- AbstractAsyncWriter
- AbstractBAMFileIndex
- AbstractFeatureCodec
- AbstractFeatureReader
- AbstractFeatureReader.ComponentMethods
- AbstractIndex
- AbstractIndex.BlockStats
- AbstractIndex.IndexType
- AbstractIterator
- AbstractJavascriptFilter
- AbstractLocusInfo
- AbstractLocusIterator
- AbstractProgressLogger
- AbstractRecordAndOffset
- AbstractRecordAndOffset.AlignmentType
- AbstractSAMHeaderRecord
- AbstractVCFCodec
- AggregateFilter
- AlignedFilter
- AlignmentBlock
- AlignmentContext
- AlignmentSpan
- Allele
- AllRefsTabixIndexCreator
- AsciiFeatureCodec
- AsciiLineReader
- AsciiLineReaderIterator
- AsciiWriter
- AsyncBlockCompressedInputStream
- AsyncBufferedIterator
- AsyncFastqWriter
- AsyncVariantContextWriter
- BAIEntry
- BamFileIoUtils
- BAMFileReader
- BAMFileSpan
- BAMFileWriter
- BAMIndex
- BAMIndexer
- BAMIndexMerger
- BAMIndexMetaData
- BamIndexValidator
- BamIndexValidator.IndexValidationStringency
- BAMQueryMultipleIntervalsIteratorFilter
- BAMRecord
- BAMRecordCodec
- BAMSBIIndexer
- BAMStartingAtIteratorFilter
- BAMStreamWriter
- BaseQualityScore
- Bases
- BasicFastqWriter
- BCF2Codec
- BCF2Codec.LazyData
- BCF2Codec.SitesInfoForDecoding
- BCF2Decoder
- BCF2Encoder
- BCF2FieldEncoder
- BCF2FieldEncoder.AtomicInt
- BCF2FieldEncoder.Flag
- BCF2FieldEncoder.Float
- BCF2FieldEncoder.GenericInts
- BCF2FieldEncoder.IntArray
- BCF2FieldEncoder.StringOrCharacter
- BCF2FieldWriter
- BCF2FieldWriter.FTGenotypesWriter
- BCF2FieldWriter.GenericSiteWriter
- BCF2FieldWriter.GenotypesWriter
- BCF2FieldWriter.GTWriter
- BCF2FieldWriter.IGFGenotypesWriter
- BCF2FieldWriter.IntegerTypeGenotypesWriter
- BCF2FieldWriter.SiteWriter
- BCF2FieldWriter.StaticallyTypeGenotypesWriter
- BCF2FieldWriterManager
- BCF2GenotypeFieldDecoders
- BCF2GenotypeFieldDecoders.Decoder
- BCF2LazyGenotypesDecoder
- BCF2Type
- BCF2Utils
- BCFVersion
- BEDCodec
- BEDCodec.StartOffset
- BEDFeature
- BetaIntegerCodec
- BetaIntegerEncoding
- Bin
- BinaryCodec
- BinaryFeatureCodec
- BinaryTagCodec
- BinList
- BinningIndexBuilder
- BinningIndexBuilder.FeatureToBeIndexed
- BinningIndexContent
- BinningIndexContent.BinList
- BinomialCoefficientUtil
- BinWithOffset
- BitInputStream
- BitOutputStream
- Block
- Block
- BlockCompressedFilePointerUtil
- BlockCompressedIndexedFastaSequenceFile
- BlockCompressedInputStream
- BlockCompressedInputStream.DecompressedBlock
- BlockCompressedInputStream.FileTermination
- BlockCompressedOutputStream
- BlockCompressedStreamConstants
- BlockCompressionMethod
- BlockContentType
- BlockGunzipper
- BrowseableBAMIndex
- BufferedLineReader
- ByteArrayLenEncoding
- ByteArraySeekableStream
- ByteArrayStopEncoding
- BZIP2ExternalCompressor
- CanonicalHuffmanByteEncoding
- CanonicalHuffmanIntegerEncoding
- ChrIndex
- Chunk
- Cigar
- CigarElement
- CigarOperator
- CigarUtil
- ClassFinder
- CloseableIterator
- CloseableTribbleIterator
- CloserUtil
- CodecLineParsingException
- CodeUtil
- CollectionUtil
- CollectionUtil.DefaultingMap
- CollectionUtil.DefaultingMap.Factory
- CollectionUtil.MultiMap
- CollectionUtil.Partitioner
- CommonInfo
- ComparableTuple
- CompoundFilter
- CompressionHeader
- CompressionHeaderEncodingMap
- CompressionHeaderFactory
- CompressorCache
- Container
- ContainerFactory
- ContainerHeader
- ContentDigests
- ContentDigests.KNOWN_DIGESTS
- CoordinateSortedPairInfoMap
- CoordinateSortedPairInfoMap.Codec
- CoordMath
- CoordSpanInputSteam
- CoreCodec
- CountingInputStream
- CountRecords
- CRAIEntry
- CRAIIndex
- CRAIIndexMerger
- CRAMBAIIndexer
- CRAMCodec
- CRAMCompressionRecord
- CramContainerHeaderIterator
- CramContainerIterator
- CRAMContainerStreamWriter
- CRAMCRAIIndexer
- CRAMEncoding
- CRAMEncodingStrategy
- CRAMException
- CRAMFileReader
- CRAMFileWriter
- CramHeader
- CRAMIndexer
- CramInt
- CramIntArray
- CramIO
- CRAMIterator
- CRAMLazyReferenceSource
- CramRecordReader
- CRAMRecordReadFeatures
- CramRecordWriter
- CRAMReferenceRegion
- CRAMReferenceSource
- CramSpanContainerIterator
- CRAMVersion
- CramVersions
- CRC32InputStream
- CRC32OutputStream
- CSIIndex
- CustomGzipOutputStream
- CustomReaderFactory
- CustomReaderFactory.ICustomReaderFactory
- DataSeries
- DataSeriesReader
- DataSeriesType
- DataSeriesWriter
- DateParser
- DateParser.InvalidDateException
- DefaultBitInputStream
- DefaultBitOutputStream
- Defaults
- DefaultSAMRecordFactory
- DeflaterFactory
- DelegatingIterator
- DeleteOnExitPathHook
- Deletion
- DiskBackedQueue
- DiskBasedBAMFileIndex
- DownsamplingIterator
- DownsamplingIteratorFactory
- DownsamplingIteratorFactory.Strategy
- DuplicateReadFilter
- DuplicateScoringStrategy
- DuplicateScoringStrategy.ScoringStrategy
- DuplicateSet
- DuplicateSetIterator
- DynamicIndexCreator
- EdgeReadIterator
- EdgingRecordAndOffset
- EdgingRecordAndOffset.Type
- EnaRefService
- EncodingDescriptor
- EncodingFactory
- EncodingID
- ExampleBinaryCodec
- ExampleSamUsage
- ExternalByteArrayCodec
- ExternalByteArrayEncoding
- ExternalByteEncoding
- ExternalCompressor
- ExternalEncoding
- ExternalIntegerEncoding
- ExternalLongEncoding
- FailsVendorReadQualityFilter
- FastaReferenceWriter
- FastaReferenceWriterBuilder
- FastaSequenceFile
- FastaSequenceIndex
- FastaSequenceIndexCreator
- FastaSequenceIndexEntry
- FastGenotype
- FastLineReader
- FastqConstants
- FastqConstants.FastqExtensions
- FastqEncoder
- FastqQualityFormat
- FastqReader
- FastqReader.LineType
- FastqRecord
- FastqWriter
- FastqWriterFactory
- Feature
- FeatureCodec
- FeatureCodecHeader
- FeatureReader
- FileAppendStreamLRUCache
- FileExtensions
- FileTruncatedException
- FilteringIterator
- FilteringIterator
- FilteringSamIterator
- FilteringVariantContextIterator
- FormatUtil
- FTPClient
- FTPHelper
- FTPReply
- FTPStream
- FTPUtils
- FullBEDFeature
- GammaIntegerEncoding
- GaveUpException
- GeneralUtils
- GenomicIndexUtil
- Genotype
- GenotypeBuilder
- GenotypeJEXLContext
- GenotypeLikelihoods
- GenotypeLikelihoods.GenotypeLikelihoodsAllelePair
- GenotypeQualityFilter
- GenotypesContext
- GenotypeType
- Gff3BaseData
- Gff3Codec
- Gff3Codec.DecodeDepth
- Gff3Codec.Gff3Directive
- Gff3Constants
- Gff3Feature
- Gff3FeatureImpl
- Gff3Writer
- GolombIntegerEncoding
- GolombLongEncoding
- GolombRiceIntegerEncoding
- GZIIndex
- GZIIndex.GZIIndexer
- GZIIndex.IndexEntry
- GZIPExternalCompressor
- HardClip
- HardyWeinbergCalculation
- Header
- HeterozygosityFilter
- Histogram
- Histogram.Bin
- HTTPHelper
- HttpUtils
- HuffmanBitCode
- HuffmanCanoncialCodeGenerator
- HuffmanParams
- HuffmanParamsCalculator
- Index
- IndexCreator
- IndexedFastaSequenceFile
- IndexFactory
- IndexFactory.IndexBalanceApproach
- IndexFactory.IndexType
- IndexMerger
- IndexToTable
- IndicesAreEqual
- InflaterFactory
- InputStreamUtils
- InsertBase
- Insertion
- InsertSizeFilter
- Interval
- Interval
- IntervalCodec
- IntervalCoordinateComparator
- IntervalFilter
- IntervalIndexCreator
- IntervalKeepPairFilter
- IntervalList
- IntervalList.IntervalMergerIterator
- IntervalListCodec
- IntervalListReferenceSequenceMask
- IntervalListWriter
- IntervalTree
- IntervalTree
- IntervalTree.Node
- IntervalTree.ValuesIterator
- IntervalTreeIndex
- IntervalTreeIndex.ChrIndex
- IntervalTreeMap
- IntervalUtil
- IntervalUtil.IntervalCombiner
- IntGenotypeFieldAccessors
- IntGenotypeFieldAccessors.Accessor
- IntGenotypeFieldAccessors.ADAccessor
- IntGenotypeFieldAccessors.DPAccessor
- IntGenotypeFieldAccessors.GQAccessor
- IntGenotypeFieldAccessors.PLAccessor
- IOUtil
- ISeekableStreamFactory
- Iso8601Date
- IterableAdapter
- IterableOnceIterator
- Iterables
- ITF8
- JavascriptSamRecordFilter
- JavascriptVariantFilter
- JexlMissingValueTreatment
- Lazy
- Lazy.LazyInitializer
- LazyGenotypesContext
- LazyGenotypesContext.LazyData
- LazyGenotypesContext.LazyParser
- LiftOver
- LiftOver.PartialLiftover
- LinearIndex
- LinearIndex
- LinearIndex.ChrIndex
- LinearIndexCreator
- LineIterator
- LineIteratorImpl
- LineReader
- LineReader
- ListMap
- LittleEndianInputStream
- LittleEndianOutputStream
- Locatable
- LocationAware
- Locus
- LocusComparator
- LocusImpl
- Log
- Log.LogLevel
- LongLineBufferedReader
- LTF8
- LZMAExternalCompressor
- MappingQualityFilter
- MathUtils
- MathUtils.RunningStat
- Md5CalculatingInputStream
- Md5CalculatingOutputStream
- MergingIterator
- MergingSamRecordIterator
- MetricBase
- MetricsFile
- Murmur3
- MutableFeature
- MutableIndex
- MutableInt
- NameAwareCodec
- NotPrimaryAlignmentFilter
- NotPrimarySkippingIterator
- Options
- OverclippedReadFilter
- OverlapDetector
- Padding
- ParsingUtils
- PassingVariantFilter
- PeekableIterator
- PeekIterator
- Positional
- PositionalBufferedStream
- PositionalOutputStream
- PrintReadsExample
- PrintVariantsExample
- ProcessExecutor
- ProcessExecutor.ExitStatusAndOutput
- ProfileIndexReading
- ProgressLogger
- ProgressLoggerInterface
- QualityEncodingDetector
- QualityEncodingDetector.FileContext
- QualityUtil
- QueryInterval
- RANS
- RANS.ORDER
- RANSExternalCompressor
- RAWExternalCompressor
- ReadableSeekableStreamByteChannel
- ReadBase
- ReadFeature
- ReadNameFilter
- ReadTag
- ReferenceCache
- ReferenceContext
- ReferenceContextType
- ReferenceSequence
- ReferenceSequenceFile
- ReferenceSequenceFileFactory
- ReferenceSequenceFileWalker
- ReferenceSequenceMask
- ReferenceSource
- RefSkip
- RelativeIso8601Date
- RemoteURLHelper
- ReservedTagConstants
- ResourceLimitedMap
- ResourceLimitedMapFunctor
- RuntimeEOFException
- RuntimeIOException
- RuntimeScriptException
- SAMBinaryTagAndUnsignedArrayValue
- SAMBinaryTagAndValue
- SamConstants
- SAMException
- SAMFileHeader
- SAMFileHeader.GroupOrder
- SAMFileHeader.PgIdGenerator
- SAMFileHeader.SortOrder
- SamFileHeaderMerger
- SamFiles
- SAMFileSource
- SAMFileSpan
- SamFileValidator
- SamFileValidator.ValidationMetrics
- SAMFileWriter
- SAMFileWriterFactory
- SAMFileWriterImpl
- SAMFlag
- SamFlagField
- SAMFormatException
- SAMHeaderRecordComparator
- SamIndexes
- SamInputResource
- SAMLineParser
- SamLocusAndReferenceIterator
- SamLocusAndReferenceIterator.SAMLocusAndReference
- SamLocusIterator
- SamLocusIterator.LocusInfo
- SamLocusIterator.RecordAndOffset
- SamPairUtil
- SamPairUtil.PairOrientation
- SamPairUtil.SetMateInfoIterator
- SAMProgramRecord
- SamReader
- SamReader.AssertingIterator
- SamReader.Indexing
- SamReader.PrimitiveSamReader
- SamReader.PrimitiveSamReaderToSamReaderAdapter
- SamReader.ReaderImplementation
- SamReader.Type
- SamReaderFactory
- SamReaderFactory.Option
- SAMReadGroupRecord
- SAMReadGroupRecord.PlatformValue
- SAMRecord
- SAMRecord.SAMTagAndValue
- SAMRecordComparator
- SAMRecordCoordinateComparator
- SAMRecordDuplicateComparator
- SAMRecordFactory
- SamRecordFilter
- SamRecordIntervalIteratorFactory
- SAMRecordIterator
- SAMRecordQueryHashComparator
- SAMRecordQueryNameComparator
- SAMRecordSetBuilder
- SamRecordTrackingBuffer
- SamRecordWithOrdinal
- SAMSequenceDictionary
- SAMSequenceDictionaryCodec
- SAMSequenceDictionaryExtractor
- SAMSequenceRecord
- SAMSortOrderChecker
- SamStreams
- SAMTag
- SAMTagUtil
- SAMTestUtil
- SAMTestUtil.SanityCheckFailedException
- SAMTextHeaderCodec
- SAMTextWriter
- SAMUtils
- SAMValidationError
- SAMValidationError.Severity
- SAMValidationError.Type
- SBIIndex
- SBIIndex.Header
- SBIIndexMerger
- SBIIndexWriter
- Scores
- SecondaryAlignmentFilter
- SecondaryAlignmentSkippingIterator
- SecondaryOrSupplementaryFilter
- SecondaryOrSupplementarySkippingIterator
- SeekableBufferedStream
- SeekableFileStream
- SeekableFTPStream
- SeekableFTPStreamHelper
- SeekableHTTPStream
- SeekableMemoryStream
- SeekablePathStream
- SeekableStream
- SeekableStreamFactory
- SequenceRegion
- SequenceUtil
- SequenceUtil.SequenceListsDifferException
- SimpleBEDFeature
- SimpleFeature
- Slice
- SliceBlocks
- SliceBlocksReadStreams
- SliceBlocksWriteStreams
- SliceFactory
- SnappyLoader
- SnpFilter
- SoftClip
- SolexaNoiseFilter
- SolexaQualityConverter
- SortingCollection
- SortingCollection.Codec
- SortingLongCollection
- SortingVariantContextWriter
- SQTagUtil
- SQTagUtil.SQBase
- SRAAccession
- SRAAlignmentIterator
- SRAFileReader
- SRAIndex
- SRAIndexedSequenceFile
- SRAIterator
- SRAIterator.RecordRangeInfo
- SRALazyRecord
- SRAUnalignmentIterator
- SRAUtils
- StopWatch
- Strand
- StreamBasedTabixIndexCreator
- StringHeader
- StringLineReader
- StringUtil
- StructuralVariantType
- SubexponentialIntegerEncoding
- Substitution
- SubstitutionMatrix
- SynchronousLineReader
- TabixFeatureReader
- TabixFormat
- TabixIndex
- TabixIndexCreator
- TabixIndexMerger
- TabixIteratorLineReader
- TabixReader
- TabixReader.Iterator
- TabixReader.TIndex
- TabixReader.TPair64
- TabixUtils
- TabixUtils.TIndex
- TabixUtils.TIntv
- TabixUtils.TPair64
- TagFilter
- TagValueAndUnsignedArrayFlag
- TempStreamFactory
- TerminatorlessBlockCompressedOutputStream
- TestUtil
- TextCigarCodec
- TextTagCodec
- TimeChannel
- TimeRandomAccessFile
- Tribble
- TribbleException
- TribbleException.CorruptedIndexFile
- TribbleException.FeatureFileDoesntExist
- TribbleException.InternalCodecException
- TribbleException.InvalidDecodeLine
- TribbleException.InvalidHeader
- TribbleException.MalformedFeatureFile
- TribbleException.TabixReaderFailure
- TribbleException.UnableToCreateCorrectIndexType
- TribbleException.UnableToReadIndexFile
- TribbleIndexCreator
- TribbleIndexedFeatureReader
- TrimmingUtil
- Tuple
- UnsortedFileException
- URLHelper
- URLHelperFactory
- UserPasswordInput
- Utils
- ValidationStringency
- ValidationUtils
- VariantContext
- VariantContext.Type
- VariantContext.Validation
- VariantContextBuilder
- VariantContextComparator
- VariantContextFilter
- VariantContextUtils
- VariantContextUtils.JexlVCMatchExp
- VariantContextWriter
- VariantContextWriterBuilder
- VariantContextWriterBuilder.OutputType
- VCF3Codec
- VCFAltHeaderLine
- VCFCodec
- VCFCompoundHeaderLine
- VCFCompoundHeaderLine.SupportedHeaderLineType
- VCFConstants
- VCFContigHeaderLine
- VCFEncoder
- VCFFileReader
- VCFFilterHeaderLine
- VCFFormatHeaderLine
- VCFHeader
- VCFHeader.HEADER_FIELDS
- VCFHeaderLine
- VCFHeaderLineCount
- VCFHeaderLineTranslator
- VCFHeaderLineType
- VCFHeaderReader
- VCFHeaderVersion
- VCFIDHeaderLine
- VCFInfoHeaderLine
- VCFIterator
- VCFIteratorBuilder
- VCFMetaHeaderLine
- VCFPassThruTextTransformer
- VCFPedigreeHeaderLine
- VCFPercentEncodedTextTransformer
- VCFReader
- VCFRecordCodec
- VCFSampleHeaderLine
- VCFSimpleHeaderLine
- VCFStandardHeaderLines
- VCFTextTransformer
- VCFUtils
- VersionHeader
- WholeGenomeReferenceSequenceMask
- WholeReadClippedFilter