All Classes
AbstractAlignmentEntryFilter
AbstractAlignmentReader
AbstractAlignmentToCompactMode
AbstractCommandLineMode
AbstractConcatAlignmentReader
AbstractGobyMode
AbstractMethylationAdapter
AbstractOutputFormat
AggregatePeaksByPeakDistanceMode
AggregatePeaksByRPKMDifferenceMode
AlignedCountNormalization
AlignedSequence
AlignmentCollectionHandler
AlignmentHelper
AlignmentPositionComparator
AlignmentProcessorFactory
AlignmentProcessorInterface
AlignmentQualityFilter
AlignmentReader
AlignmentReaderFactory
AlignmentReaderImpl
Alignments
Alignments.AlignmentCollection
Alignments.AlignmentCollection.Builder
Alignments.AlignmentCollectionOrBuilder
Alignments.AlignmentEntry
Alignments.AlignmentEntry.Builder
Alignments.AlignmentEntryOrBuilder
Alignments.AlignmentHeader
Alignments.AlignmentHeader.Builder
Alignments.AlignmentHeaderOrBuilder
Alignments.AlignmentIndex
Alignments.AlignmentIndex.Builder
Alignments.AlignmentIndexOrBuilder
Alignments.AlignmentTooManyHits
Alignments.AlignmentTooManyHits.Builder
Alignments.AlignmentTooManyHitsOrBuilder
Alignments.AmbiguousLocation
Alignments.AmbiguousLocation.Builder
Alignments.AmbiguousLocationOrBuilder
Alignments.IdentifierInfo
Alignments.IdentifierInfo.Builder
Alignments.IdentifierInfoOrBuilder
Alignments.IdentifierMapping
Alignments.IdentifierMapping.Builder
Alignments.IdentifierMappingOrBuilder
Alignments.ReadOriginInfo
Alignments.ReadOriginInfo.Builder
Alignments.ReadOriginInfoOrBuilder
Alignments.RelatedAlignmentEntry
Alignments.RelatedAlignmentEntry.Builder
Alignments.RelatedAlignmentEntryOrBuilder
Alignments.SequenceVariation
Alignments.SequenceVariation.Builder
Alignments.SequenceVariationOrBuilder
AlignmentSliceHelper
AlignmentStats
AlignmentTooManyHitsReader
AlignmentTooManyHitsWriter
AlignmentToPileupMode
AlignmentToPileupMode.OutputFormat
AlignmentToTextMode
AlignmentToTextWriter
AlignmentWriter
AlignmentWriterImpl
AlleleFrequencyOutputFormat
Annotation
AnnotationAveragingWriter
AnnotationCount
AnnotationCountInterface
AnnotationCountIterateAlignments
AnnotationLength
AnnotationPenaltyMode
AnnotationRPKM
AnnotationsToCountsMode
AnnotationWeightCount
AnyTransitionCountsIterator
ATGCCorrectionWeight
AtLeastAQuarterFilter
ATProportionWeight
AverageCalculator
AverageFisherRCalculator
BarcodeDecoderMode
BarcodeMatcher
BarcodeMatcherResult
BaseProportionWeight
BaseStatsMode
BenjaminiHochbergAdjustment
BestScoreAmbiguityAlignmentFilter
BestScoreOnlyAlignmentFilter
BetweenGroupSequenceVariationOutputFormat
BinningStrategy
BisulfiteConversionMode
BonferroniAdjustment
BranchingDetectorMode
BufferedSortingAlignmentWriter
BufferedSortingSamBamWriter
BuggyDeltaStatisticAdaptor
BuildSequenceCacheMode
BullardUpperQuartileNormalization
By5BinningStrategy
BZip2ChunkCodec
CachingCountsArchiveReader
ChiSquareTestAdaptor
ChiSquareTestCalculator
ChunkCodec
ChunkCodecHelper
CodecHelper
ColorSpaceConverter
ColumnField
ColumnFields
ColumnInfo
ColumnMetaInfo
Columns
ColumnType
CommonIndelArtifactFilter
CompactAlignmentToAnnotationCountsMode
CompactAlignmentToCountsMode
CompactAlignmentToReadSetMode
CompactAlignmentToTranscriptCountsMode
CompactFileStatsMode
CompactToFastaMode
CompactToFastaMode.OutputFormat
CompactToSAMMode
CompareGroupsVCFOutputFormat
CompressedRead
ComputeCount
ComputeCountInterface
ComputeStartCount
ComputeWeightCount
ConcatAlignmentReader
ConcatenateAlignmentMode
ConcatenateCompactReadsMode
ConcatenatePermutations
ConcatSortedAlignmentReader
CountAdaptiveBinningAdaptor
CountArchiveToPeakAnnotationsMode
CountBinningAdapterI
CountBinningAdaptor
CountCalculator
CountFixer
CountFixerInterface
CountFixerNoThresholdingEffect
CountIndexBuilder
CountRawSampleIdsCalculator
CountsAggregatorI
CountsArchiveReader
CountsArchiveToBedGraphMode
CountsArchiveToUnionPeaksAnnotationMode
CountsArchiveToWiggleMode
CountsArchiveWriter
CountsReader
CountsReaderI
CountsWriter
CountsWriterHelperI
CountsWriterI
CountWriterHelper
CountWriterHelper2
CovariateInfo
CovariateStrategy
CoverageAnalysis
CoverageMode
CumulativeArrayKeeperFast
DataProvider
DefaultAlignmentProcessorFactory
DefaultAlignmentReaderFactory
DeltaStatisticAdaptor
DeNovoDMRfinder
DiffAlignmentMode
DifferentialExpressionAnalysis
DifferentialExpressionCalculator
DifferentialExpressionCalculator.ElementType
DifferentialExpressionInfo
DifferentialExpressionResults
DifferentiallyMethylatedRegion
DifferentiallyMethylatedRegion
DiploidFilter
DiscoverSequenceVariantsMode
DiscoverVariantIterateSortedAlignments
DiscoverVariantPositionData
DisplaySequenceVariationsMode
DistinctIntValueCounterBitSet
DistinctIntValueCounterInterface
DoInParallel
DualRandomAccessSequenceCache
DummyFormatConfigurator
DummyObservationWriter
DummyProcessor
DummyProcessorUnsorted
DumpTargetInfo
DynamicOptionClient
DynamicOptionRegistry
ElementIndexComparator
EmpiricalPMode
EmpiricalPValueEstimator
EntropicIndelArtifactFilter
EntryFlagHelper
EquivalentIndelRegion
EquivalentIndelRegionCalculator
EstimatedDistribution
EstimatedTestDistributions
EvidenceCombinator
ExportableAlignmentEntryData
ExportSplicingEvents
ExtractSplicingEventsMode
FalseDiscoveryRateMode
FastArithmeticCoder
FastArithmeticCoderI
FastArithmeticCoderOrder1
FastArithmeticCoderPlus
FastArithmeticDecoder
FastArithmeticDecoderI
FastArithmeticDecoderOrder1
FastArithmeticDecoderPlus
FastaToCompactMode
FastBufferedMessageChunksReader
FastSmallAndLog10BinningStrategy
FastXEntry
FastXReader
FDRAdjustment
FenwickTree
FileExtensionHelper
FileExtensionHelper.CompactFileType
FileSlice
FilesToAttributesMode
FisherExact
FisherExact.AlternativeHypothesis
FisherExact.Result
FisherExactRCalculator
FisherExactTestAdaptor
FisherExactTestCalculator
FoldChangeCalculator
FoldChangeForExonPairs
FoldChangeMagnitudeCalculator
FormatConfigurator
FormatFieldCounter
FormulaWeightAnnotationCount
FormulaWeightAnnotationCount.FormulaChoice
FormulaWeightCount
FrequencyTable
GCProportionWeight
GenericToolsDriver
GenomicRange
GenotypeFilter
GenotypesOutputFormat
GobyConfiguration
GobyDriver
GobyException
GobyQuickSeqvar
GobyRengine
GobyRuntimeException
GobySamRecord
GobySamSegment
GobyVersion
GrepReader
GroupAssociations
GroupComparison
GZipChunkCodec
GzipOutputStreamWithCustomLevel
HeaderUtil
HeptamerInfo
HeptamerWeight
HeptamerWeightsMode
HiCMerge
HitBoundedPriorityQueue
HybridChunkCodec1
HybridChunkCodec2
IndelCountOutputFormat
InfoForTarget
InfoOutput
InformativeColumns
InformativeDouble
InformativeNonZeroNonNaN
Interval
InvalidChecksumException
IOUtil
IsDone
IterateAlignments
IterateAlignmentsCodeSample
IterateSortedAlignments
IterateSortedAlignmentsListImpl
IterateSortedAlignmentsListImpl2
IterateSortedAlignmentsToPileup
LastParser
LastToCompactMode
LeftOverFilter
LinearBinningStrategy
LocalSortProcessor
Log10BinningStrategy
Log2BinningStrategy
Log2FoldChangeCalculator
LogGCCorrectionWeight
LoggingOutputStream
LongNamedCounter
MakeBisulfiteFastaExample
MaxCombinator
MedianCombinator
Merge
MergeCompactAlignmentsMode
MessageChunksReader
MessageChunksWriter
MethylationData
MethylationFormat
MethylationRateDifferenceStatisticAdaptor
MethylationRateVCFOutputFormat
MethylationRegion
MethylationRegionsOutputFormat
MethylationSimilarityMatch
MethylationSite
MethylationSiteIterator
MethylCountInfo
MethylCountProvider
MethylCountProviderFromRegionsOutputFormat
MethylCountProviderTestSupport
MethylRateInfo
MethylSimilarityScan
MethylStats
MethylStatsMode
MinCombinator
ModifyAlignmentsCodeSample
MotifMatcher
MoveToFrontCoder
MultiReads
NamedCounters
NonAmbiguousAlignmentReader
NonAmbiguousAlignmentReaderFactory
NoOpPermutation
NoOpPermutationReader
NormalizationMethod
NotCompressedChunkCodec
NoUpgradeAlignmentReaderFactory
NullChunkCodec
NullResettableObjectPool
ObservationWriter
ObservationWriter.TypeOfPair
ObservedIndel
OffsetCountsReader
OneBinStrategy
OutputInfo
OutputInfoFromWriter
OverlapResult
ParseAlignmentEntriesCodeSample
ParseAlignmentEntriesWithIndexCodeSample
ParseReadsCodeSample
PassThroughStatisticAdaptor
Peak
PeakAggregator
PercentMismatchesQualityFilter
PermutationReader
PermutationReaderInterface
PermutationWriter
PicardFastaIndexedSequence
PlantIndels
PositionAdapter
PositionBaseInfo
PositionFacadeAlignmentReader
PositionToBasesMap
PostBarcodeMatcher
PreBarcodeMatcher
PrintWeights
ProtobuffCollectionHandler
PTestMciProviderStatisticAdaptor
PTestStatisticAdaptor
PVAlueProvider
QFast
QualityEncoding
QualityScoreFilter
QueryIndexPermutation
QueryIndexPermutationInterface
QueueResettableObjectPool
RandomAccessAnnotations
RandomAccessSequenceCache
RandomAccessSequenceInterface
RandomAccessSequenceTestSupport
Range
Ranges
Read
Read.ReadSortByEnd
Read.ReadSortByStart
ReadCodec
ReadCodec2
ReadCodecImpl
ReadGroupHelper
ReadIndexStats
ReadNameToIndex
ReadOriginInfo
ReadProtobuffCollectionHandler
ReadQualityStatsMode
Reads
Reads.MetaData
Reads.MetaData.Builder
Reads.MetaDataOrBuilder
Reads.ReadCollection
Reads.ReadCollection.Builder
Reads.ReadCollectionOrBuilder
Reads.ReadEntry
Reads.ReadEntry.Builder
Reads.ReadEntryOrBuilder
ReadSet
ReadSetToTextMode
ReadsLoader
ReadsReader
ReadsToText
ReadsToTextWriter
ReadsToWeightsMode
ReadsWriter
ReadsWriterImpl
ReadWithIndex
RealignmentProcessor
ReferenceLocation
ReformatCompactReadsMode
RegionAveragingWriter
RegionWriter
RegisterThis
Release1_9_7_2
RemoveIndelArtifactsFilter
RenameWeights
RepositionableInputStream
Resettable
ResettableObjectPoolInterface
RpkmLikeNormalizationMethod
RunParallelMode
SamComparison
SamComparisonInterface
SAMComparisonMode
SamExtractReadsMode
SamHelper
SamPerPositionComparison
SampleCountCalculator
SampleCountInfo
SamplePair
SamplePairEnumerator
SampleQualityScoresMode
SampleStats
SampleTotalCount
SamRecordGenomicPositionComparator
SAMRecordIterable
SamRecordParser
SAMToCompactMode
SAMToCompactOldMode
SAMToCompactSamHelperMode
ScanReferenceSequence
Segment
SequenceDigests
SequenceEncoder
SequenceVariationOutputFormat
SequenceVariationPool
SequenceVariationStats2Mode
SequenceVariationStatsMode
SimulateBisulfiteReads
SimulateReadsMode
SitesInFixedWindow
SkipToListIterator
SkipToSortedReader
SlidingCountArray
SmallAndLog10BinningStrategy
SomaticVariationOutputFormat
Sort1Mode
SortedAnnotations
SortIterateAlignments
SortMode
SplicedSamHelper
SplicedSamHelper.Limits
SplitCompactReadsMode
SplitFastaMode
SplitTranscriptsMode
Stat3StatisticAdaptor
Stat4StatisticAdaptor
Stat5MciProviderStatisticAdaptor
Stat5StatisticAdaptor
StatisticAdaptor
StatisticCalculator
StatisticComparator
StatsMode
StreamSignal
SubSequenceMotifMatcher
SuggestPositionSlicesMode
SummedCombinator
TabToColumnInfoMode
TallyBasesMode
TallyReadsMode
TestSkipTo
Timer
TranscriptBestScoreAlignmentFilter
TranscriptsAlignmentFilter
TrimMode
TSVWriter
TTestCalculator
UnboundedFifoPool
UnionAlgorithmSkeleton
UnionDumpIterator
UpgradeMode
UpgradeTo1_9_6
UpgradeTo1_9_8_2
VCFCompareMode
VCFParser
VCFSubsetMode
VcfToTabMode
VCFWriter
VersionMode
WarningCounter
WeightCalculator
WeightParameters
WeightsInfo
WiggleWindow
WithinGroupVariabilityMode