All Classes
AbstractAlignmentMerger
AbstractAlignmentMerger.UnmappingReadStrategy
AbstractIlluminaPositionFileReader
AbstractInputParser
AbstractMarkDuplicatesCommandLineProgram
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
AbstractOpticalDuplicateFinderCommandLineProgram
AbstractWgsMetricsCollector
AccumulateVariantCallingMetrics
AdapterMarker
AdapterPair
AdapterUtility
AddCommentsToBam
AddOrReplaceReadGroups
AlignmentSummaryMetrics
AlignmentSummaryMetrics.Category
AlignmentSummaryMetricsCollector
AlleleBalanceFilter
Alpha
AnnotationException
AsyncIterator
AtomicIterator
BaitDesigner
BaitDesigner.DesignStrategy
BamIndexStats
BamToBfq
BamToBfqWriter
BarcodeFileFaker
BarcodeFileReader
BaseBclReader
BaseDistributionByCycleMetrics
BaseIlluminaDataProvider
BasicInputParser
BciFileFaker
BclData
BclFileFaker
BclIndexReader
BclQualityEvaluationStrategy
BclReader
BedToIntervalList
BestEndMapqPrimaryAlignmentStrategy
BestMapqPrimaryAlignmentSelectionStrategy
BuildBamIndex
ByIntervalListVariantContextIterator
CalculateReadGroupChecksum
CallingMetricAccumulator
CallingMetricAccumulator.Result
Casava18ReadNameEncoder
CbclData
CbclReader
CheckFingerprint
CheckIlluminaDirectory
CheckTerminatorBlock
ChimeraUtil
CircularByteBuffer
ClassFinder
CleanSam
ClippingUtility
ClocsFileFaker
ClocsFileReader
ClusterCrosscheckMetrics
ClusterData
ClusterDataToSamConverter
ClusteredCrosscheckMetric
CollectAlignmentSummaryMetrics
CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
CollectBaseDistributionByCycle
CollectGcBiasMetrics
CollectHiSeqXPfFailMetrics
CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
CollectHiSeqXPfFailMetrics.ReadClassifier
CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
CollectHsMetrics
CollectIlluminaBasecallingMetrics
CollectIlluminaLaneMetrics
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
CollectIndependentReplicateMetrics
CollectInsertSizeMetrics
CollectJumpingLibraryMetrics
CollectMultipleMetrics
CollectMultipleMetrics.Program
CollectMultipleMetrics.ProgramInterface
CollectOxoGMetrics
CollectOxoGMetrics.CpcgMetrics
CollectQualityYieldMetrics
CollectQualityYieldMetrics.QualityYieldMetrics
CollectQualityYieldMetrics.QualityYieldMetricsCollector
CollectRawWgsMetrics
CollectRawWgsMetrics.RawWgsMetrics
CollectRnaSeqMetrics
CollectRrbsMetrics
CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
CollectSequencingArtifactMetrics
CollectTargetedMetrics
CollectTargetedPcrMetrics
CollectVariantCallingMetrics
CollectVariantCallingMetrics.VariantCallingDetailMetrics
CollectVariantCallingMetrics.VariantCallingSummaryMetrics
CollectWgsMetrics
CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
CollectWgsMetrics.WgsMetrics
CollectWgsMetrics.WgsMetricsCollector
CollectWgsMetricsWithNonZeroCoverage
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
CommandLineDefaults
CommandLineProgram
CommandLineProgramGroup
CommandLineSyntaxTranslater
CompareMetrics
CompareSAMs
ConvertSequencingArtifactToOxoG
CounterManager
CountingDuplicateFilter
CountingFilter
CountingMapQFilter
CountingPairedFilter
CreateSequenceDictionary
CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
CrosscheckFingerprints
CrosscheckMetric
CrosscheckMetric.DataType
CrosscheckMetric.FingerprintResult
CrosscheckReadGroupFingerprints
CsvInputParser
DbSnpBitSetUtil
DbSnpBitSetUtil.DbSnpBitSets
DelimitedTextFileWithHeaderIterator
DepthFilter
DiploidGenotype
DiploidHaplotype
DiskBasedReadEndsForMarkDuplicatesMap
DownsampleSam
DuplicationMetrics
EarliestFragmentPrimaryAlignmentSelectionStrategy
EmpiricalPhasingMetricsOutReader
EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
ErrorSummaryMetrics
EstimateLibraryComplexity
ExtractIlluminaBarcodes
ExtractIlluminaBarcodes.BarcodeMetric
ExtractIlluminaBarcodes.PerTileBarcodeExtractor
ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch
ExtractSequences
Fasta
FastqToSam
FastWgsMetricsCollector
FifoBuffer
FileChannelJDKBugWorkAround
FileFaker
FilterApplyingVariantIterator
FilterFileFaker
FilterFileReader
FilterSamReads
FilterSamReads.Filter
FilterVcf
FindMendelianViolations
Fingerprint
FingerprintChecker
FingerprintIdDetails
Fingerprinting
FingerprintingDetailMetrics
FingerprintingSummaryMetrics
FingerprintResults
FisherStrandFilter
FixMateInformation
FixVcfHeader
FourChannelIntensityData
GA4GHScheme
GA4GHSchemeWithMissingAsHomRef
GatherBamFiles
GatherVcfs
GcBiasDetailMetrics
GcBiasMetrics
GcBiasMetricsCollector
GcBiasSummaryMetrics
GcBiasUtils
Gene
GeneAnnotationReader
GenotypeConcordance
GenotypeConcordance.Alleles
GenotypeConcordanceContingencyMetrics
GenotypeConcordanceCounts
GenotypeConcordanceDetailMetrics
GenotypeConcordanceScheme
GenotypeConcordanceSchemeFactory
GenotypeConcordanceStateCodes
GenotypeConcordanceStates
GenotypeConcordanceStates.CallState
GenotypeConcordanceStates.ContingencyState
GenotypeConcordanceStates.TruthAndCallStates
GenotypeConcordanceStates.TruthState
GenotypeConcordanceSummaryMetrics
GenotypeFilter
GenotypeQualityFilter
GraphUtils
GraphUtils.Graph
GvcfMetricAccumulator
HaplotypeBlock
HaplotypeMap
HaplotypeProbabilities
HaplotypeProbabilities.Genotype
HaplotypeProbabilitiesFromContaminatorSequence
HaplotypeProbabilitiesFromGenotype
HaplotypeProbabilitiesFromGenotypeLikelihoods
HaplotypeProbabilitiesFromSequence
HaplotypeProbabilityOfNormalGivenTumor
HelpConstants
HsMetricCollector
HsMetrics
Illumina
IlluminaBasecallingMetrics
IlluminaBasecallsConverter
IlluminaBasecallsToFastq
IlluminaBasecallsToFastq.ReadNameFormat
IlluminaBasecallsToSam
IlluminaDataProvider
IlluminaDataProviderFactory
IlluminaDataType
IlluminaFileUtil
IlluminaFileUtil.SupportedIlluminaFormat
IlluminaLaneMetrics
IlluminaMetricsCode
IlluminaPhasingMetrics
IlluminaReadNameEncoder
IlluminaUtil
IlluminaUtil.IlluminaAdapterPair
IndependentReplicateMetric
InsertSizeMetrics
InsertSizeMetricsCollector
IntensityChannel
IntervalArgumentCollection
IntervalListScatterer
IntervalListScatterer.Mode
IntervalListToBed
IntervalListTools
IntervalListTools.Action
Intervals
Iterators
JumpingLibraryMetrics
LanePhasingMetricsCollector
LibraryIdGenerator
LiftOverIntervalList
LiftoverVcf
LocsFileFaker
LocsFileReader
LocusFunction
MakeSitesOnlyVcf
MarkDuplicates
MarkDuplicates.DuplicateTaggingPolicy
MarkDuplicates.DuplicateType
MarkDuplicatesWithMateCigar
MarkDuplicatesWithMateCigarIterator
MarkIlluminaAdapters
MarkQueue
MatchResults
MathUtil
MathUtil.LogMath
MeanQualityByCycle
MendelianViolationMetrics
MendelianViolationsByFamily
MergeableMetricBase
MergeableMetricBase.MergeByAdding
MergeableMetricBase.MergeByAssertEquals
MergeableMetricBase.MergingIsManual
MergeableMetricBase.NoMergingIsDerived
MergeableMetricBase.NoMergingKeepsValue
MergeBamAlignment
MergeSamFiles
MergeVcfs
MetricAccumulationLevel
Metrics
MMapBackedIteratorFactory
MostDistantPrimaryAlignmentSelectionStrategy
MultiLevelCollector
MultilevelMetrics
MultiTileBclFileFaker
MultiTileBclFileUtil
MultiTileBclParser
MultiTileFileUtil
MultiTileFilterParser
MultiTileLocsFileFaker
MultiTileLocsParser
MultiTileParser
NewIlluminaBasecallsConverter
NewIlluminaDataProvider
None
NonNFastaSize
NormalizeFasta
OpticalDuplicateFinder
OptionalReferenceArgumentCollection
OutputMapping
PairedVariantSubContextIterator
PairedVariantSubContextIterator.VcfTuple
ParameterizedFileUtil
PedFile
PerTileFileUtil
PerTileParser
PerTilePerCycleFileUtil
PerUnitMetricCollector
PhysicalLocation
PhysicalLocationForMateCigar
PhysicalLocationForMateCigarSet
PhysicalLocationInt
PhysicalLocationShort
PicardCommandLine
PicardException
PicardHelpDoclet
PicardHelpDocWorkUnitHandler
PosFileFaker
PosFileReader
PositionBasedDownsampleSam
PosParser
PredicateFilterDecoratingClosableIterator
PrimaryAlignmentSelectionStrategy
PropertyUtils
QdFilter
QualityScoreDistribution
QuerySortedReadPairIteratorUtil
QuerySortedReadPairIteratorUtil.ReadPair
Range
ReadData
ReadDescriptor
ReadEnds
ReadEndsForMarkDuplicates
ReadEndsForMarkDuplicatesCodec
ReadEndsForMarkDuplicatesMap
ReadEndsForMarkDuplicatesWithBarcodes
ReadEndsForMarkDuplicatesWithBarcodesCodec
ReadEndsForMateCigar
ReadNameEncoder
ReadNameParser
ReadStructure
ReadType
ReferenceArgumentCollection
RefFlatReader
RefFlatReader.RefFlatColumns
ReflectionUtil
RenameSampleInVcf
ReorderSam
ReorderSam.ReorderSamReferenceArgumentCollection
ReplaceSamHeader
RepresentativeReadIndexer
RepresentativeReadIndexerCodec
RequiredReferenceArgumentCollection
RevertOriginalBaseQualitiesAndAddMateCigar
RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
RevertSam
RevertSam.FileType
RExecutor
RnaSeqMetrics
RnaSeqMetricsCollector
RnaSeqMetricsCollector.StrandSpecificity
RrbsCpgDetailMetrics
RrbsMetricsCollector
RrbsSummaryMetrics
SamAlignmentMerger
SamFormatConverter
SamOrBam
SAMRecordAndReference
SAMRecordAndReferenceMultiLevelCollector
SAMRecordMultiLevelCollector
SamRecordWithOrdinalAndSetDuplicateReadFlag
SamToFastq
ScatterIntervalsByNs
ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
SequencingArtifactMetrics
SequencingArtifactMetrics.BaitBiasDetailMetrics
SequencingArtifactMetrics.BaitBiasSummaryMetrics
SequencingArtifactMetrics.PreAdapterDetailMetrics
SequencingArtifactMetrics.PreAdapterSummaryMetrics
SetNmAndUqTags
SetNmMdAndUqTags
Sex
SimpleMarkDuplicatesWithMateCigar
SinglePassSamProgram
Snp
SortSam
SortVcf
SplitSamByLibrary
SplitVcfs
StandardOptionDefinitions
TabbedInputParser
TabbedTextFileWithHeaderParser
TargetedPcrMetrics
TargetedPcrMetricsCollector
TargetMetricsCollector
TargetMetricsCollector.Coverage
Test
Testing
TheoreticalSensitivity
TheoreticalSensitivity.RouletteWheel
ThreadPoolExecutorWithExceptions
Tile
TileIndex
TileIndex.TileIndexRecord
TileMetricsOutReader
TileMetricsOutReader.IlluminaLaneTileCode
TileMetricsOutReader.IlluminaTileMetrics
TileMetricsOutReader.TileMetricsVersion
TileMetricsUtil
TilePhasingValue
TileTemplateRead
UmiAwareMarkDuplicatesWithMateCigar
UmiGraph
UmiMetrics
UnsignedTypeUtil
UpdateVcfSequenceDictionary
ValidateSamFile
ValidateSamFile.Mode
VariantAccumulatorExecutor
VariantAccumulatorExecutor.MultiThreadedChunkBased
VariantFilter
VariantIteratorProducer
VariantProcessor
VariantProcessor.Accumulator
VariantProcessor.AccumulatorGenerator
VariantProcessor.Builder
VariantProcessor.ResultMerger
VariantType
VcfFileSegment
VcfFileSegmentGenerator
VcfFormatConverter
VcfOrBcf
VcfToIntervalList
VcfUtils
ViewSam
ViewSam.AlignmentStatus
ViewSam.PfStatus
WgsMetricsProcessor
WgsMetricsProcessorImpl