All Classes

  • 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