All Classes

  • 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
  • AsyncWriterPool
  • 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
  • HtsgetBAMFileReader
  • HtsgetClass
  • HtsgetErrorResponse
  • HtsgetFormat
  • HtsgetMalformedResponseException
  • HtsgetRequest
  • HtsgetRequestField
  • HtsgetResponse
  • HtsgetResponse.Block
  • HtsPath
  • 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
  • InvertFilter
  • IOPath
  • 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
  • SAMRecordPrefetchingIterator
  • 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
  • Writer