All Classes
AbstractAlignmentMerger
AbstractIlluminaPositionFileReader
AbstractInputParser
AbstractMarkDuplicatesCommandLineProgram
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
AbstractOpticalDuplicateFinderCommandLineProgram
AdapterMarker
AdapterPair
AdapterUtility
AddCommentsToBam
AddOrReplaceReadGroups
AlignmentSummaryMetrics
AlignmentSummaryMetrics.Category
AlignmentSummaryMetricsCollector
AlleleBalanceFilter
Alpha
AnnotationException
AsyncIterator
AtomicIterator
BaitDesigner
BaitDesigner.DesignStrategy
BamIndexStats
BamToBfq
BamToBfqWriter
BarcodeFileFaker
BarcodeFileReader
BaseDistributionByCycleMetrics
BasicInputParser
BciFileFaker
BclData
BclFileFaker
BclIndexReader
BclQualityEvaluationStrategy
BclReader
BedToIntervalList
BestEndMapqPrimaryAlignmentStrategy
BestMapqPrimaryAlignmentSelectionStrategy
BuildBamIndex
ByIntervalListVariantContextIterator
CalculateHsMetrics
CalculateReadGroupChecksum
CallingMetricAccumulator
CallingMetricAccumulator.Result
Casava18ReadNameEncoder
CheckFingerprint
CheckIlluminaDirectory
CheckTerminatorBlock
ChimeraUtil
CircularByteBuffer
ClassFinder
CleanSam
ClippingUtility
ClocsFileFaker
ClocsFileReader
ClusterData
ClusterDataToSamConverter
CollectAlignmentSummaryMetrics
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
CollectRawWgsMetrics
CollectRawWgsMetrics.RawWgsMetrics
CollectRnaSeqMetrics
CollectRrbsMetrics
CollectSequencingArtifactMetrics
CollectTargetedMetrics
CollectTargetedPcrMetrics
CollectVariantCallingMetrics
CollectVariantCallingMetrics.VariantCallingDetailMetrics
CollectVariantCallingMetrics.VariantCallingSummaryMetrics
CollectWgsMetrics
CollectWgsMetrics.WgsMetrics
CollectWgsMetricsFromQuerySorted
CollectWgsMetricsFromQuerySorted.FILTERING_STRINGENCY
CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
CollectWgsMetricsFromSampledSites
CollectWgsMetricsFromSampledSites.SampledWgsMetrics
CollectWgsMetricsWithNonZeroCoverage
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
CommandLineDefaults
CommandLineParseException
CommandLineParser
CommandLineParser.ClpEnum
CommandLineParser.OptionDefinition
CommandLineParser.OptionDefinitionByPrintOrderComparator
CommandLineParserDefinitionException
CommandLineProgram
CommandLineProgramGroup
CommandLineProgramProperties
CompareMetrics
CompareSAMs
ConvertSequencingArtifactToOxoG
CountingDuplicateFilter
CountingFilter
CountingMapQFilter
CountingPairedFilter
CreateHtmlDocForProgram
CreateHtmlDocForStandardOptions
CreateSequenceDictionary
CrosscheckReadGroupFingerprints
CsvInputParser
DbSnpBitSetUtil
DbSnpBitSetUtil.DbSnpBitSets
DelimitedTextFileWithHeaderIterator
DepthFilter
DiploidGenotype
DiploidHaplotype
DiskBasedReadEndsForMarkDuplicatesMap
DownsampleSam
DuplicationMetrics
EarliestFragmentPrimaryAlignmentSelectionStrategy
ErrorSummaryMetrics
EstimateLibraryComplexity
ExtractIlluminaBarcodes
ExtractIlluminaBarcodes.BarcodeMetric
ExtractSequences
Fasta
FastqToSam
FifoBuffer
FileChannelJDKBugWorkAround
FileFaker
FilterApplyingVariantIterator
FilterFileFaker
FilterFileReader
FilterSamReads
FilterSamReads.Filter
FilterVcf
Fingerprint
FingerprintChecker
Fingerprinting
FingerprintingDetailMetrics
FingerprintingSummaryMetrics
FingerprintResults
FisherStrandFilter
FixMateInformation
FixVcfHeader
FourChannelIntensityData
GA4GHScheme
GA4GHSchemeWithMissingAsHomRef
GatherBamFiles
GatherVcfs
GcBiasDetailMetrics
GcBiasMetrics
GcBiasMetricsCollector
GcBiasSummaryMetrics
GcBiasUtils
Gene
GeneAnnotationReader
GenotypeConcordance
GenotypeConcordanceContingencyMetrics
GenotypeConcordanceCounts
GenotypeConcordanceDetailMetrics
GenotypeConcordanceScheme
GenotypeConcordanceSchemeFactory
GenotypeConcordanceStateCodes
GenotypeConcordanceStates
GenotypeConcordanceStates.CallState
GenotypeConcordanceStates.ContingencyState
GenotypeConcordanceStates.TruthAndCallStates
GenotypeConcordanceStates.TruthState
GenotypeConcordanceSummaryMetrics
GenotypeFilter
GenotypeQualityFilter
GenotypeReader
GenotypeReader.VariantIterator
GvcfMetricAccumulator
HaplotypeBlock
HaplotypeMap
HaplotypeProbabilities
HaplotypeProbabilities.Genotype
HaplotypeProbabilitiesFromContaminatorSequence
HaplotypeProbabilitiesFromGenotype
HaplotypeProbabilitiesFromGenotypeLikelihoods
HaplotypeProbabilitiesFromSequence
HaplotypeProbabilityOfNormalGivenTumor
HsMetricCollector
HsMetrics
Illumina
IlluminaBasecallingMetrics
IlluminaBasecallsConverter
IlluminaBasecallsConverter.ClusterDataConverter
IlluminaBasecallsConverter.ConvertedClusterDataWriter
IlluminaBasecallsToFastq
IlluminaBasecallsToFastq.ReadNameFormat
IlluminaBasecallsToSam
IlluminaDataProvider
IlluminaDataProviderFactory
IlluminaDataType
IlluminaFileUtil
IlluminaFileUtil.SupportedIlluminaFormat
IlluminaLaneMetrics
IlluminaMetricsCode
IlluminaPhasingMetrics
IlluminaReadNameEncoder
IlluminaUtil
IlluminaUtil.IlluminaAdapterPair
IndependentReplicateMetric
InsertSizeMetrics
InsertSizeMetricsCollector
IntensityChannel
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
MergeableMetricBase
MergeableMetricBase.MergeByAdding
MergeableMetricBase.MergeByAssertEquals
MergeableMetricBase.MergingIsManual
MergeableMetricBase.NoMergingIsDerived
MergeableMetricBase.NoMergingKeepsValue
MergeBamAlignment
MergeSamFiles
MergeVcfs
MetricAccumulationLevel
Metrics
MetricsDoclet
MMapBackedIteratorFactory
MostDistantPrimaryAlignmentSelectionStrategy
MultiLevelCollector
MultilevelMetrics
MultiTileBclFileFaker
MultiTileBclFileUtil
MultiTileBclParser
MultiTileFileUtil
MultiTileFilterParser
MultiTileLocsFileFaker
MultiTileLocsParser
MultiTileParser
NestedOptions
None
NonNFastaSize
NormalizeFasta
OpticalDuplicateFinder
Option
OutputMapping
PairedVariantSubContextIterator
PairedVariantSubContextIterator.VcfTuple
ParameterizedFileUtil
PedFile
PerTileFileUtil
PerTileParser
PerTilePerCycleFileUtil
PerUnitMetricCollector
PhysicalLocation
PhysicalLocationForMateCigar
PhysicalLocationForMateCigarSet
PhysicalLocationInt
PhysicalLocationShort
PicardCommandLine
PicardException
PosFileFaker
PosFileReader
PositionalArguments
PositionBasedDownsampleSam
PosParser
PredicateFilterDecoratingClosableIterator
PrimaryAlignmentSelectionStrategy
QdFilter
QualityScoreDistribution
QuerySortedReadPairIteratorUtil
QuerySortedReadPairIteratorUtil.ReadPair
Range
ReadData
ReadDescriptor
ReadEnds
ReadEndsForMarkDuplicates
ReadEndsForMarkDuplicatesCodec
ReadEndsForMarkDuplicatesMap
ReadEndsForMarkDuplicatesWithBarcodes
ReadEndsForMarkDuplicatesWithBarcodesCodec
ReadEndsForMateCigar
ReadNameEncoder
ReadNameParser
ReadStructure
ReadType
RefFlatReader
RefFlatReader.RefFlatColumns
RenameSampleInVcf
ReorderSam
ReplaceSamHeader
RevertOriginalBaseQualitiesAndAddMateCigar
RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
RevertSam
RevertSam.FileType
RExecutor
RnaSeqMetrics
RnaSeqMetricsCollector
RnaSeqMetricsCollector.StrandSpecificity
RrbsCpgDetailMetrics
RrbsMetricsCollector
RrbsSummaryMetrics
SamAlignmentMerger
SamFormatConverter
SamOrBam
SAMRecordAndReference
SAMRecordAndReferenceMultiLevelCollector
SAMRecordMultiLevelCollector
SamRecordWithOrdinalAndSetDuplicateReadFlag
SamToFastq
ScatterIntervalsByNs
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
Tile
TileIndex
TileIndex.TileIndexRecord
TileMetricsOutReader
TileMetricsOutReader.IlluminaLaneTileCode
TileMetricsOutReader.IlluminaTileMetrics
TileMetricsUtil
TilePhasingValue
TileTemplateRead
UmiAwareMarkDuplicatesWithMateCigar
UmiGraph
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
ViewSam
ViewSam.AlignmentStatus
ViewSam.PfStatus