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Package Hierarchies:
htsjdk.samtools
,
org.broadinstitute.hellbender
,
org.broadinstitute.hellbender.cmdline
,
org.broadinstitute.hellbender.cmdline.argumentcollections
,
org.broadinstitute.hellbender.cmdline.GATKPlugin
,
org.broadinstitute.hellbender.cmdline.programgroups
,
org.broadinstitute.hellbender.engine
,
org.broadinstitute.hellbender.engine.datasources
,
org.broadinstitute.hellbender.engine.filters
,
org.broadinstitute.hellbender.engine.spark
,
org.broadinstitute.hellbender.engine.spark.datasources
,
org.broadinstitute.hellbender.exceptions
,
org.broadinstitute.hellbender.metrics
,
org.broadinstitute.hellbender.metrics.analysis
,
org.broadinstitute.hellbender.tools
,
org.broadinstitute.hellbender.tools.copynumber
,
org.broadinstitute.hellbender.tools.copynumber.arguments
,
org.broadinstitute.hellbender.tools.copynumber.caller
,
org.broadinstitute.hellbender.tools.copynumber.datacollection
,
org.broadinstitute.hellbender.tools.copynumber.denoising
,
org.broadinstitute.hellbender.tools.copynumber.formats
,
org.broadinstitute.hellbender.tools.copynumber.formats.collections
,
org.broadinstitute.hellbender.tools.copynumber.formats.metadata
,
org.broadinstitute.hellbender.tools.copynumber.formats.records
,
org.broadinstitute.hellbender.tools.copynumber.gcnv
,
org.broadinstitute.hellbender.tools.copynumber.models
,
org.broadinstitute.hellbender.tools.copynumber.plotting
,
org.broadinstitute.hellbender.tools.copynumber.segmentation
,
org.broadinstitute.hellbender.tools.copynumber.utils
,
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
,
org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging
,
org.broadinstitute.hellbender.tools.copynumber.utils.optimization
,
org.broadinstitute.hellbender.tools.copynumber.utils.segmentation
,
org.broadinstitute.hellbender.tools.examples
,
org.broadinstitute.hellbender.tools.examples.metrics.multi
,
org.broadinstitute.hellbender.tools.examples.metrics.single
,
org.broadinstitute.hellbender.tools.exome
,
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter
,
org.broadinstitute.hellbender.tools.funcotator
,
org.broadinstitute.hellbender.tools.funcotator.dataSources
,
org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic
,
org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode
,
org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf
,
org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv
,
org.broadinstitute.hellbender.tools.funcotator.mafOutput
,
org.broadinstitute.hellbender.tools.funcotator.vcfOutput
,
org.broadinstitute.hellbender.tools.genomicsdb
,
org.broadinstitute.hellbender.tools.readersplitters
,
org.broadinstitute.hellbender.tools.spark
,
org.broadinstitute.hellbender.tools.spark.bwa
,
org.broadinstitute.hellbender.tools.spark.pathseq
,
org.broadinstitute.hellbender.tools.spark.pathseq.loggers
,
org.broadinstitute.hellbender.tools.spark.pipelines
,
org.broadinstitute.hellbender.tools.spark.pipelines.metrics
,
org.broadinstitute.hellbender.tools.spark.sv
,
org.broadinstitute.hellbender.tools.spark.sv.discovery
,
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
,
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
,
org.broadinstitute.hellbender.tools.spark.sv.evidence
,
org.broadinstitute.hellbender.tools.spark.sv.utils
,
org.broadinstitute.hellbender.tools.spark.transforms
,
org.broadinstitute.hellbender.tools.spark.transforms.bqsr
,
org.broadinstitute.hellbender.tools.spark.transforms.markduplicates
,
org.broadinstitute.hellbender.tools.spark.utils
,
org.broadinstitute.hellbender.tools.spark.validation
,
org.broadinstitute.hellbender.tools.validation
,
org.broadinstitute.hellbender.tools.walkers
,
org.broadinstitute.hellbender.tools.walkers.annotator
,
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
,
org.broadinstitute.hellbender.tools.walkers.bqsr
,
org.broadinstitute.hellbender.tools.walkers.contamination
,
org.broadinstitute.hellbender.tools.walkers.filters
,
org.broadinstitute.hellbender.tools.walkers.genotyper
,
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
,
org.broadinstitute.hellbender.tools.walkers.haplotypecaller
,
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
,
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
,
org.broadinstitute.hellbender.tools.walkers.markduplicates
,
org.broadinstitute.hellbender.tools.walkers.mutect
,
org.broadinstitute.hellbender.tools.walkers.qc
,
org.broadinstitute.hellbender.tools.walkers.realignmentfilter
,
org.broadinstitute.hellbender.tools.walkers.rnaseq
,
org.broadinstitute.hellbender.tools.walkers.validation
,
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
,
org.broadinstitute.hellbender.tools.walkers.variantutils
,
org.broadinstitute.hellbender.tools.walkers.vqsr
,
org.broadinstitute.hellbender.transformers
,
org.broadinstitute.hellbender.utils
,
org.broadinstitute.hellbender.utils.activityprofile
,
org.broadinstitute.hellbender.utils.artifacts
,
org.broadinstitute.hellbender.utils.baq
,
org.broadinstitute.hellbender.utils.bwa
,
org.broadinstitute.hellbender.utils.clipping
,
org.broadinstitute.hellbender.utils.codecs
,
org.broadinstitute.hellbender.utils.codecs.gencode
,
org.broadinstitute.hellbender.utils.codecs.sampileup
,
org.broadinstitute.hellbender.utils.codecs.table
,
org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable
,
org.broadinstitute.hellbender.utils.collections
,
org.broadinstitute.hellbender.utils.config
,
org.broadinstitute.hellbender.utils.downsampling
,
org.broadinstitute.hellbender.utils.fasta
,
org.broadinstitute.hellbender.utils.fragments
,
org.broadinstitute.hellbender.utils.functional
,
org.broadinstitute.hellbender.utils.gcs
,
org.broadinstitute.hellbender.utils.genotyper
,
org.broadinstitute.hellbender.utils.haplotype
,
org.broadinstitute.hellbender.utils.help
,
org.broadinstitute.hellbender.utils.hmm
,
org.broadinstitute.hellbender.utils.illumina
,
org.broadinstitute.hellbender.utils.io
,
org.broadinstitute.hellbender.utils.iterators
,
org.broadinstitute.hellbender.utils.locusiterator
,
org.broadinstitute.hellbender.utils.logging
,
org.broadinstitute.hellbender.utils.mcmc
,
org.broadinstitute.hellbender.utils.nio
,
org.broadinstitute.hellbender.utils.pairhmm
,
org.broadinstitute.hellbender.utils.param
,
org.broadinstitute.hellbender.utils.pileup
,
org.broadinstitute.hellbender.utils.python
,
org.broadinstitute.hellbender.utils.R
,
org.broadinstitute.hellbender.utils.read
,
org.broadinstitute.hellbender.utils.read.markduplicates
,
org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
,
org.broadinstitute.hellbender.utils.read.mergealignment
,
org.broadinstitute.hellbender.utils.recalibration
,
org.broadinstitute.hellbender.utils.recalibration.covariates
,
org.broadinstitute.hellbender.utils.reference
,
org.broadinstitute.hellbender.utils.report
,
org.broadinstitute.hellbender.utils.runtime
,
org.broadinstitute.hellbender.utils.samples
,
org.broadinstitute.hellbender.utils.smithwaterman
,
org.broadinstitute.hellbender.utils.solver
,
org.broadinstitute.hellbender.utils.spark
,
org.broadinstitute.hellbender.utils.svd
,
org.broadinstitute.hellbender.utils.test
,
org.broadinstitute.hellbender.utils.test.testers
,
org.broadinstitute.hellbender.utils.text
,
org.broadinstitute.hellbender.utils.tsv
,
org.broadinstitute.hellbender.utils.variant
,
org.broadinstitute.hellbender.utils.variant.writers
,
picard
,
picard.analysis
,
picard.analysis.artifacts
,
picard.analysis.directed
,
picard.analysis.replicates
,
picard.annotation
,
picard.cmdline
,
picard.cmdline.argumentcollections
,
picard.cmdline.programgroups
,
picard.fastq
,
picard.filter
,
picard.fingerprint
,
picard.illumina
,
picard.illumina.parser
,
picard.illumina.parser.fakers
,
picard.illumina.parser.readers
,
picard.illumina.quality
,
picard.metrics
,
picard.nio
,
picard.pedigree
,
picard.reference
,
picard.sam
,
picard.sam.markduplicates
,
picard.sam.markduplicates.util
,
picard.sam.util
,
picard.util
,
picard.util.help
,
picard.vcf
,
picard.vcf.filter
,
picard.vcf.MendelianViolations
,
picard.vcf.processor
,
picard.vcf.processor.util
Class Hierarchy
java.lang.Object
org.broadinstitute.hellbender.utils.read.mergealignment.
AbstractAlignmentMerger
org.broadinstitute.hellbender.utils.read.mergealignment.
SamAlignmentMerger
picard.sam.
AbstractAlignmentMerger
picard.sam.
SamAlignmentMerger
java.util.AbstractCollection<E> (implements java.util.Collection<E>)
java.util.AbstractList<E> (implements java.util.List<E>)
java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
org.broadinstitute.hellbender.utils.collections.
ExpandingArrayList
<E>
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
KBestHaplotypeFinder
java.util.AbstractSet<E> (implements java.util.Set<E>)
org.broadinstitute.hellbender.utils.
GenomeLocSortedSet
org.broadinstitute.hellbender.utils.collections.
IndexedSet
<E>
java.util.TreeSet<E> (implements java.lang.Cloneable, java.util.NavigableSet<E>, java.io.Serializable)
picard.fingerprint.
FingerprintUtils.VariantContextSet
org.broadinstitute.hellbender.tools.spark.utils.
HopscotchCollection
<T>
org.broadinstitute.hellbender.tools.spark.utils.
HopscotchMultiMap
<K,V,T>
org.broadinstitute.hellbender.tools.spark.utils.
HopscotchUniqueMultiMap
<K,V,T>
org.broadinstitute.hellbender.tools.spark.utils.
HopscotchSet
<T> (implements java.util.Set<E>)
org.broadinstitute.hellbender.tools.spark.utils.
HopscotchMap
<K,V,T>
org.broadinstitute.hellbender.engine.
AbstractConcordanceWalker.TruthVersusEval
(implements htsjdk.samtools.util.Locatable)
java.util.concurrent.AbstractExecutorService (implements java.util.concurrent.ExecutorService)
java.util.concurrent.ThreadPoolExecutor
picard.util.
ThreadPoolExecutorWithExceptions
htsjdk.tribble.AbstractFeatureCodec<FEATURE_TYPE,SOURCE> (implements htsjdk.tribble.FeatureCodec<FEATURE_TYPE,SOURCE>)
htsjdk.tribble.AsciiFeatureCodec<T>
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.
AnnotatedIntervalCodec
org.broadinstitute.hellbender.utils.codecs.sampileup.
SAMPileupCodec
org.broadinstitute.hellbender.utils.codecs.table.
TableCodec
org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.
XsvLocatableTableCodec
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfCodec
org.jgrapht.graph.AbstractGraph<V,E> (implements org.jgrapht.Graph<V,E>)
org.jgrapht.graph.AbstractBaseGraph<V,E> (implements java.lang.Cloneable, org.jgrapht.Graph<V,E>, java.io.Serializable)
org.jgrapht.graph.DefaultDirectedGraph<V,E> (implements org.jgrapht.DirectedGraph<V,E>)
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
BaseGraph
<V,E>
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.
ReadThreadingGraph
(implements org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
KmerSearchableGraph
<V,E>)
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.
TestingReadThreadingGraph
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
SeqGraph
picard.illumina.parser.readers.
AbstractIlluminaPositionFileReader
(implements htsjdk.samtools.util.CloseableIterator<T>)
picard.illumina.parser.readers.
ClocsFileReader
picard.illumina.parser.readers.
LocsFileReader
picard.illumina.parser.readers.
PosFileReader
picard.illumina.parser.readers.
AbstractIlluminaPositionFileReader.PositionInfo
org.apache.commons.math3.distribution.AbstractIntegerDistribution (implements org.apache.commons.math3.distribution.IntegerDistribution, java.io.Serializable)
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.
BetaBinomialDistribution
htsjdk.samtools.util.AbstractIterator<E> (implements java.util.Iterator<E>)
picard.util.
AbstractInputParser
(implements htsjdk.samtools.util.CloseableIterator<T>, java.lang.Iterable<T>)
picard.util.
BasicInputParser
picard.util.
CsvInputParser
picard.util.
TabbedInputParser
java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
htsjdk.samtools.util.CollectionUtil.DefaultingMap<K,V>
picard.vcf.MendelianViolations.
MendelianViolationsByFamily
java.util.LinkedHashMap<K,V> (implements java.util.Map<K,V>)
org.broadinstitute.hellbender.utils.
LRUCache
<K,V>
java.util.TreeMap<K,V> (implements java.lang.Cloneable, java.util.NavigableMap<K,V>, java.io.Serializable)
org.broadinstitute.hellbender.utils.haplotype.
EventMap
picard.fingerprint.
Fingerprint
picard.pedigree.
PedFile
org.broadinstitute.hellbender.utils.read.markduplicates.
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
(implements java.lang.AutoCloseable)
picard.sam.markduplicates.util.
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
htsjdk.samtools.util.AbstractProgressLogger (implements htsjdk.samtools.util.ProgressLoggerInterface)
org.broadinstitute.hellbender.utils.runtime.
ProgressLogger
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
AbstractRecordCollection
<METADATA,RECORD>
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
AbstractLocatableCollection
<METADATA,RECORD>
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
AbstractSampleLocatableCollection
<RECORD>
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
AlleleFractionSegmentCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
AllelicCountCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
CalledCopyRatioSegmentCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
CopyRatioCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
CopyRatioSegmentCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
IntegerCopyNumberSegmentCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
ModeledSegmentCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
MultidimensionalSegmentCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
SimpleCountCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
AnnotatedIntervalCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
SimpleIntervalCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
AbstractSampleRecordCollection
<RECORD>
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
BaselineCopyNumberCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
CopyNumberPosteriorDistributionCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
ParameterDecileCollection
<T>
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
CoveragePerContigCollection
picard.analysis.
AbstractWgsMetricsCollector
<T>
picard.analysis.
CollectWgsMetrics.WgsMetricsCollector
picard.analysis.
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
picard.analysis.
FastWgsMetricsCollector
org.broadinstitute.hellbender.utils.activityprofile.
ActivityProfile
org.broadinstitute.hellbender.utils.activityprofile.
BandPassActivityProfile
org.broadinstitute.hellbender.utils.activityprofile.
ActivityProfileState
picard.util.
AdapterMarker
org.broadinstitute.hellbender.transformers.
AdapterTrimTransformer
(implements org.broadinstitute.hellbender.transformers.
ReadTransformer
)
picard.analysis.
AdapterUtility
org.broadinstitute.hellbender.utils.mcmc.
AdaptiveMetropolisSampler
org.broadinstitute.hellbender.engine.spark.
AddContextDataToReadSpark
org.broadinstitute.hellbender.engine.spark.
AddContextDataToReadSparkOptimized
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.spark.
AddContextDataToReadSparkOptimized.SubdivideAndFillReadsIterator
(implements java.util.Iterator<E>, java.io.Serializable)
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
AFCalculationResult
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
AFCalculator
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
AlleleFrequencyCalculator
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
GeneralPloidyExactAFCalculator
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
IndependentAllelesDiploidExactAFCalculator
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
ReferenceDiploidExactAFCalculator
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
AFCalculatorProvider
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
ConcurrentAFCalculatorProvider
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
FixedAFCalculatorProvider
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
GeneralPloidyFailOverAFCalculatorProvider
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
AFPriorProvider
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
CustomAFPriorProvider
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
HeterozygosityAFPriorProvider
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
AggregatedSubHaplotypeFinder
<F>
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
AlignedAssembly
org.broadinstitute.hellbender.tools.spark.sv.evidence.
AlignedAssemblyOrExcuse
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
AlignedContig
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
AlignedContigGenerator
org.broadinstitute.hellbender.tools.spark.sv.
StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser
(implements scala.Serializable)
org.broadinstitute.hellbender.tools.spark.sv.discovery.
SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SAMFormattedContigAlignmentParser
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.
AlignmentContext
(implements org.broadinstitute.hellbender.utils.
HasGenomeLocation
, htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.utils.locusiterator.
AlignmentContextIteratorBuilder
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
AlignmentInterval
org.broadinstitute.hellbender.utils.locusiterator.
AlignmentStateMachine
org.broadinstitute.hellbender.utils.read.
AlignmentUtils
org.broadinstitute.hellbender.utils.read.
AlignmentUtils.MismatchCount
htsjdk.variant.variantcontext.Allele (implements java.lang.Comparable<T>, java.io.Serializable)
org.broadinstitute.hellbender.utils.haplotype.
Haplotype
picard.vcf.filter.
AlleleBalanceFilter
(implements picard.vcf.filter.
VariantFilter
)
org.broadinstitute.hellbender.utils.downsampling.
AlleleBiasedDownsamplingUtils
org.broadinstitute.hellbender.tools.copynumber.segmentation.
AlleleFractionKernelSegmenter
org.broadinstitute.hellbender.tools.copynumber.models.
AlleleFractionModeller
org.broadinstitute.hellbender.tools.copynumber.models.
AlleleFractionPrior
org.broadinstitute.hellbender.tools.copynumber.formats.records.
AlleleFractionSegment
(implements htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.utils.genotyper.
AlleleList.ActualPermutation
<A> (implements org.broadinstitute.hellbender.utils.genotyper.
AlleleListPermutation
<A>)
org.broadinstitute.hellbender.utils.genotyper.
AlleleList.NonPermutation
<A> (implements org.broadinstitute.hellbender.utils.genotyper.
AlleleListPermutation
<A>)
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.
AllelePileupCounter
org.broadinstitute.hellbender.tools.walkers.genotyper.
AlleleSubsettingUtils
picard.util.
AlleleSubsettingUtils
org.broadinstitute.hellbender.tools.copynumber.formats.records.
AllelicCount
(implements htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.tools.copynumber.datacollection.
AllelicCountCollector
org.broadinstitute.hellbender.utils.iterators.
AllLocusIterator
(implements java.util.Iterator<E>)
org.broadinstitute.hellbender.tools.copynumber.formats.records.
AnnotatedInterval
(implements htsjdk.tribble.Feature, htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.
AnnotatedInterval
(implements htsjdk.tribble.Feature, htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.
AnnotatedIntervalCollection
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.
AnnotatedIntervalHeader
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.
AnnotatedIntervalUtils
org.broadinstitute.hellbender.tools.spark.sv.discovery.
AnnotatedVariantProducer
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.copynumber.formats.records.
AnnotationSet
org.broadinstitute.hellbender.tools.walkers.annotator.
AnnotationUtils
org.broadinstitute.hellbender.utils.svd.
ApacheSingularValueDecomposer
(implements org.broadinstitute.hellbender.utils.svd.
SingularValueDecomposer
)
org.broadinstitute.hellbender.tools.spark.transforms.
ApplyBQSRSparkFn
org.broadinstitute.hellbender.tools.
ApplyBQSRUniqueArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.
ApplyBQSRArgumentCollection
org.broadinstitute.hellbender.utils.test.
ArgumentsBuilder
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.
ArtifactStatisticsScorer
org.broadinstitute.hellbender.utils.read.
ArtificialBAMBuilder
org.broadinstitute.hellbender.utils.read.
ArtificialReadIterator
(implements java.lang.Iterable<T>, java.util.Iterator<E>)
org.broadinstitute.hellbender.utils.read.
ArtificialReadQueryIterator
org.broadinstitute.hellbender.utils.read.
ArtificialReadUtils
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
AssemblyBasedCallerGenotypingEngine.CalledHaplotypes
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
AssemblyBasedCallerUtils
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
AssemblyContigAlignmentsConfigPicker
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
AssemblyContigWithFineTunedAlignments
org.broadinstitute.hellbender.engine.
AssemblyRegion
(implements htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.engine.
AssemblyRegionIterator
(implements java.util.Iterator<E>)
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
AssemblyRegionTrimmer
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
AssemblyRegionTrimmer.Result
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
AssemblyRegionTrimmerArgumentCollection
org.broadinstitute.hellbender.engine.spark.
AssemblyRegionWalkerContext
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
AssemblyResult
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
AssemblyResultSet
org.broadinstitute.hellbender.utils.runtime.
AsynchronousStreamWriterService
<T>
picard.util.
AsyncIterator
<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
picard.fastq.
BamToBfqWriter
org.broadinstitute.hellbender.utils.baq.
BAQ
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.baq.
BAQ.BAQCalculationResult
picard.illumina.parser.readers.
BarcodeFileReader
(implements htsjdk.samtools.util.CloseableIterator<T>)
org.apache.commons.math3.analysis.solvers.BaseAbstractUnivariateSolver<FUNC> (implements org.apache.commons.math3.analysis.solvers.BaseUnivariateSolver<FUNC>)
org.apache.commons.math3.analysis.solvers.AbstractUnivariateSolver (implements org.apache.commons.math3.analysis.solvers.UnivariateSolver)
org.broadinstitute.hellbender.utils.solver.
RobustBrentSolver
picard.illumina.parser.readers.
BaseBclReader
picard.illumina.parser.readers.
BclReader
(implements htsjdk.samtools.util.CloseableIterator<T>)
picard.illumina.parser.readers.
CbclReader
(implements htsjdk.samtools.util.CloseableIterator<T>)
picard.illumina.parser.readers.
BaseBclReader.CycleData
picard.illumina.parser.readers.
BaseBclReader.TileData
picard.cmdline.programgroups.
BaseCallingProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
BaseEdge
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
MultiSampleEdge
picard.illumina.parser.
BaseIlluminaDataProvider
(implements java.lang.AutoCloseable, java.lang.Iterable<T>, java.util.Iterator<E>)
picard.illumina.parser.
IlluminaDataProvider
picard.illumina.parser.
NewIlluminaDataProvider
org.broadinstitute.hellbender.transformers.
BaseQualityClipReadTransformer
(implements org.broadinstitute.hellbender.transformers.
ReadTransformer
)
org.broadinstitute.hellbender.transformers.
BaseQualityReadTransformer
(implements org.broadinstitute.hellbender.transformers.
ReadTransformer
)
org.broadinstitute.hellbender.utils.recalibration.
BaseRecalibrationEngine
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.recalibration.
BaseRecalibrationEngine.BQSRReferenceWindowFunction
(implements org.broadinstitute.hellbender.utils.
SerializableFunction
<T,R>)
org.broadinstitute.hellbender.tools.spark.transforms.bqsr.
BaseRecalibratorEngineSparkWrapper
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.transforms.
BaseRecalibratorSparkFn
org.broadinstitute.hellbender.utils.test.
BaseTest
org.broadinstitute.hellbender.utils.test.
BaseTest.TestDataProvider
org.broadinstitute.hellbender.utils.
BaseUtils
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
BaseVertex
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.
MultiDeBruijnVertex
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
SeqVertex
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.
BasicSomaticShortMutationValidator
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.
BasicValidationResult
(implements htsjdk.samtools.util.Locatable)
picard.illumina.parser.
BclData
picard.illumina.parser.
CbclData
picard.illumina.parser.readers.
BclIndexReader
picard.illumina.parser.readers.
BclQualityEvaluationStrategy
org.broadinstitute.hellbender.utils.read.mergealignment.
BestEndMapqPrimaryAlignmentStrategy
(implements org.broadinstitute.hellbender.utils.read.mergealignment.
PrimaryAlignmentSelectionStrategy
)
picard.sam.
BestEndMapqPrimaryAlignmentStrategy
(implements picard.sam.
PrimaryAlignmentSelectionStrategy
)
org.broadinstitute.hellbender.utils.read.mergealignment.
BestMapqPrimaryAlignmentSelectionStrategy
(implements org.broadinstitute.hellbender.utils.read.mergealignment.
PrimaryAlignmentSelectionStrategy
)
picard.sam.
BestMapqPrimaryAlignmentSelectionStrategy
(implements picard.sam.
PrimaryAlignmentSelectionStrategy
)
org.broadinstitute.hellbender.transformers.
BQSRReadTransformer
(implements org.broadinstitute.hellbender.transformers.
ReadTransformer
)
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
BreakpointComplications
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
BreakpointComplications.IntraChrStrandSwitchBreakpointComplications
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointDensityFilter
(implements java.util.Iterator<E>)
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.ExternalEvidence
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.ReadEvidence
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.DiscordantReadPairEvidence
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.InterContigPair
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.OutiesPair
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.SameStrandPair
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.WeirdTemplateSize
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.LargeIndel
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.MateUnmapped
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.SplitRead
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.TemplateSizeAnomaly
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidenceClusterer
(implements java.util.function.Function<T,R>)
org.broadinstitute.hellbender.engine.spark.
BroadcastJoinReadsWithRefBases
org.broadinstitute.hellbender.engine.spark.
BroadcastJoinReadsWithVariants
org.broadinstitute.hellbender.utils.gcs.
BucketUtils
org.broadinstitute.hellbender.utils.logging.
BunnyLog
org.broadinstitute.hellbender.tools.spark.bwa.
BwaArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.bwa.
BwaMemAlignmentUtils
org.broadinstitute.hellbender.utils.bwa.
BwaMemIndexCache
org.broadinstitute.hellbender.tools.spark.bwa.
BwaSparkEngine
(implements java.lang.AutoCloseable)
picard.vcf.
ByIntervalListVariantContextIterator
(implements java.util.Iterator<E>)
org.broadinstitute.hellbender.utils.iterators.
ByteArrayIterator
(implements java.util.Iterator<E>)
picard.vcf.
CallingMetricAccumulator
(implements picard.vcf.processor.
VariantProcessor.Accumulator
<RESULT>)
picard.vcf.
GvcfMetricAccumulator
picard.vcf.
CallingMetricAccumulator.Result
picard.fastq.
Casava18ReadNameEncoder
(implements picard.fastq.
ReadNameEncoder
)
picard.analysis.
ChimeraUtil
org.broadinstitute.hellbender.utils.read.
CigarUtils
picard.util.
CircularByteBuffer
picard.cmdline.
ClassFinder
org.broadinstitute.hellbender.utils.
ClassUtils
org.broadinstitute.hellbender.utils.clipping.
ClippingOp
picard.util.
ClippingUtility
org.broadinstitute.hellbender.tools.
ClipReads.ClippingData
picard.illumina.parser.
ClusterData
picard.illumina.
ClusterDataToSamConverter
org.broadinstitute.hellbender.tools.spark.sv.utils.
CNVInputReader
picard.analysis.
CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
(implements picard.cmdline.argumentcollections.
ReferenceArgumentCollection
)
picard.illumina.quality.
CollectHiSeqXPfFailMetrics.ReadClassifier
picard.illumina.
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
picard.analysis.
CollectQualityYieldMetrics.QualityYieldMetricsCollector
picard.analysis.
CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
(implements picard.cmdline.argumentcollections.
ReferenceArgumentCollection
)
picard.analysis.
CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
(implements picard.cmdline.argumentcollections.
IntervalArgumentCollection
)
picard.cmdline.
CommandLineDefaults
org.broadinstitute.barclay.argparser.CommandLinePluginDescriptor<T>
org.broadinstitute.hellbender.cmdline.GATKPlugin.
GATKAnnotationPluginDescriptor
org.broadinstitute.hellbender.cmdline.GATKPlugin.
GATKReadFilterPluginDescriptor
org.broadinstitute.hellbender.cmdline.
CommandLineProgram
(implements org.broadinstitute.barclay.argparser.CommandLinePluginProvider)
org.broadinstitute.hellbender.tools.walkers.bqsr.
AnalyzeCovariates
org.broadinstitute.hellbender.tools.
BwaMemIndexImageCreator
org.broadinstitute.hellbender.tools.walkers.contamination.
CalculateContamination
org.broadinstitute.hellbender.tools.copynumber.
CallCopyRatioSegments
org.broadinstitute.hellbender.tools.walkers.vqsr.
CNNVariantTrain
org.broadinstitute.hellbender.tools.walkers.vqsr.
CNNVariantWriteTensors
org.broadinstitute.hellbender.tools.
ConvertHeaderlessHadoopBamShardToBam
org.broadinstitute.hellbender.tools.spark.
CreateHadoopBamSplittingIndex
org.broadinstitute.hellbender.tools.walkers.mutect.
CreateSomaticPanelOfNormals
org.broadinstitute.hellbender.tools.copynumber.
DenoiseReadCounts
org.broadinstitute.hellbender.tools.copynumber.
DetermineGermlineContigPloidy
org.broadinstitute.hellbender.tools.walkers.vqsr.
FilterVariantTranches
org.broadinstitute.hellbender.tools.walkers.bqsr.
GatherBQSRReports
org.broadinstitute.hellbender.tools.walkers.vqsr.
GatherTranches
org.broadinstitute.hellbender.tools.
GatherVcfsCloud
org.broadinstitute.hellbender.engine.
GATKTool
org.broadinstitute.hellbender.engine.
AbstractConcordanceWalker
org.broadinstitute.hellbender.tools.walkers.validation.
Concordance
org.broadinstitute.hellbender.tools.copynumber.
AnnotateIntervals
org.broadinstitute.hellbender.engine.
AssemblyRegionWalker
org.broadinstitute.hellbender.tools.examples.
ExampleAssemblyRegionWalker
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
HaplotypeCaller
org.broadinstitute.hellbender.tools.walkers.mutect.
Mutect2
org.broadinstitute.hellbender.tools.copynumber.utils.
CombineSegmentBreakpoints
org.broadinstitute.hellbender.engine.
FeatureWalker
<F>
org.broadinstitute.hellbender.tools.examples.
ExampleFeatureWalker
org.broadinstitute.hellbender.tools.genomicsdb.
GenomicsDBImport
org.broadinstitute.hellbender.tools.
GetSampleName
org.broadinstitute.hellbender.engine.
IntervalWalker
org.broadinstitute.hellbender.tools.examples.
ExampleIntervalWalker
org.broadinstitute.hellbender.engine.
LocusWalker
org.broadinstitute.hellbender.tools.walkers.rnaseq.
ASEReadCounter
org.broadinstitute.hellbender.tools.walkers.qc.
CheckPileup
org.broadinstitute.hellbender.tools.copynumber.
CollectAllelicCounts
org.broadinstitute.hellbender.tools.examples.
ExampleLocusWalker
org.broadinstitute.hellbender.tools.walkers.qc.
Pileup
org.broadinstitute.hellbender.tools.copynumber.utils.
MergeAnnotatedRegions
org.broadinstitute.hellbender.tools.copynumber.
PostprocessGermlineCNVCalls
org.broadinstitute.hellbender.tools.copynumber.
PreprocessIntervals
org.broadinstitute.hellbender.engine.
ReadWalker
org.broadinstitute.hellbender.tools.walkers.bqsr.
ApplyBQSR
org.broadinstitute.hellbender.tools.walkers.bqsr.
BaseRecalibrator
org.broadinstitute.hellbender.tools.
ClipReads
org.broadinstitute.hellbender.tools.copynumber.
CollectReadCounts
org.broadinstitute.hellbender.tools.
CountBases
org.broadinstitute.hellbender.tools.
CountReads
org.broadinstitute.hellbender.tools.examples.
ExamplePostTraversalPythonExecutor
org.broadinstitute.hellbender.tools.examples.
ExampleReadWalkerWithReference
org.broadinstitute.hellbender.tools.examples.
ExampleReadWalkerWithVariants
org.broadinstitute.hellbender.tools.examples.
ExampleStreamingPythonExecutor
org.broadinstitute.hellbender.tools.
FixMisencodedBaseQualityReads
org.broadinstitute.hellbender.tools.
FlagStat
org.broadinstitute.hellbender.tools.
LeftAlignIndels
org.broadinstitute.hellbender.tools.
PrintReads
org.broadinstitute.hellbender.tools.walkers.
RevertBaseQualityScores
org.broadinstitute.hellbender.tools.
SplitReads
org.broadinstitute.hellbender.engine.
TwoPassReadWalker
org.broadinstitute.hellbender.tools.walkers.rnaseq.
SplitNCigarReads
org.broadinstitute.hellbender.tools.walkers.
UnmarkDuplicates
org.broadinstitute.hellbender.tools.walkers.
SplitIntervals
org.broadinstitute.hellbender.tools.copynumber.utils.
TagGermlineEvents
org.broadinstitute.hellbender.engine.
VariantWalkerBase
org.broadinstitute.hellbender.engine.
MultiVariantWalker
org.broadinstitute.hellbender.tools.walkers.vqsr.
ApplyVQSR
org.broadinstitute.hellbender.tools.walkers.contamination.
GetPileupSummaries
org.broadinstitute.hellbender.engine.
MultiVariantWalkerGroupedOnStart
org.broadinstitute.hellbender.tools.walkers.
CombineGVCFs
org.broadinstitute.hellbender.tools.walkers.vqsr.
VariantRecalibrator
org.broadinstitute.hellbender.engine.
VariantWalker
org.broadinstitute.hellbender.tools.
AnnotatePairOrientation
org.broadinstitute.hellbender.tools.walkers.validation.
AnnotateVcfWithBamDepth
org.broadinstitute.hellbender.tools.walkers.validation.
AnnotateVcfWithExpectedAlleleFraction
org.broadinstitute.hellbender.tools.walkers.variantutils.
CalculateGenotypePosteriors
org.broadinstitute.hellbender.tools.walkers.validation.
CalculateMixingFractions
org.broadinstitute.hellbender.tools.walkers.vqsr.
CNNScoreVariants
org.broadinstitute.hellbender.tools.walkers.validation.
CountFalsePositives
org.broadinstitute.hellbender.tools.walkers.
CountVariants
org.broadinstitute.hellbender.tools.examples.
ExampleVariantWalker
org.broadinstitute.hellbender.tools.walkers.realignmentfilter.
FilterAlignmentArtifacts
org.broadinstitute.hellbender.tools.exome.
FilterByOrientationBias
org.broadinstitute.hellbender.tools.walkers.mutect.
FilterMutectCalls
org.broadinstitute.hellbender.tools.
FixCallSetSampleOrdering
org.broadinstitute.hellbender.tools.funcotator.
Funcotator
org.broadinstitute.hellbender.tools.walkers.
GenotypeGVCFs
org.broadinstitute.hellbender.tools.walkers.validation.
RemoveNearbyIndels
org.broadinstitute.hellbender.tools.walkers.variantutils.
SelectVariants
org.broadinstitute.hellbender.engine.
TwoPassVariantWalker
org.broadinstitute.hellbender.tools.examples.
ExampleTwoPassVariantWalker
org.broadinstitute.hellbender.tools.walkers.variantutils.
UpdateVCFSequenceDictionary
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.
ValidateBasicSomaticShortMutations
org.broadinstitute.hellbender.tools.walkers.variantutils.
ValidateVariants
org.broadinstitute.hellbender.tools.walkers.annotator.
VariantAnnotator
org.broadinstitute.hellbender.tools.walkers.filters.
VariantFiltration
org.broadinstitute.hellbender.tools.walkers.variantutils.
VariantsToTable
org.broadinstitute.hellbender.tools.copynumber.
GermlineCNVCaller
org.broadinstitute.hellbender.tools.
IndexFeatureFile
org.broadinstitute.hellbender.tools.copynumber.
ModelSegments
org.broadinstitute.hellbender.tools.spark.pathseq.
PathSeqBuildKmers
org.broadinstitute.hellbender.tools.spark.pathseq.
PathSeqBuildReferenceTaxonomy
org.broadinstitute.hellbender.cmdline.
PicardCommandLineProgram
org.broadinstitute.hellbender.utils.read.markduplicates.
AbstractOpticalDuplicateFinderCommandLineProgram
org.broadinstitute.hellbender.utils.read.markduplicates.
AbstractMarkDuplicatesCommandLineProgram
org.broadinstitute.hellbender.tools.walkers.markduplicates.
MarkDuplicatesGATK
org.broadinstitute.hellbender.tools.walkers.markduplicates.
EstimateLibraryComplexityGATK
org.broadinstitute.hellbender.tools.validation.
CompareBaseQualities
org.broadinstitute.hellbender.cmdline.
PicardCommandLineProgramExecutor
org.broadinstitute.hellbender.tools.copynumber.plotting.
PlotDenoisedCopyRatios
org.broadinstitute.hellbender.tools.copynumber.plotting.
PlotModeledSegments
org.broadinstitute.hellbender.engine.spark.
SparkCommandLineProgram
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.
BaseRecalibratorSparkSharded
org.broadinstitute.hellbender.tools.copynumber.
CreateReadCountPanelOfNormals
org.broadinstitute.hellbender.tools.examples.
ExampleNioCountReads
org.broadinstitute.hellbender.engine.spark.
GATKSparkTool
org.broadinstitute.hellbender.tools.spark.
ApplyBQSRSpark
org.broadinstitute.hellbender.engine.spark.
AssemblyRegionWalkerSpark
org.broadinstitute.hellbender.tools.examples.
ExampleAssemblyRegionWalkerSpark
org.broadinstitute.hellbender.tools.spark.
BaseRecalibratorSpark
org.broadinstitute.hellbender.tools.spark.pipelines.
BQSRPipelineSpark
org.broadinstitute.hellbender.tools.spark.pipelines.
BwaAndMarkDuplicatesPipelineSpark
org.broadinstitute.hellbender.tools.spark.bwa.
BwaSpark
org.broadinstitute.hellbender.tools.spark.sv.evidence.
CalcMetadataSpark
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
CollectBaseDistributionByCycleSpark
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
CollectMultipleMetricsSpark
org.broadinstitute.hellbender.tools.spark.validation.
CompareDuplicatesSpark
org.broadinstitute.hellbender.tools.spark.pipelines.
CountBasesSpark
org.broadinstitute.hellbender.tools.spark.pipelines.
CountReadsSpark
org.broadinstitute.hellbender.tools.spark.pipelines.
CountVariantsSpark
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
CpxVariantReInterpreterSpark
org.broadinstitute.hellbender.tools.spark.sv.discovery.
DiscoverVariantsFromContigAlignmentsSAMSpark
org.broadinstitute.hellbender.tools.spark.sv.utils.
ExtractOriginalAlignmentRecordsByNameSpark
org.broadinstitute.hellbender.tools.spark.sv.evidence.
ExtractSVEvidenceSpark
org.broadinstitute.hellbender.tools.spark.sv.evidence.
FindBadGenomicKmersSpark
org.broadinstitute.hellbender.tools.spark.sv.evidence.
FindBreakpointEvidenceSpark
org.broadinstitute.hellbender.tools.spark.pipelines.
FlagStatSpark
org.broadinstitute.hellbender.tools.
HaplotypeCallerSpark
org.broadinstitute.hellbender.engine.spark.
IntervalWalkerSpark
org.broadinstitute.hellbender.tools.examples.
ExampleIntervalWalkerSpark
org.broadinstitute.hellbender.engine.spark.
LocusWalkerSpark
org.broadinstitute.hellbender.tools.spark.
PileupSpark
org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.
MarkDuplicatesSpark
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
MeanQualityByCycleSpark
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
MetricsCollectorSparkTool
<T>
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
CollectInsertSizeMetricsSpark
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
CollectQualityYieldMetricsSpark
org.broadinstitute.hellbender.tools.examples.metrics.multi.
ExampleCollectMultiMetricsSpark
org.broadinstitute.hellbender.tools.examples.metrics.single.
ExampleCollectSingleMetricsSpark
org.broadinstitute.hellbender.tools.spark.
ParallelCopyGCSDirectoryIntoHDFSSpark
org.broadinstitute.hellbender.tools.spark.pathseq.
PathSeqBwaSpark
org.broadinstitute.hellbender.tools.spark.pathseq.
PathSeqFilterSpark
org.broadinstitute.hellbender.tools.spark.pathseq.
PathSeqPipelineSpark
org.broadinstitute.hellbender.tools.spark.pathseq.
PathSeqScoreSpark
org.broadinstitute.hellbender.tools.spark.pipelines.
PrintReadsSpark
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
QualityScoreDistributionSpark
org.broadinstitute.hellbender.tools.spark.pipelines.
ReadsPipelineSpark
org.broadinstitute.hellbender.engine.spark.
ReadWalkerSpark
org.broadinstitute.hellbender.tools.examples.
ExampleReadWalkerWithReferenceSpark
org.broadinstitute.hellbender.tools.spark.pipelines.
SortSamSpark
org.broadinstitute.hellbender.tools.spark.sv.
StructuralVariationDiscoveryPipelineSpark
org.broadinstitute.hellbender.tools.spark.sv.discovery.
SvDiscoverFromLocalAssemblyContigAlignmentsSpark
org.broadinstitute.hellbender.engine.spark.
VariantWalkerSpark
org.broadinstitute.hellbender.tools.examples.
ExampleVariantWalkerSpark
org.broadinstitute.hellbender.tools.spark.pipelines.
PrintVariantsSpark
picard.cmdline.
CommandLineProgram
picard.sam.markduplicates.util.
AbstractOpticalDuplicateFinderCommandLineProgram
picard.sam.markduplicates.util.
AbstractMarkDuplicatesCommandLineProgram
picard.sam.markduplicates.
MarkDuplicates
picard.sam.markduplicates.
SimpleMarkDuplicatesWithMateCigar
picard.sam.markduplicates.
UmiAwareMarkDuplicatesWithMateCigar
picard.sam.markduplicates.
MarkDuplicatesWithMateCigar
picard.sam.markduplicates.
EstimateLibraryComplexity
picard.vcf.
AccumulateVariantCallingMetrics
picard.sam.
AddCommentsToBam
picard.sam.
AddOrReplaceReadGroups
picard.util.
BaitDesigner
picard.sam.
BamIndexStats
picard.fastq.
BamToBfq
picard.util.
BedToIntervalList
picard.sam.
BuildBamIndex
picard.sam.
CalculateReadGroupChecksum
picard.fingerprint.
CheckFingerprint
picard.illumina.
CheckIlluminaDirectory
picard.sam.
CheckTerminatorBlock
picard.sam.
CleanSam
picard.fingerprint.
ClusterCrosscheckMetrics
picard.illumina.quality.
CollectHiSeqXPfFailMetrics
picard.illumina.
CollectIlluminaBasecallingMetrics
picard.illumina.
CollectIlluminaLaneMetrics
picard.analysis.replicates.
CollectIndependentReplicateMetrics
picard.analysis.
CollectJumpingLibraryMetrics
picard.analysis.
CollectMultipleMetrics
picard.analysis.
CollectOxoGMetrics
picard.analysis.
CollectRrbsMetrics
picard.analysis.directed.
CollectTargetedMetrics
<METRIC,COLLECTOR>
picard.analysis.directed.
CollectHsMetrics
picard.analysis.directed.
CollectTargetedPcrMetrics
picard.vcf.
CollectVariantCallingMetrics
picard.analysis.
CollectWgsMetrics
picard.analysis.
CollectRawWgsMetrics
picard.analysis.
CollectWgsMetricsWithNonZeroCoverage
picard.analysis.
CompareMetrics
picard.sam.
CompareSAMs
picard.analysis.artifacts.
ConvertSequencingArtifactToOxoG
picard.sam.
CreateSequenceDictionary
picard.fingerprint.
CrosscheckFingerprints
picard.fingerprint.
CrosscheckReadGroupFingerprints
picard.sam.
DownsampleSam
picard.illumina.
ExtractIlluminaBarcodes
picard.reference.
ExtractSequences
picard.sam.
FastqToSam
picard.util.
FifoBuffer
picard.sam.
FilterSamReads
picard.vcf.filter.
FilterVcf
picard.vcf.MendelianViolations.
FindMendelianViolations
picard.sam.
FixMateInformation
picard.vcf.
FixVcfHeader
picard.sam.
GatherBamFiles
picard.vcf.
GatherVcfs
picard.vcf.
GenotypeConcordance
picard.fingerprint.
IdentifyContaminant
picard.illumina.
IlluminaBasecallsToFastq
picard.illumina.
IlluminaBasecallsToSam
picard.util.
IntervalListToBed
picard.util.
IntervalListTools
picard.util.
LiftOverIntervalList
picard.vcf.
LiftoverVcf
picard.vcf.
MakeSitesOnlyVcf
picard.illumina.
MarkIlluminaAdapters
picard.sam.
MergeBamAlignment
picard.sam.
MergeSamFiles
picard.vcf.
MergeVcfs
picard.reference.
NonNFastaSize
picard.reference.
NormalizeFasta
picard.sam.
PositionBasedDownsampleSam
picard.vcf.
RenameSampleInVcf
picard.sam.
ReorderSam
picard.sam.
ReplaceSamHeader
picard.sam.
RevertOriginalBaseQualitiesAndAddMateCigar
picard.sam.
RevertSam
picard.sam.
SamFormatConverter
picard.sam.
SamToFastq
picard.sam.
SamToFastqWithTags
picard.util.
ScatterIntervalsByNs
picard.sam.
SetNmMdAndUqTags
picard.sam.
SetNmAndUqTags
picard.analysis.
SinglePassSamProgram
picard.analysis.
CollectAlignmentSummaryMetrics
picard.analysis.
CollectBaseDistributionByCycle
picard.analysis.
CollectGcBiasMetrics
picard.analysis.
CollectInsertSizeMetrics
picard.analysis.
CollectQualityYieldMetrics
picard.analysis.
CollectRnaSeqMetrics
picard.analysis.artifacts.
CollectSequencingArtifactMetrics
picard.analysis.
MeanQualityByCycle
picard.analysis.
QualityScoreDistribution
picard.sam.
SortSam
picard.vcf.
SortVcf
picard.sam.
SplitSamByLibrary
picard.sam.
SplitSamByNumberOfReads
picard.vcf.
SplitVcfs
picard.vcf.
UpdateVcfSequenceDictionary
picard.sam.
ValidateSamFile
picard.vcf.
VcfFormatConverter
picard.vcf.
VcfToIntervalList
picard.sam.
ViewSam
picard.cmdline.
CommandLineSyntaxTranslater
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
CommonSuffixSplitter
org.broadinstitute.hellbender.tools.validation.
CompareMatrix
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.
CompressedDataList
<T> (implements java.lang.Iterable<T>)
org.broadinstitute.hellbender.tools.walkers.validation.
ConcordanceSummaryRecord
org.broadinstitute.hellbender.utils.config.
ConfigFactory
org.apache.hadoop.conf.Configured (implements org.apache.hadoop.conf.Configurable)
org.apache.hadoop.fs.FileSystem (implements java.io.Closeable)
org.apache.hadoop.fs.FilterFileSystem
org.apache.hadoop.fs.ChecksumFileSystem
org.apache.hadoop.fs.LocalFileSystem
org.broadinstitute.hellbender.engine.spark.
NonChecksumLocalFileSystem
org.broadinstitute.hellbender.tools.spark.pathseq.
ContainsKmerReadFilterSpark
(implements org.apache.spark.api.java.function.Function<T1,R>)
org.broadinstitute.hellbender.tools.walkers.contamination.
ContaminationRecord
org.broadinstitute.hellbender.utils.recalibration.covariates.
ContextCovariate
(implements org.broadinstitute.hellbender.utils.recalibration.covariates.
Covariate
)
org.broadinstitute.hellbender.engine.
ContextShard
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
ContigAlignmentsModifier
org.broadinstitute.hellbender.tools.copynumber.arguments.
CopyNumberArgumentValidationUtils
org.broadinstitute.hellbender.tools.copynumber.formats.
CopyNumberFormatsUtils
org.broadinstitute.hellbender.tools.copynumber.formats.records.
CopyNumberPosteriorDistribution
org.broadinstitute.hellbender.cmdline.programgroups.
CopyNumberProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
org.broadinstitute.hellbender.tools.copynumber.arguments.
CopyNumberStandardArgument
org.broadinstitute.hellbender.tools.copynumber.formats.records.
CopyRatio
(implements htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.tools.copynumber.segmentation.
CopyRatioKernelSegmenter
org.broadinstitute.hellbender.tools.copynumber.models.
CopyRatioModeller
org.broadinstitute.hellbender.tools.copynumber.formats.records.
CopyRatioSegment
(implements htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.tools.copynumber.formats.records.
CalledCopyRatioSegment
picard.analysis.
CounterManager
picard.analysis.
CounterManager.Counter
picard.filter.
CountingFilter
(implements htsjdk.samtools.filter.SamRecordFilter)
picard.filter.
CountingDuplicateFilter
picard.filter.
CountingMapQFilter
picard.filter.
CountingPairedFilter
org.broadinstitute.hellbender.engine.filters.
CountingVariantFilter
(implements org.broadinstitute.hellbender.engine.filters.
VariantFilter
)
org.broadinstitute.hellbender.engine.filters.
CountingVariantFilter.CountingAndVariantFilter
org.broadinstitute.hellbender.utils.collections.
CountSet
(implements java.util.Set<E>)
org.broadinstitute.hellbender.utils.recalibration.covariates.
CovariateKeyCache
org.broadinstitute.hellbender.cmdline.programgroups.
CoverageAnalysisProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
org.broadinstitute.hellbender.tools.copynumber.formats.records.
CoveragePerContig
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
CpxVariantInterpreter
picard.sam.
CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
(implements picard.cmdline.argumentcollections.
ReferenceArgumentCollection
)
org.broadinstitute.hellbender.utils.config.
CustomBooleanConverter
(implements org.aeonbits.owner.Converter<T>)
org.broadinstitute.hellbender.utils.recalibration.covariates.
CycleCovariate
(implements org.broadinstitute.hellbender.utils.recalibration.covariates.
Covariate
)
org.broadinstitute.hellbender.utils.tsv.
DataLine
org.broadinstitute.hellbender.tools.funcotator.
DataSourceFuncotationFactory
(implements java.io.Closeable)
org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.
CosmicFuncotationFactory
org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.
GencodeFuncotationFactory
org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.
LocatableXsvFuncotationFactory
org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.
SimpleKeyXsvFuncotationFactory
org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.
VcfFuncotationFactory
org.broadinstitute.hellbender.tools.funcotator.dataSources.
DataSourceUtils
org.broadinstitute.hellbender.cmdline.argumentcollections.
DbsnpArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.variant.
DbSnpBitSetUtil
picard.util.
DbSnpBitSetUtil
org.broadinstitute.hellbender.utils.variant.
DbSnpBitSetUtil.DbSnpBitSets
picard.util.
DbSnpBitSetUtil.DbSnpBitSets
org.broadinstitute.hellbender.utils.mcmc.
DecileCollection
(implements java.io.Serializable)
picard.util.
DelimitedTextFileWithHeaderIterator
(implements htsjdk.samtools.util.CloseableIterator<T>)
picard.util.
DelimitedTextFileWithHeaderIterator.Row
org.broadinstitute.hellbender.cmdline.
DeprecatedToolsRegistry
picard.vcf.filter.
DepthFilter
(implements picard.vcf.filter.
GenotypeFilter
)
picard.cmdline.programgroups.
DiagnosticsAndQCProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
org.broadinstitute.hellbender.utils.
Dirichlet
org.broadinstitute.hellbender.utils.read.markduplicates.
DiskBasedReadEndsForMarkDuplicatesMap
(implements org.broadinstitute.hellbender.utils.read.markduplicates.
ReadEndsForMarkDuplicatesMap
)
picard.sam.markduplicates.util.
DiskBasedReadEndsForMarkDuplicatesMap
(implements picard.sam.markduplicates.util.
ReadEndsForMarkDuplicatesMap
)
org.broadinstitute.barclay.help.DocWorkUnit (implements java.lang.Comparable<T>)
org.broadinstitute.hellbender.utils.help.
GATKDocWorkUnit
org.broadinstitute.barclay.help.DocWorkUnitHandler
org.broadinstitute.barclay.help.DefaultDocWorkUnitHandler
org.broadinstitute.hellbender.utils.help.
GATKHelpDocWorkUnitHandler
picard.util.help.
PicardHelpDocWorkUnitHandler
org.broadinstitute.hellbender.tools.
DownsampleableSparkReadShard
(implements java.io.Serializable, org.broadinstitute.hellbender.engine.
Shard
<T>)
org.broadinstitute.hellbender.utils.downsampling.
Downsampler
<T>
org.broadinstitute.hellbender.utils.downsampling.
LevelingDownsampler
<T,E>
org.broadinstitute.hellbender.utils.downsampling.
ReadsDownsampler
org.broadinstitute.hellbender.utils.downsampling.
FractionalDownsampler
org.broadinstitute.hellbender.utils.downsampling.
MutectDownsampler
org.broadinstitute.hellbender.utils.downsampling.
PassThroughDownsampler
org.broadinstitute.hellbender.utils.downsampling.
PositionalDownsampler
org.broadinstitute.hellbender.utils.downsampling.
ReservoirDownsampler
org.broadinstitute.hellbender.utils.downsampling.
DownsamplingMethod
(implements java.io.Serializable)
org.broadinstitute.hellbender.transformers.
DUSTReadTransformer
(implements org.broadinstitute.hellbender.transformers.
ReadTransformer
)
org.broadinstitute.hellbender.utils.read.mergealignment.
EarliestFragmentPrimaryAlignmentSelectionStrategy
(implements org.broadinstitute.hellbender.utils.read.mergealignment.
PrimaryAlignmentSelectionStrategy
)
picard.sam.
EarliestFragmentPrimaryAlignmentSelectionStrategy
(implements picard.sam.
PrimaryAlignmentSelectionStrategy
)
picard.illumina.parser.readers.
EmpiricalPhasingMetricsOutReader
(implements java.util.Iterator<E>)
picard.illumina.parser.readers.
EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
org.broadinstitute.hellbender.tools.spark.sv.evidence.
EvidenceTargetLink
org.broadinstitute.hellbender.tools.spark.sv.evidence.
EvidenceTargetLinkClusterer
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
ExactACcounts
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
ExactACset
org.broadinstitute.hellbender.tools.examples.metrics.multi.
ExampleMultiMetricsCollectorSpark
(implements org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
MetricsCollectorSpark
<T>, java.io.Serializable)
org.broadinstitute.hellbender.cmdline.programgroups.
ExampleProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
org.broadinstitute.hellbender.tools.examples.metrics.single.
ExampleSingleMetricsCollectorSpark
(implements org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
MetricsCollectorSpark
<T>, java.io.Serializable)
org.broadinstitute.hellbender.cmdline.
ExomeStandardArgumentDefinitions
picard.illumina.
ExtractIlluminaBarcodes.PerTileBarcodeExtractor
(implements java.lang.Runnable)
picard.illumina.
ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch
org.broadinstitute.hellbender.utils.test.
FakeReferenceSource
org.broadinstitute.hellbender.tools.walkers.validation.
FalsePositiveRecord
org.broadinstitute.hellbender.tools.walkers.variantutils.
FamilyLikelihoods
org.broadinstitute.hellbender.utils.reference.
FastaReferenceWriter
(implements java.lang.AutoCloseable)
org.broadinstitute.hellbender.engine.
FeatureContext
org.broadinstitute.hellbender.engine.
FeatureDataSource
<T> (implements java.lang.AutoCloseable, org.broadinstitute.hellbender.engine.
GATKDataSource
<T>)
org.broadinstitute.hellbender.engine.
FeatureInput
<T> (implements java.io.Serializable)
org.broadinstitute.hellbender.engine.
FeatureManager
(implements java.lang.AutoCloseable)
org.broadinstitute.hellbender.tools.spark.sv.evidence.
FermiLiteAssemblyHandler
picard.illumina.parser.fakers.
FileFaker
picard.illumina.parser.fakers.
BarcodeFileFaker
picard.illumina.parser.fakers.
BciFileFaker
picard.illumina.parser.fakers.
BclFileFaker
picard.illumina.parser.fakers.
ClocsFileFaker
picard.illumina.parser.fakers.
FilterFileFaker
picard.illumina.parser.fakers.
LocsFileFaker
picard.illumina.parser.fakers.
MultiTileBclFileFaker
picard.illumina.parser.fakers.
MultiTileLocsFileFaker
picard.illumina.parser.fakers.
PosFileFaker
org.broadinstitute.hellbender.tools.walkers.validation.
FilterAnalysisRecord
picard.vcf.filter.
FilterApplyingVariantIterator
(implements htsjdk.samtools.util.CloseableIterator<T>)
picard.illumina.parser.readers.
FilterFileReader
(implements java.util.Iterator<E>)
org.broadinstitute.hellbender.tools.spark.sv.evidence.
FindBreakpointEvidenceSpark.AssembledEvidenceResults
org.broadinstitute.hellbender.tools.spark.sv.evidence.
FindBreakpointEvidenceSpark.IntPair
picard.fingerprint.
FingerprintChecker
picard.fingerprint.
FingerprintIdDetails
picard.fingerprint.
FingerprintResults
picard.fingerprint.
FingerprintUtils
org.broadinstitute.hellbender.utils.
FisherExactTest
picard.vcf.filter.
FisherStrandFilter
(implements picard.vcf.filter.
VariantFilter
)
org.broadinstitute.hellbender.tools.
FlagStat.FlagStatus
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.utils.
FlatMapGluer
<I,O> (implements java.util.Iterator<E>)
org.broadinstitute.hellbender.utils.hmm.
ForwardBackwardAlgorithm
picard.illumina.parser.
FourChannelIntensityData
org.broadinstitute.hellbender.utils.fragments.
FragmentCollection
<T>
org.broadinstitute.hellbender.utils.fragments.
FragmentUtils
org.broadinstitute.hellbender.tools.funcotator.
FuncotatorArgumentDefinitions
org.broadinstitute.hellbender.tools.funcotator.
FuncotatorUtils
org.broadinstitute.hellbender.cmdline.GATKPlugin.
GATKAnnotationArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.cmdline.GATKPlugin.
DefaultGATKVariantAnnotationArgumentCollection
org.broadinstitute.hellbender.utils.
GATKProtectedVariantContextUtils
org.broadinstitute.hellbender.cmdline.GATKPlugin.
GATKReadFilterArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.cmdline.GATKPlugin.
DefaultGATKReadFilterArgumentCollection
org.broadinstitute.hellbender.utils.read.
GATKReadToBDGAlignmentRecordConverter
org.broadinstitute.hellbender.engine.spark.
GATKRegistrator
(implements org.apache.spark.serializer.KryoRegistrator)
org.broadinstitute.hellbender.utils.report.
GATKReport
org.broadinstitute.hellbender.utils.report.
GATKReportColumn
org.broadinstitute.hellbender.utils.report.
GATKReportColumnFormat
org.broadinstitute.hellbender.utils.report.
GATKReportTable
org.broadinstitute.hellbender.tools.spark.sv.utils.
GATKSVVCFConstants
org.broadinstitute.hellbender.tools.spark.sv.utils.
GATKSVVCFHeaderLines
org.broadinstitute.hellbender.utils.variant.
GATKVariantContextUtils
org.broadinstitute.hellbender.utils.variant.
GATKVariantContextUtils.AlleleMapper
org.broadinstitute.hellbender.utils.variant.
GATKVCFConstants
org.broadinstitute.hellbender.utils.variant.
GATKVCFHeaderLines
org.broadinstitute.hellbender.tools.copynumber.denoising.
GCBiasCorrector
picard.analysis.
GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
(implements picard.metrics.
PerUnitMetricCollector
<BEAN,HKEY,ARGTYPE>)
picard.analysis.
GcBiasUtils
org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.
GencodeFuncotation
(implements org.broadinstitute.hellbender.tools.funcotator.
Funcotation
)
org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.
GencodeFuncotationBuilder
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfFeature
(implements java.lang.Comparable<T>, htsjdk.tribble.Feature)
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfCDSFeature
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfExonFeature
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfGeneFeature
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfSelenocysteineFeature
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfStartCodonFeature
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfStopCodonFeature
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfTranscriptFeature
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfUTRFeature
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfFeature.OptionalField
<T>
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfFeatureBaseData
picard.annotation.
Gene.Transcript
picard.annotation.
Gene.Transcript.Exon
picard.annotation.
GeneAnnotationReader
org.broadinstitute.hellbender.utils.
GenomeLoc
(implements java.lang.Comparable<T>, org.broadinstitute.hellbender.utils.
HasGenomeLocation
, htsjdk.samtools.util.Locatable, java.io.Serializable)
org.broadinstitute.hellbender.utils.
GenomeLocParser
org.broadinstitute.hellbender.tools.genomicsdb.
GenomicsDBConstants
org.broadinstitute.hellbender.utils.test.
GenomicsDBTestUtils
org.broadinstitute.hellbender.tools.walkers.genotyper.
GenotypeAlleleCounts
(implements java.lang.Comparable<T>)
org.broadinstitute.hellbender.tools.walkers.genotyper.
GenotypeCalculationArgumentCollection
(implements java.io.Serializable)
picard.vcf.
GenotypeConcordance.Alleles
picard.vcf.
GenotypeConcordanceCounts
picard.vcf.
GenotypeConcordanceScheme
picard.vcf.
GA4GHScheme
picard.vcf.
GA4GHSchemeWithMissingAsHomRef
picard.vcf.
GenotypeConcordanceSchemeFactory
picard.vcf.
GenotypeConcordanceStates
picard.vcf.
GenotypeConcordanceStates.TruthAndCallStates
(implements java.lang.Comparable<T>)
org.broadinstitute.hellbender.utils.
GenotypeCounts
org.broadinstitute.hellbender.tools.walkers.genotyper.
GenotypeLikelihoodCalculator
org.broadinstitute.hellbender.tools.walkers.genotyper.
GenotypeLikelihoodCalculators
picard.vcf.filter.
GenotypeQualityFilter
(implements picard.vcf.filter.
GenotypeFilter
)
org.broadinstitute.hellbender.utils.
GenotypeUtils
org.broadinstitute.hellbender.tools.walkers.genotyper.
GenotypingData
<A> (implements org.broadinstitute.hellbender.utils.genotyper.
AlleleList
<A>, org.broadinstitute.hellbender.utils.genotyper.
SampleList
)
org.broadinstitute.hellbender.tools.walkers.genotyper.
GenotypingEngine
<Config>
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
AssemblyBasedCallerGenotypingEngine
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
HaplotypeCallerGenotypingEngine
org.broadinstitute.hellbender.tools.walkers.mutect.
SomaticGenotypingEngine
org.broadinstitute.hellbender.tools.walkers.genotyper.
MinimalGenotypingEngine
org.broadinstitute.hellbender.tools.walkers.genotyper.
GenotypingGivenAllelesUtils
org.broadinstitute.hellbender.tools.walkers.genotyper.
GenotypingLikelihoods
<A> (implements org.broadinstitute.hellbender.utils.genotyper.
AlleleList
<A>, org.broadinstitute.hellbender.utils.genotyper.
SampleList
)
org.broadinstitute.hellbender.tools.copynumber.arguments.
GermlineCallingArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.copynumber.gcnv.
GermlineCNVNamingConstants
org.broadinstitute.hellbender.tools.copynumber.gcnv.
GermlineCNVVariantComposer
<DATA>
org.broadinstitute.hellbender.tools.copynumber.gcnv.
GermlineCNVIntervalVariantComposer
org.broadinstitute.hellbender.tools.copynumber.gcnv.
GermlineCNVSegmentVariantComposer
org.broadinstitute.hellbender.tools.copynumber.arguments.
GermlineContigPloidyModelArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.copynumber.arguments.
GermlineDenoisingModelArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.walkers.mutect.
GermlineProbabilityCalculator
org.broadinstitute.hellbender.utils.mcmc.
GibbsSampler
<V,S,T>
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
GraphUtils
picard.util.
GraphUtils
picard.util.
GraphUtils.Graph
<Node>
org.broadinstitute.barclay.help.GSONWorkUnit
org.broadinstitute.hellbender.utils.help.
GATKGSONWorkUnit
org.broadinstitute.hellbender.utils.variant.writers.
GVCFWriter
(implements htsjdk.variant.variantcontext.writer.VariantContextWriter)
org.broadinstitute.hellbender.utils.haplotype.
HaplotypeBAMDestination
org.broadinstitute.hellbender.utils.haplotype.
SAMFileDestination
org.broadinstitute.hellbender.utils.haplotype.
HaplotypeBAMWriter
(implements java.lang.AutoCloseable)
picard.fingerprint.
HaplotypeBlock
(implements java.lang.Comparable<T>)
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
HaplotypeCallerEngine
(implements org.broadinstitute.hellbender.engine.
AssemblyRegionEvaluator
)
org.broadinstitute.hellbender.tools.
HaplotypeCallerSpark.ReferenceMultiSourceAdapter
(implements org.broadinstitute.hellbender.engine.
ReferenceDataSource
, htsjdk.samtools.reference.ReferenceSequenceFile, java.io.Serializable)
org.broadinstitute.hellbender.tools.
HaplotypeCallerSpark.ShardingArgumentCollection
(implements java.io.Serializable)
picard.fingerprint.
HaplotypeMap
picard.fingerprint.
HaplotypeProbabilities
picard.fingerprint.
HaplotypeProbabilitiesFromGenotype
picard.fingerprint.
HaplotypeProbabilitiesFromGenotypeLikelihoods
picard.fingerprint.
HaplotypeProbabilitiesFromSequence
picard.fingerprint.
HaplotypeProbabilitiesFromContaminatorSequence
picard.fingerprint.
HaplotypeProbabilityOfNormalGivenTumor
org.broadinstitute.hellbender.tools.copynumber.formats.collections.
HDF5SimpleCountCollection
org.broadinstitute.hellbender.tools.copynumber.denoising.
HDF5SVDReadCountPanelOfNormals
(implements org.broadinstitute.hellbender.tools.copynumber.denoising.
SVDReadCountPanelOfNormals
)
org.broadinstitute.hellbender.tools.copynumber.utils.
HDF5Utils
org.broadinstitute.hellbender.utils.read.
HeaderlessSAMRecordCoordinateComparator
(implements java.util.Comparator<T>, java.io.Serializable)
org.broadinstitute.hellbender.utils.help.
HelpConstants
picard.util.help.
HelpConstants
org.broadinstitute.barclay.help.HelpDoclet
org.broadinstitute.hellbender.utils.help.
GATKHelpDoclet
picard.util.help.
PicardHelpDoclet
org.broadinstitute.hellbender.tools.walkers.genotyper.
HeterogeneousPloidyModel
(implements org.broadinstitute.hellbender.tools.walkers.genotyper.
PloidyModel
)
org.broadinstitute.hellbender.tools.walkers.annotator.
HeterozygosityCalculator
org.broadinstitute.hellbender.utils.
Histogram
org.broadinstitute.hellbender.utils.read.mergealignment.
HitsForInsert
org.broadinstitute.hellbender.tools.walkers.genotyper.
HomogeneousPloidyModel
(implements org.broadinstitute.hellbender.tools.walkers.genotyper.
PloidyModel
)
org.broadinstitute.hellbender.utils.variant.
HomoSapiensConstants
org.broadinstitute.hellbender.tools.copynumber.arguments.
HybridADVIArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.copynumber.arguments.
GermlineCNVHybridADVIArgumentCollection
org.broadinstitute.hellbender.tools.copynumber.arguments.
GermlineContigPloidyHybridADVIArgumentCollection
org.broadinstitute.hellbender.utils.
IGVUtils
picard.illumina.
IlluminaBasecallsConverter
<CLUSTER_OUTPUT_RECORD>
picard.illumina.parser.
IlluminaDataProviderFactory
picard.illumina.parser.
IlluminaFileUtil
picard.fastq.
IlluminaReadNameEncoder
(implements picard.fastq.
ReadNameEncoder
)
picard.util.
IlluminaUtil
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
ImpreciseVariantDetector
org.broadinstitute.hellbender.tools.walkers.genotyper.
IndependentSampleGenotypesModel
org.broadinstitute.hellbender.utils.genotyper.
IndexedAlleleList
<A> (implements org.broadinstitute.hellbender.utils.genotyper.
AlleleList
<A>)
htsjdk.samtools.reference.IndexedFastaSequenceFile (implements java.io.Closeable)
org.broadinstitute.hellbender.utils.fasta.
CachingIndexedFastaSequenceFile
org.broadinstitute.hellbender.utils.genotyper.
IndexedSampleList
(implements org.broadinstitute.hellbender.utils.genotyper.
SampleList
)
org.broadinstitute.hellbender.utils.
IndexRange
org.broadinstitute.hellbender.utils.
IndexUtils
java.io.InputStream (implements java.io.Closeable)
htsjdk.samtools.seekablestream.SeekableStream
org.broadinstitute.hellbender.utils.nio.
ChannelAsSeekableStream
org.broadinstitute.hellbender.utils.runtime.
InputStreamSettings
picard.analysis.directed.
InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
(implements picard.metrics.
PerUnitMetricCollector
<BEAN,HKEY,ARGTYPE>)
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
InsertSizeMetricsCollectorSpark
(implements org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
MetricsCollectorSpark
<T>, java.io.Serializable)
org.broadinstitute.hellbender.tools.copynumber.formats.records.
IntegerCopyNumberSegment
(implements htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.tools.copynumber.gcnv.
IntegerCopyNumberState
(implements java.lang.Comparable<T>)
org.broadinstitute.hellbender.utils.test.
IntegrationTestSpec
org.broadinstitute.hellbender.utils.
IntegrationUtils
htsjdk.samtools.util.Interval (implements java.lang.Cloneable, java.lang.Comparable<T>, htsjdk.samtools.util.Locatable)
picard.annotation.
Gene
(implements java.lang.Iterable<T>)
org.broadinstitute.hellbender.utils.locusiterator.
IntervalAlignmentContextIterator
(implements java.util.Iterator<E>)
org.broadinstitute.hellbender.cmdline.argumentcollections.
IntervalArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.cmdline.argumentcollections.
OptionalIntervalArgumentCollection
org.broadinstitute.hellbender.cmdline.argumentcollections.
RequiredIntervalArgumentCollection
org.broadinstitute.hellbender.tools.copynumber.formats.records.
IntervalCopyNumberGenotypingData
(implements htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.tools.spark.sv.evidence.
IntervalCoverageFinder
(implements java.lang.Iterable<T>)
picard.util.
IntervalListScatterer
org.broadinstitute.hellbender.utils.iterators.
IntervalLocusIterator
(implements java.util.Iterator<E>)
org.broadinstitute.hellbender.utils.iterators.
IntervalOverlappingIterator
<T> (implements java.util.Iterator<E>)
picard.cmdline.programgroups.
IntervalsManipulationProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
org.broadinstitute.hellbender.utils.collections.
IntervalsSkipList
<T> (implements java.io.Serializable)
org.broadinstitute.hellbender.utils.collections.
IntervalsSkipListOneContig
<T> (implements java.io.Serializable)
org.broadinstitute.hellbender.utils.
IntervalUtils
org.broadinstitute.hellbender.engine.spark.
IntervalWalkerContext
org.broadinstitute.hellbender.tools.spark.utils.
IntHistogram
org.broadinstitute.hellbender.tools.spark.utils.
IntHistogram.CDF
org.broadinstitute.hellbender.utils.io.
IOUtils
picard.util.
Iterators
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
KBestHaplotype
(implements java.lang.Comparable<T>)
org.broadinstitute.hellbender.tools.copynumber.utils.segmentation.
KernelSegmenter
<DATA>
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
Kmer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
KmerCleaner
(implements java.lang.Iterable<T>)
org.broadinstitute.hellbender.tools.spark.sv.evidence.
KmerCounter
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
KMerCounter
org.broadinstitute.hellbender.tools.spark.sv.evidence.
KSWindowFinder
org.broadinstitute.hellbender.utils.
KV
<K,V>
picard.illumina.
LanePhasingMetricsCollector
org.broadinstitute.hellbender.tools.spark.utils.
LargeLongHopscotchSet
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.read.markduplicates.
LibraryIdGenerator
picard.sam.markduplicates.util.
LibraryIdGenerator
org.broadinstitute.hellbender.tools.spark.sv.evidence.
LibraryStatistics
org.broadinstitute.hellbender.utils.locusiterator.
LIBSDownsamplingInfo
(implements java.io.Serializable)
picard.util.
LiftoverUtils
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
LikelihoodEngineArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.locusiterator.
LocusIteratorByState
(implements java.util.Iterator<E>)
org.broadinstitute.hellbender.engine.spark.
LocusWalkerContext
org.broadinstitute.hellbender.utils.
LoggingUtils
org.broadinstitute.hellbender.tools.spark.utils.
LongBloomFilter
org.broadinstitute.hellbender.tools.spark.utils.
LongHopscotchSet
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
LowWeightChainPruner
<V,E>
org.broadinstitute.hellbender.
Main
org.broadinstitute.hellbender.utils.
MannWhitneyU
org.broadinstitute.hellbender.utils.
MannWhitneyU.RankedData
org.broadinstitute.hellbender.utils.
MannWhitneyU.Result
org.broadinstitute.hellbender.utils.
MannWhitneyU.TestStatistic
org.broadinstitute.hellbender.transformers.
MappingQualityReadTransformer
(implements org.broadinstitute.hellbender.transformers.
ReadTransformer
)
org.broadinstitute.hellbender.cmdline.argumentcollections.
MarkDuplicatesSparkArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.
MarkDuplicatesSparkRecord
org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.
PairedEnds
org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.
EmptyFragment
org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.
Fragment
org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.
Pair
(implements picard.sam.util.
PhysicalLocation
)
org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.
Passthrough
org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.
MarkDuplicatesSparkUtils
org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.
MarkDuplicatesSparkUtils.IndexPair
<T>
org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.
MarkDuplicatesSparkUtils.PairedEndsCoordinateComparator
(implements java.util.Comparator<T>, java.io.Serializable)
picard.sam.markduplicates.
MarkDuplicatesWithMateCigarIterator
(implements htsjdk.samtools.SAMRecordIterator)
picard.sam.markduplicates.util.
MarkQueue
picard.fingerprint.
MatchResults
(implements java.lang.Comparable<T>)
picard.util.
MathUtil
picard.util.
MathUtil.LogMath
org.broadinstitute.hellbender.utils.
MathUtils
org.broadinstitute.hellbender.utils.
MathUtils.RunningAverage
org.broadinstitute.hellbender.utils.
MatrixSummaryUtils
org.broadinstitute.hellbender.utils.samples.
MendelianViolation
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.
MetadataUtils
org.broadinstitute.hellbender.cmdline.programgroups.
MetagenomicsProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
org.broadinstitute.hellbender.cmdline.argumentcollections.
MetricAccumulationLevelArgumentCollection
(implements java.io.Serializable)
htsjdk.samtools.metrics.MetricBase
org.broadinstitute.hellbender.metrics.analysis.
BaseDistributionByCycleMetrics
picard.analysis.
BaseDistributionByCycleMetrics
picard.illumina.quality.
CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
picard.illumina.quality.
CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
picard.analysis.
CollectOxoGMetrics.CpcgMetrics
picard.analysis.
CollectQualityYieldMetrics.QualityYieldMetrics
picard.fingerprint.
CrosscheckMetric
picard.fingerprint.
ClusteredCrosscheckMetric
org.broadinstitute.hellbender.tools.examples.metrics.single.
ExampleSingleMetrics
(implements java.io.Serializable)
picard.illumina.
ExtractIlluminaBarcodes.BarcodeMetric
picard.analysis.
FingerprintingDetailMetrics
picard.analysis.
FingerprintingSummaryMetrics
picard.metrics.
GcBiasMetrics
picard.vcf.
GenotypeConcordanceContingencyMetrics
picard.vcf.
GenotypeConcordanceDetailMetrics
picard.vcf.
GenotypeConcordanceSummaryMetrics
picard.illumina.
IlluminaBasecallingMetrics
picard.illumina.
IlluminaLaneMetrics
picard.illumina.
IlluminaPhasingMetrics
picard.analysis.
JumpingLibraryMetrics
picard.analysis.
MergeableMetricBase
picard.vcf.
CollectVariantCallingMetrics.VariantCallingSummaryMetrics
picard.vcf.
CollectVariantCallingMetrics.VariantCallingDetailMetrics
picard.analysis.
CollectWgsMetrics.WgsMetrics
picard.analysis.
CollectRawWgsMetrics.RawWgsMetrics
picard.analysis.
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
picard.sam.
DuplicationMetrics
org.broadinstitute.hellbender.utils.read.markduplicates.
GATKDuplicationMetrics
(implements java.io.Serializable)
picard.analysis.artifacts.
ErrorSummaryMetrics
picard.analysis.replicates.
IndependentReplicateMetric
picard.vcf.MendelianViolations.
MendelianViolationMetrics
picard.metrics.
MultilevelMetrics
picard.analysis.
AlignmentSummaryMetrics
picard.analysis.
GcBiasDetailMetrics
picard.analysis.
GcBiasSummaryMetrics
picard.analysis.directed.
HsMetrics
picard.analysis.
InsertSizeMetrics
picard.analysis.
RnaSeqMetrics
picard.analysis.
RrbsCpgDetailMetrics
picard.analysis.
RrbsSummaryMetrics
picard.analysis.directed.
TargetedPcrMetrics
picard.analysis.directed.
TargetMetrics
org.broadinstitute.hellbender.metrics.
MultiLevelMetrics
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.examples.metrics.multi.
ExampleMultiMetrics
(implements java.io.Serializable)
org.broadinstitute.hellbender.metrics.
InsertSizeMetrics
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.pathseq.loggers.
PSFilterMetrics
org.broadinstitute.hellbender.tools.spark.pathseq.loggers.
PSScoreMetrics
org.broadinstitute.hellbender.metrics.
QualityYieldMetrics
(implements java.io.Serializable)
picard.analysis.artifacts.
SequencingArtifactMetrics.BaitBiasDetailMetrics
picard.analysis.artifacts.
SequencingArtifactMetrics.BaitBiasSummaryMetrics
picard.analysis.artifacts.
SequencingArtifactMetrics.PreAdapterDetailMetrics
picard.analysis.artifacts.
SequencingArtifactMetrics.PreAdapterSummaryMetrics
picard.sam.markduplicates.
UmiMetrics
org.broadinstitute.hellbender.metrics.
MetricsArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.examples.metrics.multi.
ExampleMultiMetricsArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.examples.metrics.single.
ExampleSingleMetricsArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.metrics.
InsertSizeMetricsArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.metrics.
QualityYieldMetricsArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.metrics.
MetricsUtils
org.broadinstitute.hellbender.utils.test.
MiniClusterUtils
org.broadinstitute.hellbender.utils.variant.
MinimalVariant
(implements org.broadinstitute.hellbender.utils.variant.
GATKVariant
, java.io.Serializable)
org.broadinstitute.hellbender.tools.walkers.contamination.
MinorAlleleFractionRecord
(implements htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.transformers.
MisencodedBaseQualityReadTransformer
(implements org.broadinstitute.hellbender.transformers.
ReadTransformer
)
org.broadinstitute.hellbender.tools.walkers.validation.
MixingFraction
picard.illumina.parser.readers.
MMapBackedIteratorFactory
org.broadinstitute.hellbender.tools.copynumber.formats.records.
ModeledSegment
(implements htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.tools.copynumber.formats.records.
ModeledSegment.SimplePosteriorSummary
org.broadinstitute.hellbender.utils.read.mergealignment.
MostDistantPrimaryAlignmentSelectionStrategy
(implements org.broadinstitute.hellbender.utils.read.mergealignment.
PrimaryAlignmentSelectionStrategy
)
picard.sam.
MostDistantPrimaryAlignmentSelectionStrategy
(implements picard.sam.
PrimaryAlignmentSelectionStrategy
)
org.broadinstitute.hellbender.tools.copynumber.segmentation.
MultidimensionalKernelSegmenter
org.broadinstitute.hellbender.tools.copynumber.models.
MultidimensionalModeller
org.broadinstitute.hellbender.tools.copynumber.formats.records.
MultidimensionalSegment
(implements htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.utils.read.mergealignment.
MultiHitAlignedReadIterator
(implements htsjdk.samtools.util.CloseableIterator<T>)
org.broadinstitute.hellbender.engine.
MultiIntervalLocalReadShard
(implements org.broadinstitute.hellbender.engine.
MultiIntervalShard
<T>)
org.broadinstitute.hellbender.metrics.
MultiLevelCollector
<METRIC_TYPE,HISTOGRAM_KEY,ARGTYPE>
org.broadinstitute.hellbender.metrics.
SAMRecordAndReferenceMultiLevelCollector
<BEAN,HKEY>
org.broadinstitute.hellbender.metrics.
SAMRecordMultiLevelCollector
<BEAN,HKEY>
picard.metrics.
MultiLevelCollector
<METRIC_TYPE,Histogram_KEY,ARGTYPE>
picard.analysis.
GcBiasMetricsCollector
picard.analysis.directed.
InsertSizeMetricsCollector
picard.metrics.
SAMRecordAndReferenceMultiLevelCollector
<BEAN,HKEY>
picard.analysis.
AlignmentSummaryMetricsCollector
picard.analysis.
RrbsMetricsCollector
picard.metrics.
SAMRecordMultiLevelCollector
<BEAN,HKEY>
picard.analysis.directed.
RnaSeqMetricsCollector
picard.analysis.directed.
TargetMetricsCollector
<METRIC_TYPE>
picard.analysis.directed.
HsMetricCollector
picard.analysis.directed.
TargetedPcrMetricsCollector
org.broadinstitute.hellbender.metrics.
MultiLevelReducibleCollector
<METRIC_TYPE,HISTOGRAM_KEY,ARGTYPE,UNIT_COLLECTOR> (implements java.io.Serializable)
org.broadinstitute.hellbender.tools.examples.metrics.multi.
ExampleMultiMetricsCollector
(implements java.io.Serializable)
org.broadinstitute.hellbender.metrics.
InsertSizeMetricsCollector
(implements java.io.Serializable)
picard.illumina.parser.
MultiTileBclParser
picard.illumina.parser.
MultiTileParser
<OUTPUT_RECORD>
picard.illumina.parser.
MultiTileFilterParser
picard.illumina.parser.
MultiTileLocsParser
org.broadinstitute.hellbender.engine.
MultiVariantDataSource
(implements java.lang.AutoCloseable, org.broadinstitute.hellbender.engine.
GATKDataSource
<T>)
org.broadinstitute.hellbender.tools.walkers.mutect.
Mutect2Engine
(implements org.broadinstitute.hellbender.engine.
AssemblyRegionEvaluator
)
org.broadinstitute.hellbender.tools.walkers.mutect.
Mutect2FilteringEngine
org.broadinstitute.hellbender.utils.
NativeUtils
org.broadinstitute.hellbender.transformers.
NDNCigarReadTransformer
(implements org.broadinstitute.hellbender.transformers.
ReadTransformer
)
org.broadinstitute.hellbender.utils.collections.
NestedIntegerArray
<T> (implements java.io.Serializable)
org.broadinstitute.hellbender.utils.collections.
NestedIntegerArray.Leaf
<T>
picard.illumina.
NewIlluminaBasecallsConverter
<CLUSTER_OUTPUT_RECORD>
org.broadinstitute.hellbender.utils.nio.
NioBam
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
NovelAdjacencyAndAltHaplotype
org.broadinstitute.hellbender.utils.
Nucleotide.Counter
org.broadinstitute.hellbender.utils.svd.
OjAlgoSingularValueDecomposer
(implements org.broadinstitute.hellbender.utils.svd.
SingularValueDecomposer
)
org.broadinstitute.hellbender.utils.logging.
OneShotLogger
org.broadinstitute.hellbender.cmdline.argumentcollections.
OpticalDuplicatesArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.
OptimizationUtils
org.broadinstitute.hellbender.cmdline.argumentcollections.
OptionalFeatureInputArgumentCollection
(implements java.io.Serializable)
picard.cmdline.argumentcollections.
OptionalReferenceArgumentCollection
(implements picard.cmdline.argumentcollections.
ReferenceArgumentCollection
)
org.broadinstitute.hellbender.cmdline.argumentcollections.
OptionalVariantInputArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.
OrientationBiasFilterConstants
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.
OrientationBiasFilterer
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.
OrientationBiasUtils
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.
OrientationSampleTransitionSummary
picard.cmdline.programgroups.
OtherProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
org.apache.hadoop.mapreduce.OutputFormat<K,V>
org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,V>
org.seqdoop.hadoop_bam.AnySAMOutputFormat<K>
org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat<K>
org.broadinstitute.hellbender.engine.spark.datasources.
ReadsSparkSink.SparkSAMOutputFormat
org.broadinstitute.hellbender.engine.spark.datasources.
ReadsSparkSink.SparkHeaderlessSAMOutputFormat
org.seqdoop.hadoop_bam.BAMOutputFormat<K>
org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat<K>
org.broadinstitute.hellbender.engine.spark.datasources.
ReadsSparkSink.SparkBAMOutputFormat
org.broadinstitute.hellbender.engine.spark.datasources.
ReadsSparkSink.SparkHeaderlessBAMOutputFormat
org.seqdoop.hadoop_bam.CRAMOutputFormat<K>
org.seqdoop.hadoop_bam.KeyIgnoringCRAMOutputFormat<K>
org.broadinstitute.hellbender.engine.spark.datasources.
ReadsSparkSink.SparkCRAMOutputFormat
org.broadinstitute.hellbender.engine.spark.datasources.
ReadsSparkSink.SparkHeaderlessCRAMOutputFormat
org.seqdoop.hadoop_bam.VCFOutputFormat<K>
org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat<K>
org.broadinstitute.hellbender.engine.spark.datasources.
VariantsSparkSink.SparkVCFOutputFormat
org.broadinstitute.hellbender.engine.spark.datasources.
VariantsSparkSink.SparkHeaderlessVCFOutputFormat
picard.illumina.parser.
OutputMapping
org.broadinstitute.hellbender.tools.funcotator.
OutputRenderer
(implements java.lang.AutoCloseable)
org.broadinstitute.hellbender.tools.funcotator.mafOutput.
MafOutputRenderer
org.broadinstitute.hellbender.tools.funcotator.vcfOutput.
VcfOutputRenderer
java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
org.apache.commons.io.output.ThresholdingOutputStream
org.broadinstitute.hellbender.utils.io.
HardThresholdingOutputStream
org.broadinstitute.hellbender.utils.runtime.
OutputStreamSettings
org.broadinstitute.hellbender.tools.walkers.rnaseq.
OverhangFixingManager
org.broadinstitute.hellbender.tools.walkers.rnaseq.
OverhangFixingManager.Splice
org.broadinstitute.hellbender.tools.walkers.rnaseq.
OverhangFixingManager.SplitRead
org.broadinstitute.hellbender.tools.spark.sv.utils.
PairedStrandedIntervals
org.broadinstitute.hellbender.tools.spark.sv.utils.
PairedStrandedIntervalTree
<V> (implements java.lang.Iterable<T>)
org.broadinstitute.hellbender.tools.spark.sv.utils.
PairedStrandedIntervalTree.PairedStrandedIntervalTreeIterator
(implements java.util.Iterator<E>)
org.broadinstitute.hellbender.tools.spark.sv.utils.
PairedStrandedIntervalTree.PairedStrandedIntervalTreeOverlapperIterator
(implements java.util.Iterator<E>)
picard.vcf.
PairedVariantSubContextIterator
(implements java.util.Iterator<E>)
picard.vcf.
PairedVariantSubContextIterator.VcfTuple
org.broadinstitute.hellbender.utils.pairhmm.
PairHMM
(implements java.io.Closeable)
org.broadinstitute.hellbender.utils.pairhmm.
Log10PairHMM
org.broadinstitute.hellbender.utils.pairhmm.
LoglessPairHMM
org.broadinstitute.hellbender.utils.pairhmm.
VectorLoglessPairHMM
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
PairHMMLikelihoodCalculationEngine
(implements org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
ReadLikelihoodCalculationEngine
)
org.broadinstitute.hellbender.utils.pairhmm.
PairHMMModel
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
PairHMMNativeArgumentCollection
org.broadinstitute.hellbender.utils.mcmc.
Parameter
<T,U>
picard.illumina.parser.
ParameterizedFileUtil
picard.illumina.parser.
MultiTileBclFileUtil
picard.illumina.parser.
MultiTileFileUtil
<OUTPUT_RECORD>
picard.illumina.parser.
PerTileFileUtil
picard.illumina.parser.
PerTileOrPerRunFileUtil
picard.illumina.parser.
PerTilePerCycleFileUtil
org.broadinstitute.hellbender.utils.mcmc.
ParameterizedModel
<V1,S1,T1>
org.broadinstitute.hellbender.utils.mcmc.
ParameterizedModel.GibbsBuilder
<V2,S2,T2>
org.broadinstitute.hellbender.utils.mcmc.
ParameterizedState
<T>
org.broadinstitute.hellbender.utils.param.
ParamUtils
org.broadinstitute.hellbender.tools.spark.sv.evidence.
PartitionCrossingChecker
org.apache.spark.Partitioner (implements scala.Serializable)
org.broadinstitute.hellbender.tools.spark.sv.utils.
ComplexityPartitioner
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
Path
<T,E>
picard.nio.
PathHelper
org.broadinstitute.hellbender.utils.nio.
PathLineIterator
(implements java.lang.AutoCloseable, java.lang.Iterable<T>)
picard.pedigree.
PedFile.PedTrio
org.broadinstitute.hellbender.utils.samples.
PedReader
org.broadinstitute.hellbender.tools.walkers.mutect.
PerAlleleCollection
<X>
org.broadinstitute.hellbender.tools.copynumber.utils.optimization.
PersistenceOptimizer
picard.illumina.parser.
PerTileParser
<ILLUMINA_DATA>
picard.illumina.parser.
PosParser
org.broadinstitute.hellbender.tools.examples.metrics.multi.
PerUnitExampleMultiMetricsCollector
(implements org.broadinstitute.hellbender.metrics.
PerUnitMetricCollector
<BEAN,HKEY,ARGTYPE>, java.io.Serializable)
org.broadinstitute.hellbender.metrics.
PerUnitInsertSizeMetricsCollector
(implements org.broadinstitute.hellbender.metrics.
PerUnitMetricCollector
<BEAN,HKEY,ARGTYPE>, java.io.Serializable)
picard.sam.util.
PGTagArgumentCollection
picard.sam.markduplicates.util.
PhysicalLocationForMateCigarSet
picard.sam.util.
PhysicalLocationInt
(implements picard.sam.util.
PhysicalLocation
)
picard.sam.util.
PhysicalLocationShort
picard.sam.markduplicates.util.
PhysicalLocationForMateCigar
picard.sam.markduplicates.util.
ReadEnds
picard.sam.markduplicates.util.
ReadEndsForMarkDuplicates
(implements java.lang.Cloneable)
picard.sam.markduplicates.util.
ReadEndsForMarkDuplicatesWithBarcodes
picard.sam.markduplicates.util.
ReadEndsForMateCigar
picard.cmdline.
PicardCommandLine
org.broadinstitute.hellbender.utils.pileup.
PileupElement
org.broadinstitute.hellbender.tools.walkers.contamination.
PileupSummary
(implements htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.tools.walkers.variantutils.
PosteriorProbabilitiesUtils
org.broadinstitute.hellbender.tools.walkers.variantutils.
PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions
org.broadinstitute.hellbender.utils.mcmc.
PosteriorSummary
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.mcmc.
PosteriorSummaryUtils
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.
PowerCalculationUtils
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.
PreAdapterOrientationScorer
picard.vcf.processor.util.
PredicateFilterDecoratingClosableIterator
<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
org.broadinstitute.hellbender.utils.read.
PrimaryAlignmentKey
(implements java.lang.Comparable<T>)
org.broadinstitute.hellbender.utils.genotyper.
ProbabilityVector
org.broadinstitute.hellbender.utils.runtime.
ProcessControllerBase
<CAPTURE_POLICY>
org.broadinstitute.hellbender.utils.runtime.
ProcessController
org.broadinstitute.hellbender.utils.runtime.
StreamingProcessController
org.broadinstitute.hellbender.utils.runtime.
ProcessControllerBase.OutputCapture
(implements java.util.concurrent.Callable<V>)
org.broadinstitute.hellbender.utils.runtime.
ProcessOutput
org.broadinstitute.hellbender.utils.runtime.
ProcessSettings
org.broadinstitute.hellbender.engine.
ProgressMeter
org.broadinstitute.hellbender.utils.codecs.
ProgressReportingDelegatingCodec
<A,B> (implements htsjdk.tribble.FeatureCodec<FEATURE_TYPE,SOURCE>)
picard.util.
PropertyUtils
org.broadinstitute.hellbender.tools.spark.pathseq.
PSBuildReferenceTaxonomyUtils
org.broadinstitute.hellbender.tools.spark.pathseq.
PSBwaAligner
org.broadinstitute.hellbender.tools.spark.pathseq.
PSBwaAlignerSpark
(implements java.lang.AutoCloseable)
org.broadinstitute.hellbender.tools.spark.pathseq.
PSBwaArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.pathseq.
PSBwaFilter
org.broadinstitute.hellbender.tools.spark.pathseq.
PSBwaUtils
org.broadinstitute.hellbender.tools.spark.pathseq.
PSFilter
(implements java.lang.AutoCloseable)
org.broadinstitute.hellbender.tools.spark.pathseq.
PSFilterArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.pathseq.loggers.
PSFilterEmptyLogger
(implements org.broadinstitute.hellbender.tools.spark.pathseq.loggers.
PSFilterLogger
)
org.broadinstitute.hellbender.tools.spark.pathseq.loggers.
PSFilterFileLogger
(implements org.broadinstitute.hellbender.tools.spark.pathseq.loggers.
PSFilterLogger
)
org.broadinstitute.hellbender.tools.spark.pathseq.
PSKmerCollection
org.broadinstitute.hellbender.tools.spark.pathseq.
PSKmerBloomFilter
org.broadinstitute.hellbender.tools.spark.pathseq.
PSKmerSet
org.broadinstitute.hellbender.tools.spark.pathseq.
PSKmerUtils
org.broadinstitute.hellbender.tools.spark.pathseq.
PSPairedUnpairedSplitterSpark
org.broadinstitute.hellbender.tools.spark.pathseq.
PSPathogenAlignmentHit
org.broadinstitute.hellbender.tools.spark.pathseq.
PSPathogenReferenceTaxonProperties
org.broadinstitute.hellbender.tools.spark.pathseq.
PSPathogenTaxonScore
org.broadinstitute.hellbender.tools.spark.pathseq.
PSScoreArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.pathseq.loggers.
PSScoreFileLogger
(implements org.broadinstitute.hellbender.tools.spark.pathseq.loggers.
PSScoreLogger
)
org.broadinstitute.hellbender.tools.spark.pathseq.
PSScorer
org.broadinstitute.hellbender.tools.spark.pathseq.
PSTaxonomyConstants
org.broadinstitute.hellbender.tools.spark.pathseq.
PSTaxonomyDatabase
org.broadinstitute.hellbender.tools.spark.pathseq.
PSTree
org.broadinstitute.hellbender.tools.spark.pathseq.
PSTreeNode
org.broadinstitute.hellbender.tools.spark.pathseq.
PSUtils
picard.vcf.filter.
QdFilter
(implements picard.vcf.filter.
VariantFilter
)
org.broadinstitute.hellbender.tools.spark.sv.evidence.
QNameAndInterval
(implements java.util.Map.Entry<K,V>)
org.broadinstitute.hellbender.tools.spark.sv.evidence.
QNameFinder
(implements java.util.function.Function<T,R>)
org.broadinstitute.hellbender.tools.spark.sv.evidence.
QNameIntervalFinder
(implements java.util.function.Function<T,R>)
org.broadinstitute.hellbender.tools.spark.sv.evidence.
QNameKmerizer
(implements java.util.function.Function<T,R>)
org.broadinstitute.hellbender.tools.spark.sv.evidence.
QNamesForKmersFinder
(implements java.util.function.Function<T,R>)
org.broadinstitute.hellbender.utils.recalibration.covariates.
QualityScoreCovariate
(implements org.broadinstitute.hellbender.utils.recalibration.covariates.
Covariate
)
org.broadinstitute.hellbender.utils.
QualityUtils
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
QualityYieldMetricsCollectorSpark
(implements org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
MetricsCollectorSpark
<T>, java.io.Serializable)
org.broadinstitute.hellbender.utils.recalibration.
QualQuantizer
org.broadinstitute.hellbender.utils.recalibration.
QualQuantizer.QualInterval
(implements java.lang.Comparable<T>)
org.broadinstitute.hellbender.utils.recalibration.
QuantizationInfo
(implements java.io.Serializable)
picard.util.
QuerySortedReadPairIteratorUtil
picard.util.
QuerySortedReadPairIteratorUtil.ReadPair
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
RandomLikelihoodCalculationEngine
(implements org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
ReadLikelihoodCalculationEngine
)
picard.illumina.parser.
Range
org.broadinstitute.hellbender.utils.iterators.
ReadCachingIterator
(implements java.util.Iterator<E>)
org.broadinstitute.hellbender.tools.spark.sv.evidence.
ReadClassifier
(implements java.util.function.Function<T,R>)
org.broadinstitute.hellbender.utils.clipping.
ReadClipper
org.broadinstitute.hellbender.tools.
ClipReads.ReadClipperWithData
org.broadinstitute.hellbender.utils.test.
ReadClipperTestUtils
org.broadinstitute.hellbender.utils.read.
ReadConstants
org.broadinstitute.hellbender.engine.
ReadContextData
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.read.
ReadCoordinateComparator
(implements java.util.Comparator<T>, java.io.Serializable)
org.broadinstitute.hellbender.utils.recalibration.covariates.
ReadCovariates
picard.illumina.parser.
ReadData
picard.cmdline.programgroups.
ReadDataManipulationProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
picard.illumina.parser.
ReadDescriptor
org.broadinstitute.hellbender.utils.read.markduplicates.
ReadEnds
(implements picard.sam.util.
PhysicalLocation
)
org.broadinstitute.hellbender.utils.read.markduplicates.
ReadEndsForMarkDuplicates
org.broadinstitute.hellbender.utils.read.markduplicates.
ReadEndsForMarkDuplicatesCodec
(implements htsjdk.samtools.util.SortingCollection.Codec<T>)
picard.sam.markduplicates.util.
ReadEndsForMarkDuplicatesCodec
(implements htsjdk.samtools.util.SortingCollection.Codec<T>)
picard.sam.markduplicates.util.
ReadEndsForMarkDuplicatesWithBarcodesCodec
java.io.Reader (implements java.io.Closeable, java.lang.Readable)
org.broadinstitute.hellbender.utils.codecs.
LineIteratorReader
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
ReadErrorCorrector
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
ReadErrorCorrector.CorrectionSet
org.broadinstitute.hellbender.tools.readersplitters.
ReaderSplitter
<T>
org.broadinstitute.hellbender.tools.readersplitters.
ReadGroupSplitter
<T>
org.broadinstitute.hellbender.tools.readersplitters.
LibraryNameSplitter
org.broadinstitute.hellbender.tools.readersplitters.
ReadGroupIdSplitter
org.broadinstitute.hellbender.tools.readersplitters.
SampleNameSplitter
org.broadinstitute.hellbender.engine.filters.
ReadFilter
(implements java.util.function.Predicate<T>, java.io.Serializable)
org.broadinstitute.hellbender.engine.filters.
AlignmentAgreesWithHeaderReadFilter
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.filters.
AmbiguousBaseReadFilter
org.broadinstitute.hellbender.tools.spark.pathseq.
ContainsKmerReadFilter
org.broadinstitute.hellbender.engine.filters.
CountingReadFilter
org.broadinstitute.hellbender.engine.filters.
CountingReadFilter.CountingAndReadFilter
org.broadinstitute.hellbender.engine.filters.
FragmentLengthReadFilter
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.pathseq.
HostAlignmentReadFilter
org.broadinstitute.hellbender.engine.filters.
LibraryReadFilter
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.filters.
MappingQualityReadFilter
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.pathseq.
MarkedOpticalDuplicateReadFilter
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.filters.
MetricsReadFilter
org.broadinstitute.hellbender.engine.filters.
NotOpticalDuplicateReadFilter
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.filters.
OverclippedReadFilter
org.broadinstitute.hellbender.engine.filters.
PlatformReadFilter
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.filters.
PlatformUnitReadFilter
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.filters.
ReadFilter.ReadFilterBinOp
org.broadinstitute.hellbender.engine.filters.
ReadFilter.ReadFilterAnd
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.AllowAllReadsReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.CigarContainsNoNOperator
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.FirstOfPairReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.GoodCigarReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.HasReadGroupReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.MappedReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.MappingQualityAvailableReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.MappingQualityNotZeroReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.MatchingBasesAndQualsReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.MateDifferentStrandReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.MateOnSameContigOrNoMappedMateReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.NonZeroFragmentLengthReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.NonZeroReferenceLengthAlignmentReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.NotDuplicateReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.NotSecondaryAlignmentReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.NotSupplementaryAlignmentReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.PairedReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.PassesVendorQualityCheckReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.PrimaryLineReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.ProperlyPairedReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.ReadLengthEqualsCigarLengthReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.SecondOfPairReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.SeqIsStoredReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.ValidAlignmentEndReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary.ValidAlignmentStartReadFilter
org.broadinstitute.hellbender.engine.filters.
ReadGroupBlackListReadFilter
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.filters.
ReadGroupReadFilter
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.filters.
ReadLengthReadFilter
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.filters.
ReadNameReadFilter
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.filters.
ReadStrandFilter
org.broadinstitute.hellbender.engine.filters.
SampleReadFilter
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.filters.
WellformedReadFilter
org.broadinstitute.hellbender.cmdline.
ReadFilterArgumentDefinitions
org.broadinstitute.hellbender.utils.iterators.
ReadFilteringIterator
(implements java.lang.Iterable<T>, java.util.Iterator<E>)
org.broadinstitute.hellbender.engine.filters.
ReadFilterLibrary
org.broadinstitute.hellbender.tools.spark.utils.
ReadFilterSparkifier
(implements org.apache.spark.api.java.function.Function<T1,R>)
org.broadinstitute.hellbender.utils.recalibration.covariates.
ReadGroupCovariate
(implements org.broadinstitute.hellbender.utils.recalibration.covariates.
Covariate
)
org.broadinstitute.hellbender.cmdline.argumentcollections.
ReadInputArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.cmdline.argumentcollections.
OptionalReadInputArgumentCollection
org.broadinstitute.hellbender.cmdline.argumentcollections.
RequiredReadInputArgumentCollection
org.broadinstitute.hellbender.utils.genotyper.
ReadLikelihoods
<A> (implements org.broadinstitute.hellbender.utils.genotyper.
AlleleList
<A>, org.broadinstitute.hellbender.utils.genotyper.
SampleList
)
org.broadinstitute.hellbender.utils.genotyper.
UnfilledReadsLikelihoods
<A>
org.broadinstitute.hellbender.utils.genotyper.
ReadLikelihoods.BestAllele
org.broadinstitute.hellbender.tools.spark.sv.evidence.
ReadMetadata
org.broadinstitute.hellbender.tools.spark.sv.evidence.
ReadMetadata.LibraryRawStatistics
org.broadinstitute.hellbender.tools.spark.sv.evidence.
ReadMetadata.PartitionBounds
org.broadinstitute.hellbender.tools.spark.sv.evidence.
ReadMetadata.PartitionStatistics
picard.sam.util.
ReadNameParser
picard.sam.markduplicates.util.
OpticalDuplicateFinder
org.broadinstitute.hellbender.utils.read.markduplicates.
SerializableOpticalDuplicatesFinder
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.pileup.
ReadPileup
(implements java.lang.Iterable<T>)
org.broadinstitute.hellbender.utils.read.
ReadQueryNameComparator
(implements java.util.Comparator<T>, java.io.Serializable)
org.broadinstitute.hellbender.utils.recalibration.
ReadRecalibrationInfo
org.broadinstitute.hellbender.engine.
ReadsContext
(implements java.lang.Iterable<T>)
org.broadinstitute.hellbender.engine.
ReadsDataSource
(implements java.lang.AutoCloseable, org.broadinstitute.hellbender.engine.
GATKDataSource
<T>)
org.broadinstitute.hellbender.utils.downsampling.
ReadsDownsamplingIterator
(implements java.lang.Iterable<T>, java.util.Iterator<E>)
org.broadinstitute.hellbender.tools.spark.sv.evidence.
ReadsForQNamesFinder
(implements java.lang.Iterable<T>)
org.broadinstitute.hellbender.utils.nio.
ReadsIterable
(implements java.lang.Iterable<T>, java.io.Serializable)
org.broadinstitute.hellbender.utils.read.markduplicates.
ReadsKey
org.broadinstitute.hellbender.utils.test.
ReadsPreprocessingPipelineTestData
org.broadinstitute.hellbender.engine.spark.datasources.
ReadsSparkSink
org.broadinstitute.hellbender.engine.spark.datasources.
ReadsSparkSource
(implements java.io.Serializable)
picard.illumina.parser.
ReadStructure
picard.illumina.parser.
ReadStructure.Substructure
(implements java.lang.Iterable<T>)
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.
ReadThreadingAssembler
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
ReadThreadingAssemblerArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.utils.
ReadTransformerSparkifier
(implements org.apache.spark.api.java.function.Function<T1,R>)
org.broadinstitute.hellbender.utils.iterators.
ReadTransformingIterator
(implements java.lang.Iterable<T>, java.util.Iterator<E>)
org.broadinstitute.hellbender.utils.read.
ReadUtils
org.broadinstitute.hellbender.engine.spark.
ReadWalkerContext
org.broadinstitute.hellbender.tools.walkers.realignmentfilter.
RealignmentArgumentCollection
org.broadinstitute.hellbender.tools.walkers.realignmentfilter.
RealignmentEngine
org.broadinstitute.hellbender.tools.walkers.realignmentfilter.
RealignmentEngine.RealignmentResult
org.broadinstitute.hellbender.utils.recalibration.
RecalDatum
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.recalibration.
RecalibrationArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.recalibration.
RecalibrationReport
org.broadinstitute.hellbender.utils.recalibration.
RecalibrationTables
(implements java.lang.Iterable<T>, java.io.Serializable)
org.broadinstitute.hellbender.utils.recalibration.
RecalUtils
org.apache.hadoop.mapreduce.RecordWriter<K,V>
org.seqdoop.hadoop_bam.VCFRecordWriter<K>
org.seqdoop.hadoop_bam.KeyIgnoringVCFRecordWriter<K>
org.broadinstitute.hellbender.engine.spark.datasources.
VariantsSparkSink.GvcfKeyIgnoringVCFRecordWriter
<K>
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
ReducibleAnnotationData
<T>
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AlleleSpecificAnnotationData
<T>
org.broadinstitute.hellbender.utils.reference.
ReferenceBases
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
ReferenceConfidenceModel
org.broadinstitute.hellbender.tools.walkers.
ReferenceConfidenceVariantContextMerger
org.broadinstitute.hellbender.tools.walkers.
ReferenceConfidenceVariantContextMerger.VCWithNewAlleles
org.broadinstitute.hellbender.engine.
ReferenceContext
(implements java.lang.Iterable<T>)
org.broadinstitute.hellbender.engine.datasources.
ReferenceFileSource
(implements org.broadinstitute.hellbender.engine.datasources.
ReferenceSource
, java.io.Serializable)
org.broadinstitute.hellbender.engine.
ReferenceFileSource
(implements org.broadinstitute.hellbender.engine.
ReferenceDataSource
)
org.broadinstitute.hellbender.engine.datasources.
ReferenceHadoopSource
(implements org.broadinstitute.hellbender.engine.datasources.
ReferenceSource
, java.io.Serializable)
org.broadinstitute.hellbender.cmdline.argumentcollections.
ReferenceInputArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.cmdline.argumentcollections.
OptionalReferenceInputArgumentCollection
org.broadinstitute.hellbender.cmdline.argumentcollections.
RequiredReferenceInputArgumentCollection
org.broadinstitute.hellbender.engine.
ReferenceMemorySource
(implements org.broadinstitute.hellbender.engine.
ReferenceDataSource
)
org.broadinstitute.hellbender.engine.datasources.
ReferenceMultiSource
(implements org.broadinstitute.hellbender.engine.datasources.
ReferenceSource
, java.io.Serializable)
picard.cmdline.programgroups.
ReferenceProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
org.broadinstitute.hellbender.engine.
ReferenceShard
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.spark.datasources.
ReferenceTwoBitSource
(implements org.broadinstitute.hellbender.engine.datasources.
ReferenceSource
, java.io.Serializable)
org.broadinstitute.hellbender.utils.reference.
ReferenceUtils
org.broadinstitute.hellbender.engine.datasources.
ReferenceWindowFunctions
org.broadinstitute.hellbender.engine.datasources.
ReferenceWindowFunctions.FixedWindowFunction
(implements org.broadinstitute.hellbender.utils.
SerializableFunction
<T,R>)
picard.annotation.
RefFlatReader
picard.util.
ReflectionUtil
picard.sam.
ReorderSam.ReorderSamReferenceArgumentCollection
(implements picard.cmdline.argumentcollections.
ReferenceArgumentCollection
)
picard.sam.util.
RepresentativeReadIndexer
picard.sam.markduplicates.util.
RepresentativeReadIndexerCodec
(implements htsjdk.samtools.util.SortingCollection.Codec<T>)
org.broadinstitute.hellbender.cmdline.argumentcollections.
RequiredFeatureInputArgumentCollection
(implements java.io.Serializable)
picard.cmdline.argumentcollections.
RequiredReferenceArgumentCollection
(implements picard.cmdline.argumentcollections.
ReferenceArgumentCollection
)
org.broadinstitute.hellbender.cmdline.argumentcollections.
RequiredVariantInputArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.io.
Resource
picard.util.
RExecutor
picard.analysis.directed.
RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
(implements picard.metrics.
PerUnitMetricCollector
<BEAN,HKEY,ARGTYPE>)
org.broadinstitute.hellbender.utils.runtime.
RuntimeUtils
org.broadinstitute.hellbender.utils.test.
SamAssertionUtils
org.broadinstitute.hellbender.utils.read.
SamComparison
org.broadinstitute.hellbender.utils.read.
SAMFileGATKReadWriter
(implements org.broadinstitute.hellbender.utils.read.
GATKReadWriter
)
org.broadinstitute.hellbender.utils.test.testers.
SamFileTester
(implements org.broadinstitute.hellbender.utils.test.
CommandLineProgramTester
)
org.broadinstitute.hellbender.utils.test.testers.
CleanSamTester
org.broadinstitute.hellbender.utils.codecs.sampileup.
SAMPileupElement
org.broadinstitute.hellbender.utils.codecs.sampileup.
SAMPileupFeature
(implements htsjdk.tribble.Feature)
org.broadinstitute.hellbender.utils.samples.
Sample
(implements java.lang.Comparable<T>)
org.broadinstitute.hellbender.utils.samples.
SampleDB
org.broadinstitute.hellbender.utils.samples.
SampleDBBuilder
org.broadinstitute.hellbender.utils.iterators.
SamReaderQueryingIterator
(implements htsjdk.samtools.util.CloseableIterator<T>, java.lang.Iterable<T>)
org.broadinstitute.hellbender.metrics.
SAMRecordAndReference
picard.metrics.
SAMRecordAndReference
htsjdk.samtools.
SAMRecordSparkCodec
(implements htsjdk.samtools.util.SortingCollection.Codec<T>)
org.broadinstitute.hellbender.utils.read.
SAMRecordToGATKReadAdapter
(implements org.broadinstitute.hellbender.utils.read.
GATKRead
, java.io.Serializable)
org.broadinstitute.hellbender.utils.read.
BDGAlignmentRecordToGATKReadAdapter
org.broadinstitute.hellbender.utils.iterators.
SAMRecordToReadIterator
(implements java.lang.Iterable<T>, java.util.Iterator<E>)
htsjdk.samtools.util.SamRecordWithOrdinal
org.broadinstitute.hellbender.utils.read.markduplicates.
SamRecordWithOrdinalAndSetDuplicateReadFlag
picard.sam.markduplicates.util.
SamRecordWithOrdinalAndSetDuplicateReadFlag
org.broadinstitute.hellbender.utils.
SATagBuilder
picard.util.
ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
(implements picard.cmdline.argumentcollections.
ReferenceArgumentCollection
)
org.broadinstitute.hellbender.utils.runtime.
ScriptExecutor
org.broadinstitute.hellbender.utils.python.
PythonExecutorBase
org.broadinstitute.hellbender.utils.python.
PythonScriptExecutor
org.broadinstitute.hellbender.utils.python.
StreamingPythonScriptExecutor
org.broadinstitute.hellbender.utils.R.
RScriptExecutor
org.broadinstitute.hellbender.utils.nio.
SeekableByteChannelPrefetcher
(implements java.nio.channels.SeekableByteChannel)
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
SegmentedCpxVariantSimpleVariantExtractor
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants
org.broadinstitute.hellbender.tools.funcotator.
SequenceComparison
org.broadinstitute.hellbender.utils.
SequenceDictionaryUtils
org.broadinstitute.hellbender.cmdline.argumentcollections.
SequenceDictionaryValidationArgumentCollection.NoValidationCollection
(implements org.broadinstitute.hellbender.cmdline.argumentcollections.
SequenceDictionaryValidationArgumentCollection
)
org.broadinstitute.hellbender.cmdline.argumentcollections.
SequenceDictionaryValidationArgumentCollection.StandardValidationCollection
(implements org.broadinstitute.hellbender.cmdline.argumentcollections.
SequenceDictionaryValidationArgumentCollection
)
picard.analysis.artifacts.
SequencingArtifactMetrics
com.esotericsoftware.kryo.Serializer<T>
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
AlignedAssembly.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
AlignedAssemblyOrExcuse.Serializer
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
AlignedContig.Serializer
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
AlignmentInterval.Serializer
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
AssemblyContigWithFineTunedAlignments.Serializer
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
BreakpointComplications.IntraChrStrandSwitchBreakpointComplications.Serializer
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications.Serializer
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.ExternalEvidence.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.InterContigPair.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.LargeIndel.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.MateUnmapped.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.OutiesPair.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.ReadEvidence.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.SameStrandPair.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.SplitRead.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.TemplateSizeAnomaly.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
BreakpointEvidence.WeirdTemplateSize.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
EvidenceTargetLink.Serializer
org.broadinstitute.hellbender.tools.spark.utils.
HopscotchCollection.Serializer
<T>
org.broadinstitute.hellbender.tools.spark.utils.
HopscotchMap.Serializer
org.broadinstitute.hellbender.tools.spark.utils.
HopscotchMultiMap.Serializer
org.broadinstitute.hellbender.tools.spark.utils.
HopscotchSet.Serializer
org.broadinstitute.hellbender.tools.spark.utils.
HopscotchUniqueMultiMap.Serializer
org.broadinstitute.hellbender.tools.spark.utils.
IntHistogram.CDF.Serializer
org.broadinstitute.hellbender.tools.spark.utils.
IntHistogram.Serializer
org.broadinstitute.hellbender.engine.spark.
JsonSerializer
<T>
org.broadinstitute.hellbender.tools.spark.sv.utils.
KmerAndCount.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
KmerAndInterval.Serializer
org.broadinstitute.hellbender.tools.spark.utils.
LargeLongHopscotchSet.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
LibraryStatistics.Serializer
org.broadinstitute.hellbender.tools.spark.utils.
LongBloomFilter.Serializer
org.broadinstitute.hellbender.tools.spark.utils.
LongHopscotchSet.Serializer
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
NovelAdjacencyAndAltHaplotype.Serializer
org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.
Pair.Serializer
org.broadinstitute.hellbender.tools.spark.sv.utils.
PairedStrandedIntervalTree.Serializer
<T>
org.broadinstitute.hellbender.tools.spark.pathseq.
PSKmerBloomFilter.Serializer
org.broadinstitute.hellbender.tools.spark.pathseq.
PSKmerSet.Serializer
org.broadinstitute.hellbender.tools.spark.pathseq.
PSTaxonomyDatabase.Serializer
org.broadinstitute.hellbender.tools.spark.pathseq.
PSTree.Serializer
org.broadinstitute.hellbender.tools.spark.pathseq.
PSTreeNode.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
QNameAndInterval.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
ReadMetadata.LibraryRawStatistics.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
ReadMetadata.PartitionBounds.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
ReadMetadata.PartitionStatistics.Serializer
org.broadinstitute.hellbender.tools.spark.sv.evidence.
ReadMetadata.Serializer
org.broadinstitute.hellbender.engine.spark.
SAMRecordSerializer
org.broadinstitute.hellbender.engine.spark.
SAMRecordToGATKReadAdapterSerializer
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
SimpleChimera.Serializer
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
SimpleNovelAdjacencyAndChimericAlignmentEvidence.Serializer
org.broadinstitute.hellbender.tools.spark.sv.utils.
Strand.Serializer
org.broadinstitute.hellbender.tools.spark.sv.utils.
StrandedInterval.Serializer
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVFastqUtils.FastqRead.Serializer
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVInterval.Serializer
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVIntervalTree.Serializer
<T>
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVKmerLong.Serializer
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVKmerShort.Serializer
org.broadinstitute.hellbender.tools.spark.utils.
SetSizeUtils
org.broadinstitute.hellbender.engine.
ShardBoundary
(implements htsjdk.samtools.util.Locatable, java.io.Serializable)
org.broadinstitute.hellbender.engine.
ShardBoundaryShard
<T> (implements java.io.Serializable, org.broadinstitute.hellbender.engine.
Shard
<T>)
org.broadinstitute.hellbender.utils.iterators.
ShardedIntervalIterator
(implements java.util.Iterator<E>)
org.broadinstitute.hellbender.engine.
ShardToMultiIntervalShardAdapter
<T> (implements org.broadinstitute.hellbender.engine.
MultiIntervalShard
<T>, java.io.Serializable, org.broadinstitute.hellbender.engine.
Shard
<T>)
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
SharedSequenceMerger
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
SharedVertexSequenceSplitter
org.broadinstitute.hellbender.cmdline.programgroups.
ShortVariantDiscoveryProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
org.broadinstitute.hellbender.engine.spark.
ShuffleJoinReadsWithRefBases
org.broadinstitute.hellbender.engine.spark.
ShuffleJoinReadsWithVariants
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.
SimpleAnnotatedIntervalWriter
(implements org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.
AnnotatedIntervalWriter
)
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
SimpleChimera
org.broadinstitute.hellbender.tools.copynumber.caller.
SimpleCopyRatioCaller
org.broadinstitute.hellbender.tools.copynumber.formats.records.
SimpleCount
(implements htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging.
SimpleGermlineTagger
org.broadinstitute.hellbender.utils.
SimpleInterval
(implements htsjdk.samtools.util.Locatable, java.io.Serializable)
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.
SimpleLocatableMetadata
(implements org.broadinstitute.hellbender.tools.copynumber.formats.metadata.
LocatableMetadata
)
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
SimpleNovelAdjacencyAndChimericAlignmentEvidence
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.
SimpleNovelAdjacencyInterpreter
org.broadinstitute.hellbender.transformers.
SimpleRepeatMaskTransformer
(implements org.broadinstitute.hellbender.transformers.
ReadTransformer
)
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.
SimpleSampleLocatableMetadata
(implements org.broadinstitute.hellbender.tools.copynumber.formats.metadata.
SampleLocatableMetadata
)
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.
SimpleSampleMetadata
(implements org.broadinstitute.hellbender.tools.copynumber.formats.metadata.
SampleMetadata
)
org.broadinstitute.hellbender.utils.svd.
SimpleSVD
(implements org.broadinstitute.hellbender.utils.svd.
SVD
)
org.broadinstitute.hellbender.tools.spark.sv.utils.
SingleSequenceReferenceAligner
<T,U> (implements java.lang.AutoCloseable)
org.broadinstitute.hellbender.utils.mcmc.
SliceSampler
org.broadinstitute.hellbender.utils.smithwaterman.
SmithWatermanIntelAligner
(implements org.broadinstitute.hellbender.utils.smithwaterman.
SmithWatermanAligner
)
org.broadinstitute.hellbender.utils.smithwaterman.
SmithWatermanJavaAligner
(implements org.broadinstitute.hellbender.utils.smithwaterman.
SmithWatermanAligner
)
picard.fingerprint.
Snp
(implements java.lang.Comparable<T>)
org.broadinstitute.hellbender.tools.walkers.mutect.
SomaticLikelihoodsEngine
org.broadinstitute.hellbender.engine.spark.
SparkCommandLineArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.spark.
SparkContextFactory
org.broadinstitute.hellbender.utils.spark.
SparkConverter
org.broadinstitute.hellbender.engine.spark.
SparkSharder
org.broadinstitute.hellbender.utils.svd.
SparkSingularValueDecomposer
(implements org.broadinstitute.hellbender.utils.svd.
SingularValueDecomposer
)
org.broadinstitute.hellbender.utils.test.
SparkTestUtils
org.broadinstitute.hellbender.utils.spark.
SparkUtils
org.broadinstitute.hellbender.cmdline.
StandardArgumentDefinitions
org.broadinstitute.hellbender.tools.walkers.genotyper.
StandardCallerArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
AssemblyBasedCallerArgumentCollection
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
HaplotypeCallerArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.walkers.mutect.
M2ArgumentCollection
org.broadinstitute.hellbender.tools.walkers.mutect.
M2FiltersArgumentCollection
org.broadinstitute.hellbender.tools.walkers.genotyper.
UnifiedArgumentCollection
org.broadinstitute.hellbender.utils.recalibration.covariates.
StandardCovariateList
(implements java.lang.Iterable<T>, java.io.Serializable)
picard.cmdline.
StandardOptionDefinitions
org.broadinstitute.hellbender.tools.spark.sv.utils.
StrandedInterval
org.broadinstitute.hellbender.utils.runtime.
StreamOutput
org.broadinstitute.hellbender.utils.runtime.
CapturedStreamOutput
org.broadinstitute.hellbender.utils.runtime.
CapturedStreamOutputSnapshot
org.broadinstitute.hellbender.transformers.
StripMateNumberTransformer
(implements org.broadinstitute.hellbender.transformers.
ReadTransformer
)
org.broadinstitute.hellbender.cmdline.programgroups.
StructuralVariantDiscoveryProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
org.broadinstitute.hellbender.tools.spark.sv.
StructuralVariationDiscoveryArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.sv.
StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.sv.
StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.walkers.mutect.
SubsettedLikelihoodMatrix
<A> (implements org.broadinstitute.hellbender.utils.genotyper.
LikelihoodMatrix
<A>)
org.broadinstitute.hellbender.tools.spark.sv.utils.
SvCigarUtils
org.broadinstitute.hellbender.tools.copynumber.denoising.
SVDDenoisedCopyRatioResult
org.broadinstitute.hellbender.tools.copynumber.denoising.
SVDDenoisingUtils
org.broadinstitute.hellbender.utils.svd.
SVDFactory
org.broadinstitute.hellbender.tools.spark.sv.discovery.
SvDiscoverFromLocalAssemblyContigAlignmentsSpark.AssemblyContigsClassifiedByAlignmentSignatures
org.broadinstitute.hellbender.tools.spark.sv.discovery.
SvDiscoveryInputMetaData
org.broadinstitute.hellbender.tools.spark.sv.discovery.
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.utils.
SVFastqUtils
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVFastqUtils.FastqRead
(implements org.broadinstitute.hellbender.utils.fermi.FermiLiteAssembler.BasesAndQuals)
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVFastqUtils.Mapping
(implements htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVFileUtils
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVInterval
(implements java.lang.Comparable<T>)
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVIntervalTree
<V> (implements java.lang.Iterable<T>)
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.ValuesIterator
<V1> (implements java.util.Iterator<E>)
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVKmer
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVKmerLong
(implements java.lang.Comparable<T>)
org.broadinstitute.hellbender.tools.spark.sv.utils.
KmerAndCount
(implements java.util.Map.Entry<K,V>)
org.broadinstitute.hellbender.tools.spark.sv.evidence.
KmerAndInterval
(implements java.util.Map.Entry<K,V>)
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVKmerShort
(implements java.lang.Comparable<T>)
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVKmerizer
(implements java.util.Iterator<E>)
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVDUSTFilteredKmerizer
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVKmerizer.ASCIICharSequence
(implements java.lang.CharSequence)
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVLocation
(implements java.lang.Comparable<T>)
org.broadinstitute.hellbender.tools.spark.sv.evidence.
SVReadFilter
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVReferenceUtils
org.broadinstitute.hellbender.tools.spark.sv.discovery.
SvType
org.broadinstitute.hellbender.tools.spark.sv.discovery.
BreakEndVariantType
org.broadinstitute.hellbender.tools.spark.sv.discovery.
BreakEndVariantType.InvSuspectBND
org.broadinstitute.hellbender.tools.spark.sv.discovery.
BreakEndVariantType.TransLocBND
org.broadinstitute.hellbender.tools.spark.sv.discovery.
SimpleSVType
org.broadinstitute.hellbender.tools.spark.sv.discovery.
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.utils.
SVUtils
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVUtils.IteratorFilter
<T> (implements java.util.Iterator<E>)
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVVCFReader
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVVCFWriter
org.broadinstitute.hellbender.utils.smithwaterman.
SWNativeAlignerWrapper
(implements org.broadinstitute.hellbender.utils.smithwaterman.
SmithWatermanAligner
)
org.broadinstitute.hellbender.utils.solver.
SynchronizedUnivariateSolver
org.broadinstitute.hellbender.utils.solver.
SynchronizedUnivariateSolver.UnivariateSolverSummary
picard.util.
TabbedTextFileWithHeaderParser
(implements java.lang.Iterable<T>)
picard.util.
TabbedTextFileWithHeaderParser.Row
org.broadinstitute.hellbender.utils.tsv.
TableColumnCollection
org.broadinstitute.hellbender.utils.codecs.table.
TableFeature
(implements htsjdk.tribble.Feature)
org.broadinstitute.hellbender.tools.funcotator.dataSources.
TableFuncotation
(implements org.broadinstitute.hellbender.tools.funcotator.
Funcotation
)
org.broadinstitute.hellbender.utils.tsv.
TableReader
<R> (implements java.io.Closeable, java.lang.Iterable<T>)
org.broadinstitute.hellbender.tools.walkers.validation.
ConcordanceSummaryRecord.Reader
org.broadinstitute.hellbender.utils.mcmc.
ParameterReader
<T>
org.broadinstitute.hellbender.utils.tsv.
TableUtils
org.broadinstitute.hellbender.utils.tsv.
TableWriter
<R> (implements java.io.Closeable)
org.broadinstitute.hellbender.tools.walkers.validation.
ConcordanceSummaryRecord.Writer
org.broadinstitute.hellbender.utils.mcmc.
ParameterWriter
<T>
picard.analysis.directed.
TargetMetricsCollector.Coverage
picard.analysis.directed.
TargetMetricsCollector.PerUnitTargetMetricCollector
(implements picard.metrics.
PerUnitMetricCollector
<BEAN,HKEY,ARGTYPE>)
picard.
Test
picard.cmdline.programgroups.
Testing
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
org.broadinstitute.hellbender.cmdline.
TestProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
org.broadinstitute.hellbender.utils.text.
TextFormattingUtils
org.broadinstitute.hellbender.tools.spark.sv.utils.
TextMDCodec
org.broadinstitute.hellbender.tools.spark.sv.utils.
TextMDCodec.MDElement
org.broadinstitute.hellbender.tools.spark.sv.utils.
TextMDCodec.DeletionMDElement
org.broadinstitute.hellbender.tools.spark.sv.utils.
TextMDCodec.MatchMDElement
org.broadinstitute.hellbender.tools.spark.sv.utils.
TextMDCodec.MismatchMDElement
picard.analysis.
TheoreticalSensitivity
picard.analysis.
TheoreticalSensitivity.RouletteWheel
java.lang.Throwable (implements java.io.Serializable)
java.lang.Exception
java.lang.RuntimeException
org.broadinstitute.hellbender.exceptions.
GATKException
org.broadinstitute.hellbender.tools.funcotator.
FuncotatorUtils.TranscriptCodingSequenceException
org.broadinstitute.hellbender.exceptions.
GATKException.MissingReadField
org.broadinstitute.hellbender.exceptions.
GATKException.ReadAttributeTypeMismatch
org.broadinstitute.hellbender.exceptions.
GATKException.ShouldNeverReachHereException
org.broadinstitute.hellbender.utils.runtime.
ScriptExecutorException
org.broadinstitute.hellbender.utils.python.
PythonScriptExecutorException
org.broadinstitute.hellbender.utils.R.
RScriptExecutorException
picard.
PicardException
picard.annotation.
AnnotationException
org.broadinstitute.hellbender.exceptions.
PicardNonZeroExitException
org.broadinstitute.hellbender.exceptions.
UserException
org.broadinstitute.hellbender.exceptions.
UserException.BadInput
org.broadinstitute.hellbender.exceptions.
UserException.Require2BitReferenceForBroadcast
org.broadinstitute.hellbender.exceptions.
UserException.BadTempDir
org.broadinstitute.hellbender.exceptions.
UserException.CannotExecuteScript
org.broadinstitute.hellbender.exceptions.
UserException.CannotHandleGzippedRef
org.broadinstitute.hellbender.exceptions.
UserException.CouldNotCreateOutputFile
org.broadinstitute.hellbender.exceptions.
UserException.CouldNotIndexFile
org.broadinstitute.hellbender.exceptions.
UserException.CouldNotReadInputFile
org.broadinstitute.hellbender.exceptions.
UserException.EmptyIntersection
org.broadinstitute.hellbender.exceptions.
UserException.FailsStrictValidation
org.broadinstitute.hellbender.exceptions.
UserException.HardwareFeatureException
org.broadinstitute.hellbender.exceptions.
UserException.IncompatibleRecalibrationTableParameters
org.broadinstitute.hellbender.exceptions.
UserException.IncompatibleSequenceDictionaries
org.broadinstitute.hellbender.exceptions.
UserException.LexicographicallySortedSequenceDictionary
org.broadinstitute.hellbender.exceptions.
UserException.MalformedBAM
org.broadinstitute.hellbender.exceptions.
UserException.HeaderMissingReadGroup
org.broadinstitute.hellbender.exceptions.
UserException.ReadMissingReadGroup
org.broadinstitute.hellbender.exceptions.
UserException.MalformedFile
org.broadinstitute.hellbender.exceptions.
UserException.MalformedGenomeLoc
org.broadinstitute.hellbender.exceptions.
UserException.MalformedRead
org.broadinstitute.hellbender.exceptions.
UserException.MisencodedQualityScoresRead
org.broadinstitute.hellbender.exceptions.
UserException.MissingContigInSequenceDictionary
org.broadinstitute.hellbender.exceptions.
UserException.MissingIndex
org.broadinstitute.hellbender.exceptions.
UserException.MissingReference
org.broadinstitute.hellbender.exceptions.
UserException.MissingReferenceDictFile
org.broadinstitute.hellbender.exceptions.
UserException.MissingReferenceFaiFile
org.broadinstitute.hellbender.exceptions.
UserException.NoSuitableCodecs
org.broadinstitute.hellbender.exceptions.
UserException.UnimplementedFeature
org.broadinstitute.hellbender.exceptions.
UserException.WrongFeatureType
picard.illumina.parser.
Tile
picard.illumina.parser.
TileIndex
(implements java.lang.Iterable<T>)
picard.illumina.parser.
TileIndex.TileIndexRecord
picard.illumina.parser.readers.
TileMetricsOutReader
(implements java.util.Iterator<E>)
picard.illumina.parser.readers.
TileMetricsOutReader.IlluminaLaneTileCode
picard.illumina.parser.readers.
TileMetricsOutReader.IlluminaTileMetrics
picard.illumina.parser.
TileMetricsUtil
picard.illumina.parser.
TilePhasingValue
org.broadinstitute.hellbender.tools.walkers.vqsr.
TrainingSet
org.broadinstitute.hellbender.tools.walkers.vqsr.
Tranche
org.broadinstitute.hellbender.tools.walkers.vqsr.
VQSLODTranche
org.broadinstitute.hellbender.tools.walkers.vqsr.
Tranche.TrancheComparator
<T> (implements java.util.Comparator<T>)
org.broadinstitute.hellbender.tools.walkers.vqsr.
Tranche.TrancheTruthSensitivityComparator
(implements java.util.Comparator<T>)
org.broadinstitute.hellbender.tools.walkers.vqsr.
TrancheManager
org.broadinstitute.hellbender.tools.walkers.vqsr.
TrancheManager.SelectionMetric
org.broadinstitute.hellbender.tools.walkers.vqsr.
TrancheManager.TruthSensitivityMetric
org.broadinstitute.hellbender.engine.
TraversalParameters
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.samples.
Trio
picard.sam.markduplicates.
UmiGraph
picard.sam.markduplicates.
UmiUtil
org.broadinstitute.hellbender.utils.
UniqueIDWrapper
<A>
org.broadinstitute.hellbender.utils.solver.
UnivariateSolverJobDescription
org.broadinstitute.hellbender.utils.solver.
UnivariateSolverSpecifications
org.broadinstitute.hellbender.utils.
UnsignedTypeUtil
picard.util.
UnsignedTypeUtil
org.broadinstitute.hellbender.utils.
Utils
picard.vcf.processor.
VariantAccumulatorExecutor.MultiThreadedChunkBased
<A,R> (implements picard.vcf.processor.
VariantAccumulatorExecutor
<ACCUMULATOR,RESULT>)
org.broadinstitute.hellbender.tools.walkers.annotator.
VariantAnnotation
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
Annotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
GenotypeAnnotation
org.broadinstitute.hellbender.tools.walkers.annotator.
DepthPerAlleleBySample
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
, org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
DepthPerSampleHC
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardHCAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
OxoGReadCounts
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
PerAlleleAnnotation
org.broadinstitute.hellbender.tools.walkers.annotator.
BaseQuality
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
FragmentLength
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
MappingQuality
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
ReadPosition
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
StrandArtifact
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
StrandBiasBySample
org.broadinstitute.hellbender.tools.walkers.annotator.
UniqueAltReadCount
org.broadinstitute.hellbender.tools.walkers.annotator.
InfoFieldAnnotation
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_InbreedingCoeff
(implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_QualByDepth
(implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_StandardAnnotation
, org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
ReducibleAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_RMSMappingQuality
(implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_StandardAnnotation
, org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
ReducibleAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
ChromosomeCounts
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
Coverage
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
, org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
GenotypeSummaries
org.broadinstitute.hellbender.tools.walkers.annotator.
MappingQualityZero
org.broadinstitute.hellbender.tools.walkers.annotator.
PedigreeAnnotation
org.broadinstitute.hellbender.tools.walkers.annotator.
ExcessHet
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
InbreedingCoeff
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
PossibleDeNovo
org.broadinstitute.hellbender.tools.walkers.annotator.
QualByDepth
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
RankSumTest
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
Annotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_RankSumTest
(implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
ReducibleAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_BaseQualityRankSumTest
(implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_MappingQualityRankSumTest
(implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_ReadPosRankSumTest
(implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
BaseQualityRankSumTest
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
ClippingRankSumTest
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardHCAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
LikelihoodRankSumTest
org.broadinstitute.hellbender.tools.walkers.annotator.
MappingQualityRankSumTest
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
ReadPosRankSumTest
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
ReferenceBases
org.broadinstitute.hellbender.tools.walkers.annotator.
RMSMappingQuality
(implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
ReducibleAnnotation
, org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
SampleList
org.broadinstitute.hellbender.tools.walkers.annotator.
StrandBiasTest
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_StrandBiasTest
(implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
ReducibleAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_FisherStrand
(implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_StrandOddsRatio
(implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
FisherStrand
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
StrandOddsRatio
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
TandemRepeat
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
VariantAnnotatorEngine
org.broadinstitute.hellbender.tools.walkers.annotator.
VariantAnnotatorEngine.VAExpression
htsjdk.variant.variantcontext.VariantContext (implements htsjdk.tribble.Feature, java.io.Serializable)
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVContext
org.broadinstitute.hellbender.tools.walkers.genotyper.
VariantCallContext
org.broadinstitute.hellbender.utils.test.
VariantContextTestUtils
org.broadinstitute.hellbender.utils.variant.
VariantContextVariantAdapter
(implements org.broadinstitute.hellbender.utils.variant.
GATKVariant
, java.io.Serializable)
org.broadinstitute.hellbender.tools.walkers.vqsr.
VariantDataManager
picard.cmdline.programgroups.
VariantEvaluationProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
picard.cmdline.programgroups.
VariantFilteringProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
org.broadinstitute.hellbender.engine.filters.
VariantFilterLibrary
org.broadinstitute.hellbender.engine.filters.
VariantIDsVariantFilter
(implements org.broadinstitute.hellbender.engine.filters.
VariantFilter
)
picard.vcf.processor.
VariantIteratorProducer
picard.cmdline.programgroups.
VariantManipulationProgramGroup
(implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
org.broadinstitute.hellbender.tools.walkers.annotator.
VariantOverlapAnnotator
picard.vcf.processor.
VariantProcessor
<RESULT,ACCUMULATOR>
picard.vcf.processor.
VariantProcessor.Builder
<A,R>
org.broadinstitute.hellbender.tools.walkers.vqsr.
VariantRecalibratorEngine
org.broadinstitute.hellbender.engine.
VariantShard
org.broadinstitute.hellbender.engine.datasources.
VariantsSource
org.broadinstitute.hellbender.engine.spark.datasources.
VariantsSparkSink
org.broadinstitute.hellbender.engine.spark.datasources.
VariantsSparkSource
org.broadinstitute.hellbender.engine.filters.
VariantTypesVariantFilter
(implements org.broadinstitute.hellbender.engine.filters.
VariantFilter
)
org.broadinstitute.hellbender.utils.variant.
VariantUtils
org.broadinstitute.hellbender.engine.spark.
VariantWalkerContext
picard.vcf.processor.
VcfFileSegment
picard.vcf.processor.
VcfFileSegmentGenerator
org.broadinstitute.hellbender.utils.variant.
VcfUtils
picard.vcf.
VcfUtils
org.broadinstitute.hellbender.utils.hmm.
ViterbiAlgorithm
picard.analysis.
WgsMetricsProcessorImpl
<T> (implements picard.analysis.
WgsMetricsProcessor
)
org.broadinstitute.hellbender.utils.test.
XorWrapper
(implements java.nio.channels.SeekableByteChannel)
org.broadinstitute.hellbender.utils.text.
XReadLines
(implements java.lang.AutoCloseable, java.lang.Iterable<T>, java.util.Iterator<E>)
org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.
XsvTableFeature
(implements htsjdk.tribble.Feature)
Interface Hierarchy
org.broadinstitute.hellbender.utils.illumina.
AdapterPair
picard.util.
AdapterPair
org.broadinstitute.hellbender.utils.genotyper.
AlleleList
<A>
org.broadinstitute.hellbender.utils.genotyper.
AlleleListPermutation
<A> (also extends org.broadinstitute.hellbender.utils.collections.
Permutation
<E>)
org.broadinstitute.hellbender.utils.genotyper.
LikelihoodMatrix
<A>
org.broadinstitute.hellbender.tools.walkers.annotator.
Annotation
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
AS_StandardAnnotation
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
ReducibleAnnotation
org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
org.broadinstitute.hellbender.tools.walkers.annotator.
StandardHCAnnotation
org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
org.broadinstitute.hellbender.engine.
AssemblyRegionEvaluator
picard.util.
AtomicIterator
<T>
java.lang.AutoCloseable
java.io.Closeable
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.
AnnotatedIntervalWriter
org.broadinstitute.hellbender.utils.read.
GATKReadWriter
org.broadinstitute.hellbender.utils.smithwaterman.
SmithWatermanAligner
org.broadinstitute.hellbender.tools.spark.pathseq.loggers.
PSFilterLogger
org.broadinstitute.hellbender.tools.spark.pathseq.loggers.
PSScoreLogger
org.broadinstitute.hellbender.engine.
ReferenceDataSource
(also extends org.broadinstitute.hellbender.engine.
GATKDataSource
<T>)
picard.analysis.
CollectMultipleMetrics.ProgramInterface
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
CollectMultipleMetricsSpark.SparkCollectorProvider
org.broadinstitute.hellbender.utils.test.
CommandLineProgramTester
org.broadinstitute.hellbender.utils.mcmc.
DataCollection
org.broadinstitute.hellbender.utils.hmm.
ForwardBackwardAlgorithm.Result
<D,T,S>
org.broadinstitute.hellbender.tools.funcotator.
Funcotation
java.util.function.Function<T,R>
org.broadinstitute.hellbender.utils.
SerializableFunction
<T,R> (also extends java.io.Serializable)
org.broadinstitute.hellbender.transformers.
ReadTransformer
(also extends java.util.function.UnaryOperator<T>)
java.util.function.UnaryOperator<T>
org.broadinstitute.hellbender.tools.walkers.genotyper.
AlleleLikelihoodMatrixMapper
<A>
org.broadinstitute.hellbender.transformers.
ReadTransformer
(also extends org.broadinstitute.hellbender.utils.
SerializableFunction
<T,R>)
picard.vcf.filter.
GenotypeFilter
org.broadinstitute.hellbender.utils.
HasGenomeLocation
org.broadinstitute.hellbender.utils.hmm.
HMM
<D,T,S>
org.broadinstitute.hellbender.utils.functional.
IntBiConsumer
picard.cmdline.argumentcollections.
IntervalArgumentCollection
org.broadinstitute.hellbender.utils.functional.
IntToDoubleBiFunction
java.lang.Iterable<T>
org.broadinstitute.hellbender.engine.
GATKDataSource
<T>
org.broadinstitute.hellbender.engine.
ReferenceDataSource
(also extends java.lang.AutoCloseable)
org.broadinstitute.hellbender.engine.
MultiIntervalShard
<T>
org.broadinstitute.hellbender.engine.
Shard
<T> (also extends htsjdk.samtools.util.Locatable)
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.
KmerSearchableGraph
<V,E>
htsjdk.samtools.util.Locatable
org.broadinstitute.hellbender.utils.read.
GATKRead
org.broadinstitute.hellbender.utils.variant.
GATKVariant
org.broadinstitute.hellbender.engine.
Shard
<T> (also extends java.lang.Iterable<T>)
org.broadinstitute.hellbender.tools.spark.utils.
LongIterator
org.broadinstitute.hellbender.utils.
MathUtils.IntToDoubleArrayFunction
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.
Metadata
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.
LocatableMetadata
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.
SampleLocatableMetadata
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.
SampleLocatableMetadata
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.
SampleMetadata
org.broadinstitute.hellbender.utils.test.
MiniClusterUtils.MiniClusterTest
org.broadinstitute.hellbender.utils.mcmc.
ParameterEnum
org.broadinstitute.hellbender.utils.mcmc.
ParameterSampler
<U,V,S,T>
org.broadinstitute.hellbender.utils.collections.
Permutation
<E>
org.broadinstitute.hellbender.utils.genotyper.
AlleleListPermutation
<A> (also extends org.broadinstitute.hellbender.utils.genotyper.
AlleleList
<A>)
picard.metrics.
PerUnitMetricCollector
<BEAN,HKEY,ARGTYPE>
picard.sam.util.
PhysicalLocation
java.util.function.Predicate<T>
org.broadinstitute.hellbender.engine.filters.
VariantFilter
(also extends java.io.Serializable)
org.broadinstitute.hellbender.utils.read.mergealignment.
PrimaryAlignmentSelectionStrategy
picard.sam.
PrimaryAlignmentSelectionStrategy
org.broadinstitute.hellbender.utils.read.markduplicates.
ReadEndsForMarkDuplicatesMap
picard.sam.markduplicates.util.
ReadEndsForMarkDuplicatesMap
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
ReadLikelihoodCalculationEngine
picard.fastq.
ReadNameEncoder
picard.cmdline.argumentcollections.
ReferenceArgumentCollection
org.broadinstitute.hellbender.engine.datasources.
ReferenceSource
org.broadinstitute.hellbender.utils.genotyper.
SampleList
org.broadinstitute.hellbender.tools.walkers.genotyper.
PloidyModel
org.broadinstitute.hellbender.cmdline.argumentcollections.
SequenceDictionaryValidationArgumentCollection
java.io.Serializable
org.aeonbits.owner.Config
org.aeonbits.owner.Accessible
org.broadinstitute.hellbender.utils.config.
GATKConfig
(also extends org.aeonbits.owner.Mutable)
org.aeonbits.owner.Mutable
org.broadinstitute.hellbender.utils.config.
GATKConfig
(also extends org.aeonbits.owner.Accessible)
org.broadinstitute.hellbender.utils.recalibration.covariates.
Covariate
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
MetricsCollectorSpark
<T>
org.broadinstitute.hellbender.metrics.
PerUnitMetricCollector
<BEAN,HKEY,ARGTYPE>
org.broadinstitute.hellbender.utils.
SerializableFunction
<T,R> (also extends java.util.function.Function<T,R>)
org.broadinstitute.hellbender.transformers.
ReadTransformer
(also extends java.util.function.UnaryOperator<T>)
org.broadinstitute.hellbender.engine.filters.
VariantFilter
(also extends java.util.function.Predicate<T>)
org.broadinstitute.hellbender.tools.spark.sv.utils.
SingleSequenceReferenceAligner.TriFunction
<T,U,V,W>
org.broadinstitute.hellbender.utils.svd.
SingularValueDecomposer
org.broadinstitute.hellbender.utils.smithwaterman.
SmithWatermanAlignment
org.broadinstitute.hellbender.utils.svd.
SVD
org.broadinstitute.hellbender.tools.copynumber.denoising.
SVDReadCountPanelOfNormals
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVIntervalTree.Entry
<V1>
picard.vcf.processor.
VariantAccumulatorExecutor
<ACCUMULATOR,RESULT>
picard.vcf.filter.
VariantFilter
picard.vcf.processor.
VariantProcessor.Accumulator
<RESULT>
picard.vcf.processor.
VariantProcessor.AccumulatorGenerator
<ACCUMULATOR,RESULT>
picard.vcf.processor.
VariantProcessor.ResultMerger
<RESULT>
picard.analysis.
WgsMetricsProcessor
Annotation Type Hierarchy
org.broadinstitute.hellbender.engine.
DoNotSubclass
(implements java.lang.annotation.Annotation)
org.broadinstitute.hellbender.utils.config.
SystemProperty
(implements java.lang.annotation.Annotation)
picard.analysis.
MergeableMetricBase.MergeByAdding
(implements java.lang.annotation.Annotation)
picard.analysis.
MergeableMetricBase.MergeByAssertEquals
(implements java.lang.annotation.Annotation)
picard.analysis.
MergeableMetricBase.NoMergingIsDerived
(implements java.lang.annotation.Annotation)
picard.analysis.
MergeableMetricBase.MergingIsManual
(implements java.lang.annotation.Annotation)
picard.analysis.
MergeableMetricBase.NoMergingKeepsValue
(implements java.lang.annotation.Annotation)
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
org.broadinstitute.hellbender.engine.
AlignmentContext.ReadOrientation
org.broadinstitute.hellbender.engine.spark.
JoinStrategy
org.broadinstitute.hellbender.metrics.
MetricAccumulationLevel
org.broadinstitute.hellbender.tools.copynumber.arguments.
GermlineDenoisingModelArgumentCollection.CopyNumberPosteriorExpectationMode
org.broadinstitute.hellbender.tools.copynumber.arguments.
HybridADVIArgumentCollection.HybridADVIArgument
org.broadinstitute.hellbender.tools.copynumber.
DetermineGermlineContigPloidy.RunMode
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.
Metadata.Type
org.broadinstitute.hellbender.tools.copynumber.formats.records.
CalledCopyRatioSegment.Call
org.broadinstitute.hellbender.tools.copynumber.
GermlineCNVCaller.RunMode
org.broadinstitute.hellbender.tools.copynumber.models.
AlleleFractionParameter
(implements org.broadinstitute.hellbender.utils.mcmc.
ParameterEnum
)
org.broadinstitute.hellbender.tools.copynumber.models.
CopyRatioParameter
(implements org.broadinstitute.hellbender.utils.mcmc.
ParameterEnum
)
org.broadinstitute.hellbender.tools.copynumber.utils.segmentation.
KernelSegmenter.ChangepointSortOrder
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.
OrientationBiasFilterSummaryTableColumn
org.broadinstitute.hellbender.tools.funcotator.
AminoAcid
org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.
GencodeFuncotation.VariantType
org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.
GencodeFuncotation.VariantClassification
org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.
SimpleKeyXsvFuncotationFactory.XsvDataKeyType
org.broadinstitute.hellbender.tools.funcotator.
FuncotatorArgumentDefinitions.DataSourceType
org.broadinstitute.hellbender.tools.funcotator.
FuncotatorArgumentDefinitions.OutputFormatType
org.broadinstitute.hellbender.tools.funcotator.
TranscriptSelectionMode
org.broadinstitute.hellbender.tools.
GatherVcfsCloud.GatherType
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
CollectMultipleMetricsSpark.SparkCollectors
(implements org.broadinstitute.hellbender.tools.spark.pipelines.metrics.
CollectMultipleMetricsSpark.SparkCollectorProvider
)
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
AssemblyContigWithFineTunedAlignments.AlignmentSignatureBasicType
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
AssemblyContigWithFineTunedAlignments.ReasonForAlignmentClassificationFailure
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
ContigAlignmentsModifier.AlnModType
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
ContigAlignmentsModifier.AlnModType.ModTypeString
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.
StrandSwitch
org.broadinstitute.hellbender.tools.spark.sv.discovery.
SimpleSVType.TYPES
org.broadinstitute.hellbender.tools.spark.sv.evidence.
TemplateFragmentOrdinal
org.broadinstitute.hellbender.tools.spark.sv.utils.
Strand
org.broadinstitute.hellbender.tools.spark.sv.utils.
SVKmer.Base
org.broadinstitute.hellbender.tools.walkers.annotator.
StrandArtifact.ArtifactState
org.broadinstitute.hellbender.tools.walkers.contamination.
ContaminationRecord.Level
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.
AFCalculatorImplementation
org.broadinstitute.hellbender.tools.walkers.genotyper.
GenotypeAssignmentMethod
org.broadinstitute.hellbender.tools.walkers.genotyper.
GenotypeLikelihoodsCalculationModel
org.broadinstitute.hellbender.tools.walkers.genotyper.
GenotypingOutputMode
org.broadinstitute.hellbender.tools.walkers.genotyper.
OutputMode
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
AssemblyResult.Status
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
PairHMMLikelihoodCalculationEngine.PCRErrorModel
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
ReadLikelihoodCalculationEngine.Implementation
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.
ReferenceConfidenceMode
org.broadinstitute.hellbender.tools.walkers.mutect.
CreateSomaticPanelOfNormals.DuplicateSampleStrategy
org.broadinstitute.hellbender.tools.walkers.mutect.
PerAlleleCollection.Type
org.broadinstitute.hellbender.tools.walkers.rnaseq.
ASEReadCounter.OUTPUT_FORMAT
org.broadinstitute.hellbender.tools.walkers.rnaseq.
ASEReadCounter.CountPileupType
org.broadinstitute.hellbender.tools.walkers.validation.
ConcordanceState
org.broadinstitute.hellbender.tools.walkers.variantutils.
ValidateVariants.ValidationType
org.broadinstitute.hellbender.tools.walkers.vqsr.
TensorType
(implements org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum)
org.broadinstitute.hellbender.utils.activityprofile.
ActivityProfileState.Type
org.broadinstitute.hellbender.utils.artifacts.
Transition
org.broadinstitute.hellbender.utils.baq.
BAQ.CalculationMode
org.broadinstitute.hellbender.utils.baq.
BAQ.QualityMode
org.broadinstitute.hellbender.utils.
BaseUtils.Base
org.broadinstitute.hellbender.utils.
BaseUtils.BaseSubstitutionType
org.broadinstitute.hellbender.utils.clipping.
ClippingRepresentation
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfFeature.AnnotationSource
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfFeature.FeatureType
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfFeature.GenomicPhase
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfFeature.GeneTranscriptType
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfFeature.GeneTranscriptStatus
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfFeature.LocusLevel
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfFeature.FeatureTag
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfFeature.TranscriptSupportLevel
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfFeature.RemapStatus
org.broadinstitute.hellbender.utils.codecs.gencode.
GencodeGtfFeature.RemapTargetStatus
org.broadinstitute.hellbender.utils.downsampling.
DownsampleType
org.broadinstitute.hellbender.utils.
GenomeLocParser.ValidationLevel
org.broadinstitute.hellbender.utils.genotyper.
DiploidGenotype
org.broadinstitute.hellbender.utils.haplotype.
HaplotypeBAMWriter.WriterType
org.broadinstitute.hellbender.utils.illumina.
IlluminaAdapterPair
(implements org.broadinstitute.hellbender.utils.illumina.
AdapterPair
)
org.broadinstitute.hellbender.utils.
IntervalMergingRule
org.broadinstitute.hellbender.utils.
IntervalSetRule
org.broadinstitute.hellbender.utils.
IntervalUtils.IntervalBreakpointType
org.broadinstitute.hellbender.utils.
MannWhitneyU.TestType
org.broadinstitute.hellbender.utils.mcmc.
Decile
org.broadinstitute.hellbender.utils.mcmc.
ParameterizedModel.UpdateMethod
org.broadinstitute.hellbender.utils.mcmc.
ParameterTableColumn
org.broadinstitute.hellbender.utils.
NGSPlatform
org.broadinstitute.hellbender.utils.
Nucleotide
org.broadinstitute.hellbender.utils.pairhmm.
PairHMM.Implementation
org.broadinstitute.hellbender.utils.pairhmm.
VectorLoglessPairHMM.Implementation
org.broadinstitute.hellbender.utils.python.
PythonExecutorBase.PythonExecutableName
org.broadinstitute.hellbender.utils.R.
RScriptLibrary
org.broadinstitute.hellbender.utils.read.markduplicates.
MarkDuplicatesScoringStrategy
org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.
MarkDuplicatesSparkRecord.Type
org.broadinstitute.hellbender.utils.read.mergealignment.
HitsForInsert.NumPrimaryAlignmentState
org.broadinstitute.hellbender.utils.read.
ReadsWriteFormat
org.broadinstitute.hellbender.utils.read.
ReadUtils.ClippingTail
org.broadinstitute.hellbender.utils.recalibration.
EventType
org.broadinstitute.hellbender.utils.report.
GATKReportColumnFormat.Alignment
org.broadinstitute.hellbender.utils.report.
GATKReportDataType
org.broadinstitute.hellbender.utils.report.
GATKReportTable.TableDataHeaderFields
org.broadinstitute.hellbender.utils.report.
GATKReportTable.Sorting
org.broadinstitute.hellbender.utils.report.
GATKReportTable.TableNameHeaderFields
org.broadinstitute.hellbender.utils.report.
GATKReportVersion
org.broadinstitute.hellbender.utils.runtime.
ProcessControllerBase.ProcessStream
org.broadinstitute.hellbender.utils.runtime.
StreamLocation
org.broadinstitute.hellbender.utils.samples.
Affection
org.broadinstitute.hellbender.utils.samples.
PedigreeValidationType
org.broadinstitute.hellbender.utils.samples.
PedReader.MissingPedField
org.broadinstitute.hellbender.utils.samples.
PedReader.Field
org.broadinstitute.hellbender.utils.samples.
Sex
org.broadinstitute.hellbender.utils.
SequenceDictionaryUtils.SequenceDictionaryCompatibility
org.broadinstitute.hellbender.utils.
SequencerFlowClass
org.broadinstitute.hellbender.utils.smithwaterman.
SmithWatermanAligner.Implementation
org.broadinstitute.hellbender.utils.smithwaterman.
SmithWatermanJavaAligner.State
org.broadinstitute.hellbender.utils.solver.
SynchronizedUnivariateSolver.UnivariateSolverStatus
org.broadinstitute.hellbender.utils.
Trilean
org.broadinstitute.hellbender.utils.variant.
DbSnpVariantType
org.broadinstitute.hellbender.utils.variant.
GATKVariantContextUtils.GenotypeMergeType
org.broadinstitute.hellbender.utils.variant.
GATKVariantContextUtils.FilteredRecordMergeType
org.broadinstitute.hellbender.utils.variant.
GATKVCFIndexType
picard.analysis.
AlignmentSummaryMetrics.Category
picard.analysis.
CollectMultipleMetrics.Program
(implements picard.analysis.
CollectMultipleMetrics.ProgramInterface
)
picard.analysis.
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
picard.analysis.
MetricAccumulationLevel
picard.analysis.artifacts.
Transition
picard.analysis.artifacts.
Transition.Base
picard.analysis.directed.
RnaSeqMetricsCollector.StrandSpecificity
picard.annotation.
LocusFunction
picard.annotation.
RefFlatReader.RefFlatColumns
picard.fingerprint.
CrosscheckMetric.FingerprintResult
picard.fingerprint.
CrosscheckMetric.DataType
picard.fingerprint.
DiploidGenotype
picard.fingerprint.
DiploidHaplotype
picard.fingerprint.
HaplotypeProbabilities.Genotype
picard.illumina.
IlluminaBasecallsToFastq.ReadNameFormat
picard.illumina.parser.
IlluminaDataType
picard.illumina.parser.
IlluminaFileUtil.SupportedIlluminaFormat
picard.illumina.parser.
IlluminaMetricsCode
picard.illumina.parser.
IntensityChannel
picard.illumina.parser.
ReadType
picard.illumina.parser.
TileTemplateRead
picard.illumina.parser.readers.
TileMetricsOutReader.TileMetricsVersion
picard.illumina.quality.
CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
picard.nio.
PathHelper.PathProviders
picard.pedigree.
Sex
picard.sam.
AbstractAlignmentMerger.UnmappingReadStrategy
picard.sam.
FilterSamReads.Filter
(implements org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum)
picard.sam.
RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
picard.sam.
RevertSam.FileType
(implements org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum)
picard.sam.
ValidateSamFile.Mode
picard.sam.
ViewSam.AlignmentStatus
picard.sam.
ViewSam.PfStatus
picard.sam.markduplicates.
MarkDuplicates.DuplicateTaggingPolicy
picard.sam.markduplicates.
MarkDuplicates.DuplicateType
picard.util.
BaitDesigner.DesignStrategy
picard.util.
IlluminaUtil.IlluminaAdapterPair
(implements picard.util.
AdapterPair
)
picard.util.
IntervalListScatterer.Mode
picard.util.
IntervalListTools.Action
(implements org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum)
picard.util.
VariantType
picard.vcf.
GenotypeConcordanceStateCodes
picard.vcf.
GenotypeConcordanceStates.TruthState
picard.vcf.
GenotypeConcordanceStates.CallState
picard.vcf.
GenotypeConcordanceStates.ContingencyState
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