- AbstractAlignmentMerger
- AbstractAlignmentMerger.UnmappingReadStrategy
- AbstractIlluminaPositionFileReader
- AbstractInputParser
- AbstractMarkDuplicatesCommandLineProgram
- AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
- AbstractOpticalDuplicateFinderCommandLineProgram
- AbstractWgsMetricsCollector
- AccumulateQualityYieldMetrics
- AccumulateVariantCallingMetrics
- AdapterMarker
- AdapterPair
- AdapterUtility
- AddCommentsToBam
- AddOATag
- AddOrReplaceReadGroups
- AlignmentSummaryMetrics
- AlignmentSummaryMetrics.Category
- AlignmentSummaryMetricsCollector
- AlleleBalanceFilter
- AlleleSubsettingUtils
- AnnotationException
- ArraysControlInfo
- AsyncIterator
- AtomicIterator
- BafRegressMetrics
- BaitDesigner
- BaitDesigner.DesignStrategy
- BamIndexStats
- BamToBfq
- BamToBfqWriter
- BarcodeEditDistanceQuery
- BarcodeExtractor
- BarcodeExtractor.BarcodeMatch
- BarcodeFileFaker
- BarcodeFileReader
- BarcodeMetric
- BaseBclReader
- BaseCalculator
- BaseCallingProgramGroup
- BasecallsConverter
- BasecallsConverter.ClusterDataConverter
- BasecallsConverter.ConvertedClusterDataWriter
- BasecallsConverterBuilder
- BaseDistributionByCycleMetrics
- BaseErrorAggregation
- BaseErrorCalculator
- BaseErrorMetric
- BaseIlluminaDataProvider
- BasicInputParser
- BciFileFaker
- BclData
- BclFileFaker
- BclIndexFaker
- BclIndexReader
- BclQualityEvaluationStrategy
- BclReader
- BedToIntervalList
- BestEndMapqPrimaryAlignmentStrategy
- BestMapqPrimaryAlignmentSelectionStrategy
- BpmToNormalizationManifestCsv
- Build37ExtendedIlluminaManifest
- Build37ExtendedIlluminaManifestRecord
- Build37ExtendedIlluminaManifestRecord.Flag
- Build37ExtendedIlluminaManifestRecordCreator
- BuildBamIndex
- ByIntervalListVariantContextIterator
- CalculateFingerprintMetrics
- CalculateReadGroupChecksum
- CallingMetricAccumulator
- CallingMetricAccumulator.Result
- CappedHaplotypeProbabilities
- Casava18ReadNameEncoder
- CbclData
- CbclReader
- CheckDuplicateMarking
- CheckDuplicateMarking.Mode
- CheckFingerprint
- CheckIlluminaDirectory
- CheckTerminatorBlock
- ChimeraUtil
- CircularByteBuffer
- ClassFinder
- CleanSam
- ClippingUtility
- ClocsFileFaker
- ClocsFileReader
- ClusterCrosscheckMetrics
- ClusterData
- ClusterDataToSamConverter
- ClusteredCrosscheckMetric
- CollectAlignmentSummaryMetrics
- CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
- CollectArraysVariantCallingMetrics
- CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
- CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
- CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
- CollectBaseDistributionByCycle
- CollectDuplicateMetrics
- 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
- CollectQualityYieldMetrics.QualityYieldMetricsFlow
- CollectRawWgsMetrics
- CollectRawWgsMetrics.RawWgsMetrics
- CollectRnaSeqMetrics
- CollectRrbsMetrics
- CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
- CollectSamErrorMetrics
- CollectSequencingArtifactMetrics
- CollectTargetedMetrics
- CollectTargetedPcrMetrics
- CollectVariantCallingMetrics
- CollectVariantCallingMetrics.VariantCallingDetailMetrics
- CollectVariantCallingMetrics.VariantCallingSummaryMetrics
- CollectWgsMetrics
- CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
- CollectWgsMetrics.WgsMetricsCollector
- CollectWgsMetricsWithNonZeroCoverage
- CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
- CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
- CombineGenotypingArrayVcfs
- CommandLineDefaults
- CommandLineProgram
- CommandLineSyntaxTranslater
- CompareGtcFiles
- CompareMetrics
- CompareSAMs
- ConvertHaplotypeDatabaseToVcf
- ConvertSequencingArtifactToOxoG
- CounterManager
- CountingAdapterFilter
- CountingDuplicateFilter
- CountingFilter
- CountingMapQFilter
- CountingPairedFilter
- CreateBafRegressMetricsFile
- CreateExtendedIlluminaManifest
- CreateSequenceDictionary
- CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
- CreateVerifyIDIntensityContaminationMetricsFile
- CrosscheckFingerprints
- CrosscheckMetric
- CrosscheckMetric.DataType
- CrosscheckMetric.FingerprintResult
- CrosscheckReadGroupFingerprints
- CsvInputParser
- DbSnpBitSetUtil
- DbSnpBitSetUtil.DbSnpBitSets
- DelimitedTextFileWithHeaderIterator
- DepthFilter
- DiagnosticsAndQCProgramGroup
- DiploidGenotype
- DiploidHaplotype
- DiskBasedReadEndsForMarkDuplicatesMap
- DistanceMetric
- DownsampleSam
- DuplicationMetrics
- DuplicationMetricsFactory
- EarliestFragmentPrimaryAlignmentSelectionStrategy
- EmpiricalPhasingMetricsOutReader
- EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
- EmptyOutputArgumentCollection
- ErrorMetric
- ErrorSummaryMetrics
- EstimateLibraryComplexity
- ExtractBarcodesProgram
- ExtractFingerprint
- ExtractIlluminaBarcodes
- ExtractIlluminaBarcodes.PerTileBarcodeExtractor
- ExtractSequences
- FastqToSam
- FastWgsMetricsCollector
- FifoBuffer
- FileFaker
- FilterApplyingVariantIterator
- FilterFileFaker
- FilterFileReader
- FilterSamReads
- FilterSamReads.Filter
- FilterVcf
- FindMendelianViolations
- Fingerprint
- FingerprintChecker
- FingerprintIdDetails
- FingerprintingDetailMetrics
- FingerprintingSummaryMetrics
- FingerprintMetrics
- FingerprintResults
- FingerprintUtils
- FingerprintUtils.VariantContextSet
- FisherStrandFilter
- FixMateInformation
- FixVcfHeader
- FlowBasedDuplicationMetrics
- 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
- GenotypingArraysProgramGroup
- GraphUtils
- GraphUtils.Graph
- GtcToVcf
- GvcfMetricAccumulator
- HaplotypeBlock
- HaplotypeMap
- HaplotypeProbabilities
- HaplotypeProbabilities.Genotype
- HaplotypeProbabilitiesFromContaminatorSequence
- HaplotypeProbabilitiesFromGenotype
- HaplotypeProbabilitiesFromGenotypeLikelihoods
- HaplotypeProbabilitiesFromSequence
- HaplotypeProbabilityOfNormalGivenTumor
- HelpConstants
- HsMetricCollector
- HsMetrics
- IdentifyContaminant
- IlluminaAdpcFileWriter
- IlluminaAdpcFileWriter.Record
- IlluminaBasecallingMetrics
- IlluminaBasecallsToFastq
- IlluminaBasecallsToFastq.ReadNameFormat
- IlluminaBasecallsToSam
- IlluminaBPMFile
- IlluminaBPMLocusEntry
- IlluminaDataProviderFactory
- IlluminaDataType
- IlluminaFileUtil
- IlluminaFileUtil.SupportedIlluminaFormat
- IlluminaGenotype
- IlluminaLaneMetrics
- IlluminaManifest
- IlluminaManifestRecord
- IlluminaManifestRecord.IlluminaStrand
- IlluminaMetricsCode
- IlluminaPhasingMetrics
- IlluminaReadNameEncoder
- IlluminaUtil
- IlluminaUtil.IlluminaAdapterPair
- IndelErrorCalculator
- IndelErrorMetric
- IndependentReplicateMetric
- InfiniumDataFile
- InfiniumEGTFile
- InfiniumFileTOC
- InfiniumGTCFile
- InfiniumGTCRecord
- InfiniumNormalizationManifest
- InfiniumTransformation
- InfiniumVcfFields
- InfiniumVcfFields.GENOTYPE_VALUES
- InsertSizeMetrics
- InsertSizeMetricsCollector
- IntensityChannel
- IntervalArgumentCollection
- IntervalListScatter
- IntervalListScatterer
- IntervalListScattererByBaseCount
- IntervalListScattererByIntervalCount
- IntervalListScattererByIntervalCountWithDistributedRemainder
- IntervalListScattererWithoutSubdivision
- IntervalListScattererWithoutSubdivisionWithOverflow
- IntervalListScattererWithSubdivision
- IntervalListScatterMode
- IntervalListToBed
- IntervalListTools
- IntervalListTools.Action
- IntervalsManipulationProgramGroup
- Iterators
- JumpingLibraryMetrics
- LanePhasingMetricsCollector
- LibraryIdGenerator
- LiftOverHaplotypeMap
- LiftOverIntervalList
- LiftoverUtils
- LiftoverVcf
- LocsFileFaker
- LocsFileReader
- LocusFunction
- MakeSitesOnlyVcf
- MakeVcfSampleNameMap
- MarkDuplicates
- MarkDuplicates.DuplicateTaggingPolicy
- MarkDuplicates.DuplicateType
- MarkDuplicatesForFlowArgumentCollection
- MarkDuplicatesForFlowHelper
- MarkDuplicatesHelper
- MarkDuplicatesWithMateCigar
- MarkDuplicatesWithMateCigarIterator
- MarkIlluminaAdapters
- MarkQueue
- MatchResults
- MathUtil
- MathUtil.LogMath
- MeanQualityByCycle
- MemoryBasedReadEndsForMarkDuplicatesMap
- MendelianViolationMetrics
- MendelianViolationsByFamily
- MergeableMetricBase
- MergeableMetricBase.MergeByAdding
- MergeableMetricBase.MergeByAssertEquals
- MergeableMetricBase.MergingIsManual
- MergeableMetricBase.NoMergingIsDerived
- MergeableMetricBase.NoMergingKeepsValue
- MergeBamAlignment
- MergePedIntoVcf
- MergeSamFiles
- MergeVcfs
- MetricAccumulationLevel
- MMapBackedIteratorFactory
- MostDistantPrimaryAlignmentSelectionStrategy
- MultiLevelCollector
- MultilevelMetrics
- MultiTileBclFileFaker
- MultiTileBclFileUtil
- MultiTileBclParser
- MultiTileFileUtil
- MultiTileFilterParser
- MultiTileLocsFileFaker
- MultiTileLocsParser
- MultiTileParser
- NonNFastaSize
- NormalizeFasta
- OpticalDuplicateFinder
- OptionalReferenceArgumentCollection
- OtherProgramGroup
- OutputArgumentCollection
- OutputMapping
- OverlappingErrorMetric
- OverlappingReadsErrorCalculator
- Pair
- PairedVariantSubContextIterator
- PairedVariantSubContextIterator.VcfTuple
- PanelMetricsBase
- ParameterizedFileUtil
- PathProvider
- PedFile
- PerTileFileUtil
- PerTileOrPerRunFileUtil
- PerTileParser
- PerTilePerCycleFileUtil
- PerUnitMetricCollector
- PGTagArgumentCollection
- PhysicalLocation
- PhysicalLocationForMateCigar
- PhysicalLocationForMateCigarSet
- PhysicalLocationInt
- PhysicalLocationShort
- PicardCommandLine
- PicardException
- PicardHtsPath
- PosFileFaker
- PosFileReader
- PositionBasedDownsampleSam
- PosParser
- PredicateFilterDecoratingClosableIterator
- PrimaryAlignmentKey
- PrimaryAlignmentSelectionStrategy
- PropertyUtils
- QdFilter
- QualityScoreDistribution
- QuerySortedReadPairIteratorUtil
- QuerySortedReadPairIteratorUtil.ReadPair
- Range
- ReadBaseStratification
- ReadBaseStratification.BinnedReadCycleStratifier
- ReadBaseStratification.CigarOperatorsInReadStratifier
- ReadBaseStratification.CollectionStratifier
- ReadBaseStratification.Consensus
- ReadBaseStratification.ConsensusStratifier
- ReadBaseStratification.CycleBin
- ReadBaseStratification.FlowCellTileStratifier
- ReadBaseStratification.FlowCellXStratifier
- ReadBaseStratification.FlowCellYStratifier
- ReadBaseStratification.GCContentStratifier
- ReadBaseStratification.IndelLengthStratifier
- ReadBaseStratification.IndelsInReadStratifier
- ReadBaseStratification.LongShortHomopolymer
- ReadBaseStratification.LongShortHomopolymerStratifier
- ReadBaseStratification.MismatchesInReadStratifier
- ReadBaseStratification.NsInReadStratifier
- ReadBaseStratification.PairOrientation
- ReadBaseStratification.PairStratifier
- ReadBaseStratification.ProperPaired
- ReadBaseStratification.ReadDirection
- ReadBaseStratification.ReadOrdinality
- ReadBaseStratification.RecordAndOffsetStratifier
- ReadData
- ReadDataManipulationProgramGroup
- ReadDescriptor
- ReadEnds
- ReadEndsForMarkDuplicates
- ReadEndsForMarkDuplicatesCodec
- ReadEndsForMarkDuplicatesMap
- ReadEndsForMarkDuplicatesWithBarcodes
- ReadEndsForMarkDuplicatesWithBarcodesCodec
- ReadEndsForMateCigar
- ReadNameEncoder
- ReadNameParser
- ReadStructure
- ReadType
- ReferenceArgumentCollection
- ReferenceProgramGroup
- RefFlatReader
- RefFlatReader.RefFlatColumns
- ReflectionUtil
- RenameSampleInVcf
- ReorderSam
- ReplaceSamHeader
- RepresentativeReadIndexer
- RepresentativeReadIndexerCodec
- RequiredOutputArgumentCollection
- RequiredReferenceArgumentCollection
- RevertOriginalBaseQualitiesAndAddMateCigar
- RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
- RevertSam
- RevertSam.FileType
- RExecutor
- RnaSeqMetrics
- RnaSeqMetricsCollector
- RnaSeqMetricsCollector.StrandSpecificity
- RrbsCpgDetailMetrics
- RrbsMetricsCollector
- RrbsSummaryMetrics
- SamAlignmentMerger
- SamComparison
- SamComparison.AlignmentComparison
- SAMComparisonArgumentCollection
- SamComparisonMetric
- SamFormatConverter
- SAMRecordAndReference
- SAMRecordAndReferenceMultiLevelCollector
- SAMRecordMultiLevelCollector
- SamRecordWithOrdinalAndSetDuplicateReadFlag
- SamToBfqWriter
- SamToFastq
- SamToFastqWithTags
- ScatterIntervalsByNs
- ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
- SequenceDictionaryUtils
- SequenceDictionaryUtils.SamSequenceRecordsIterator
- SequencingArtifactMetrics
- SequencingArtifactMetrics.BaitBiasDetailMetrics
- SequencingArtifactMetrics.BaitBiasSummaryMetrics
- SequencingArtifactMetrics.PreAdapterDetailMetrics
- SequencingArtifactMetrics.PreAdapterSummaryMetrics
- SetNmAndUqTags
- SetNmMdAndUqTags
- Sex
- SimpleErrorCalculator
- SimpleMarkDuplicatesWithMateCigar
- SingleBarcodeDistanceMetric
- SinglePassSamProgram
- Snp
- SortedBasecallsConverter
- SortGff
- SortSam
- SortVcf
- SplitSamByLibrary
- SplitSamByNumberOfReads
- SplitVcfs
- StandardOptionDefinitions
- TabbedInputParser
- TabbedTextFileWithHeaderParser
- TargetedPcrMetrics
- TargetedPcrMetricsCollector
- TargetMetrics
- TargetMetricsBase
- TargetMetricsCollector
- TargetMetricsCollector.Coverage
- Test
- Testing
- TheoreticalSensitivity
- TheoreticalSensitivity.RouletteWheel
- TheoreticalSensitivityMetrics
- ThreadPoolExecutorUtil
- ThreadPoolExecutorWithExceptions
- Tile
- TileIndex
- TileIndex.TileIndexRecord
- TileMetricsOutReader
- TileMetricsOutReader.IlluminaLaneTileCode
- TileMetricsOutReader.IlluminaTileMetrics
- TileMetricsOutReader.TileMetricsVersion
- TileMetricsUtil
- TilePhasingValue
- TileTemplateRead
- Transition
- Transition.Base
- UmiAwareMarkDuplicatesWithMateCigar
- UmiGraph
- UmiMetrics
- UnsignedTypeUtil
- UnsortedBasecallsConverter
- UpdateVcfSequenceDictionary
- ValidateSamFile
- ValidateSamFile.Mode
- VariantAccumulatorExecutor
- VariantAccumulatorExecutor.MultiThreadedChunkBased
- VariantEvaluationProgramGroup
- VariantFilter
- VariantFilteringProgramGroup
- VariantIteratorProducer
- VariantManipulationProgramGroup
- VariantProcessor
- VariantProcessor.Accumulator
- VariantProcessor.AccumulatorGenerator
- VariantProcessor.Builder
- VariantProcessor.ResultMerger
- VariantType
- VcfFileSegment
- VcfFileSegmentGenerator
- VcfFormatConverter
- VcfPathSegment
- VcfPathSegmentGenerator
- VcfToAdpc
- VcfToIntervalList
- VcfToIntervalList.VARIANT_ID_TYPES
- VcfUtils
- VerifyIDIntensityContaminationMetrics
- ViewSam
- ViewSam.AlignmentStatus
- ViewSam.PfStatus
- WgsMetrics
- WgsMetricsProcessor
- WgsMetricsProcessorImpl