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
BAMCodec
BAMCodecV1_0
BAMDecoder
BAMDecoderOptions
BAMDecoderV1_0
BAMEncoder
BAMEncoderOptions
BAMEncoderV1_0
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
BetaAPI
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
Bundle
BundleBuilder
BundleJSON
BundleResource
BundleResourceBase
BundleResourceType
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
CRAMCodec
CRAMCodecV2_1
CRAMCodecV3_0
CRAMCompressionRecord
CramContainerHeaderIterator
CramContainerIterator
CRAMContainerStreamWriter
CRAMCRAIIndexer
CRAMDecoder
CRAMDecoderOptions
CRAMDecoderV2_1
CRAMDecoderV3_0
CRAMEncoder
CRAMEncoderOptions
CRAMEncoderV2_1
CRAMEncoderV3_0
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
FASTACodecV1_0
FASTADecoderV1_0
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
HaploidReferenceCodec
HaploidReferenceDecoder
HaploidReferenceDecoderOptions
HaploidReferenceEncoder
HaploidReferenceEncoderOptions
HaploidReferenceFormats
HaploidReferenceResolver
HapRefDecoderOptions
HardClip
HardyWeinbergCalculation
Header
HeterozygosityFilter
Histogram
Histogram.Bin
HtsCodec
HtsCodecRegistry
HtsCodecResolver
HtsContentType
HtsDecoder
HtsDecoderOptions
HtsDefaultRegistry
HtsEncoder
HtsEncoderOptions
HtsgetBAMCodec
HtsgetBAMCodecV1_2
HtsgetBAMDecoder
HtsgetBAMDecoderV1_2
HtsgetBAMFileReader
HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter
HtsgetClass
HtsgetErrorResponse
HtsgetFormat
HtsgetMalformedResponseException
HtsgetPOSTRequest
HtsgetRequest
HtsgetRequestField
HtsgetResponse
HtsgetResponse.Block
HtsHeader
HtsInterval
HtsIntervalUtils
HtsjdkException
HtsjdkIOException
HtsjdkPluginException
HtsjdkUnsupportedOperationException
HtsPath
HtsQuery
HtsQueryInterval
HtsQueryRule
HtsRecord
HtsVersion
HTTPHelper
HttpUtils
HuffmanBitCode
HuffmanCanoncialCodeGenerator
HuffmanParams
HuffmanParamsCalculator
Index
IndexCreator
IndexedFastaSequenceFile
IndexFactory
IndexFactory.IndexBalanceApproach
IndexFactory.IndexType
IndexMerger
IndexToTable
IndicesAreEqual
InflaterFactory
InputStreamResource
InputStreamUtils
InsertBase
Insertion
InsertSizeFilter
InternalAPI
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
IOPathResource
IOPathUtils
IOUtil
IOUtils
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
OutputStreamResource
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
ReadsBundle
ReadsCodec
ReadsCodecUtils
ReadsDecoder
ReadsDecoderOptions
ReadsEncoder
ReadsEncoderOptions
ReadsFormats
ReadsQuery
ReadsResolver
ReadTag
ReferenceCache
ReferenceContext
ReferenceContextType
ReferenceSequence
ReferenceSequenceFile
ReferenceSequenceFileFactory
ReferenceSequenceFileWalker
ReferenceSequenceMask
ReferenceSource
RefSkip
RelativeIso8601Date
RemoteURLHelper
ReservedTagConstants
ResourceLimitedMap
ResourceLimitedMapFunctor
RuntimeEOFException
RuntimeIOException
RuntimeScriptException
SAMBinaryTagAndUnsignedArrayValue
SAMBinaryTagAndValue
SAMCodec
SAMCodecV1_0
SamConstants
SAMDecoder
SAMDecoderV1_0
SAMEncoder
SAMEncoderV1_0
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
SeekableStreamResource
SequenceRegion
SequenceUtil
SequenceUtil.SequenceListsDifferException
SignatureStream
SimpleAllele
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
Upgradeable
URLHelper
URLHelperFactory
UserPasswordInput
Utils
ValidationStringency
ValidationUtils
VariantContext
VariantContext.Type
VariantContext.Validation
VariantContextBuilder
VariantContextComparator
VariantContextFilter
VariantContextUtils
VariantContextUtils.JexlVCMatchExp
VariantContextWriter
VariantContextWriterBuilder
VariantContextWriterBuilder.OutputType
VariantsCodec
VariantsCodecUtils
VariantsDecoder
VariantsDecoderOptions
VariantsEncoder
VariantsEncoderOptions
VariantsFormats
VariantsResolver
VCF3Codec
VCFAltHeaderLine
VCFCodec
VCFCodec
VCFCodecV3_2
VCFCodecV3_3
VCFCodecV4_0
VCFCodecV4_1
VCFCodecV4_2
VCFCodecV4_3
VCFCompoundHeaderLine
VCFCompoundHeaderLine.SupportedHeaderLineType
VCFConstants
VCFContigHeaderLine
VCFDecoder
VCFDecoderV3_2
VCFDecoderV3_3
VCFDecoderV4_0
VCFDecoderV4_1
VCFDecoderV4_2
VCFDecoderV4_3
VCFEncoder
VCFEncoder
VCFEncoderV3_2
VCFEncoderV3_3
VCFEncoderV4_0
VCFEncoderV4_1
VCFEncoderV4_2
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