- AcgtTree
- AlleleCountStats
- ArrayUtil
- AutoHashMap
- Average
- AverageInt
- BasesChangeCounter
- BBCompressionUtils
- BBFileHeader
- BBFileReader
- BBTotalSummaryBlock
- BBZoomLevelFormat
- BBZoomLevelHeader
- BBZoomLevels
- BedAnnotationOutputFormatter
- BedFeature
- BedFileIterator
- BedOutputFormatter
- BigBedDataBlock
- BigBedFileIterator
- BigBedIterator
- BigWigDataBlock
- BigWigIterator
- BigWigSection
- BigWigSectionHeader
- BigWigSectionHeader.WigItemType
- BinarySequence
- Binomial
- BinSeqFileIterator
- BioType
- BitUtil
- BlackBoxEvent
- BlastResultEntry
- BlastResultFileIterator
- BooleanMutable
- BPTree
- BPTreeChildNode
- BPTreeChildNodeItem
- BPTreeHeader
- BPTreeLeafNode
- BPTreeLeafNodeItem
- BPTreeNode
- CatalystActivity
- Cds
- Chromosome
- ChromosomeSimpleName
- ChrPosScoreList
- ChrPosStats
- CircularCorrection
- CochranArmitageTest
- Coder
- CodonChange
- CodonChangeDel
- CodonChangeDup
- CodonChangeIns
- CodonChangeInterval
- CodonChangeInv
- CodonChangeMixed
- CodonChangeMnp
- CodonChangeSnp
- CodonChangeStructural
- CodonTable
- CodonTables
- CombinatorialIterator
- CommandLine
- CompareByValue
- CompareByValue
- CompareEffects
- CompareToEnsembl
- CompareToVep
- Compartment
- Complex
- ConcurrentActor
- ConcurrentFactory
- ConcurrentProperties
- Config
- CountByKey
- CountByType
- Counter
- CounterDouble
- CountFragments
- CountReads
- CountReadsOnMarkers
- Coverage
- CoverageByType
- CoverageChr
- CreateSpliceSiteTestCase
- Custom
- CytoBands
- Depolymerisation
- Diff
- DistanceResult
- DnaAndQualitySequence
- DnaAndQualitySequenceWithId
- DnaCoder
- DnaNSequence
- DnaQualityCoder
- DnaQualSubsequenceComparator
- DnaSeqFileIterator
- DnaSeqIdFileIterator
- DnaSeqPeFileIterator
- DnaSequence
- DnaSequenceByte
- DnaSequenceId
- DnaSequencePe
- DnaSubsequenceComparator
- Download
- Downstream
- EffectType
- EffFormatVersion
- Embl
- EmblFile
- EnrichmentAlgorithm
- EnrichmentAlgorithm.EnrichmentAlgorithmType
- EnrichmentAlgorithmGreedy
- EnrichmentAlgorithmGreedyVariableSize
- Entity
- Entity.TransferFunction
- Event
- ExecuteOsCommand
- Exon
- Exon.ExonSpliceType
- ExonSpliceCharacterizer
- FastaFileIterator
- Fastq2Fastq
- FastqFileIterator
- FastqSplit
- FastqTools
- FastqTrimmer
- FastqTrimmerAdrian
- FastqTrimmerMedian
- Feature
- Feature.Type
- FeatureCoordinates
- Features
- FeaturesFile
- FileIndexChrPos
- FileIterator
- Filter
- FindRareAaIntervals
- FisherExactTest
- FisherPValueAlgorithm
- FisherPValueGreedyAlgorithm
- FloatStats
- FrameType
- GenBank
- GenBankFile
- Gene
- Gene.GeneType
- GeneCountByTypeTable
- GeneIds
- GenericMarker
- GenericMarkerFileIterator
- Genes
- GeneSet
- GeneSets
- GeneSetsRanked
- GeneStats
- Genome
- GenomicSequences
- Genotypes
- GenotypeStats
- GenotypeVector
- Gff3FileIterator
- GffMarker
- GffType
- GoogleBarChart
- GoogleChartVenn
- GoogleGenePercentBar
- GoogleGeneRegionChart
- GoogleGeneRegionNumExonsChart
- GoogleHistogram
- GoogleLineChart
- GooglePlot
- GooglePlotInt
- GoTerm
- GoTerms
- Gpr
- GprHtml
- GprSeq
- Gtex
- GtexExperiment
- Gtf2Marker
- GuessTableTypes
- HashLongLongArray
- Hgvs
- HgvsDna
- HgvsProtein
- HomHetStats
- Hypergeometric
- IdGenerator
- IdMap
- IdMapper
- IdMapperEntry
- IntegrationTest
- Intergenic
- IntergenicConserved
- Interval
- IntervalAndSubIntervals
- IntervalComparatorByEnd
- IntervalComparatorByStart
- IntervalForest
- IntervalNode
- IntervalNodeOri
- IntervalSetIterator
- IntervalTree
- IntervalTreeArray
- IntervalTreeOri
- IntHisto
- Intron
- IntronConserved
- IntStats
- Iterator2Iterable
- Itree
- IubString
- Jaspar
- KeyValue
- LeadingEdgeFractionAlgorithm
- LineChrPos
- LineClassFileIterator
- LineFileIterator
- LineFilter
- LineSeqFileIterator
- LittleEndianInputStream
- LogStats
- LogStats.RequestResult
- LossOfFunction
- Marker
- MarkerFileIterator
- MarkerParentId
- Markers
- MarkerSeq
- MarkerSerializer
- MarkerTypes
- MarkerUtil
- MarkerWithFrame
- Master
- MasterEff
- MasterVcf
- MasterVcfStr
- MatrixEntry
- MatrixEntryFileIterator
- MicroCosmEntry
- MicroCosmFileIterator
- MicroRnaBindingSite
- MineMarkerIntervals
- MineTwoMarkerIntervals
- Monitor
- Motif
- MotifFileIterator
- MotifLogo
- MultivalueHashMap
- NeedlemanWunsch
- NeedlemanWunschOverlap
- NextProt
- NextProtDb
- NextProtParser
- NextProtParserV2
- Nmer
- NmerCount
- NmerCountWc
- NoneAlgorithm
- NormalDistribution
- NullReader
- ObservedOverExpected
- ObservedOverExpectedCHG
- ObservedOverExpectedCHH
- ObservedOverExpectedCpG
- OpenBitSet
- OsCmdQueue
- OsCmdRunner
- OutputFormatter
- Overlap
- OverlapDnaSeq
- OverlapFilter
- OverlapFilterCompareAllAll
- OverlapFilterDnaId
- OverlapRessult
- Parser
- Pathway
- Pcingola
- PdbFile
- PedEntry
- PedFamily
- PedFileIterator
- PedGenotype
- PedigreeEnrty
- PedPedigree
- PlinkMap
- Polymerisation
- PosStats
- Progress
- PromoterSequences
- ProteinInteractionLocus
- ProteinProteinInteractionLocus
- ProteinStructuralInteractionLocus
- PurityChange
- PvaluesList
- Pwm
- PwmAndSeqs
- Qseq2Fastq
- Qseq2FastqSplit
- RandMarker
- RankSumNoReplacementPdf
- RankSumNoReplacementSimulate
- RankSumPdf
- RankSumPValueAlgorithm
- RankSumPValueGreedyAlgorithm
- RareAminoAcid
- Reaction
- Reaction.RegulationType
- Reactome
- ReadsOnMarkersModel
- Regulation
- RegulationBedFileIterator
- RegulationConsensusMultipleBed
- RegulationFileConsensus
- RegulationFileIterator
- RegulationFileSplitBytType
- RegulationGffFileIterator
- ReSampleInt
- ReSampleMap
- ReSampleMapRank
- Result
- Result
- RPChromosomeRegion
- RPTree
- RPTreeChildNode
- RPTreeChildNodeItem
- RPTreeHeader
- RPTreeLeafNode
- RPTreeLeafNodeItem
- RPTreeNode
- RPTreeNodeProxy
- SamEntry
- SamFileIterator
- SamHeader
- SamHeaderRecord
- SamHeaderRecordSq
- SamplingStats
- ScoreList
- ScoreList.ScoreSummary
- SeekableBufferedReader
- SeekableFileStream
- SeekableStream
- SequenceComplexity
- SequenceIndexer
- SequenceReference
- SequenceRotator
- Sex
- SmithWaterman
- SnpEff
- SnpEff.GeneDatabaseFormat
- SnpEff.InputFormat
- SnpEff.OutputFormat
- SnpEffCmdAcat
- SnpEffCmdBuild
- SnpEffCmdBuildNextProt
- SnpEffCmdCds
- SnpEffCmdClosest
- SnpEffCmdCount
- SnpEffCmdDatabases
- SnpEffCmdDownload
- SnpEffCmdDump
- SnpEffCmdDump.DumpFormat
- SnpEffCmdEff
- SnpEffCmdGenes2Bed
- SnpEffCmdGsa
- SnpEffCmdLen
- SnpEffCmdPdb
- SnpEffCmdProtein
- SnpEffCmdSeq
- SnpEffCmdShow
- SnpEffCmdSpliceAnalysis
- SnpEffCmdTranslocationsReport
- SnpEffectPredictor
- SnpEffPredictorFactory
- SnpEffPredictorFactoryEmbl
- SnpEffPredictorFactoryFeatures
- SnpEffPredictorFactoryGenBank
- SnpEffPredictorFactoryGenesFile
- SnpEffPredictorFactoryGff
- SnpEffPredictorFactoryGff2
- SnpEffPredictorFactoryGff3
- SnpEffPredictorFactoryGtf22
- SnpEffPredictorFactoryKnownGene
- SnpEffPredictorFactoryRand
- SnpEffPredictorFactoryRefSeq
- SpliceSite
- SpliceSiteAcceptor
- SpliceSiteBranch
- SpliceSiteBranchU12
- SpliceSiteDonor
- SpliceSiteRegion
- SpliceTypes
- StartMaster
- StartMasterVcf
- StreamGobbler
- SubsequenceComparator
- SuffixIndexerNmer
- Svg
- SvgBnd
- SvgCds
- SvgExon
- SvgGene
- SvgIntron
- SvgNextProt
- SvgScale
- SvgSpacer
- SvgTranscript
- SvgTranslocation
- TabixIndex
- TabixInterval
- TabixIterator
- TabixReader
- TableFile
- TestCasesAlign
- TestCasesAnn
- TestCasesAnnParse
- TestCasesApplyDel
- TestCasesApplyIns
- TestCasesApplyMixed
- TestCasesApplyMnp
- TestCasesApplySnp
- TestCasesBase
- TestCasesBaseApply
- TestCasesBinomial
- TestCasesBuild
- TestCasesCds
- TestCasesChiSquare
- TestCasesCircular
- TestCasesCochranArmitage
- TestCasesCodonTable
- TestCasesCytoBands
- TestCasesDel
- TestCasesDels
- TestCasesDnaNSequence
- TestCasesDnaOverlap
- TestCasesDnaSequence
- TestCasesDnaSequenceByte
- TestCasesEffectCollapse
- TestCasesEffectCollapse2
- TestCasesFasta
- TestCasesFileIndexChrPos
- TestCasesFisherExactTest
- TestCasesGenePvalueList
- TestCasesGenomicSequences
- TestCasesGenotypeVector
- TestCasesHgvs
- TestCasesHgvsBase
- TestCasesHgvsDnaDup
- TestCasesHgvsDnaDupNegative
- TestCasesHgvsExon
- TestCasesHgvsIntron
- TestCasesHgvsProtDup
- TestCasesHypergeometric
- TestCasesIns
- TestCasesIntegratioBuildPdb
- TestCasesIntegrationApply
- TestCasesIntegrationBase
- TestCasesIntegrationCancer
- TestCasesIntegrationCanonical
- TestCasesIntegrationCircularGenome
- TestCasesIntegrationCodingTag
- TestCasesIntegrationConfig
- TestCasesIntegrationCutsomIntervals
- TestCasesIntegrationDelEtc
- TestCasesIntegrationDup
- TestCasesIntegrationEff
- TestCasesIntegrationEmbl
- TestCasesIntegrationErrors
- TestCasesIntegrationExonFrame
- TestCasesIntegrationFilterTranscripts
- TestCasesIntegrationGenBank
- TestCasesIntegrationGenomicSequences
- TestCasesIntegrationGff3
- TestCasesIntegrationGtf22
- TestCasesIntegrationHgvs
- TestCasesIntegrationHgvsDel
- TestCasesIntegrationHgvsDnaDup
- TestCasesIntegrationHgvsFrameShift
- TestCasesIntegrationHgvsHard
- TestCasesIntegrationHgvsIns
- TestCasesIntegrationHgvsLarge
- TestCasesIntegrationHgvsMnps
- TestCasesIntegrationHgvsUpDownStream
- TestCasesIntegrationHugeDeletions
- TestCasesIntegrationInsEtc
- TestCasesIntegrationInsVep
- TestCasesIntegrationLof
- TestCasesIntegrationMarkerSeq
- TestCasesIntegrationMissenseSilentRatio
- TestCasesIntegrationMixedVariants
- TestCasesIntegrationMnp
- TestCasesIntegrationMotif
- TestCasesIntegrationNextProt
- TestCasesIntegrationNmd
- TestCasesIntegrationNoChange
- TestCasesIntegrationProtein
- TestCasesIntegrationProteinInteraction
- TestCasesIntegrationRefSeq
- TestCasesIntegrationRegulation
- TestCasesIntegrationSequenceOntology
- TestCasesIntegrationSnp
- TestCasesIntegrationSnpEff
- TestCasesIntegrationSnpEffMultiThread
- TestCasesIntegrationSnpEnsembl
- TestCasesIntegrationSpliceRegion
- TestCasesIntegrationStructural
- TestCasesIntegrationTranscript
- TestCasesIntegrationTranscriptError
- TestCasesIntegrationVariant
- TestCasesIntegrationVcfs
- TestCasesIntergenic
- TestCasesIntervals
- TestCasesIntervalTree
- TestCasesIntervalTreeArray
- TestCasesIntervalTreeOri
- TestCasesIntervalVariant
- TestCasesIntStats
- TestCasesIubString
- TestCasesJaspar
- TestCasesMarkerUtils
- TestCasesMnps
- TestCasesNmers
- TestCasesOverlap
- TestCasesProteinInteraction
- TestCasesReactome
- TestCasesSeekableReader
- TestCasesSequenceIndexer
- TestCasesSnps
- TestCasesSpliceRegion
- TestCasesSpliceSite
- TestCasesStructuralDel
- TestCasesStructuralDup
- TestCasesStructuralInv
- TestCasesStructuralTranslocations
- TestCasesVariantDecompose
- TestCasesVariantRealignment
- TestCasesVcf
- TestCasesZzz
- TestSuiteHgvs
- TestSuiteIntegration
- TestSuiteUnity
- TfamEntry
- Timer
- TPair64
- Transcript
- TranscriptSet
- TranscriptSupportLevel
- TranslocationReport
- TsTvStats
- Tuple
- TxtSerializable
- Upstream
- Utr
- Utr3prime
- Utr5prime
- Variant
- Variant.VariantType
- VariantBnd
- VariantEffect
- VariantEffect.Coding
- VariantEffect.EffectImpact
- VariantEffect.ErrorWarningType
- VariantEffect.FunctionalClass
- VariantEffectFilter
- VariantEffectFusion
- VariantEffects
- VariantEffectStats
- VariantEffectStructural
- VariantFileIterator
- VariantNonRef
- VariantRealign
- VariantStats
- VariantTxtFileIterator
- VariantTypeStats
- VariantVcfEntry
- VariantWithScore
- VcfAnnotator
- VcfAnnotatorChain
- VcfConsequence
- VcfConsequenceHeader
- VcfEffect
- VcfEntry
- VcfEntry.AlleleFrequencyType
- VcfFileIterator
- VcfGenotype
- VcfHapMapFileIterator
- VcfHeader
- VcfHeaderEntry
- VcfHeaderFormat
- VcfHeaderInfo
- VcfHeaderInfo.VcfInfoNumber
- VcfInfoType
- VcfLof
- VcfNmd
- VcfOutputFormatter
- VcfRefAltAlign
- VcfStats
- VcfWorkQueue
- VersionCheck
- WigItem
- Work
- Worker
- WorkerEff
- WorkerVcf
- WorkerVcfStr
- ZoomDataBlock
- ZoomDataRecord
- ZoomLevelIterator
- ZoomLevelIterator.EmptyIterator