMsg() AbstractIlluminaPositionFileReader
Create a string that will be included in any NoSuchElementException thrown by the next() method
makeExceptionMsg() ClocsFileReader
makeExceptionMsg() LocsFileReader
makeExceptionMsg() PosFileReader
makeFeatureInterval(T) FeatureWalker
This method can be overridden if you need to customize the interval for a given feature.
makeFeatureInterval(T) FuncotateSegments
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.
makeFromAlleles(String, String, int, List<String>) GATKVariantContextUtils
For testing purposes only.
makeGenotypeCall(GenotypeBuilder, double[], List<Allele>) GnarlyGenotyperEngine
For a genotype with likelihoods that has a no-call GT, determine the most likely genotype from PLs and set it
We use a GenotypeLikelihoodCalculator to convert from the best PL index to the indexes of the alleles for that
genotype so we can set the GenotypeBuilder with the alleles
makeGenotypeCall(int, GenotypeBuilder, GenotypeAssignmentMethod, double[], List<Allele>, List<Allele>) GATKVariantContextUtils
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, File, Set<String>, boolean) CollectMultipleMetrics.ProgramInterface
makeInstance(String, String, File, File, Set<MetricAccumulationLevel>, File, File, File, Set<String>) CollectMultipleMetrics.ProgramInterface
makeInstanceOf(Class<T>) ClassUtils
Create objects of a concrete class.
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
makeLocationString(String, int, String, int) SvType
makeLocationString(NovelAdjacencyAndAltHaplotype) SvType
makeMergedVariantContext(List<VariantContext>) AssemblyBasedCallerUtils
makeNewHMM(PairHMMNativeArguments) PairHMM.Implementation
makeOneBpInterval(String, int) SVUtils
Given chromosome name and requested position (1-based coordinate system),
return a 1 bp long interval that spans only the requested base.
makeOREdge(Collection<BaseEdge>, int) 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() Mutect2
makePostReadFilterTransformer() SplitNCigarReads
makePostVariantFilterTransformer() VariantWalkerBase
Returns the post-filter variant transformer (simple or composite) that will be applied to the variants after filtering.
makePostVariantFilterTransformer() Funcotator
makePreReadFilterTransformer() GATKTool
Returns the pre-filter read transformer (simple or composite) that will be applied to the reads before filtering.
makePreReadFilterTransformer() SplitNCigarReads
makePreVariantFilterTransformer() VariantWalkerBase
Returns the pre-filter variant transformer (simple or composite) that will be applied to the variants before filtering.
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
makeReaderMaybeGzipped(Path) 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
makeReadGroupCollector(SAMReadGroupRecord) MultiLevelCollector
makeReadGroupCollector(SAMReadGroupRecord) MultiLevelReducibleCollector
makeReadGroupCollector(SAMReadGroupRecord) MultiLevelCollector
makeReads() ArtificialBAMBuilder
Create a read stream based on the parameters.
makeReadThreadingAssembler() HaplotypeCallerReadThreadingAssemblerArgumentCollection
makeReadThreadingAssembler() MutectReadThreadingAssemblerArgumentCollection
makeReadThreadingAssembler() ReadThreadingAssemblerArgumentCollection
makeReducedAnnotationString(VariantContext, Map<Allele, Double>) AS_StrandBiasTest
makeReferenceArgumentCollection() CollectAlignmentSummaryMetrics
makeReferenceArgumentCollection() CollectRrbsMetrics
makeReferenceArgumentCollection() CommandLineProgram
makeReferenceArgumentCollection() CreateSequenceDictionary
makeReferenceArgumentCollection() DownsampleSam
makeReferenceArgumentCollection() ScatterIntervalsByNs
makeReferenceArgumentCollection() LiftoverVcf
makeReferenceConfidenceVariantContext(int, byte[], String, int, ReadPileup, Locatable, int, boolean, List<VariantContext>) ReferenceConfidenceModel
makeSampleCollector(SAMReadGroupRecord) MultiLevelCollector
makeSampleCollector(SAMReadGroupRecord) MultiLevelReducibleCollector
makeSampleCollector(SAMReadGroupRecord) MultiLevelCollector
makeSeekable(List<File>, BclQualityEvaluationStrategy, int[]) BclReader
makeSequenceDictionary(File) CreateSequenceDictionary
Read all the sequences from the given reference file, and convert into SAMSequenceRecords
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
makeSortingCollection() SequenceDictionaryUtils
makeSourceFromStream(InputStream) GencodeGtfCodec
makeSourceFromStream(InputStream) ProgressReportingDelegatingCodec
makeStandardHCReadFilters() HaplotypeCallerEngine
makeStandardMutect2PostFilterReadTransformer(Path, boolean) Mutect2Engine
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
makeTruthVariantFilter() EvaluateInfoFieldConcordance
makeTruthVariantFilter() MergeMutect2CallsWithMC3
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.
makeVariantAnnotations() Mutect2
makeVariantFilter() VariantWalkerSpark
makeVariantFilter() VariantWalkerBase
Returns the variant filter (simple or composite) that will be applied to the variants before calling #apply.
makeVariantFilter() Funcotator
makeVariantFilter(boolean) FuncotatorEngine
makeVariantFilter() FilterAlignmentArtifacts
makeVariantFilter() SelectVariants
Create filters for variant types, ids, and genomic intervals.
makeVariantFilter() CNNScoreVariants
makeVCFHeader(SAMSequenceDictionary, Set<VCFHeaderLine>) HaplotypeCallerEngine
Create a VCF header.
MakeVcfSampleNameMap picard.vcf
Creates a TSV from sample name to VCF/GVCF path, with one line per input.
MakeVcfSampleNameMap() MakeVcfSampleNameMap
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
MANIFEST_FILE InfiniumVcfFields
MANIFEST_FILE_HEADER_NAMES IlluminaManifest
MANIFEST_FILE_NAME DataSourceUtils
manifestFileParser IlluminaManifest
manifestName InfiniumEGTFile
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
MAP_FILE MergePedIntoVcf
MAP_INFO_HEADER_NAME IlluminaManifest
MAP_NAME_VALUE_DELIMITER FuncotatorArgumentDefinitions
MAP_QUAL_RANK_SUM_KEY GATKVCFConstants
mapAlleles(LikelihoodMatrix<EVIDENCE, A>) AlleleLikelihoodMatrixMapper
MAPPABILITY CopyNumberAnnotations
MAPPABILITY_TRACK_PATH_LONG_NAME AnnotateIntervals
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_DEPTH_DEPRECATED GATKVCFConstants
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
MappingQualityFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
MappingQualityFilter(double, int) MappingQualityFilter
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
mappingQualityStratifier ReadBaseStratification
Stratifies into the mapping-quality of the read under consideration
MappingQualityZero org.broadinstitute.hellbender.tools.walkers.annotator
Count of all reads with MAPQ = 0 across all samples
MappingQualityZero() MappingQualityZero
MAPPINGS_DIFFER SamComparisonMetric
The number of primary records which are mapped in both files but do not meet criteria to be counted in MAPPINGS_MATCH.
MAPPINGS_MATCH SamComparisonMetric
The number of primary records for which mappings match in files.
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[]
marginalize(Map<B, List<A>>) AlleleLikelihoods
Perform marginalization from an allele set to another (smaller one) taking the maximum value
for each evidence in the original allele subset.
marginalize(Map<B, List<A>>, Locatable) AlleleLikelihoods
Perform marginalization from an allele set to another (smaller one) taking the maximum value
for each unit of evidence in the original allele subset.
mark(JavaRDD<GATKRead>, SAMFileHeader, MarkDuplicatesScoringStrategy, OpticalDuplicateFinder, int, boolean, MarkDuplicates.DuplicateTaggingPolicy) 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.
mark(JavaRDD<GATKRead>, SAMFileHeader, OpticalDuplicateFinder, MarkDuplicatesSparkArgumentCollection, int) MarkDuplicatesSpark
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.
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
MarkDuplicates on Spark
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.TransientFieldPhysicalLocationComparator org.broadinstitute.hellbender.tools.spark.transforms.markduplicates
Comparator for TransientFieldPhysicalLocation objects by their attributes and strandedness.
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
MASKED_ANY_BASE FuncotatorConstants
A character representing any base as used in VCF files and IUPAC base standards.
MASKED_ANY_BASE_STRING FuncotatorConstants
A String representing any base as used in VCF files and IUPAC base standards.
maskExtension VariantFiltration
maskName VariantFiltration
When using the --mask argument, the mask-name will be annotated in the variant record.
matchAllelesOnly(VariantContext, VariantContext) GATKVariantContextUtils
Attempt to match allele ref/alt pairs, even if the allele pairs in the given variant contexts are equivalent,
but not exact.
MATCHED_NORMAL_LONG_NAME 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
matchOnKeyOrDefault(Set<Map.Entry<String, String>>, String, String) FuncotationFilter
Given a set of extracted funcotations of a variant, return a Stream of values that belong to the key.
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_CONTIG_TAG_NAME AddOriginalAlignmentTags
MATE_DIFFERENT_STRAND ReadFilterLibrary
MATE_ON_SAME_CONTIG_OR_NO_MAPPED_MATE ReadFilterLibrary
MATE_UNMAPPED_AND_UNMAPPED_READ_FILTER ReadFilterLibrary
MateDifferentStrandReadFilter() ReadFilterLibrary.MateDifferentStrandReadFilter
mateIsReverseStrand() GATKRead
mateIsReverseStrand() SAMRecordToGATKReadAdapter
mateIsUnmapped() GATKRead
mateIsUnmapped() SAMRecordToGATKReadAdapter
mateIsUnplaced() GATKRead
Does the reads mate have a position assigned to it for sorting purposes..
mateIsUnplaced() SAMRecordToGATKReadAdapter
MateOnSameContigOrNoMappedMateReadFilter() ReadFilterLibrary.MateOnSameContigOrNoMappedMateReadFilter
MateUnmappedAndUnmappedReadFilter() ReadFilterLibrary.MateUnmappedAndUnmappedReadFilter
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(GenomeLoc) GenomeLoc
Returns the maximum GenomeLoc of this and other
max(Function<Double, Double>, double, double, double) OptimizationUtils
max(DoubleUnaryOperator, double, double, double, double, double, int) OptimizationUtils
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_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH CommandLineProgram
CommandLineProgramProperties oneLineSummary attribute must be shorted than this in order to maintain
reasonable help output formatting.
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_ALTERNATE_ALLELES_LONG_NAME GenotypeCalculationArgumentCollection
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_CHANGEPOINTS_PER_CHROMOSOME ContaminationSegmenter
MAX_COMBINED_DISTANCE MultiVariantWalkerGroupedOnStart
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_DEPTH_LONG_NAME CollectF1R2CountsArgumentCollection
MAX_DEPTH_LONG_NAME LearnReadOrientationModel
MAX_DEPTH_PER_SAMPLE_NAME LocusWalker
MAX_DIFF_RATE EstimateLibraryComplexity
MAX_DISCARD_FRACTION RevertSam
MAX_DISTANCE_TO_FILTERED_CALL_ON_SAME_HAPLOTYPE_LONG_NAME M2FiltersArgumentCollection
MAX_DUST_SCORE StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
MAX_EDIT_DISTANCE_TO_JOIN UmiAwareMarkDuplicatesWithMateCigar
MAX_EM_ITERATIONS_LONG_NAME LearnReadOrientationModel
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
Hard filter thresholds
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_PROBABILITY_LONG_NAME CreateSomaticPanelOfNormals
MAX_GROUP_RATIO EstimateLibraryComplexity
MAX_INDEL_LENGTH_LONG_NAME LeftAlignAndTrimVariants
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_LEADING_BASES_LONG_NAME LeftAlignAndTrimVariants
MAX_LOCI CollectSamErrorMetrics
MAX_MASKED_BASES_LONG_NAME PSFilterArgumentCollection
MAX_MASKED_BASES_SHORT_NAME PSFilterArgumentCollection
MAX_MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_LONG_NAME M2FiltersArgumentCollection
MAX_MERGE_DISTANCE MergeAnnotatedRegionsByAnnotation
MAX_MISMATCH_RATE CollectRrbsMetrics
MAX_MISMATCHES ExtractIlluminaBarcodes
MAX_MNP_DISTANCE_LONG_NAME AssemblyBasedCallerArgumentCollection
MAX_MNP_DISTANCE_SHORT_NAME AssemblyBasedCallerArgumentCollection
MAX_N_INDEL_INFORMATIVE_READS ReferenceConfidenceModel
MAX_N_RATIO_LONG_NAME M2FiltersArgumentCollection
MAX_NO_CALLS ExtractIlluminaBarcodes
MAX_NORMAL_QUAL_SUM Mutect2Engine
MAX_NUM_INTERVALS_TO_IMPORT_IN_PARALLEL GenomicsDBImport
MAX_NUMBER_OF_VALUES_PER_HDF5_MATRIX HDF5Utils
MAX_NUMT_FRACTION_LONG_NAME M2FiltersArgumentCollection
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 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_SIZE_FOR_HISTOGRAM IndelLengthHistogram
MAX_SPLICES_TO_KEEP OverhangFixingManager
MAX_STARTS_LONG_NAME AssemblyRegionWalker
MAX_SUSPICIOUS_READS_PER_ALIGNMENT_START_LONG_NAME M2ArgumentCollection
MAX_TARGET_COVERAGE PanelMetricsBase
The maximum coverage of reads that mapped to target regions of an experiment.
MAX_TO_MERGE ScatterIntervalsByNs
MAX_TRAINING_EPOCHS_LONG_NAME HybridADVIArgumentCollection
MAX_VALIDATION_NORMAL_COUNT_LONG_NAME ValidateBasicSomaticShortMutations
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 AssemblyRegionArgumentCollection
maxCallableImpreciseVariantDeletionSize StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsSparkArgumentCollection
maxCombinedDistance MultiVariantWalkerGroupedOnStart
maxDepth CollectF1R2CountsArgumentCollection
maxDepthPerSample LocusWalker
maxDepthPerSample LocusWalkerSpark
maxDistanceToFilteredCallOnSameHaplotype M2FiltersArgumentCollection
maxDUSTScore StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
maxElementIndex(double[]) MathUtils
maxElementIndex(double[], int, int) MathUtils
maxElementIndex(double[], int) MathUtils
maxElementIndex(int[]) MathUtils
maxEnd() SVIntervalTree
Return the interval having the largest ending value.
maxEventsInRegion M2FiltersArgumentCollection
maxFalsePositiveRate M2FiltersArgumentCollection
maxFASTQSize StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
maxFragmentLength FragmentLengthReadFilter
maxGermlineProbability CreateSomaticPanelOfNormals
maxGQ GVCFBlock
maxHaplotypeLength PairHMM
maximalInterestingDistance BarcodeEditDistanceQuery
maximal edit distance between reads and barcodes to be considered
maximum() InsertSizeDistribution
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_GC_CONTENT_LONG_NAME FilterIntervals
MAXIMUM_INSERT_SIZE CollectSequencingArtifactMetrics
MAXIMUM_INSERT_SIZE CollectOxoGMetrics
MAXIMUM_MAPPABILITY_LONG_NAME FilterIntervals
MAXIMUM_MAPPING_QUALITY_NAME ReadFilterArgumentDefinitions
MAXIMUM_NUMBER_OF_SEGMENTS_PER_CHROMOSOME_LONG_NAME ModelSegments
MAXIMUM_NUMBER_OF_SMOOTHING_ITERATIONS_LONG_NAME ModelSegments
MAXIMUM_SEGMENTAL_DUPLICATION_CONTENT_LONG_NAME FilterIntervals
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
maximumLikelihoodOverAllAlleles(int, int) AlleleLikelihoods
maximumSpan AssemblyRegionTrimmer.Result
Maximum available range for the trimmed variant region.
maxIndelSize LeftAlignAndTrimVariants
Maximum indel size to realign.
maxLeadingBases LeftAlignAndTrimVariants
Distance in reference to look back before allele
maxMADTolerance InsertSizeMetricsArgumentCollection
maxMappingQualityScore MappingQualityReadFilter
maxMedianFragmentLengthDifference M2FiltersArgumentCollection
maxMnpDistance AssemblyBasedCallerArgumentCollection
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.
maxNuMTFraction M2FiltersArgumentCollection
maxPopulationAlleleFrequency M2ArgumentCollection
In tumor-only mode, we discard variants with population allele frequencies greater than this threshold.
maxProbPropagationDistance AssemblyRegionWalker
maxProbPropagationDistance AssemblyRegionArgumentCollection
maxProbPropagationDistance ActivityProfile
maxQualityScore UnifiedArgumentCollection
maxReadLength ReadLengthReadFilter
maxReadLength PairHMM
maxReadsPerAlignmentStart AssemblyRegionWalker
maxReadsPerAlignmentStart AssemblyRegionArgumentCollection
maxReasonableFragmentLength RealignmentArgumentCollection
Maximum fragment length to be considered a reasonable pair alignment
maxSize() DigammaCache
maxSize() IntToDoubleFunctionCache
maxSize() Log10Cache
maxSize() Log10FactorialCache
maxSuspiciousReadsPerAlignmentStart M2ArgumentCollection
Maximum number of suspicious reads (mediocre mapping quality or too many substitutions) allowed in a downsampling stride.
maxTrackedFragmentLength StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
maxUnprunedVariants ReadThreadingAssemblerArgumentCollection
The maximum number of variants in graph the adaptive pruner will allow
maxValidationNormalCount ValidateBasicSomaticShortMutations
maybeAdvance() PerTileParser
MC3_ALT_COUNT_KEY MergeMutect2CallsWithMC3
MC3_REF_COUNT_KEY MergeMutect2CallsWithMC3
MDElement(int) TextMDCodec.MDElement
mean() InsertSizeDistribution
mean(int, boolean) VariantDataManager
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(double[]) MathUtil
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 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_R InfiniumVcfFields
MEAN_READ_LENGTH AlignmentSummaryMetrics
The mean read length of the set of reads examined.
MEAN_TARGET_COVERAGE PanelMetricsBase
The mean coverage of targets.
MEAN_THETA InfiniumVcfFields
MEAN_UMI_LENGTH UmiMetrics
Number of bases in each UMI
MEAN_X InfiniumVcfFields
MEAN_Y InfiniumVcfFields
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
meanR InfiniumEGTFile
meanTheta InfiniumEGTFile
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_AUTOSOMAL_COVERAGE_LONG_NAME M2FiltersArgumentCollection
MEDIAN_BASE_QUALITY_FILTER_NAME GATKVCFConstants
MEDIAN_BASE_QUALITY_KEY GATKVCFConstants
MEDIAN_COVERAGE 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_FRAGMENT_LENGTH_KEY 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_MAPPING_QUALITY_KEY GATKVCFConstants
MEDIAN_READ_POSITON_KEY GATKVCFConstants
MEDIAN_TARGET_COVERAGE PanelMetricsBase
The median coverage of targets.
medianAutosomalCoverage M2FiltersArgumentCollection
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?
MemoryBasedReadEndsForMarkDuplicatesMap picard.sam.markduplicates.util
Map from String to ReadEnds object.
MemoryBasedReadEndsForMarkDuplicatesMap() MemoryBasedReadEndsForMarkDuplicatesMap
MENDEL_VIOLATION_LR_KEY GATKVCFConstants
MENDELIAN_VIOLATION_QUAL_THRESHOLD VariantEval
MendelianViolation org.broadinstitute.hellbender.utils.samples
Class for the identification and tracking of mendelian violation.
MendelianViolation(double) MendelianViolation
MendelianViolation(double, boolean, boolean) MendelianViolation
MendelianViolationEvaluator org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
Mendelian violation detection and counting
a violation looks like:
Suppose dad = A/B and mom = C/D
The child can be [A or B] / [C or D].
MendelianViolationEvaluator() MendelianViolationEvaluator
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(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(MergeableMetricBase) WgsMetrics
Merges the various PCT_EXC_* metrics.
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_INPUT_INTERVALS_LONG_NAME GenomicsDBImport
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 (
MergeByAdding).
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
MergeAnnotatedRegionsByAnnotation org.broadinstitute.hellbender.tools.copynumber.utils
MergeAnnotatedRegionsByAnnotation() MergeAnnotatedRegionsByAnnotation
MergeBamAlignment picard.sam
Summary
MergeBamAlignment() MergeBamAlignment
MERGED_VCF_FILE_NAME SvDiscoverFromLocalAssemblyContigAlignmentsSpark
mergeDesignMatrices(List<AltSiteRecord>, List<AltSiteRecord>) LearnReadOrientationModel
Contract: this method must be called after grouping the design matrices by context.
mergedSampleName(String, String, boolean) GATKVariantContextUtils
mergeEvals VariantEval
If true, VariantEval will treat -eval 1 -eval 2 as separate tracks from the same underlying
variant set, and evaluate the union of the results.
mergeFingerprintsBy(Map<FingerprintIdDetails, Fingerprint>, Function<FingerprintIdDetails, String>) Fingerprint
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
mergeLinearChainVertex(LinkedList<SeqVertex>) SeqGraph
mergeListsBySetOperator(List<GenomeLoc>, List<GenomeLoc>, IntervalSetRule) IntervalUtils
merge two interval lists, using an interval set rule
MergeMutect2CallsWithMC3 org.broadinstitute.hellbender.tools.walkers.validation
MergeMutect2CallsWithMC3() MergeMutect2CallsWithMC3
MergeMutectStats org.broadinstitute.hellbender.tools.walkers.mutect
Merge the stats output by scatters of a single Mutect2 job.
MergeMutectStats() MergeMutectStats
MergePedIntoVcf picard.arrays
Class to take genotype calls from a ped file output from zCall and merge them into a vcf from autocall.
MergePedIntoVcf() MergePedIntoVcf
mergeRegions(List<AnnotatedInterval>, SAMSequenceDictionary, String, Consumer<Locatable>) AnnotatedIntervalUtils
Merge AnnotatedIntervals by whether the regions overlap.
mergeRegionsByAnnotation(List<AnnotatedInterval>, SAMSequenceDictionary, List<String>, Consumer<Locatable>, String, int) AnnotatedIntervalUtils
Merge AnnotatedIntervals by whether the given annotation values match (all annotations must match).
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.
messageDigest NioFileCopierWithProgressMeter
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
METADATA_TAG TableWriter
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
METHYLATION_REFERENCE_CONTEXT_KEY GATKVCFConstants
MethylationProgramGroup org.broadinstitute.hellbender.cmdline.programgroups
Tools that performs methylation calling and methylation-based coverage for bisulfite BAMs
MethylationProgramGroup() MethylationProgramGroup
MethylationTypeCaller org.broadinstitute.hellbender.tools.walkers
Identifies methylated bases from bisulfite sequencing data.
MethylationTypeCaller() MethylationTypeCaller
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
METRIC_TYPE AlleleFrequencyQCMetric
METRIC_VALUE AlleleFrequencyQCMetric
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
metricOutput AlleleFrequencyQC
metrics RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
METRICS MarkIlluminaAdapters
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
MetricsCollection org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
Created by knoblett on 9/15/15.
MetricsCollection() MetricsCollection
MetricsCollectorSpark T extends MetricsArgumentCollection > - Interface in org.broadinstitute.hellbender.tools.spark.pipelines.metrics
Each metrics collector has to be able to run from 4 different contexts:
- a standalone walker tool
- the
org.broadinstitute.hellbender.metrics.analysis.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(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_AF_LONG_NAME M2FiltersArgumentCollection
MIN_ASSEMBLY_LONG_NAME AssemblyRegionWalker
MIN_BASE_Q CollectSamErrorMetrics
MIN_BASE_QUAL MarkDuplicatesScoringStrategy
MIN_BASE_QUALITY_DEFAULT_CUTOFF AnnotatePairOrientation
MIN_BASE_QUALITY_LONG_NAME PSFilterArgumentCollection
MIN_BASE_QUALITY_LONG_NAME CollectF1R2CountsArgumentCollection
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_CLIPPED_READ_LENGTH_LONG_NAME PSFilterArgumentCollection
MIN_CLIPPED_READ_LENGTH_SHORT_NAME PSFilterArgumentCollection
MIN_CONTIG_SIZE_LONG_NAME SplitIntervals
MIN_COUNT AS_StrandBiasTest
MIN_DP FilterVcf
MIN_DP GenotypeConcordance
MIN_DP FindMendelianViolations
MIN_DP_FORMAT_KEY GATKVCFConstants
MIN_FRACTION_OF_MATCHING_BASES PalindromeArtifactClipReadTransformer
MIN_FRAGMENT_LENGTH_NAME ReadFilterArgumentDefinitions
MIN_GQ FilterVcf
MIN_GQ GenotypeConcordance
MIN_GQ FindMendelianViolations
MIN_GROUP_COUNT EstimateLibraryComplexity
MIN_HET_FRACTION FindMendelianViolations
MIN_HISTOGRAM_WIDTH CollectInsertSizeMetrics
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_Q CollectSamErrorMetrics
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 EstimateLibraryComplexity
MIN_MEDIAN_BASE_QUALITY_LONG_NAME M2FiltersArgumentCollection
MIN_MEDIAN_MAPPING_QUALITY_LONG_NAME M2FiltersArgumentCollection
MIN_MEDIAN_MQ_LONG_NAME CollectF1R2CountsArgumentCollection
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_PALINDROME_SIZE Mutect2Engine
MIN_PHASE_QUALITY VariantEval
MIN_PHRED_SCALED_QUAL QualityUtils
MIN_POLYMERASE_SLIPPAGE_LENGTH M2FiltersArgumentCollection
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_POWER_LONG_NAME ValidateBasicSomaticShortMutations
MIN_PVALUE AS_StrandBiasTest
MIN_Q FastqToSam
MIN_QD FilterVcf
MIN_READ_LENGTH_ARG_NAME ReadFilterArgumentDefinitions
MIN_READ_SPAN_AFTER_DEOVERLAP CpxVariantInterpreter
MIN_READS_ON_EACH_STRAND_LONG_NAME M2FiltersArgumentCollection
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_TAIL_QUALITY_WITH_ERROR_CORRECTION HaplotypeCallerEngine
MIN_TARGET_COVERAGE PanelMetricsBase
The minimum coverage of reads that mapped to target regions of an experiment.
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.
minAdapterLength PSFilterArgumentCollection
Adapter trimming will require a match of at least this length to a known adapter.
minAf M2FiltersArgumentCollection
minAF M2ArgumentCollection
minAlignerScoreDifferencePerBase RealignmentArgumentCollection
Minimum difference between best and second-best alignment for a read to be considered well-mapped
minAlignLength StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsSparkArgumentCollection
MinAlleleFractionFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
MinAlleleFractionFilter(double) MinAlleleFractionFilter
minAssemblyRegionSize AssemblyRegionWalker
minAssemblyRegionSize AssemblyRegionArgumentCollection
minBaseQuality CollectF1R2CountsArgumentCollection
minBaseQuality ASEReadCounter
If this argument is enabled, bases with quality scores lower than this threshold will not be counted.
minBaseQualityScore VariantAnnotator
Bases with a quality below this threshold will not be used for annotation.
minBaseQualityScore AssemblyBasedCallerArgumentCollection
Bases with a quality below this threshold will not be used for calling.
minBaseQualityToUseInAssembly AbstractReadThreadingGraph
minBaseQualityToUseInAssembly ReadThreadingAssembler
minBqCutoff ValidateBasicSomaticShortMutations
minCoherentEvidenceWeightPerCoverage 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
minEvidenceWeightPerCoverage StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
minFragmentLength FragmentLengthReadFilter
minGQ GVCFBlock
MinibatchSliceSampler DATA > - Class in org.broadinstitute.hellbender.utils.mcmc
Implements slice sampling of a continuous, univariate, unnormalized probability density function (PDF),
which is assumed to be unimodal.
MinibatchSliceSampler(RandomGenerator, List<DATA>, Function<Double, Double>, BiFunction<DATA, Double, Double>, double, double, double, int, double) MinibatchSliceSampler
Creates a new sampler for a bounded univariate random variable, given a random number generator, a list of data,
a continuous, univariate, unimodal, unnormalized log probability density function
(assumed to be a posterior and specified by a prior and a likelihood),
hard limits on the random variable, a step width, a minibatch size, and a minibatch approximation threshold.
MinibatchSliceSampler(RandomGenerator, List<DATA>, Function<Double, Double>, BiFunction<DATA, Double, Double>, double, int, double) MinibatchSliceSampler
Creates a new sampler for an unbounded univariate random variable, given a random number generator, a list of data,
a continuous, univariate, unimodal, unnormalized log probability density function
(assumed to be a posterior and specified by a prior and a likelihood),
a step width, a minibatch size, and a minibatch approximation threshold.
minIdentity 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) MinimalGenotypingEngine
Creates a new unified genotyping given the UG configuration parameters and the targeted set of samples
MinimalGenotypingEngine(UnifiedArgumentCollection, SampleList, 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() InsertSizeDistribution
MINIMUM_ALLELE_FRACTION_LONG_NAME M2ArgumentCollection
MINIMUM_ALLELE_FRACTION_SHORT_NAME M2ArgumentCollection
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_GC_CONTENT_LONG_NAME FilterIntervals
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_MAPPABILITY_LONG_NAME FilterIntervals
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_READ_LENGTH_AFTER_TRIMMING AssemblyBasedCallerUtils
MINIMUM_SEGMENTAL_DUPLICATION_CONTENT_LONG_NAME FilterIntervals
MINIMUM_TOTAL_ALLELE_COUNT_CASE_LONG_NAME ModelSegments
MINIMUM_TOTAL_ALLELE_COUNT_NORMAL_LONG_NAME ModelSegments
MINIMUM_UNSCRUPULOUS_HOM_REF_ALT_FRACTION_THRESHOLD ContaminationModel
minimumAlleleIndex() GenotypeAlleleCounts
Returns the smallest allele index present in the genotype.
minimumBaseQuality BarcodeEditDistanceQuery
minimal base quality to condiser informative
minimumPct InsertSizeMetricsArgumentCollection
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
minMedianMapQual CollectF1R2CountsArgumentCollection
minMedianReadPosition M2FiltersArgumentCollection
minMismatchDifferencePerBase RealignmentArgumentCollection
Minimum ratio between the number of mismatches in the second best and best alignments
minMQ StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsSparkArgumentCollection
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
MinorAlleleFractionRecord org.broadinstitute.hellbender.tools.walkers.contamination
Created by David Benjamin on 2/13/17.
MinorAlleleFractionRecord(SimpleInterval, double) MinorAlleleFractionRecord
MinorAlleleFractionRecord.MinorAlleleFractionTableReader org.broadinstitute.hellbender.tools.walkers.contamination
MinorAlleleFractionTableReader(Path) MinorAlleleFractionRecord.MinorAlleleFractionTableReader
minOverlapper(SVInterval) SVIntervalTree
Find the earliest interval in the tree that overlaps the specified interval.
minPower UnifiedArgumentCollection
minPower ValidateBasicSomaticShortMutations
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.
minReadsOnEachStrand M2FiltersArgumentCollection
minSeedLength PSFilterArgumentCollection
Controls the sensitivity of BWA alignment to the host reference.
minSeedLength RealignmentArgumentCollection
BWA-mem minimum seed length
minSlippageLength M2FiltersArgumentCollection
MINUTE_IN_MS NioFileCopierWithProgressMeter
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.
mismatchesInReadStratifier ReadBaseStratification
Stratifies according to the overall mismatches (from NM) that the read has against the reference, NOT
including the current base.
MismatchesInReadStratifier() ReadBaseStratification.MismatchesInReadStratifier
MismatchMDElement() TextMDCodec.MismatchMDElement
mismatchQualities AlignmentUtils.MismatchCount
MISSING_LEFT SamComparisonMetric
The number of primary records which are found in right file but not found in left file
MISSING_RIGHT SamComparisonMetric
The number of primary records which are found in left file but not found in right file
MISSING_SITES_HOM_REF GenotypeConcordance
MISSING_VAL_LONG_NAME VariantFiltration
MissingContigInSequenceDictionary(String, SAMSequenceDictionary) UserException.MissingContigInSequenceDictionary
MissingIndex(String) UserException.MissingIndex
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
MissingReferenceGziFile(Path, Path) UserException.MissingReferenceGziFile
mitochondria M2FiltersArgumentCollection
mitochondria M2ArgumentCollection
Mitochondria mode changes default values for --tumor-lod-to-emit and --initial-tumor-lod to 0 to increase sensitivity.
MITOCHONDRIA_MODE_LONG_NAME M2ArgumentCollection
MITOCHONDRIAL_CONTIG_NAMES FuncotatorConstants
Set containing known valid names for Mitochondrial chromosomes.
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
MODULES_TO_USE VariantEval
See the -list argument to view available modules.
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_IDENTIFIER_TAG MarkDuplicates
MOLECULAR_INDEX_BASE_QUALITY_TAG IlluminaBasecallsToSam
MOLECULAR_INDEX_TAG IlluminaBasecallsToSam
molecularBarcode ReadStructure
MolecularIndex ReadType
Molten org.broadinstitute.hellbender.tools.walkers.varianteval.util
Molten for @Analysis modules.
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.
MS_TO_SEC NioFileCopierWithProgressMeter
msBetweenCallsToRead SeekableByteChannelPrefetcher
msCopyingData SeekableByteChannelPrefetcher
msWaitingForData SeekableByteChannelPrefetcher
MTAC Mutect2
MTFAC FilterMutectCalls
MULTIALLELIC_FILTER_NAME GATKVCFConstants
MultiallelicFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
MultiallelicFilter(int) MultiallelicFilter
MultiallelicSummary org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
MultiallelicSummary() MultiallelicSummary
MultiallelicSummary.Type org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
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.
MultiplePassReadWalker org.broadinstitute.hellbender.engine
A MultiplePassReadWalker traverses input reads multiple times.
MultiplePassReadWalker() MultiplePassReadWalker
MultiplePassReadWalker.GATKReadConsumer org.broadinstitute.hellbender.engine
Implemented by MultiplePassReadWalker-derived tools.
MultiplePassVariantWalker org.broadinstitute.hellbender.engine
A VariantWalker that makes multiple passes through the variants.
MultiplePassVariantWalker() MultiplePassVariantWalker
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.
MultiVariantInputArgumentCollection org.broadinstitute.hellbender.cmdline.argumentcollections
Class that defines the variant arguments used for a MultiVariantWalker.
MultiVariantInputArgumentCollection() MultiVariantInputArgumentCollection
multiVariantInputArgumentCollection MultiVariantWalker
MultiVariantInputArgumentCollection.DefaultMultiVariantInputArgumentCollection org.broadinstitute.hellbender.cmdline.argumentcollections
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 mutations 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.filtering
Mutect2FilteringEngine(M2FiltersArgumentCollection, VCFHeader, File) Mutect2FilteringEngine
Mutect2VariantFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
Mutect2VariantFilter() Mutect2VariantFilter
MUTECT_FILTER_NAMES GATKVCFConstants
MUTECT_STATS_SHORT_NAME Mutect2
MutectDownsampler org.broadinstitute.hellbender.utils.downsampling
MutectDownsampler(int, int, int) MutectDownsampler
MutectReadThreadingAssemblerArgumentCollection org.broadinstitute.hellbender.tools.walkers.haplotypecaller
MutectReadThreadingAssemblerArgumentCollection() MutectReadThreadingAssemblerArgumentCollection
MutectStats org.broadinstitute.hellbender.tools.walkers.mutect
MutectStats(String, double) MutectStats
mvRefHet_Var MendelianViolationEvaluator
mvRefRef_Het MendelianViolationEvaluator
mvRefRef_Var MendelianViolationEvaluator
mvRefVar_Ref MendelianViolationEvaluator
mvRefVar_Var MendelianViolationEvaluator
mvVarHet_Ref MendelianViolationEvaluator
mvVarVar_Het MendelianViolationEvaluator
mvVarVar_Ref MendelianViolationEvaluator
P95_GREEN CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The 95th Intensity Percentile for the green color channel for this sample
P95_RED CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The 95th Intensity Percentile for the red color channel for this sample
P_95_GREEN InfiniumVcfFields
P_95_RED InfiniumVcfFields
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
padded ShardBoundary
paddedHaplotypeLength PairHMM
paddedInterval ShardBoundary
paddedMaxHaplotypeLength PairHMM
paddedMaxReadLength PairHMM
paddedReadLength PairHMM
paddedShardBoundary() ReadlessAssemblyRegion
paddedShardBoundary() ShardBoundary
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, Map<String, Byte>) Pair
Pair X extends java.lang.Comparable<X >,Y extends java.lang.Comparable<Y >> - Class in picard.sam.util
Simple Pair class.
Pair(X, Y) 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 global 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
PairStratifier(ReadBaseStratification.RecordAndOffsetStratifier<T>, ReadBaseStratification.RecordAndOffsetStratifier<R>) ReadBaseStratification.PairStratifier
PairStratifierFactory(ReadBaseStratification.RecordAndOffsetStratifier<T>, ReadBaseStratification.RecordAndOffsetStratifier<S>, String) ReadBaseStratification
A factory for generating "pair" stratifier instances from two stratifiers and a string
PalindromeArtifactClipReadTransformer org.broadinstitute.hellbender.transformers
Trims (hard clips) soft-clipped bases due to the following artifact:
When a sequence and its reverse complement occur near opposite ends of a fragment DNA damage (especially in the case
of FFPE samples and ancient DNA) can disrupt base-pairing causing a single-strand loop of the sequence and its reverse
complement, after which end repair copies the true 5' end of the fragment onto the 3' end of the fragment.
PalindromeArtifactClipReadTransformer(ReferenceDataSource, int) PalindromeArtifactClipReadTransformer
PANEL_OF_NORMALS_LONG_NAME M2ArgumentCollection
PANEL_OF_NORMALS_SHORT_NAME M2ArgumentCollection
PanelMetricsBase picard.analysis.directed
A base class for Metrics for targeted panels.
PanelMetricsBase() PanelMetricsBase
PanelOfNormalsFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
PanelOfNormalsFilter() PanelOfNormalsFilter
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.
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
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.
parseClusterRecordsFromTileMetricsV3(Collection<File>, Map<Integer, File>, ReadStructure) TileMetricsUtil
parseCommaDelimitedArgList(String) PSUtils
parseDirective(String) CollectSamErrorMetrics
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) ContigChimericAlignmentIterativeInterpreter
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
parseQualList(VariantContext) AS_QualByDepth
parseRawDataString(ReducibleAnnotationData<Histogram>) AS_RankSumTest
parseRawDataString(ReducibleAnnotationData<Double>) AS_RMSMappingQuality
parseRawDataString(ReducibleAnnotationData<List<Integer>>) AS_StrandBiasTest
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
partitionPrecision SomaticGVCFBlockCombiner
PartitionStatistics(Iterator<GATKRead>, SVReadFilter, int, Map<String, String>) ReadMetadata.PartitionStatistics
PASS_FILTER FilterApplyingVariantIterator
The "PASS"ing filter String.
PASSES_FILTERS VariantFilterLibrary
PASSES_VENDOR_QUALITY_CHECK ReadFilterLibrary
passesCallThreshold(double) GenotypingEngine
passesEmitThreshold(double, boolean) GenotypingEngine
PassesFiltersVariantFilter() VariantFilterLibrary.PassesFiltersVariantFilter
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?
passesThreshold(Allele, double) AFCalculationResult
Are we confident that an allele is present
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 V extends BaseVertex ,E extends BaseEdge > - Class in org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
A path thought a BaseGraph
class to keep track of paths
Path(V, BaseGraph<V, E>) Path
Create a new Path containing no edges and starting at initialVertex
Path(List<E>, V, BaseGraph<V, E>) Path
Constructor that does not check arguments' validity i.e.
Path(Path<V, E>, E) Path
Create a new Path extending p with edge
Path(Path<V, E>, List<E>) Path
Create a new Path extending p with edge
Path(E, Path<V, E>) Path
Prepend a path with an edge.
pathExists(JavaSparkContext, Path) SparkUtils
Determine if the targetPath exists.
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.
PathProvider picard.nio
A class whose purpose is to initialize the various plugins that provide Path support.
PATHS RuntimeUtils
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
PathSpecifier org.broadinstitute.hellbender.engine
Default implementation for PathURI.
PathSpecifier(String) PathSpecifier
If the raw input string already contains a scheme (including a "file" scheme), assume its already
properly escape/encoded.
PathURI org.broadinstitute.hellbender.engine
Interface for htsjdk input/output URIs.
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_INDEL_QUAL_LONG_NAME M2ArgumentCollection
PCR_SLIPPAGE_RATE_LONG_NAME M2FiltersArgumentCollection
PCR_SNV_QUAL_LONG_NAME M2ArgumentCollection
pcrErrorModel LikelihoodEngineArgumentCollection
When calculating the likelihood of variants, we can try to correct for PCR errors that cause indel artifacts.
pcrIndelQual M2ArgumentCollection
pcrSnvQual M2ArgumentCollection
PCT_100X WgsMetrics
The fraction of bases that attained at least 100X sequence coverage in post-filtering bases.
PCT_10X WgsMetrics
The fraction of bases that attained at least 10X sequence coverage in post-filtering bases.
PCT_15X WgsMetrics
The fraction of bases that attained at least 15X sequence coverage in post-filtering bases.
PCT_1X WgsMetrics
The fraction of bases that attained at least 1X sequence coverage in post-filtering bases.
PCT_20X WgsMetrics
The fraction of bases that attained at least 20X sequence coverage in post-filtering bases.
PCT_25X WgsMetrics
The fraction of bases that attained at least 25X sequence coverage in post-filtering bases.
PCT_30X WgsMetrics
The fraction of bases that attained at least 30X sequence coverage in post-filtering bases.
PCT_40X WgsMetrics
The fraction of bases that attained at least 40X sequence coverage in post-filtering bases.
PCT_50X WgsMetrics
The fraction of bases that attained at least 50X sequence coverage in post-filtering bases.
PCT_5X WgsMetrics
The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.
PCT_60X WgsMetrics
The fraction of bases that attained at least 60X sequence coverage in post-filtering bases.
PCT_70X WgsMetrics
The fraction of bases that attained at least 70X sequence coverage in post-filtering bases.
PCT_80X WgsMetrics
The fraction of bases that attained at least 80X sequence coverage in post-filtering bases.
PCT_90X 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 or aligned with MQ0 and match to a known adapter sequence right from the
start of the read (indication of adapter-dimer pairs).
PCT_AMPLIFIED_BASES 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 CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The fraction of high confidence SNPs in dbSNP
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_ADAPTER PanelMetricsBase
The fraction of aligned bases in reads that have MQ=0 and whose 5' end consists of adapter sequence.
PCT_EXC_ADAPTER WgsMetrics
The fraction of aligned bases that were filtered out because they were in reads with mapping quality 0 and the looked like adapter reads.
PCT_EXC_BASEQ PanelMetricsBase
The fraction of aligned bases that were filtered out because they were of low base quality.
PCT_EXC_BASEQ WgsMetrics
The fraction of aligned bases that were filtered out because they were of low base quality (lower than MIN_BASE_QUALITY).
PCT_EXC_CAPPED WgsMetrics
The fraction of aligned bases that were filtered out because they would have raised coverage above COVERAGE_CAP.
PCT_EXC_DUPE PanelMetricsBase
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
PCT_EXC_DUPE WgsMetrics
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
PCT_EXC_MAPQ PanelMetricsBase
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
PCT_EXC_MAPQ WgsMetrics
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (lower than MIN_MAPPING_QUALITY).
PCT_EXC_OFF_TARGET PanelMetricsBase
The fraction of aligned bases that were filtered out because they did not align over a target base.
PCT_EXC_OVERLAP PanelMetricsBase
The fraction of aligned bases that were filtered out because they were the second observation from
an insert with overlapping reads.
PCT_EXC_OVERLAP WgsMetrics
The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
PCT_EXC_TOTAL WgsMetrics
The total fraction of aligned bases excluded due to all filters.
PCT_EXC_UNPAIRED 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_MIX VerifyIDIntensityContaminationMetrics
The percent mixture (contamination) of the sample for ID
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 PanelMetricsBase
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 PanelMetricsBase
The fraction of unique reads passing filter, PF_UNIQUE_READS/TOTAL_READS.
PCT_PF_UQ_READS_ALIGNED PanelMetricsBase
The fraction of unique reads passing filter that align to the reference,
PF_UQ_READS_ALIGNED/PF_UNIQUE_READS.
PCT_R1_TRANSCRIPT_STRAND_READS 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 aligned 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 PanelMetricsBase
The fraction of all target bases achieving 100X or greater coverage.
PCT_TARGET_BASES_10X PanelMetricsBase
The fraction of all target bases achieving 10X or greater coverage.
PCT_TARGET_BASES_1X PanelMetricsBase
The fraction of all target bases achieving 1X or greater coverage.
PCT_TARGET_BASES_20X PanelMetricsBase
The fraction of all target bases achieving 20X or greater coverage.
PCT_TARGET_BASES_2X PanelMetricsBase
The fraction of all target bases achieving 2X or greater coverage.
PCT_TARGET_BASES_30X PanelMetricsBase
The fraction of all target bases achieving 30X or greater coverage.
PCT_TARGET_BASES_40X PanelMetricsBase
The fraction of all target bases achieving 40X or greater coverage.
PCT_TARGET_BASES_50X PanelMetricsBase
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.
PED_FILE MergePedIntoVcf
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
pending AbstractReadThreadingGraph
Sequences added for read threading before we've actually built the graph
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.
percent_of_sites_with_more_than_2_alleles IndelSummary
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 an 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.
permute(double[], RandomDataGenerator) MathUtil
permute the input array randomly (using a RandomDataGenerator)
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>, ConcurrentHashMap<String, ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch>, ExtractIlluminaBarcodes.BarcodeMetric, IlluminaDataProviderFactory, int, int, int, int, List<File>, List<AbstractIlluminaPositionFileReader.PositionInfo>, File[], DistanceMetric) ExtractIlluminaBarcodes.PerTileBarcodeExtractor
PerTileBarcodeExtractor(int, File, Map<String, ExtractIlluminaBarcodes.BarcodeMetric>, ConcurrentHashMap<String, ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch>, ExtractIlluminaBarcodes.BarcodeMetric, IlluminaDataProviderFactory, int, int, int, int, DistanceMetric) 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, 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 PanelMetricsBase
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 PanelMetricsBase
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 PanelMetricsBase
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 TargetMetricsBase
Tracks the number of read pairs that we see that are PF (used to calculate library size)
PF_SELECTED_UNIQUE_PAIRS TargetMetricsBase
Tracks the number of unique PF_SELECTED_PAIRS we see (used to calc library size)
PF_STATUS ViewSam
PF_UNIQUE_READS PanelMetricsBase
The number of PF_READS that are not marked as duplicates.
PF_UQ_BASES_ALIGNED PanelMetricsBase
The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
PF_UQ_READS_ALIGNED PanelMetricsBase
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.
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>) AssemblyBasedCallerUtils
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.
phredScaledPosteriorAnnotationName() ContaminationFilter
phredScaledPosteriorAnnotationName() FilteredHaplotypeFilter
phredScaledPosteriorAnnotationName() GermlineFilter
phredScaledPosteriorAnnotationName() HardFilter
phredScaledPosteriorAnnotationName() Mutect2VariantFilter
phredScaledPosteriorAnnotationName() NormalArtifactFilter
phredScaledPosteriorAnnotationName() PolymeraseSlippageFilter
phredScaledPosteriorAnnotationName() ReadOrientationFilter
phredScaledPosteriorAnnotationName() StrandArtifactFilter
phredScaledPosteriorAnnotationName() TumorEvidenceFilter
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.arrays - package picard.arrays
picard.arrays.illumina - package picard.arrays.illumina
picard.cmdline - package picard.cmdline
picard.cmdline.argumentcollections - package picard.cmdline.argumentcollections
picard.cmdline.programgroups - package picard.cmdline.programgroups
picard.fastq - package picard.fastq
picard.filter - package picard.filter
picard.fingerprint - package picard.fingerprint
picard.illumina - package picard.illumina
picard.illumina.parser - package picard.illumina.parser
picard.illumina.parser.fakers - package picard.illumina.parser.fakers
picard.illumina.parser.readers - package picard.illumina.parser.readers
picard.illumina.quality - package picard.illumina.quality
picard.metrics - package picard.metrics
picard.nio - package picard.nio
picard.pedigree - package picard.pedigree
picard.reference - package picard.reference
picard.sam - package picard.sam
picard.sam.markduplicates - package picard.sam.markduplicates
picard.sam.markduplicates.util - package picard.sam.markduplicates.util
picard.sam.SamErrorMetric - package picard.sam.SamErrorMetric
picard.sam.util - package picard.sam.util
picard.util - package picard.util
picard.util.help - package picard.util.help
picard.util.IntervalList - package picard.util.IntervalList
picard.vcf - package picard.vcf
picard.vcf.filter - package picard.vcf.filter
picard.vcf.MendelianViolations - package picard.vcf.MendelianViolations
picard.vcf.processor - package picard.vcf.processor
picard.vcf.processor.util - package picard.vcf.processor.util
PICARD_INTERVAL_FILE_EXTENSION SplitIntervals
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
PileupSummary.PileupSummaryComparator org.broadinstitute.hellbender.tools.walkers.contamination
PileupSummaryComparator(SAMSequenceDictionary) PileupSummary.PileupSummaryComparator
PIPELINE_MAX_ALT_COUNT GnarlyGenotyper
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.
ploidy VariantEval
PLOIDY_HEADER_NAME IlluminaManifest
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
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.
POINTS_PER_SEGMENTATION_WINDOW ContaminationSegmenter
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.
POLYMERASE_SLIPPAGE GATKVCFConstants
POLYMERASE_SLIPPAGE_QUAL_KEY GATKVCFConstants
PolymeraseSlippageFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
PolymeraseSlippageFilter(int, double) PolymeraseSlippageFilter
PolymorphicNuMTFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
PolymorphicNuMTFilter(double) PolymorphicNuMTFilter
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_KEY 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 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(File) PossibleDeNovo
PossibleDeNovo() PossibleDeNovo
postDiNucleotideStratifier ReadBaseStratification
Stratifies a base onto the reference base that it covers and the following base, possibly reverse complemented if the read
has been reversed by the aligner.
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
posteriorProbabilityOfError(VariantContext, double, int) Mutect2FilteringEngine
posteriorProbabilityOfNormalArtifact(double) Mutect2FilteringEngine
posteriors(double[], double[]) NaturalLogUtils
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.
postProcessForHaplotypeFinding(File, Locatable) AbstractReadThreadingGraph
postProcessForHaplotypeFinding(File, Locatable) JunctionTreeLinkedDeBruinGraph
Generate the junction trees and prune them (optionally printing the graph stages as output)
postProcessForHaplotypeFinding(File, Locatable) ReadThreadingGraph
PostprocessGermlineCNVCalls org.broadinstitute.hellbender.tools.copynumber
Postprocesses the output of
GermlineCNVCaller and generates VCF files as well as a concatenated denoised
copy ratio file.
PostprocessGermlineCNVCalls() PostprocessGermlineCNVCalls
POTENTIAL_POLYMORPHIC_NUMT_FILTER_NAME GATKVCFConstants
POWER_HEADER_LINE ValidateBasicSomaticShortMutations
POWER_INFO_FIELD_KEY ValidateBasicSomaticShortMutations
PowerCalculationUtils org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
PPV ValidationReport
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
preDiNucleotideStratifier ReadBaseStratification
Stratifies a base onto the reference base that it covers and the preceding base, possibly reverse complemented if the read
has been reversed by the aligner.
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.
preprocessIntervalList(IntervalList) IntervalListScatterer
A function that will be called on an IntervalList prior to splitting it into sub-lists, and is a point where
implementations can chose to impose some conditions on the lists, for example, merging overlapping/abutting intervals,
removing duplicates, etc.
preprocessIntervalList(IntervalList) IntervalListScattererWithSubdivision
PreprocessIntervals org.broadinstitute.hellbender.tools.copynumber
Prepares bins for coverage collection.
PreprocessIntervals() PreprocessIntervals
preprocessReads() AbstractReadThreadingGraph
preprocessReads() JunctionTreeLinkedDeBruinGraph
preprocessReads() ReadThreadingGraph
Since we want to duplicate non-unique kmers in the graph code we must determine what those kmers are
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
previousReadBaseStratifier ReadBaseStratification
Stratifies bases into the previous (uppercase) base as it was read from the sequencer (i.e.
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
PrimaryAlignmentKey picard.sam.util
It is useful to define a key such that the key will occur at most once among the primary alignments in a given file
(assuming the file is valid).
PrimaryAlignmentKey(SAMRecord) 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_StrandBiasTest
PRINT_SUMMARY_LONG_NAME CompareDuplicatesSpark
PrintBGZFBlockInformation org.broadinstitute.hellbender.tools
A diagnostic tool that prints information about the compressed blocks in a BGZF format file,
such as a .vcf.gz file or a .bam file.
PrintBGZFBlockInformation() PrintBGZFBlockInformation
printDebugHistograms() ReadThreadingAssembler
Print the generated graphs to the graphWriter
printDecoratedExceptionMessage(PrintStream, Exception, String) Main
Prints the given message (may be null) to the provided stream, adding adornments and formatting.
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.
PrintMissingComp org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
PrintMissingComp() PrintMissingComp
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
PrintReadsHeader org.broadinstitute.hellbender.tools
PrintReadsHeader() PrintReadsHeader
PrintReadsSpark org.broadinstitute.hellbender.tools.spark.pipelines
PrintReadsSpark() PrintReadsSpark
printReport() SamComparison
printSettings() CommandLineProgram
Output a curated set of important settings to the logger.
printSimplifiedGraph(File, int) JunctionTreeLinkedDeBruinGraph
Print out the graph in the dot language for visualization for the graph after merging the graph into a seq graph.
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
printVersionInfo(PrintStream) Main
Prints version information for the toolkit, including versions of important libraries.
prior TrainingSet
PRIOR_ERROR ErrorMetric
PRIOR_Q CollectSamErrorMetrics
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) InsertSizeDistribution
probability(int) BetaBinomialDistribution
PROBABILITY DownsampleSam
PROBABILITY CollectSamErrorMetrics
probabilityOfSequencingError(Datum) SomaticClusteringModel
PROBE_A InfiniumVcfFields
PROBE_B InfiniumVcfFields
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(ReadPileup, ReferenceContext) F1R2CountsCollector
process ProcessControllerBase
process() VariantProcessor
PROCESS_SINGLE_TILE IlluminaBasecallsToSam
processAlignments(JavaRDD<LocusWalkerContext>, JavaSparkContext) LocusWalkerSpark
Process the alignments and write output.
processAlignments(JavaRDD<LocusWalkerContext>, JavaSparkContext) CollectAllelicCountsSpark
processAlignments(JavaRDD<LocusWalkerContext>, JavaSparkContext) ExampleLocusWalkerSpark
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
processAssemblyRegions(JavaRDD<AssemblyRegionWalkerContext>, JavaSparkContext) HaplotypeCallerSpark
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
ProcessControllerAckResult org.broadinstitute.hellbender.utils.runtime
Command acknowledgements that are returned from a process managed by StreamingProcessController.
ProcessControllerAckResult(boolean) ProcessControllerAckResult
Creates an ack result, for ACK or NCK.
ProcessControllerAckResult(String) ProcessControllerAckResult
Creates an (negative NKM) ack result, with a message.
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
processDeletionLocus(SamLocusIterator.RecordAndOffset, SamLocusIterator.LocusInfo) CollectSamErrorMetrics
Checks if the same record has been seen at the previous locus already, thereby determining
whether or not a deletion has already been processed.
processedMultiIndelRatio MultiallelicSummary
processedMultiSnpRatio MultiallelicSummary
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
processReads(JavaRDD<ReadWalkerContext>, JavaSparkContext) ExampleReadWalkerWithVariantsSpark
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
processTranscriptList(Set<String>) FuncotatorEngine
Processes the given Set into a list of transcript IDs.
processVariants(JavaRDD<VariantWalkerContext>, JavaSparkContext) VariantWalkerSpark
Process the variants and write output.
processVariants(JavaRDD<VariantWalkerContext>, JavaSparkContext) ExampleVariantWalkerSpark
processVariants(JavaRDD<VariantWalkerContext>, JavaSparkContext) PrintVariantsSpark
produceAnnotatedVcFromAssemblyEvidence(SvType, SimpleNovelAdjacencyAndChimericAlignmentEvidence, Broadcast<ReferenceMultiSparkSource>, Broadcast<SAMSequenceDictionary>, Broadcast<SVIntervalTree<VariantContext>>, String) AnnotatedVariantProducer
produceAnnotatedVcFromEvidenceTargetLink(EvidenceTargetLink, SvType) AnnotatedVariantProducer
produceLinkedAssemblyBasedVariants(Tuple2<SvType, SvType>, SimpleNovelAdjacencyAndChimericAlignmentEvidence, Broadcast<ReferenceMultiSparkSource>, 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.
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 MergeBamAlignment
PROGRAM_GROUP_NAME AbstractMarkDuplicatesCommandLineProgram
PROGRAM_GROUP_NAME MergeBamAlignment
PROGRAM_GROUP_VERSION AbstractMarkDuplicatesCommandLineProgram
PROGRAM_GROUP_VERSION MergeBamAlignment
PROGRAM_RECORD_ID AbstractMarkDuplicatesCommandLineProgram
PROGRAM_RECORD_ID MergeBamAlignment
PROGRAM_RECORD_ID_SHORT_NAME StandardArgumentDefinitions
PROGRAM_RECORD_ID_SHORT_NAME StandardOptionDefinitions
programName SparkCommandLineProgram
PROGRESS_STEP_INTERVAL CollectSamErrorMetrics
progressBytesRead NioFileCopierWithProgressMeter
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
progressPercentDisplayIncrement NioFileCopierWithProgressMeter
ProgressReportingDelegatingCodec A extends htsjdk.tribble.Feature,B > - Class in org.broadinstitute.hellbender.utils.codecs
This class is useful when we want to report progress when indexing.
ProgressReportingDelegatingCodec() ProgressReportingDelegatingCodec
ProgressReportingDelegatingCodec(FeatureCodec<A, B>, double) ProgressReportingDelegatingCodec
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
ProteinChangeInfo org.broadinstitute.hellbender.tools.funcotator
Class representing the change in the protein sequence for a specific reference/alternate allele pair in a variant.
PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN MarkIlluminaAdapters
pruneJunctionTrees(int) JunctionTreeLinkedDeBruinGraph
Traverse all of the junction trees in the graph and remove branches supported by < minimumEdgeWeight edges recursively.
pruneLowWeightChains(BaseGraph<V, E>) ChainPruner
pruningLogOddsThreshold ReadThreadingAssemblerArgumentCollection
Log-10 likelihood ratio threshold for adaptive pruning algorithm.
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
PURINE Nucleotide
PushPullTransformer T > - Interface in org.broadinstitute.hellbender.utils.iterators
A class that receives a stream of elements and transforms or filters them in some way, such as by downsampling with
a
Downsampler.
PushToPullIterator T > - Class in org.broadinstitute.hellbender.utils.iterators
Iterator wrapper around our generic PushPullTransformer) interface.
PushToPullIterator(Iterator<T>, PushPullTransformer<T>) PushToPullIterator
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(List<Object>, V) StratificationManager
put(T, int...) NestedIntegerArray
Insert a value at the position specified by the given keys.
put(int, int[][][]) CovariateKeyCache
Store the given array in the cache.
put(int, String, ReadEndsForMarkDuplicates) DiskBasedReadEndsForMarkDuplicatesMap
put(int, String, ReadEndsForMarkDuplicates) MemoryBasedReadEndsForMarkDuplicatesMap
put(int, String, ReadEndsForMarkDuplicates) ReadEndsForMarkDuplicatesMap
Store the element in the map with the given key.
putAll(Map<? extends List<Object>, ? extends V>) StratificationManager
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
PYRIMIDINE Nucleotide
PYTHON_EXTENSION PythonExecutorBase
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 InfiniumVcfFields
R ReadEnds
R_LIBRARY_SUFFIX RScriptLibrary
RANDOM_SEED DownsampleSam
RANDOM_SEED_FOR_CHAIN_GENERATION HMM
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
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.
rate(long, long) VariantEvaluator
ratio(long, long) VariantEvaluator
ratio_of_1_and_2_to_3_bp_deletions IndelSummary
ratio_of_1_and_2_to_3_bp_insertions IndelSummary
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_GENOTYPE_COUNT_KEY GATKVCFConstants
RAW_MAP_QUAL_RANK_SUM_KEY GATKVCFConstants
RAW_MAPPING_QUALITY_WITH_DEPTH_KEY GATKVCFConstants
RAW_QUAL_APPROX_KEY GATKVCFConstants
RAW_RMS_MAPPING_QUALITY_DEPRECATED 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, double, int, Histogram<Integer>, int) CollectRawWgsMetrics.RawWgsMetrics
rawXIntensity InfiniumGTCRecord
rawYIntensity InfiniumGTCRecord
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.InvertedDuplicationBreakpointComplications>) BreakpointComplications.InvertedDuplicationBreakpointComplications.Serializer
read(Kryo, Input, Class<BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications>) BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications.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(File) BasicValidationResult
read(char[], int, int) LineIteratorReader
Reads lines from the buffer, and if empty from the underlying line-iterator.
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(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
read1IndexInFile ReadEndsForMarkDuplicates
read1ReferenceIndex ReadEnds
read2 QuerySortedReadPairIteratorUtil.ReadPair
READ2_ALIGNED_BAM MergeBamAlignment
READ2_MAX_BASES_TO_WRITE SamToFastq
READ2_TRIM MergeBamAlignment
READ2_TRIM SamToFastq
read2Coordinate ReadEnds
read2IndexInFile ReadEndsForMarkDuplicates
read2ReferenceIndex ReadEnds
READ_CHUNK_SIZE BamToBfq
READ_END BaseDistributionByCycleMetrics
READ_END BaseDistributionByCycleMetrics
READ_FILTER_LONG_NAME ReadFilterArgumentDefinitions
read_filter_packages() GATKConfig
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 ArtificialReadUtils
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_ORIENTATION_ARTIFACT_FILTER_NAME GATKVCFConstants
READ_ORIENTATION_QUAL_KEY GATKVCFConstants
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.
readAltSiteRecords(Path, int) AltSiteRecord
Code for reading sample name and alt site records from a table
readAltSiteRecords(Path) AltSiteRecord
readAndMateAreUnmapped(GATKRead) ReadUtils
Helper method for interrogating if a read and its mate (if it exists) are unmapped
readArguments GATKTool
readArguments GATKSparkTool
readArtifactPriors(File) ArtifactPriorCollection
Contract: only read from the file created by writeArtifactPriors
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
ReadBaseStratification picard.sam.SamErrorMetric
Classes, methods, and enums that deal with the stratification of read bases and reference information.
ReadBaseStratification() ReadBaseStratification
ReadBaseStratification.BinnedReadCycleStratifier picard.sam.SamErrorMetric
Stratifies into quintiles of read cycle.
ReadBaseStratification.CigarOperatorsInReadStratifier picard.sam.SamErrorMetric
Stratifies according to the number of matching cigar operators (from CIGAR string) that the read has.
ReadBaseStratification.CollectionStratifier picard.sam.SamErrorMetric
A CollectionStratifier is a stratifier that uses a collection of stratifiers to inform the stratification.
ReadBaseStratification.Consensus picard.sam.SamErrorMetric
Types of consensus reads as determined by the number of duplicates used from
first and second strands.
ReadBaseStratification.ConsensusStratifier picard.sam.SamErrorMetric
Stratify by tags used during duplex and single index consensus calling.
ReadBaseStratification.CycleBin picard.sam.SamErrorMetric
An enum designed to hold a binned version of any probability-like number (between 0 and 1)
in quintiles
ReadBaseStratification.FlowCellTileStratifier picard.sam.SamErrorMetric
Stratifies base into their read's tile which is parsed from the read-name.
ReadBaseStratification.GCContentStratifier picard.sam.SamErrorMetric
A stratifier that uses GC (of the read) to stratify.
ReadBaseStratification.IndelLengthStratifier picard.sam.SamErrorMetric
Stratifies according to the length of an insertion or deletion.
ReadBaseStratification.IndelsInReadStratifier picard.sam.SamErrorMetric
Stratifies according to the number of indel bases (from CIGAR string) that the read has.
ReadBaseStratification.LongShortHomopolymer picard.sam.SamErrorMetric
ReadBaseStratification.LongShortHomopolymerStratifier picard.sam.SamErrorMetric
Stratify bases according to the type of Homopolymer that they belong to (repeating element, final reference base and
whether the length is "long" or not).
ReadBaseStratification.MismatchesInReadStratifier picard.sam.SamErrorMetric
Stratifies according to the overall mismatches (from SAMTag.NM) that the read has against the reference, NOT
including the current base.
ReadBaseStratification.NsInReadStratifier picard.sam.SamErrorMetric
Stratify by the number of Ns found in the read.
ReadBaseStratification.PairOrientation picard.sam.SamErrorMetric
An enum for holding a reads read-pair's Orientation (i.e.
ReadBaseStratification.PairStratifier T extends java.lang.Comparable<T >,R extends java.lang.Comparable<R >> - Class in picard.sam.SamErrorMetric
A PairStratifier is a stratifier that uses two other stratifiers to inform the stratification.
ReadBaseStratification.ProperPaired picard.sam.SamErrorMetric
An enum to hold information about the "properness" of a read pair
ReadBaseStratification.ReadDirection picard.sam.SamErrorMetric
An enum for holding the direction for a read (positive strand or negative strand
ReadBaseStratification.ReadOrdinality picard.sam.SamErrorMetric
An enum to hold the ordinality of a read
ReadBaseStratification.RecordAndOffsetStratifier T extends java.lang.Comparable<T >> - Interface in picard.sam.SamErrorMetric
The main interface for a stratifier.
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.
ReadClipperWithData(GATKRead, List<ClipReads.SeqToClip>) ClipReads.ReadClipperWithData
readColumnsFromHeader(File) CopyNumberFormatsUtils
Extracts column names from a TSV file
ReadConstants org.broadinstitute.hellbender.utils.read
Constants for use with the GATKRead interface
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 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
readDirectionStratifier ReadBaseStratification
Stratifies bases into their read's Direction (i.e.
ReadEnds picard.sam.markduplicates.util
Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
ReadEnds() ReadEnds
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 picard.sam.markduplicates.util
Codec for ReadEnds that just outputs the primitive fields and reads them back.
ReadEndsForMarkDuplicatesCodec() ReadEndsForMarkDuplicatesCodec
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"
Reader(Path) ConcordanceSummaryRecord.Reader
reader(Path, 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.MateUnmappedAndUnmappedReadFilter org.broadinstitute.hellbender.engine.filters
Filter reads whose mate is unmapped as well as unmapped reads.
ReadFilterLibrary.NonChimericOriginalAlignmentReadFilter org.broadinstitute.hellbender.engine.filters
If original alignment and mate original alignment tags exist, filter reads that were originally chimeric (mates were on different contigs).
ReadFilterLibrary.NonZeroFragmentLengthReadFilter 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) MutectStats
readFromFile(File) FilterAnalysisRecord
readFromPath(Path) MinorAlleleFractionRecord
readFromPath(Path) FilterAnalysisRecord
readGroup ReadGroupReadFilter
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
readGroupIndex TransientFieldPhysicalLocation
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
readgroupStratifier ReadBaseStratification
Stratifies to the readgroup id of the read.
readHasMappedMate(GATKRead) ReadUtils
readHasMappedMate(SAMRecord) ReadUtils
readHasNoAssignedPosition(GATKRead) ReadUtils
Checks whether the provided read has an assigned position.
readHasReasonableMQ(GATKRead) ReadUtils
Used to be called isUsableRead()
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
ReadlessAssemblyRegion org.broadinstitute.hellbender.engine
ReadlessAssemblyRegion(AssemblyRegion) ReadlessAssemblyRegion
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.
readLines() XReadLines
Reads all of the lines in the file, and returns them as a list of strings
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
readMetricsFile(File) LearnReadOrientationModel
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
readNameRegex ReadNameParser
readNextLine() AbstractInputParser
readNextLine() BasicInputParser
Workhorse method that reads the next line from the underlying reader
readObject(ObjectInputStream) ContainsKmerReadFilterSpark
readOneBarcode ReadEndsForMarkDuplicatesWithBarcodes
readOrdinalityStratifier ReadBaseStratification
Stratifies bases into their read's Ordinality (i.e.
ReadOrientation org.broadinstitute.hellbender.tools.walkers.readorientation
Created by tsato on 3/28/18.
readOrientationBiasSummaryTable(File) OrientationBiasUtils
ReadOrientationFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
ReadOrientationFilter(List<File>) ReadOrientationFilter
readOrientationPriorTarGzs M2FiltersArgumentCollection
readOrientationStratifier ReadBaseStratification
Stratifies bases into their read-pair's Orientation (i.e.
readOverlapsRegion(GATKRead) AssemblyRegion
Returns true if read would overlap the extended extent of this region
ReadPair() QuerySortedReadPairIteratorUtil.ReadPair
readPairednessStratifier ReadBaseStratification
Stratifies bases into their read's Proper-pairedness
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
ReadPositionFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
ReadPositionFilter(double) ReadPositionFilter
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 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
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.
ReadsContext(ReadsContext, SimpleInterval) ReadsContext
Create a ReadsContext using the data source from the provided ReadsContext, with the supplied
interval.
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 AssemblyRegionReadShardArgumentCollection
readShardSize AssemblyRegionReadShardArgumentCollection
readShardSize LocusWalkerSpark
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
ReadsKey.KeyForFragment org.broadinstitute.hellbender.utils.read.markduplicates
Key class for representing relevant duplicate marking identifiers into a single long key for fragment data.
ReadsKey.KeyForPair org.broadinstitute.hellbender.utils.read.markduplicates
Key class for representing relevant duplicate marking identifiers into a two long key values for pair data data.
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
ReadsSparkSink org.broadinstitute.hellbender.engine.spark.datasources
ReadsSparkSink writes GATKReads to a file.
ReadsSparkSink() ReadsSparkSink
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
readStandalone(String) ReadMetadata.Serializer
Reads a read-metadata from a file or resource.
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
readSubsequence BarcodeEditDistanceQuery
list of barcode reads
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, int, boolean, double, double, int, boolean) ReadThreadingAssembler
ReadThreadingAssemblerArgumentCollection org.broadinstitute.hellbender.tools.walkers.haplotypecaller
ReadThreadingAssemblerArgumentCollection() ReadThreadingAssemblerArgumentCollection
ReadThreadingGraph org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
Note: not final but only intended 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(byte[]) RealignmentEngine
realignmentArgumentCollection FilterAlignmentArtifacts
RealignmentArgumentCollection org.broadinstitute.hellbender.tools.walkers.realignmentfilter
RealignmentArgumentCollection() RealignmentArgumentCollection
RealignmentEngine org.broadinstitute.hellbender.tools.walkers.realignmentfilter
RealignmentEngine(RealignmentArgumentCollection) RealignmentEngine
realignReadsToTheirBestHaplotype(AlleleLikelihoods<GATKRead, Haplotype>, Haplotype, Locatable, SmithWatermanAligner) AssemblyBasedCallerUtils
Returns a map with the original read as a key and the realigned read as the value.
reallyFilterOut(SAMRecord) CountingAdapterFilter
reallyFilterOut(SAMRecord) CountingDuplicateFilter
reallyFilterOut(SAMRecord) CountingFilter
Return true if we are to filter this record out, false otherwise.
reallyFilterOut(SAMRecord) CountingMapQFilter
reallyFilterOut(SAMRecord) CountingPairedFilter
ReblockGVCF org.broadinstitute.hellbender.tools.walkers.variantutils
Condense homRef blocks in a single-sample GVCF
ReblockGVCF() ReblockGVCF
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.
record(int[], double[], double, double, VariantContext) SomaticClusteringModel
Record(short, short, float, float, float, IlluminaGenotype) IlluminaAdpcFileWriter.Record
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.
recordCall(ErrorProbabilities, double) FilteringOutputStats
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
RECOVER_SWAPPED_REF_ALT LiftoverVcf
recoverAllDanglingBranches ReadThreadingAssemblerArgumentCollection
By default, the read threading assembler does not recover dangling branches that fork after splitting from the reference.
recoverDanglingHeads(int, int, boolean, SmithWatermanAligner) AbstractReadThreadingGraph
Try to recover dangling heads
recoverDanglingTails(int, int, boolean, SmithWatermanAligner) AbstractReadThreadingGraph
Try to recover dangling tails
RED CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
The red intensity value for the control.
reduce(FindBreakpointEvidenceSpark.IntPair, FindBreakpointEvidenceSpark.IntPair) FindBreakpointEvidenceSpark.IntPair
reduce(ReadMetadata.LibraryRawStatistics, ReadMetadata.LibraryRawStatistics) ReadMetadata.LibraryRawStatistics
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() Transition
ref GVCFBlock
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_CONTEXT_PADDING F1R2FilterConstants
REF_COUNT ErrorSummaryMetrics
The number of reference bases observed.
REF_FLAT CollectMultipleMetrics
REF_FLAT CollectRnaSeqMetrics
REF_HIST_EXTENSION F1R2CountsCollector
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_STRAND_HEADER_NAME IlluminaManifest
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).
refAllele SvType
refBases BAQ.BAQCalculationResult
refDepth ReferenceConfidenceResult
reference FilterFuncotations
reference PathSeqBuildKmers
reference OverhangFixingManager.Splice
REFERENCE CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
REFERENCE CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
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
REFERENCE_WINDOW_PADDING MultiVariantWalkerGroupedOnStart
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
referenceBaseStratifier ReadBaseStratification
Stratifies a base onto the reference base that it covers, possibly reverse complemented if the read
has been reversed by the aligner.
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
ReferenceConfidenceResult org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Holds information about a genotype call of a single sample reference vs.
ReferenceConfidenceResult() ReferenceConfidenceResult
ReferenceConfidenceUtils org.broadinstitute.hellbender.tools.walkers.haplotypecaller
ReferenceConfidenceUtils() ReferenceConfidenceUtils
ReferenceConfidenceVariantContextMerger org.broadinstitute.hellbender.tools.walkers
Variant context utilities related to merging variant-context instances.
ReferenceConfidenceVariantContextMerger(VariantAnnotatorEngine, VCFHeader) ReferenceConfidenceVariantContextMerger
ReferenceConfidenceVariantContextMerger(VariantAnnotatorEngine, VCFHeader, boolean) ReferenceConfidenceVariantContextMerger
ReferenceConfidenceVariantContextMerger(VariantAnnotatorEngine, VCFHeader, boolean, boolean) 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(ReferenceContext, SimpleInterval) ReferenceContext
Create a windowed ReferenceContext set up to lazily query the provided interval.
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.
referenceFasta AbstractAlignmentMerger
referenceFasta AbstractAlignmentMerger
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.
ReferenceFileSparkSource org.broadinstitute.hellbender.engine.spark.datasources
Class to load a reference sequence from a fasta file on Spark.
ReferenceFileSparkSource(String) ReferenceFileSparkSource
ReferenceFileSparkSource(Path) ReferenceFileSparkSource
ReferenceHadoopSparkSource org.broadinstitute.hellbender.engine.spark.datasources
Class to load a reference sequence from a fasta file on HDFS.
ReferenceHadoopSparkSource(String) ReferenceHadoopSparkSource
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.
ReferenceMultiSparkSource org.broadinstitute.hellbender.engine.spark.datasources
Wrapper to load a reference sequence from the Google Genomics API, or a file stored on HDFS or locally.
ReferenceMultiSparkSource() ReferenceMultiSparkSource
ReferenceMultiSparkSource(String, SerializableFunction<GATKRead, SimpleInterval>) ReferenceMultiSparkSource
referencePath PSBwaArgumentCollection
referencePath AbstractReadThreadingGraph
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
referenceSpan AlignmentInterval
ReferenceSparkSource org.broadinstitute.hellbender.engine.spark.datasources
Internal interface to load a reference sequence.
ReferenceTwoBitSparkSource org.broadinstitute.hellbender.engine.spark.datasources
A ReferenceSource impl that is backed by a .2bit representation of a reference genome.
ReferenceTwoBitSparkSource(String) ReferenceTwoBitSparkSource
ReferenceUtils org.broadinstitute.hellbender.utils.reference
A collection of static methods for dealing with references.
ReferenceWalker org.broadinstitute.hellbender.engine
A reference walker is a tool which processes each base in a given reference.
ReferenceWalker() ReferenceWalker
ReferenceWindowFunctions org.broadinstitute.hellbender.engine.spark.datasources
A library of reference window functions suitable for passing in to transforms such as AddContextDataToRead.
ReferenceWindowFunctions() ReferenceWindowFunctions
ReferenceWindowFunctions.FixedWindowFunction org.broadinstitute.hellbender.engine.spark.datasources
A function for requesting a fixed number of extra bases of reference context on either side
of each read.
referenceWindowPadding MultiVariantWalkerGroupedOnStart
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
RefuseNegativeContigAndCoordinates SVInterval.SVIntervalConstructorArgsValidator
RefuseNegativeContigs SVInterval.SVIntervalConstructorArgsValidator
RefuseNegativeCoordinates SVInterval.SVIntervalConstructorArgsValidator
RefVsAnyResult org.broadinstitute.hellbender.tools.walkers.haplotypecaller
Holds information about a genotype call of a single sample reference vs.
RefVsAnyResult(int) RefVsAnyResult
Creates a new ref-vs-alt result indicating the genotype likelihood vector capacity.
regenerateVariationEvents(int) AssemblyResultSet
regionStartLoc ActivityProfile
regionStopLoc ActivityProfile
regionWithHigherCoordOnContig SimpleChimera
regionWithLowerCoordOnContig SimpleChimera
registerClasses(Kryo) GATKRegistrator
registerFuncotationMapDependencies(Kryo) GATKRegistrator
Make sure that all FuncotationMap (which incl.
REINTERPRETED_1_SEG_CALL_VCF_FILE_NAME SvDiscoverFromLocalAssemblyContigAlignmentsSpark
REINTERPRETED_MULTI_SEG_CALL_VCF_FILE_NAME SvDiscoverFromLocalAssemblyContigAlignmentsSpark
REJECT LiftOverIntervalList
REJECT LiftoverVcf
relearnThresholdAndClearAcumulatedProbabilities() ThresholdCalculator
remap(Allele) GATKVariantContextUtils.AlleleMapper
remap(List<Allele>) GATKVariantContextUtils.AlleleMapper
remapALengthList(List<?>, int[]) ReferenceConfidenceVariantContextMerger
Given a list of per-alt-allele attributes, subset to relevant alt alleles
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.
remapRLengthList(List<?>, int[]) ReferenceConfidenceVariantContextMerger
Given a list of per-allele attributes including the reference allele, subset to relevant alleles
remove() ActivityProfileStateIterator
remove() AssemblyRegionFromActivityProfileStateIterator
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) StratificationManager
remove(Object) IndexedSet
Removes an element from the set.
remove(GenomeLoc) GenomeLocSortedSet
a simple removal of an interval contained in this list.
remove() AllLocusIterator
remove() CloseAtEndIterator
remove() PushToPullIterator
remove() ReadCachingIterator
remove() ArtificialReadIterator
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(int, String) MemoryBasedReadEndsForMarkDuplicatesMap
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_ALL_DUPLICATE_READS MarkDuplicatesSparkArgumentCollection
REMOVE_DEFAULT_ATTRIBUTE_TO_CLEAR_LONG_NAME RevertSamSpark
REMOVE_DUPLICATE_INFORMATION PositionBasedDownsampleSam
REMOVE_DUPLICATE_INFORMATION RevertSam
REMOVE_DUPLICATES AbstractMarkDuplicatesCommandLineProgram
REMOVE_FILTERED_VARIANTS_LONG_NAME FuncotatorArgumentDefinitions
REMOVE_SEQUENCING_DUPLICATE_READS MarkDuplicatesSparkArgumentCollection
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
removeAllDuplicates MarkDuplicatesSparkArgumentCollection
removeChild(int) PSTreeNode
removeDefaults RevertSamSpark
removeEach(Object) HopscotchCollection
remove each of the elements equivalent to the key
removeEldestEntry(Map.Entry<K, V>) LRUCache
removeFilteredVariants FuncotatorVariantArgumentCollection
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
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
removeSampleEvidence(int, Collection<EVIDENCE>, int) AlleleLikelihoods
removeSequencingDuplicates MarkDuplicatesSparkArgumentCollection
removeShadowedContigs StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
removeSingletonOrphanVertices() BaseGraph
Remove all vertices in the graph that have in and out degree of 0
removeSingletonOrphanVertices() AbstractReadThreadingGraph
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) AbstractReadThreadingGraph
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
renderProteinChangeString(SequenceComparison, Locatable) FuncotatorUtils
renderSamFileHeader() XsvLocatableTableCodec
Create a SAM File Header from the preamble.
renderSanitizedFuncotationForVcf(Funcotation, List<String>) FuncotatorUtils
renderTileMetricsFileFromBasecallingDirectory(File, int, boolean) TileMetricsUtil
ReorderSam picard.sam
Reorders a SAM/BAM input file according to the order of contigs in a second reference file.
ReorderSam() ReorderSam
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
replaceExtension(String, String) IOUtils
replaceExtension(File, String) IOUtils
ReplaceSamHeader picard.sam
ReplaceSamHeader() ReplaceSamHeader
replicationRateFromReplicateSets IndependentReplicateMetric
REPORTED_GENDER CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The sex, as reported by the collaborator
ReportTypeCounts() AnalyzeSaturationMutagenesis.ReportTypeCounts
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
Require2BitReferenceForBroadcast() UserException.Require2BitReferenceForBroadcast
REQUIRE_INDEX VcfFormatConverter
requiredAnnotations() BaseQualityFilter
requiredAnnotations() ChimericOriginalAlignmentFilter
requiredAnnotations() ClusteredEventsFilter
requiredAnnotations() ContaminationFilter
requiredAnnotations() DuplicatedAltReadFilter
requiredAnnotations() FilteredHaplotypeFilter
requiredAnnotations() FragmentLengthFilter
requiredAnnotations() GermlineFilter
requiredAnnotations() MappingQualityFilter
requiredAnnotations() MinAlleleFractionFilter
requiredAnnotations() MultiallelicFilter
requiredAnnotations() Mutect2VariantFilter
requiredAnnotations() NormalArtifactFilter
requiredAnnotations() NRatioFilter
requiredAnnotations() PanelOfNormalsFilter
requiredAnnotations() PolymeraseSlippageFilter
requiredAnnotations() PolymorphicNuMTFilter
requiredAnnotations() ReadOrientationFilter
requiredAnnotations() ReadPositionFilter
requiredAnnotations() StrandArtifactFilter
requiredAnnotations() StrictStrandBiasFilter
requiredAnnotations() TumorEvidenceFilter
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
RequiredStratification org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
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
requiresFeatures() DataSourceFuncotationFactory
requiresFeatures() CosmicFuncotationFactory
requiresFeatures() SimpleKeyXsvFuncotationFactory
requiresFeatures() GetPileupSummaries
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() CollectAllelicCountsSpark
requiresIntervals() CollectReadCounts
requiresIntervals() GetPileupSummaries
requiresIntervals() CountFalsePositives
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() AnalyzeSaturationMutagenesis
requiresReads() AnnotatePairOrientation
requiresReads() GetSampleName
requiresReads() PrintReadsHeader
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() RevertSamSpark
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() ReferenceWalker
requiresReference() AssemblyRegionWalkerSpark
requiresReference() GATKSparkTool
Does this tool require reference data? Tools that do should override to return true.
requiresReference() VariantLocusWalker
requiresReference() AnalyzeSaturationMutagenesis
requiresReference() AnnotateIntervals
requiresReference() CollectAllelicCounts
requiresReference() CollectAllelicCountsSpark
requiresReference() PreprocessIntervals
requiresReference() TagGermlineEvents
requiresReference() ExampleReadWalkerWithReferenceSpark
requiresReference() FuncotateSegments
requiresReference() Funcotator
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() GnarlyGenotyper
requiresReference() MethylationTypeCaller
requiresReference() FilterMutectCalls
requiresReference() CheckPileup
requiresReference() CollectF1R2Counts
requiresReference() SplitNCigarReads
requiresReference() ValidateBasicSomaticShortMutations
requiresReference() LeftAlignAndTrimVariants
Reference is required for left alignment
requiresReference() CNNScoreVariants
requiresReference() CollectSequencingArtifactMetrics
requiresReference() CollectOxoGMetrics
requiresReference() CollectWgsMetrics
requiresReference() GtcToVcf
requiresReference() CommandLineProgram
requiresReference() IdentifyContaminant
requiresReference() ExtractSequences
requiresReference() MergeBamAlignment
requiresReference() CollectSamErrorMetrics
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() CachingIndexedFastaSequenceFile
Resets the ReferenceSequenceFile so that the next call to nextSequence() will return
the first sequence in the file.
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
resetReadsDataSource() ReadWalker
Reset the reads data source so the caller can iterate through the reads again.
resetRefSeqFileWalker() AbstractAlignmentMerger
resetRefSeqFileWalker() AbstractAlignmentMerger
resetStats() Downsampler
Reset stats in the downsampler such as the number of discarded items *without* clearing the downsampler of items
resolveFilePathStringFromKnownPath(String, Path) DataSourceUtils
Resolves the path string to a full path object using the given knownPath as a sibling file.
resolveIncompatibleAlleles(Allele, VariantContext, LinkedHashSet<Allele>) GATKVariantContextUtils
resolveIntervals(File, IntervalArgumentCollection, Logger) CopyNumberArgumentValidationUtils
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.
RESOURCE_LONG_NAME StandardArgumentDefinitions
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
results IndelLengthHistogram
retainNodes(Set<Integer>) PSTree
Removes all nodes not in the given set
retrieveAllHeaderInfo() FuncotationMetadata
retrieveAllHeaderInfo() VcfFuncotationMetadata
retrieveConfiguration(File) FuncotatorUtils
Create a configuration instance from a properties file, where key names are ordered.
retrieveHeaderInfo(String) FuncotationMetadata
retrieveHeaderInfo(String) VcfFuncotationMetadata
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.
reverseComplement() GATKRead
Modify this read by reverse complementing its bases and reversing its quality scores.
reverseComplement() SAMRecordToGATKReadAdapter
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.
revertReads(JavaRDD<GATKRead>, List<String>) RevertSamSpark
Takes an individual SAMRecord and applies the set of changes/reversions to it that
have been requested by program level options.
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.
RevertSamSpark org.broadinstitute.hellbender.tools.spark
Reverts a SAM file by optionally restoring original quality scores and by removing
all alignment information.
RevertSamSpark() RevertSamSpark
RevertSamSpark.FileType org.broadinstitute.hellbender.tools.spark
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
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
rgqThreshold ReblockGVCF
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_FILE SamComparisonMetric
Right file used in comparison
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
RIlmn InfiniumGTCRecord
RMS_MAPPING_QUALITY_OLD_BEHAVIOR_OVERRIDE_ARGUMENT RMSMappingQuality
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(double...) MathUtil
returns a long array containing the rounded values of the input array
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
roundFinitePrecisionErrors(double) Mutect2FilteringEngine
roundToNDecimalPlaces(double, int) MathUtils
Rounds the double to the given number of decimal places.
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
RS_ID InfiniumVcfFields
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.
rsNames InfiniumEGTFile
rsNameToIndex InfiniumEGTFile
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
runCommandLineProgram(CommandLineProgram, String[]) Main
Run the given command line program with the raw arguments from the command line
runInDebugMode StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsSparkArgumentCollection
runLocalAssembly(AssemblyRegion, Haplotype, byte[], SimpleInterval, 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
runPipeline(JavaSparkContext) GATKSparkTool
runPipeline(JavaSparkContext) SparkCommandLineProgram
Runs the pipeline.
runPipeline(JavaSparkContext) VariantWalkerSpark
runPipeline(JavaSparkContext) CreateReadCountPanelOfNormals
runPipeline(JavaSparkContext) ExampleNioCountReads
Runs the pipeline.
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) RevertSamSpark
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
runWithoutGapsAnnotation StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
runWithoutUmapS100Annotation StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
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_FILES CompareSAMs
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
SamComparison org.broadinstitute.hellbender.utils.read
Rudimentary SAM comparer.
SamComparison(SamReader, SamReader) SamComparison
Note: the caller must make sure the SamReaders are closed properly.
SamComparison picard.sam.util
Compare two SAM/BAM files.
SamComparison(SamReader, SamReader) SamComparison
Note: the caller must make sure the SamReaders are closed properly.
SamComparison(SamReader, SamReader, String, String, SAMComparisonArgumentCollection) SamComparison
SamComparison.AlignmentComparison picard.sam.util
samComparisonArgumentCollection CompareSAMs
SAMComparisonArgumentCollection picard.sam.util
Argument collection for SAM comparison
SAMComparisonArgumentCollection() SAMComparisonArgumentCollection
SamComparisonMetric picard.sam
Metric for results of SamComparison.
SamComparisonMetric() SamComparisonMetric
same(byte, byte) Nucleotide
same(Nucleotide) Nucleotide
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
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 ActivityProfile
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 AlleleFrequencyQCMetric
SAMPLE MultiLevelMetrics
The sample to which these metrics apply.
SAMPLE SplitReads
sample AlleleFrequencyQC
Sample org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
Stratifies the eval RODs by each sample in the eval ROD.
Sample() Sample
sample AlleleLikelihoods.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 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 CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The name of the sample
SAMPLE_ALIAS GtcToVcf
SAMPLE_ALIAS InfiniumVcfFields
SAMPLE_ALIAS FingerprintMetrics
The Sample alias taken from RG header or #CHROME line
SAMPLE_ALIAS IdentifyContaminant
SAMPLE_ALIAS IlluminaBasecallsToSam
SAMPLE_ALIAS RevertSam
SAMPLE_ALIAS CollectVariantCallingMetrics.VariantCallingDetailMetrics
The name of the sample being assayed
SAMPLE_ALIAS_ARG RevertSamSpark
SAMPLE_ALIAS_SHORT_NAME StandardArgumentDefinitions
SAMPLE_ALIAS_SHORT_NAME StandardOptionDefinitions
SAMPLE_EXPRESSIONS VariantEval
SAMPLE_INDEX_LONG_NAME PostprocessGermlineCNVCalls
SAMPLE_LIST_KEY GATKVCFConstants
SAMPLE_LONG_NAME SplitReads
SAMPLE_METADATA_TAG TableUtils
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
SAMPLE_SIZE TheoreticalSensitivityMetrics
Number of samples drawn at each depth in the depth distribution.
sampleAlias RevertSamSpark
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
sampleEvidence(int) AlleleLikelihoods
Returns the units of evidence that belong to a sample sorted by their index (within that sample).
sampleEvidenceCount(int) AlleleLikelihoods
Returns the quantity of evidence that belongs to a sample in the evidence-likelihood collection.
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) AlleleLikelihoods
Returns an evidence 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.
SamplePairExtractor org.broadinstitute.hellbender.tools.funcotator.metadata
Utility class to determine the tumor normal pairs that makeup a VCF Header
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.
SampleReadFilter org.broadinstitute.hellbender.engine.filters
Keep only reads for a given sample.
SampleReadFilter() SampleReadFilter
SampleReadFilter(SAMFileHeader) SampleReadFilter
samples GenotypingEngine
samples AlleleLikelihoods
Sample list
samples() AlleleLikelihoods
Returns the samples in this evidence-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
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 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
SamSequenceRecordsIterator(File, boolean) SequenceDictionaryUtils.SamSequenceRecordsIterator
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 RevertSamSpark
SANITIZE RevertSam
sanitizeFuncotationFieldForMaf(String) FuncotatorUtils
Make sure that an individual funcotation field (i.e.
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
SB_TABLE_KEY GATKVCFConstants
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() AnalysisModuleScanner
scan the class and find all appropriate fields and tables
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.
SCANNER_NAME CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The name of the scanner used for this sample
SCANNER_NAME InfiniumVcfFields
scatter(IntervalList, int) IntervalListScatterer
Scatter an IntervalList into several IntervalLists.
SCATTER_CONTENT IntervalListTools
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() KBestHaplotype
score(GATKRead) MarkDuplicatesScoringStrategy
Given a read, compute the reads's score for mark duplicates.
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 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_IN_MS NioFileCopierWithProgressMeter
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
secondIntervalFile CompareIntervalLists
SecondOfPairReadFilter() ReadFilterLibrary.SecondOfPairReadFilter
secondPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) TwoPassVariantWalker
secondPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) ExampleTwoPassVariantWalker
secondPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) FilterFuncotations
secondPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) CNNScoreVariants
secondPassApply(VariantContext, ReadsContext, ReferenceContext, FeatureContext) FilterVariantTranches
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
SEGMENTAL_DUPLICATION_CONTENT CopyNumberAnnotations
SEGMENTAL_DUPLICATION_TRACK_PATH_LONG_NAME AnnotateIntervals
segmentationRecords() ContaminationModel
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
SegmentExonOverlaps org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment
Class that represents the exon numbers overlapped by a genomic region.
SegmentExonOverlaps(String, String) SegmentExonOverlaps
SegmentExonUtils org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment
SEGMENTS_FILE_LONG_NAME CopyNumberStandardArgument
SEGMENTS_FILE_SUFFIX ModelSegments
SELECT_EXPS VariantEval
SELECT_NAMES VariantEval
selectAlleleBiasedEvidence(Map<A, List<EVIDENCE>>, 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 an ack, returning all accumulated output
since the last call to either
sensitivity ValidationReport
SENSITIVITY_METADATA_TAG FilterStats
sensitivityAtConstantDepth(int, Histogram<Integer>, double, int, double, long) TheoreticalSensitivity
Calculates the theoretical sensitivity with a given Phred-scaled quality score distribution at a constant
depth.
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 CollectArraysVariantCallingMetrics
SEQUENCE_DICTIONARY ReorderSam
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
SequenceDictionaryIsMissingContigLengths(String, SAMSequenceDictionary) UserException.SequenceDictionaryIsMissingContigLengths
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 picard.util
Class with helper methods for generating and writing SequenceDictionary objects.
SequenceDictionaryUtils() SequenceDictionaryUtils
SequenceDictionaryUtils.SamSequenceRecordsIterator picard.util
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
SEQUENCING_QUAL_KEY GATKVCFConstants
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.
SequencingError org.broadinstitute.hellbender.tools.walkers.mutect.clustering
SequencingError() SequencingError
seqValidationArguments GATKTool
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.
serialize(Kryo, Output) PSTaxonomyDatabase
serialize(Kryo, Output) PSTree
serialize(Kryo, Output) BreakpointComplications.InvertedDuplicationBreakpointComplications
serialize(Kryo, Output) BreakpointComplications
serialize(Kryo, Output) BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications
serialize(Kryo, Output) BreakpointComplications.SmallDuplicationBreakpointComplications
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.InvertedDuplicationBreakpointComplications.Serializer
Serializer() BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications.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
serialVersionUID VariantFilter
serialVersionUID QualityYieldMetricsArgumentCollection
serialVersionUID ExampleMultiMetricsArgumentCollection
serialVersionUID ExampleSingleMetricsArgumentCollection
serialVersionUID StrandCorrectedAllele
serialVersionUID MetricsCollectorSpark
serialVersionUID DUSTReadTransformer
serialVersionUID ReadTransformer
serialVersionUID StripMateNumberTransformer
serialVersionUID VariantTransformer
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(ArtifactPrior) ArtifactPriorCollection
Add an artifact prior to the collection.
set(int, V) StratificationManager
set(int, int, double) LikelihoodMatrix
Set the likelihood of a unit of evidence 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(String, double, int) 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(int, double, int) 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() AbstractReadThreadingGraph
setAlt(Allele, X) PerAlleleCollection
setAlternateAllele(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
setAssayFormat(String) IlluminaManifest
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
setCachedPath(Path) PathSpecifier
setcDnaChange(String) GencodeFuncotation
setcDnaChange(String) GencodeFuncotationBuilder
setCds(GencodeGtfCDSFeature) GencodeGtfExonFeature
setChecksumAlgorithmAndExpectedChecksum(String, String) NioFileCopierWithProgressMeter
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.
setColumn(int, String) SimpleXSVWriter.LineBuilder
setColumn(String, String) SimpleXSVWriter.LineBuilder
setCommand(String[]) ProcessSettings
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(double, int, long, int, int, String, double, double) MetricsCollection
setData(List<VariantDatum>) VariantDataManager
setDataSourceName(String) GencodeFuncotation
setDataSourceName(String) GencodeFuncotationBuilder
setDateManufactured(String) IlluminaManifest
setDebug(boolean) AssemblyResultSet
setDebug(boolean) ReadThreadingAssembler
setDebugGraphOutputPath(File) ReadThreadingAssembler
setDebugGraphTransformations(boolean) ReadThreadingAssembler
setDebugHistogramOutput(File) 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
setDescriptorFileName(String) IlluminaManifest
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
setEstimatedQReported(double) RecalDatum
setEventMap(EventMap) Haplotype
setExonPosition(SimpleInterval) 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
setFormatTimeRemainingAsTimestamp() NioFileCopierWithProgressMeter
Sets the logger to log the time remaining in timestamp format ala 'DD:HH:MM:ss.SS'.
setFormatTimeRemainingAsWords() NioFileCopierWithProgressMeter
Sets the logger to log the time remaining in word format ala 'D days, H hours, M minutes, s seconds'.
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.
setGcCacheSize(int) ReadBaseStratification
setGcContent(Double) GencodeFuncotation
setGcContent(Double) GencodeFuncotationBuilder
setGcContent(Double) SequenceComparison
setGeneTranscriptType(GencodeGtfFeature.GeneTranscriptType) GencodeFuncotation
setGeneTranscriptType(GencodeGtfFeature.GeneTranscriptType) GencodeFuncotationBuilder
setGenomeAssembly(String) SequenceDictionaryUtils.SamSequenceRecordsIterator
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(int, String) BucketUtils
Sets max_reopens, requester_pays, and generous timeouts as the global default.
setGraphWriter(File) ReadThreadingAssembler
setHeader(SAMFileHeader) ReadFilter
setHeader(SAMFileHeader) WellformedReadFilter
setHeader(SAMFileHeader) ArtificialBAMBuilder
setHeader(SAMFileHeader) SAMRecordToGATKReadAdapter
setHeader(VCFHeader) GVCFWriter
setHeaderLine(List<String>) SimpleXSVWriter
Provides a header line to the XSV output file.
setHgGenomeBuild(String) IlluminaManifestRecord
sethInfo(VCFInfoHeaderLine) VariantAnnotatorEngine.VAExpression
setHugoSymbol(String) GencodeFuncotation
setHugoSymbol(String) GencodeFuncotationBuilder
setIdentifier(String) InfiniumDataFile
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) 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
setIsUnplaced() GATKRead
Mark the read as unmapped, and also removes mapping information from the read (i.e.
setIsUnplaced() 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) TransientFieldPhysicalLocation
setLibraryId(short) PhysicalLocationForMateCigar
setLibraryId(short) ReadEnds
setLibraryId(short) PhysicalLocation
setLibraryId(short) PhysicalLocationInt
setLocationSet(PhysicalLocationForMateCigarSet) ReadEndsForMateCigar
setLociCount(int) IlluminaManifest
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
setLongHomopolymer(int) ReadBaseStratification
defaults to 6
setManifestFileParser(CsvInputParser) IlluminaManifest
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
setMateIsUnplaced() GATKRead
Mark the read's mate as unmapped (lacking a defined position on the genome).
setMateIsUnplaced() 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
setMetadata(FuncotationMetadata) GencodeFuncotation
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
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
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
setNumAssays(int) IlluminaManifest
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
setOffset(int) InfiniumFileTOC
setOffsetX(float) InfiniumTransformation
setOffsetY(float) InfiniumTransformation
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
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) RepresentativeReadIndexerCodec
setOverrideValuesInFuncotations(List<Funcotation>) DataSourceFuncotationFactory
setOverwriteExisting(boolean) NioFileCopierWithProgressMeter
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.
setPriorError(double) ErrorMetric
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
setProteinChangeInfo(ProteinChangeInfo) SequenceComparison
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) TransientFieldPhysicalLocation
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
setRecoverAllDanglingBranches(boolean) ReadThreadingAssembler
setRecoverDanglingBranches(boolean) ReadThreadingAssembler
setRedirectErrorStream(boolean) ProcessSettings
setRef(Allele, X) PerAlleleCollection
setRefAllele(String) GencodeFuncotation
setRefAllele(Allele) GencodeFuncotationBuilder
setReferenceAllele(String) SequenceComparison
setReferenceBases(String) SequenceComparison
setReferenceContext(String) GencodeFuncotation
Set the reference context string.
setReferenceContext(String) GencodeFuncotationBuilder
setReferenceFasta(File) FingerprintChecker
setReferenceLength(long) PSPathogenTaxonScore
setReferenceSequence(File) SinglePassSamProgram
Set the reference File.
setReferenceWindow(Integer) SequenceComparison
setRegionForGenotyping(AssemblyRegion) AssemblyResultSet
Sets the region for genotyping.
setRemovePathsNotConnectedToRef(boolean) ReadThreadingAssembler
setReserved1(float) InfiniumTransformation
setReserved2(float) InfiniumTransformation
setReserved3(float) InfiniumTransformation
setReserved4(float) InfiniumTransformation
setReserved5(float) InfiniumTransformation
setReserved6(float) InfiniumTransformation
setResultState(boolean) SamRecordWithOrdinalAndSetDuplicateReadFlag
setRow(String[]) SimpleXSVWriter.LineBuilder
setRow(List<String>) SimpleXSVWriter.LineBuilder
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
setScaleX(float) InfiniumTransformation
setScaleY(float) InfiniumTransformation
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.
setShear(float) InfiniumTransformation
setSize() PSKmerSet
setSize RepresentativeReadIndexer
SetSizeUtils org.broadinstitute.hellbender.tools.spark.utils
Set size utility
SetSizeUtils() SetSizeUtils
setSkipBlankLines(boolean) AbstractInputParser
setSkipNLoci(int) ArtificialBAMBuilder
setSparkVerbosity(String) SparkCommandLineArgumentCollection
setSpecies(String) SequenceDictionaryUtils.SamSequenceRecordsIterator
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
setStatePrior(double[], double, ArtifactState) ArtifactState
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(Path) LocatableXsvFuncotationFactory
setTag(String) GATKPathSpecifier
setTagAttributes(Map<String, String>) GATKPathSpecifier
setTheta(float) InfiniumTransformation
setThreadingStartOnlyAtExistingVertex(boolean) AbstractReadThreadingGraph
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) TransientFieldPhysicalLocation
setTile(int) ClusterData
setTile(short) PhysicalLocation
setTile(short) PhysicalLocationInt
setTiles(List<Integer>) ParameterizedFileUtil
setTilesForPerRunFile(List<Integer>) ParameterizedFileUtil
setTilesForPerRunFile(List<Integer>) PerTileOrPerRunFileUtil
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
setTranscriptEndPos(Integer) GencodeFuncotation
setTranscriptEndPos(Integer) GencodeFuncotationBuilder
Set the end position (1-based, inclusive) relative to the start of the transcript of a the variant in the
GencodeFuncotation.
setTranscriptExonNumber(Integer) GencodeFuncotation
setTranscriptExonNumber(int) GencodeFuncotationBuilder
setTranscriptLength(Integer) GencodeFuncotation
setTranscriptLength(Integer) GencodeFuncotationBuilder
setTranscriptStartPos(Integer) GencodeFuncotation
setTranscriptStartPos(Integer) GencodeFuncotationBuilder
Set the start position (1-based, inclusive) relative to the start of the transcript of a the variant in the
GencodeFuncotation.
setTranscriptStrand(String) GencodeFuncotation
setTransientAttribute(Object, Object) GATKRead
This is used to access the transient attribute store in the underlying data type.
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
setupVCFWriter(Set<VCFHeaderLine>, boolean, DbsnpArgumentCollection, VariantContextWriter) GenotypeGVCFsEngine
Create a VCF header in the writer
setUri(String) SequenceDictionaryUtils.SamSequenceRecordsIterator
setUseOriginalQualities(boolean) QualityYieldMetrics
setValidated(boolean) BreakpointEvidence
setValidationStringency(ValidationStringency) FingerprintChecker
setValue(int, double) EvidenceFeatures
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
setVariantEvalWalker(VariantEval) VariantStratifier
Should only be called by VariantEvalWalker itself
setVariantType(GencodeFuncotation.VariantType) GencodeFuncotation
setVariantType(GencodeFuncotation.VariantType) GencodeFuncotationBuilder
setVerbosity(NioFileCopierWithProgressMeter.Verbosity) NioFileCopierWithProgressMeter
setVersion(String) GencodeFuncotation
setVersion(String) GencodeFuncotationBuilder
setVersion(int) InfiniumTransformation
setWalkerType(String) GATKGSONWorkUnit
setWeightThreshold(int) JunctionTreeKBestHaplotypeFinder
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) TransientFieldPhysicalLocation
setX(int) ClusterData
setX(int) PhysicalLocation
setX(int) PhysicalLocationInt
setX(int) PhysicalLocationShort
setY(int) TransientFieldPhysicalLocation
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<SB>, 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, JavaRDD<SB>, int) SparkSharder
Create an RDD of
Shard from an RDD of coordinate sorted
Locatable without using a shuffle ,
and where the intervals for shards are specified as an RDD, rather than a list.
shard(JavaSparkContext, JavaRDD<L>, Class<L>, SAMSequenceDictionary, List<SB>, 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
ShardBoundary(SimpleInterval, SimpleInterval, boolean) ShardBoundary
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 AssemblyRegionWalkerSpark
shardingArgs ReadsPipelineSpark
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
shortToByteArray(short) InfiniumDataFile
Utility method to convert a short to a byte array
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
shouldBeReblocked(VariantContext) ReblockGVCF
shouldIncludeInterval(long, double, long) IntervalListScattererWithoutSubdivision
shouldIncludeInterval(long, double, long) IntervalListScattererWithoutSubdivisionWithOverflow
ShouldNeverReachHereException(String) GATKException.ShouldNeverReachHereException
ShouldNeverReachHereException(String, Throwable) GATKException.ShouldNeverReachHereException
ShouldNeverReachHereException(Throwable) GATKException.ShouldNeverReachHereException
shouldRemoveReadsAfterGraphConstruction() AbstractReadThreadingGraph
shouldRemoveReadsAfterGraphConstruction() JunctionTreeLinkedDeBruinGraph
shouldRemoveReadsAfterGraphConstruction() ReadThreadingGraph
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 VariantWalkerSpark
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
signalEndOfInput() PushPullTransformer
Used to tell the transformer that no more items will be submitted to it, and that it should
finalize any pending items.
signalEndOfInput() GVCFBlockCombiner
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
SIMPLE_CHIMERA_VCF_FILE_NAME SvDiscoverFromLocalAssemblyContigAlignmentsSpark
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(String, AlignmentInterval, AlignmentInterval, StrandSwitch, boolean, List<String>, String) SimpleChimera
SimpleChimera(AlignmentInterval, AlignmentInterval, List<String>, String, String, SAMSequenceDictionary) SimpleChimera
Construct a new SimpleChimera from two alignment intervals.
SimpleChimera.DistancesBetweenAlignmentsOnRefAndOnRead org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
Struct to represent the (distance - 1) between boundaries of the two alignments represented by this CA,
on reference, and on read.
SimpleChimera.Serializer org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
simpleChimeraWithStichableAlignments(AlignmentInterval, AlignmentInterval) AssemblyContigAlignmentsConfigPicker
See the funny alignment signature described in ticket 4951 on GATK github
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
SimpleErrorCalculator picard.sam.SamErrorMetric
A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.
SimpleErrorCalculator() SimpleErrorCalculator
SimpleGermlineTagger org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging
This utility class performs a simple tagging of germline segments in a tumor segments file.
SimpleInsDelOrReplacementBreakpointComplications(String, String) BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications
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(String, Path, String, String, int, SimpleKeyXsvFuncotationFactory.XsvDataKeyType, LinkedHashMap<String, String>, int, boolean, 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) GATKVariantContextUtils
Merges VariantContexts into a single hybrid.
simpleMerge(Collection<VariantContext>, List<String>, int, GATKVariantContextUtils.FilteredRecordMergeType, GATKVariantContextUtils.GenotypeMergeType, boolean) GATKVariantContextUtils
Merges VariantContexts into a single hybrid.
SimpleNovelAdjacencyAndChimericAlignmentEvidence org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
SimpleNovelAdjacencyAndChimericAlignmentEvidence(NovelAdjacencyAndAltHaplotype, Iterable<SimpleChimera>) SimpleNovelAdjacencyAndChimericAlignmentEvidence
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, int, int, String, Allele, Allele, int, Map<String, Object>) 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.SupportedType org.broadinstitute.hellbender.tools.spark.sv.discovery
SimpleTsvOutputRenderer org.broadinstitute.hellbender.tools.funcotator.simpletsvoutput
This class is very versatile, but as a result, it must do some lazy loading after it receives the first write command.
SimpleXSVWriter org.broadinstitute.hellbender.utils.tsv
A simple TSV/CSV/XSV writer with support for writing in the cloud with configurable delimiter.
SimpleXSVWriter(Path, char) SimpleXSVWriter
Creates a new table writer given the file and column names.
SimpleXSVWriter(Writer, char) SimpleXSVWriter
Creates a new table writer given an initialized writer and column names.
SimpleXSVWriter.LineBuilder org.broadinstitute.hellbender.utils.tsv
Helper to allow for incremental construction of a body line using either indexes or column headings
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
SingleBarcodeDistanceMetric picard.util
A class for finding the distance between a single barcode and a barcode-read (with base qualities)
SingleBarcodeDistanceMetric(byte[], byte[], byte[], int, int) SingleBarcodeDistanceMetric
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 ReadOrientation
size() StratificationManager
How many states are held in this stratification manager?
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() 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() IntToDoubleFunctionCache
size() SeekableByteChannelPrefetcher
Returns the current size of entity to which this channel is connected.
size() ReadPileup
The number of elements in this pileup.
size() CovariateKeyCache
Returns the size of this cache.
size() StandardCovariateList
Returns the size of the list of standard covariates.
size() SimpleInterval
size() HaplotypeBlock
Returns the number of SNPs within the haplotype block.
size() DiskBasedReadEndsForMarkDuplicatesMap
size() MarkQueue
The number of records currently in this queue.
size() MemoryBasedReadEndsForMarkDuplicatesMap
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
sizeBeforeLoc(GenomeLoc) GenomeLocSortedSet
Return the number of bps before loc in the sorted set
sizeInRam() DiskBasedReadEndsForMarkDuplicatesMap
sizeInRam() MemoryBasedReadEndsForMarkDuplicatesMap
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 (PDF),
which is assumed to be unimodal.
SliceSampler(RandomGenerator, Function<Double, Double>, double, double, double) SliceSampler
Creates a new sampler for a bounded univariate random variable, given a random number generator,
a continuous, univariate, unimodal, unnormalized log probability density function,
hard limits on the random variable, and a step width.
SliceSampler(RandomGenerator, Function<Double, Double>, double) SliceSampler
Creates a new sampler for an unbounded univariate random variable, given a random number generator,
a continuous, univariate, unimodal, unnormalized log probability density function,
and a step width.
slippageRate M2FiltersArgumentCollection
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_HEADER_NAME IlluminaManifest
SNP_het_to_hom_ratio IndelSummary
SNP_HETEROZYGOSITY HomoSapiensConstants
Standard heterozygous rate for SNP variation.
SNP_MASK_LONG_NAME FastaAlternateReferenceMaker
SNP_MASK_PRIORITY_LONG_NAME FastaAlternateReferenceMaker
SNP_OUTPUT SplitVcfs
SNP_REFERENCE_BIAS CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The rate at which reference bases are observed at ref/alt heterozygous SNP sites.
SNP_to_indel_ratio IndelSummary
SNP_to_indel_ratio_for_singletons IndelSummary
snpCounter GenotypeConcordance
SNPDPPerSample VariantSummary
SnpEffPositionModifier org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
Stratifies variants as genes or coding regions, according to the effect modifier, as indicated by snpEff.
SnpEffPositionModifier() SnpEffPositionModifier
SnpEffPositionModifier.PositionModifier org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
SnpEffUtil org.broadinstitute.hellbender.tools.walkers.varianteval.util
Created with IntelliJ IDEA.
SnpEffUtil() SnpEffUtil
SnpEffUtil.EffectFunctionalClass org.broadinstitute.hellbender.tools.walkers.varianteval.util
SnpEffUtil.EffectType org.broadinstitute.hellbender.tools.walkers.varianteval.util
snpHeterozygosity GenotypeCalculationArgumentCollection
The expected heterozygosity value used to compute prior probability that a locus is non-reference.
snpHeterozygosity HaplotypeCallerGenotypingEngine
snpmask FastaAlternateReferenceMaker
SNPs from this file are used as a mask (inserting N's in the sequence) when constructing the alternate reference
snpmaskPriority FastaAlternateReferenceMaker
Gives priority to a SNP mask over an input VCF for a site.
SNPNoveltyRate MultiallelicSummary
SNPNoveltyRate VariantSummary
snpPadding ReadThreadingAssemblerArgumentCollection
snps DbSnpBitSetUtil.DbSnpBitSets
snps DbSnpBitSetUtil.DbSnpBitSets
SNPSubstitutionType(byte, byte) BaseUtils
Returns the base substitution type of the 2 state SNP
SOFT_CLIPPED_LEADING_TRAILING_RATIO_THRESHOLD ReadFilterArgumentDefinitions
SOFT_CLIPPED_RATIO_THRESHOLD ReadFilterArgumentDefinitions
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.
SoftClippedReadFilter org.broadinstitute.hellbender.engine.filters
Filter out reads where the ratio of soft-clipped bases to total bases exceeds some given value.
SoftClippedReadFilter() SoftClippedReadFilter
softClipsLengthStratifier ReadBaseStratification
Stratifies into the number of soft-clipped bases that the read has in its alignment, or
-1 if not aligned.
softClipToRegionIncludingClippedBases(GATKRead, int, int) 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
SOMATIC_ARG_LONG_NAME FuncotatorDataSourceDownloader
SOMATIC_INPUT_LONG_NAME CombineGVCFs
SomaticClusteringModel org.broadinstitute.hellbender.tools.walkers.mutect.clustering
SomaticClusteringModel(M2FiltersArgumentCollection, List<MutectStats>) SomaticClusteringModel
SomaticGenotypingEngine org.broadinstitute.hellbender.tools.walkers.mutect
SomaticGenotypingEngine(M2ArgumentCollection, Set<String>, VariantAnnotatorEngine) SomaticGenotypingEngine
SomaticGVCFBlockCombiner org.broadinstitute.hellbender.utils.variant.writers
SomaticGVCFBlockCombiner(List<Number>, int) SomaticGVCFBlockCombiner
SomaticGVCFBlockCombiner(List<Number>, int, int) SomaticGVCFBlockCombiner
SomaticGVCFWriter org.broadinstitute.hellbender.utils.variant.writers
Genome-wide VCF writer for somatic (Mutect2) output
Merges reference blocks based on TLOD
SomaticGVCFWriter(VariantContextWriter, List<Number>) SomaticGVCFWriter
Create a new GVCF writer
Should be a non-empty list of boundaries.
SomaticGVCFWriter(VariantContextWriter, List<Number>, int) SomaticGVCFWriter
somaticInput CombineGVCFs
Merge somatic GVCFs, retaining LOD and haplotype event count information in FORMAT field
Note that the Mutect2 reference confidence mode is in BETA -- the likelihoods model and output format are subject to change in subsequent versions.
somaticInput GenotypeGVCFs
"Genotype" somatic GVCFs, outputting genotypes according to confidently called alt alleles, which may lead to inconsistent ploidy
Note that the Mutect2 reference confidence mode is in BETA -- the likelihoods model and output format are subject to change in subsequent versions.
SomaticLikelihoodsEngine org.broadinstitute.hellbender.tools.walkers.mutect
Created by David Benjamin on 3/9/17.
SomaticLikelihoodsEngine() SomaticLikelihoodsEngine
somaticLogOdds(LikelihoodMatrix<EVIDENCE, Allele>) SomaticGenotypingEngine
SomaticReferenceConfidenceModel org.broadinstitute.hellbender.tools.walkers.mutect
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_LONG_NAME StandardArgumentDefinitions
SORT_ORDER_SHORT_NAME StandardArgumentDefinitions
SORT_ORDER_SHORT_NAME StandardOptionDefinitions
SortableJexlVCMatchExp org.broadinstitute.hellbender.tools.walkers.varianteval.util
SortableJexlVCMatchExp(String, Expression) SortableJexlVCMatchExp
Create a new matcher expression with name and JEXL expression exp
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 MarkDuplicates
sortLocatablesBySequenceDictionary(Collection<T>, SAMSequenceDictionary) IntervalUtils
Sort by the contig then position as specified by the index order in the given sequence dictionary.
sortOrder RevertSamSpark
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
SortSam on Spark (works on SAM/BAM/CRAM)
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
source NioFileCopierWithProgressMeter
SOURCE InfiniumVcfFields
SOURCE FingerprintMetrics
The originating file (if available) for this fingerprint
SOURCE_HEADER_NAME IlluminaManifest
SOURCE_SEQ_HEADER_NAME IlluminaManifest
SOURCE_STRAND_HEADER_NAME IlluminaManifest
SOURCE_VERSION_HEADER_NAME IlluminaManifest
sourceContigName SimpleChimera
spanByKey(JavaPairRDD<K, V>) SparkUtils
Like groupByKey, but assumes that values are already sorted by key, so no shuffle is needed,
which is much faster.
SPANNING_DELETION_SYMBOLIC_ALLELE_DEPRECATED 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_executor_memoryOverhead() GATKConfig
spark_io_compression_codec() GATKConfig
spark_kryoserializer_buffer_max() GATKConfig
SPARK_MASTER_LONG_NAME SparkCommandLineArgumentCollection
SPARK_PROGRAM_NAME_LONG_NAME SparkCommandLineProgram
SPARK_PROPERTY_NAME StandardArgumentDefinitions
SPARK_VERBOSITY_LONG_NAME SparkCommandLineArgumentCollection
sparkArgs SparkCommandLineProgram
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)
sparkReadAdapter(AlignmentRecord, SAMFileHeader) BDGAlignmentRecordToGATKReadAdapter
sparkReadAdapter(AlignmentRecord) BDGAlignmentRecordToGATKReadAdapter
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
SparkUtils org.broadinstitute.hellbender.utils.spark
Miscellaneous Spark-related utilities
sparkVariantAdapter(VariantContext) VariantContextVariantAdapter
specialArgumentsCollection CommandLineProgram
specialArgumentsCollection CommandLineProgram
SPECIES CreateSequenceDictionary
SPECIES_HEADER_NAME IlluminaManifest
specificity ValidationReport
Splice(String, int, int) OverhangFixingManager.Splice
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_StrandBiasTest
SPLIT_MULTI_ALLELIC_LONG_NAME VariantsToTable
SPLIT_MULTI_ALLELIC_SHORT_NAME VariantsToTable
SPLIT_MULTIALLELEICS_LONG_NAME LeftAlignAndTrimVariants
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
splitAnnotationArgsIntoMap(List<String>) FuncotatorEngine
Split each element of the given List into a key and value.
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
splitMultiAllelic VariantsToTable
By default, a variant record with multiple ALT alleles will be summarized in one line, with per alt-allele fields
(e.g.
splitMultiallelics LeftAlignAndTrimVariants
If this argument is set, split multiallelic records and left-align individual alleles.
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
splitVariantContextToBiallelics(VariantContext, boolean, GenotypeAssignmentMethod, boolean) GATKVariantContextUtils
Split variant context into its biallelic components if there are more than 2 alleles
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
srcFileSize NioFileCopierWithProgressMeter
srcFileSizeNumDigits NioFileCopierWithProgressMeter
STANDARD_BASES Nucleotide
List of the standard (non-redundant) nucleotide values in their preferred alphabetical order.
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_FOR_FILTERING Mutect2FilteringEngine
STANDARD_NGS SmithWatermanAligner
StandardAnnotation org.broadinstitute.hellbender.tools.walkers.annotator
This is a marker interface used to indicate which annotations are "Standard".
standardArgs HaplotypeCallerArgumentCollection
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
StandardEval org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
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
StandardStratification org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
StandardValidationCollection() SequenceDictionaryValidationArgumentCollection.StandardValidationCollection
start() ProgressMeter
Start the progress meter and produce preliminary output such as column headings.
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, File) 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
START_EXON_SUFFIX GencodeFuncotationFactory
Used when generating start exon field name for segment funcotations.
START_GENE_SUFFIX GencodeFuncotationFactory
Since gencode funcotation field names are generated dynamically, we have to search the incoming funcotation fields for the proper gencode funcotations.
START_TRANSCRIPT_DELIMITER VcfOutputRenderer
The delimiter to use when starting the information regarding a transcript.
startBatchWrite(String, List<T>) StreamingPythonScriptExecutor
Request that a batch of items be written to the stream on a background thread.
startBatchWrite(List<T>) AsynchronousStreamWriter
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
startingVC GVCFBlock
startPos ArtificialReadQueryIterator
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
states VariantStratifier
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() InsertSizeDistribution
stddev() MathUtils.RunningAverage
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.
stddev(double[], 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
stopped() ProgressMeter
Returns whether the meter has been stopped.
stopSparkContext(JavaSparkContext) SparkContextFactory
Stop a JavaSparkContext, unless it is the test context.
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_QUAL_KEY GATKVCFConstants
STRAND_SPECIFICITY CollectRnaSeqMetrics
StrandArtifactFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
StrandArtifactFilter() StrandArtifactFilter
StrandArtifactFilter.EStep org.broadinstitute.hellbender.tools.walkers.mutect.filtering
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
StrandCorrectedAllele org.broadinstitute.hellbender.tools.funcotator
Class to represent a strand-corrected Allele.
StrandCorrectedReferenceBases org.broadinstitute.hellbender.tools.funcotator
Simple container class to represent bases that have been corrected for strandedness already.
StrandCorrectedReferenceBases(String, Strand) StrandCorrectedReferenceBases
StrandCorrectedReferenceBases(byte[], Strand) StrandCorrectedReferenceBases
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.
STRATEGY DownsampleSam
StratificationManager K extends Stratifier <java.lang.Object>,V > - Class in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager
Represents the full state space of all stratification combinations
StratificationManager(List<K>) StratificationManager
Create a new StratificationManager with nodes to store data for all combinations
of the ordered list of strats
StratificationManager.Combiner V > - Interface in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager
STRATIFICATIONS_TO_USE VariantEval
Stratifier T > - Interface in org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager
A basic interface for a class to be used with the StratificationManager system
STRATIFIER_VALUE CollectSamErrorMetrics
stratify(AlignmentContext.ReadOrientation) AlignmentContext
Returns a potentially derived subcontext containing only forward, reverse, or in fact all reads
in alignment context context.
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) ReadBaseStratification.BinnedReadCycleStratifier
stratify(SAMRecord) ReadBaseStratification.CigarOperatorsInReadStratifier
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) ReadBaseStratification.CollectionStratifier
stratify(SAMRecord) ReadBaseStratification.ConsensusStratifier
stratify(SAMRecord) ReadBaseStratification.FlowCellTileStratifier
stratify(SAMRecord) ReadBaseStratification.GCContentStratifier
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) ReadBaseStratification.IndelLengthStratifier
stratify(SAMRecord) ReadBaseStratification.IndelsInReadStratifier
Returns the number of bases associated with I and D CIGAR elements.
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) ReadBaseStratification.LongShortHomopolymerStratifier
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) ReadBaseStratification.MismatchesInReadStratifier
stratify(SAMRecord) ReadBaseStratification.NsInReadStratifier
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) ReadBaseStratification.PairStratifier
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) ReadBaseStratification.RecordAndOffsetStratifier
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
STREAMING_ACK_MESSAGE StreamingToolConstants
Command acknowledgement messages used to signal positive acknowledgement ('ack'),
negative acknowledgement ('nck'), and negative acknowledgement with an accompanying
message ('nkm').
STREAMING_ACK_MESSAGE_SIZE StreamingToolConstants
STREAMING_NCK_MESSAGE StreamingToolConstants
STREAMING_NCK_WITH_MESSAGE_MAX_MESSAGE_LENGTH StreamingToolConstants
STREAMING_NCK_WITH_MESSAGE_MESSAGE StreamingToolConstants
STREAMING_NCK_WITH_MESSAGE_MESSAGE_LEN_SIZE StreamingToolConstants
Number of characters used to represent the length of the serialized message, fixed at a constant
4 characters to ensure we can deterministically know how much input to wait for when looking for
a message length in the incoming stream.
StreamingProcessController org.broadinstitute.hellbender.utils.runtime
Facade to Runtime.exec() and java.lang.Process.
StreamingProcessController(ProcessSettings) StreamingProcessController
StreamingProcessController(ProcessSettings, boolean) StreamingProcessController
Create a controller using the specified settings.
StreamingPythonScriptExecutor T > - Class in org.broadinstitute.hellbender.utils.python
Python executor used to interact with a cooperative, keep-alive Python process.
StreamingPythonScriptExecutor(boolean) 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.
StreamingToolConstants org.broadinstitute.hellbender.utils.runtime
Various constants used by StreamingProcessController that require synchronized equivalents in
the companion process, i.e., if the streaming process is written in Python, there must be
equivalent Python constants for use by the Python code.
StreamingToolConstants() StreamingToolConstants
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 AssemblyRegionWalkerSpark
strict ReadsPipelineSpark
STRICT SplitVcfs
STRICT_STRAND_BIAS_FILTER_NAME GATKVCFConstants
StrictStrandBiasFilter org.broadinstitute.hellbender.tools.walkers.mutect.filtering
StrictStrandBiasFilter(int) StrictStrandBiasFilter
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 AsynchronousStreamWriter
Convenience function that can be provided to an AsynchronousStreamWriter 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
STRONG Nucleotide
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.DiscoverVariantsFromContigAlignmentsSparkArgumentCollection org.broadinstitute.hellbender.tools.spark.sv
StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection org.broadinstitute.hellbender.tools.spark.sv
StructuralVariationDiscoveryArgumentCollection.SvEvidenceFilterType 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
SUBDIVISION_MODE IntervalListTools
SUBDIVISION_MODE_lONG_NAME SplitIntervals
SUBDIVISION_MODE_SHORT_NAME SplitIntervals
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
submit(T) PushPullTransformer
Submit one item to the transformer for consideration.
submit(Collection<T>) PushPullTransformer
submit(VariantContext) GVCFBlockCombiner
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.
subsetSomaticAlleles(VCFHeader, GenotypesContext, List<Allele>, int[]) AlleleSubsettingUtils
Remove alternate alleles from a set of genotypes turning removed alleles to no-call and dropping other per-allele attributes
SubsettedLikelihoodMatrix EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele> - Class in org.broadinstitute.hellbender.tools.walkers.mutect
Fast wrapper for a LikelihoodMatrix that uses only a subset of alleles.
SubsettedLikelihoodMatrix(LikelihoodMatrix<EVIDENCE, A>, List<A>) 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.
sum(IntToDoubleFunction) IndexRange
Sums the values of an int -> double function applied to this range
sum(double[]) MathUtils
sum(int[]) MathUtils
sum(long[]) MathUtils
sum(double[], int, int) MathUtils
Returns the sum of the elements in the array starting with start and ending before stop.
sum() Nucleotide.Counter
Return the total count of all nucleotide constants.
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
sumADsOverSamples(VariantContext, boolean, boolean) Mutect2FilteringEngine
sumArrayFunction(int, int, MathUtils.IntToDoubleArrayFunction) MathUtils
sumDoubleFunction(Collection<E>, ToDoubleFunction<E>) MathUtils
sumHistogramsFromFiles(List<MetricsFile<?, Integer>>, boolean) LearnReadOrientationModel
sumIntFunction(Collection<E>, ToIntFunction<E>) MathUtils
sumLog10(double[]) MathUtils
Returns the sum of values whose log10s we have.
summary ValidateBasicSomaticShortMutations
summary Concordance
summary EvaluateInfoFieldConcordance
SUMMARY GcBiasMetrics
SUMMARY_FILE_EXTENSION CollectRrbsMetrics
SUMMARY_FILE_SUFFIX FilterByOrientationBias
SUMMARY_LONG_NAME Concordance
SUMMARY_LONG_NAME EvaluateInfoFieldConcordance
SUMMARY_METRICS_FILE_EXTENSION GenotypeConcordance
SUMMARY_OUTPUT CollectGcBiasMetrics
SUMMARY_OUTPUT CheckFingerprint
SUMMARY_SHORT_NAME Concordance
SUMMARY_SHORT_NAME EvaluateInfoFieldConcordance
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
sumStrandCountsOverSamples(VariantContext, boolean, boolean) Mutect2FilteringEngine
SUPPORTED_ALLELES_TAG AssemblyBasedCallerUtils
supportedTypes() MultiTileParser
supportedTypes() PosParser
SUPPORTING_CALLSET_LONG_NAME GenotypeCalculationArgumentCollection
SUPPORTING_CALLSET_SHORT_NAME GenotypeCalculationArgumentCollection
SUPPORTING_CALLSETS_LONG_NAME CalculateGenotypePosteriors
SUPPORTING_CALLSETS_SHORT_NAME CalculateGenotypePosteriors
supportsCombine() VariantEvaluator
Must be overloaded to return true for evaluation modules that support the combine operation
supportsMetricAccumulationLevel() CollectMultipleMetrics.ProgramInterface
supportsSerialIteration() ReadsDataSource
supportsVariant(GATKRead, VariantContext, int) RealignmentEngine
supportVariants GenotypeCalculationArgumentCollection
Supporting external panel.
supportVariants CalculateGenotypePosteriors
Supporting external panels.
SVAlignmentLengthFilter(int) SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SVAlignmentLengthFilter
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
SvDiscoverFromLocalAssemblyContigAlignmentsSpark.StructuralVariantFilter org.broadinstitute.hellbender.tools.spark.sv.discovery
SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SVAlignmentLengthFilter org.broadinstitute.hellbender.tools.spark.sv.discovery
SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SVMappingQualityFilter org.broadinstitute.hellbender.tools.spark.sv.discovery
SvDiscoveryInputMetaData org.broadinstitute.hellbender.tools.spark.sv.discovery
SvDiscoveryInputMetaData(JavaSparkContext, StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsSparkArgumentCollection, String, String, ReadMetadata, List<SVInterval>, PairedStrandedIntervalTree<EvidenceTargetLink>, Broadcast<SVIntervalTree<VariantContext>>, SAMFileHeader, ReferenceMultiSparkSource, Set<VCFHeaderLine>, 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
svEvidenceFilterModelFile StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
svEvidenceFilterThresholdProbability StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
svEvidenceFilterType StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
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
svGenomeGapsFile StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
svGenomeUmapS100File StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
SVInterval org.broadinstitute.hellbender.tools.spark.sv.utils
Naturally collating, simple interval
WARNING: THIS IS NOT THE SAME AS THE BED COORDINATE SYSTEM OR
SimpleInterval !!!!!
SVInterval(int, int, int) SVInterval
SVInterval(int, int, int, SVInterval.SVIntervalConstructorArgsValidator) SVInterval
SVInterval.Serializer org.broadinstitute.hellbender.tools.spark.sv.utils
SVInterval.SVIntervalConstructorArgsValidator 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
SVMappingQualityFilter(int) SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SVMappingQualityFilter
SVNoveltyRate VariantSummary
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, int, int, String, Allele, Allele, int, Map<String, Object>) 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
switchToNaturalLog() AlleleLikelihoods
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
VALID_ALLELES IlluminaManifest
ValidAlignmentEndReadFilter() ReadFilterLibrary.ValidAlignmentEndReadFilter
ValidAlignmentStartReadFilter() ReadFilterLibrary.ValidAlignmentStartReadFilter
validate() GermlineCallingArgumentCollection
validate() GermlineContigPloidyModelArgumentCollection
validate() GermlineDenoisingModelArgumentCollection
validate() HybridADVIArgumentCollection
validate(T) AnnotationKey
validate() StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsSparkArgumentCollection
Explicit call this method.
validate() StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
Explicit call this method.
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_INTEGRITY_ARG_LONG_NAME FuncotatorDataSourceDownloader
VALIDATE_SAMPLE_MAP_LONG_NAME GenomicsDBImport
validateAllelesList() ReducibleAnnotationData
validateAndPrepareOutputDirectories(File...) CopyNumberArgumentValidationUtils
Validate that output directories are writeable.
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
validateArguments() PedigreeAnnotation
Provide input arguments so as to warn the user if they are providing an incorrect subset of pedigree inputs.
ValidateBasicSomaticShortMutations org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
ValidateBasicSomaticShortMutations() ValidateBasicSomaticShortMutations
ValidateBasicSomaticShortMutations.Judgment org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
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.
validateInputs(File...) CopyNumberArgumentValidationUtils
Validate that input files and/or directories are readable if they are not null (i.e., optional inputs).
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.
validateOutputFiles(File...) CopyNumberArgumentValidationUtils
Validate that output files are writeable, whether or not they already exist.
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
validateVersionCompatibility(BCFVersion, BCFVersion) GenomicsDBBCFCodec
VALIDATION_AD_HEADER_LINE ValidateBasicSomaticShortMutations
VALIDATION_AD_INFO_FIELD_KEY ValidateBasicSomaticShortMutations
VALIDATION_STRINGENCY PicardCommandLineProgram
VALIDATION_STRINGENCY CommandLineProgram
validationCaseName ValidateBasicSomaticShortMutations
validationControlName ValidateBasicSomaticShortMutations
ValidationReport org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
ValidationReport() ValidationReport
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 IlluminaGenotype
VALUE_SEPARATOR Tranche
valueCounts CompressedDataList
valueOf(String) AlignmentContext.ReadOrientation
Returns the enum constant of this type with the specified name.
valueOf(String) GATKSparkTool.ReadInputMergingPolicy
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) CollectReadCounts.Format
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) FilterFuncotations.AlleleFrequencyDataSource
Returns the enum constant of this type with the specified name.
valueOf(String) FilterFuncotations.Reference
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) FuncotatorUtils.Genus
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) RevertSamSpark.FileType
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) BreakEndVariantType.SupportedType
Returns the enum constant of this type with the specified name.
valueOf(String) TypeInferredFromSimpleChimera
Returns the enum constant of this type with the specified name.
valueOf(String) SimpleSVType.SupportedType
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) InsertSizeDistributionShape
Returns the enum constant of this type with the specified name.
valueOf(String) StructuralVariationDiscoveryArgumentCollection.SvEvidenceFilterType
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) 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) 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) AbstractReadThreadingGraph.TraversalDirection
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) ErrorType
Returns the enum constant of this type with the specified name.
valueOf(String) ThresholdCalculator.Strategy
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) ArtifactState
Returns the enum constant of this type with the specified name.
valueOf(String) ReadOrientation
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) ValidateBasicSomaticShortMutations.Judgment
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) MultiallelicSummary.Type
Returns the enum constant of this type with the specified name.
valueOf(String) VariantSummary.Type
Returns the enum constant of this type with the specified name.
valueOf(String) AlleleFrequency.StratifyingScale
Returns the enum constant of this type with the specified name.
valueOf(String) FunctionalClass.FunctionalType
Returns the enum constant of this type with the specified name.
valueOf(String) SnpEffPositionModifier.PositionModifier
Returns the enum constant of this type with the specified name.
valueOf(String) SnpEffUtil.EffectFunctionalClass
Returns the enum constant of this type with the specified name.
valueOf(String) SnpEffUtil.EffectType
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) 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) NioFileCopierWithProgressMeter.Verbosity
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(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) Build37ExtendedIlluminaManifestRecord.Flag
Returns the enum constant of this type with the specified name.
valueOf(String) IlluminaGenotype
Returns the enum constant of this type with the specified name.
valueOf(String) IlluminaManifestRecord.IlluminaStrand
Returns the enum constant of this type with the specified name.
valueOf(String) InfiniumVcfFields.GENOTYPE_VALUES
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) DistanceMetric
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) PathProvider
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) ReadBaseStratification.Consensus
Returns the enum constant of this type with the specified name.
valueOf(String) ReadBaseStratification.CycleBin
Returns the enum constant of this type with the specified name.
valueOf(String) ReadBaseStratification.LongShortHomopolymer
Returns the enum constant of this type with the specified name.
valueOf(String) ReadBaseStratification.PairOrientation
Returns the enum constant of this type with the specified name.
valueOf(String) ReadBaseStratification.ProperPaired
Returns the enum constant of this type with the specified name.
valueOf(String) ReadBaseStratification.ReadDirection
Returns the enum constant of this type with the specified name.
valueOf(String) ReadBaseStratification.ReadOrdinality
Returns the enum constant of this type with the specified name.
valueOf(String) SamComparison.AlignmentComparison
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) IntervalListScatterMode
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() GATKSparkTool.ReadInputMergingPolicy
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() CollectReadCounts.Format
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() FilterFuncotations.AlleleFrequencyDataSource
Returns an array containing the constants of this enum type, in
the order they are declared.
values() FilterFuncotations.Reference
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() FuncotatorUtils.Genus
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() RevertSamSpark.FileType
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() BreakEndVariantType.SupportedType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() TypeInferredFromSimpleChimera
Returns an array containing the constants of this enum type, in
the order they are declared.
values() SimpleSVType.SupportedType
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() InsertSizeDistributionShape
Returns an array containing the constants of this enum type, in
the order they are declared.
values() StructuralVariationDiscoveryArgumentCollection.SvEvidenceFilterType
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() 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() 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() AbstractReadThreadingGraph.TraversalDirection
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() ErrorType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ThresholdCalculator.Strategy
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() ArtifactState
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ReadOrientation
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() ValidateBasicSomaticShortMutations.Judgment
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() MultiallelicSummary.Type
Returns an array containing the constants of this enum type, in
the order they are declared.
values() VariantSummary.Type
Returns an array containing the constants of this enum type, in
the order they are declared.
values() AlleleFrequency.StratifyingScale
Returns an array containing the constants of this enum type, in
the order they are declared.
values() FunctionalClass.FunctionalType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() StratificationManager
values(List<List<Object>>) StratificationManager
values() SnpEffPositionModifier.PositionModifier
Returns an array containing the constants of this enum type, in
the order they are declared.
values() SnpEffUtil.EffectFunctionalClass
Returns an array containing the constants of this enum type, in
the order they are declared.
values() SnpEffUtil.EffectType
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() 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() NioFileCopierWithProgressMeter.Verbosity
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() Build37ExtendedIlluminaManifestRecord.Flag
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IlluminaGenotype
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IlluminaManifestRecord.IlluminaStrand
Returns an array containing the constants of this enum type, in
the order they are declared.
values() InfiniumVcfFields.GENOTYPE_VALUES
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() DistanceMetric
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() PathProvider
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() ReadBaseStratification.Consensus
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ReadBaseStratification.CycleBin
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ReadBaseStratification.LongShortHomopolymer
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ReadBaseStratification.PairOrientation
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ReadBaseStratification.ProperPaired
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ReadBaseStratification.ReadDirection
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ReadBaseStratification.ReadOrdinality
Returns an array containing the constants of this enum type, in
the order they are declared.
values() SamComparison.AlignmentComparison
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() IntervalListScatterMode
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 AlleleLikelihoods
Indexed per sample, allele and finally evidence (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))
variance() InsertSizeDistribution
VARIANT_DEPTH_KEY GATKVCFConstants
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
VariantAFEvaluator org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
VariantAFEvaluator() VariantAFEvaluator
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, 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.
VariantCallingDetailMetrics() CollectVariantCallingMetrics.VariantCallingDetailMetrics
VariantCallingSummaryMetrics() CollectVariantCallingMetrics.VariantCallingSummaryMetrics
variantChromosome SvType
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
VariantEval org.broadinstitute.hellbender.tools.walkers.varianteval
Given a variant callset, it is common to calculate various quality control metrics.
VariantEval() VariantEval
VariantEvalReportWriter org.broadinstitute.hellbender.tools.walkers.varianteval
Class for writing the GATKReport for VariantEval
Accepts a fulled evaluated (i.e., there's no more data coming) set of stratifications and evaluators
and supports writing out the data in these evaluators to a GATKReport.
VariantEvalReportWriter() VariantEvalReportWriter
VariantEvaluationProgramGroup picard.cmdline.programgroups
Tools that evaluate and refine variant calls, e.g.
VariantEvaluationProgramGroup() VariantEvaluationProgramGroup
VariantEvaluator org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
VariantEvaluator(String) VariantEvaluator
VariantEvaluator() VariantEvaluator
VariantEvalUtils org.broadinstitute.hellbender.tools.walkers.varianteval.util
VariantEvalUtils(VariantEval) VariantEvalUtils
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
VariantFilterLibrary.AllowAllVariantsVariantFilter org.broadinstitute.hellbender.engine.filters
Do not filter out any variants.
VariantFilterLibrary.NotSymbolicOrSVVariantFilter org.broadinstitute.hellbender.engine.filters
Filter out any variants that are symbolic or SV.
VariantFilterLibrary.PassesFiltersVariantFilter org.broadinstitute.hellbender.engine.filters
Filter out any variants that fail (variant-level) filters.
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
VariantLocusWalker org.broadinstitute.hellbender.engine
VariantLocusWalker processes variants from a single source, grouped by locus overlap, or optionally one
at a time in order, with optional contextual information from a reference, sets of reads, and/or supplementary sources
of Features.
VariantLocusWalker() VariantLocusWalker
VariantManipulationProgramGroup picard.cmdline.programgroups
Tools that manipulate variant call format (VCF) data
VariantManipulationProgramGroup() VariantManipulationProgramGroup
variantMultiIndelRatio MultiallelicSummary
variantMultiSnpRatio MultiallelicSummary
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
variantRate CountVariants
variantRatePerBp CountVariants
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 GetPileupSummaries
variants FastaAlternateReferenceMaker
Variants from this input file are used by this tool to construct an alternate reference.
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
variantShardSize VariantWalkerSpark
variantSource TrainingSet
VariantsSparkSink org.broadinstitute.hellbender.engine.spark.datasources
VariantsSparkSink writes variants to a VCF file in parallel using Hadoop-BAM.
VariantsSparkSink() VariantsSparkSink
VariantsSparkSource org.broadinstitute.hellbender.engine.spark.datasources
VariantsSparkSource loads Variants from files serially (using FeatureDataSource) or in parallel
using Hadoop-BAM.
VariantsSparkSource(JavaSparkContext) VariantsSparkSource
variantStart SvType
variantStop SvType
VariantsToTable org.broadinstitute.hellbender.tools.walkers.variantutils
Extract fields from a VCF file to a tab-delimited table
VariantsToTable() VariantsToTable
VariantStratifier org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
VariantStratifier() VariantStratifier
VariantSummary org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
VariantSummary() VariantSummary
VariantSummary.Type org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
VariantTransformer org.broadinstitute.hellbender.transformers
VariantType org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
Stratifies the eval variants by their type (SNP, INDEL, ETC)
VariantType() VariantType
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
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 variants from one or more sources of variants,
with optional contextual information from a reference, sets of reads, and/or supplementary sources of
Features.
VariantWalkerBase() VariantWalkerBase
VariantWalkerContext org.broadinstitute.hellbender.engine.spark
VariantWalkerContext(VariantContext, ReadsContext, ReferenceContext, FeatureContext) VariantWalkerContext
VariantWalkerSpark org.broadinstitute.hellbender.engine.spark
VariantWalkerSpark() VariantWalkerSpark
variantWasSingleton(VariantContext) VariantEvaluator
Returns true if the variant in vc was a singleton in the original input evaluation
set, regardless of variant context subsetting that has occurred.
VCF CollectIndependentReplicateMetrics
VCF VcfToAdpc
VCF CollectSamErrorMetrics
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, LinkedHashMap<String, String>, FeatureInput<? extends Feature>) VcfFuncotationFactory
VcfFuncotationFactory(String, String, Path, LinkedHashMap<String, String>, FeatureInput<? extends Feature>, boolean) VcfFuncotationFactory
VcfFuncotationMetadata org.broadinstitute.hellbender.tools.funcotator.metadata
vcfOutput SelectVariants
VcfOutputRenderer org.broadinstitute.hellbender.tools.funcotator.vcfOutput
A Funcotator output renderer for writing to VCF files.
VcfOutputRenderer(VariantContextWriter, List<DataSourceFuncotationFactory>, VCFHeader, LinkedHashMap<String, String>, LinkedHashMap<String, String>, Set<VCFHeaderLine>, Set<String>, String) VcfOutputRenderer
VcfToAdpc picard.arrays
A simple program to convert a Genotyping Arrays VCF to an ADPC file (Illumina intensity data file).
VcfToAdpc() VcfToAdpc
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 global 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 NioFileCopierWithProgressMeter
VERBOSITY CommandLineProgram
VERBOSITY_DEFAULT NioFileCopierWithProgressMeter
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
VerifyIDIntensityContaminationMetrics picard.arrays
VerifyIDIntensityContaminationMetrics() VerifyIDIntensityContaminationMetrics
version DataSourceFuncotationFactory
VERSION MafOutputRenderer
version FilterFileReader
Version number found in the FilterFile, this should equal 3
VERSION_STRING ReadMetadata.Serializer
Serialization version.
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
VQSRNegativeModelFailure(String) UserException.VQSRNegativeModelFailure
VQSRPositiveModelFailure(String) UserException.VQSRPositiveModelFailure