All Classes
AbstractAsyncWriter
AbstractBAMFileIndex
AbstractBitCodec
AbstractFeatureCodec
AbstractFeatureReader
AbstractFeatureReader.ComponentMethods
AbstractIndex
AbstractIndex.BlockStats
AbstractIndex.IndexType
AbstractIterator
AbstractJavascriptFilter
AbstractProgressLogger
AbstractReader
AbstractSAMHeaderRecord
AbstractVCFCodec
AggregateFilter
AlignedFilter
AlignmentBlock
AlignmentSpan
Allele
AsciiFeatureCodec
AsciiLineReader
AsciiLineReaderIterator
AsciiWriter
AsyncBufferedIterator
AsyncFastqWriter
AsyncVariantContextWriter
BamFileIoUtils
BAMFileSpan
BAMIndex
BAMIndexer
BAMIndexMetaData
BamIndexValidator
BamIndexValidator.IndexValidationStringency
BAMQueryMultipleIntervalsIteratorFilter
BAMRecord
BAMRecordCodec
BaseCategory
BaseCategoryType
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
BetaIntegerEncoding
Bin
BinaryCodec
BinaryFeatureCodec
BinaryTagCodec
BinList
BinningIndexBuilder
BinningIndexBuilder.FeatureToBeIndexed
BinningIndexContent
BinningIndexContent.BinList
BitCodec
BitInputStream
BitOutputStream
Block
Block
BlockCompressedFilePointerUtil
BlockCompressedInputStream
BlockCompressedInputStream.FileTermination
BlockCompressedOutputStream
BlockCompressedStreamConstants
BlockCompressionMethod
BlockContentType
BlockGunzipper
BrowseableBAMIndex
BufferedLineReader
ByteArrayLenEncoding
ByteArraySeekableStream
ByteArrayStopEncoding
ByteArrayStopEncoding.ByteArrayStopCodec
ChrIndex
Chunk
Cigar
CigarElement
CigarOperator
CigarUtil
CloseableIterator
CloseableTribbleIterator
CloserUtil
CodecLineParsingException
CodeUtil
CollectionUtil
CollectionUtil.DefaultingMap
CollectionUtil.DefaultingMap.Factory
CollectionUtil.MultiMap
CollectionUtil.Partitioner
CommonInfo
ComparableTuple
CompoundFilter
CompressionHeader
CompressionHeaderFactory
Container
ContainerFactory
ContainerIO
ContainerParser
ContentDigests
ContentDigests.KNOWN_DIGESTS
CoordinateSortedPairInfoMap
CoordinateSortedPairInfoMap.Codec
CoordMath
CoordSpanInputSteam
CountingInputStream
CountRecords
CRAIEntry
CRAIIndex
CRAIIndex.CRAIIndexException
Cram2SamRecordFactory
CramArray
CRAMBAIIndexer
CramCompressionRecord
CramCompressionRecord.BAM_FLAGS
CramContainerIterator
CRAMContainerStreamWriter
CRAMCRAIIndexer
CRAMException
CRAMFileReader
CRAMFileWriter
CramHeader
CramInt
CramIO
CRAMIterator
CramNormalizer
CramRecordReader
CRAMReferenceSource
CramSpanContainerIterator
CramVersionPolicies
CramVersions
CRC32InputStream
CRC32OutputStream
CustomReaderFactory
CustomReaderFactory.ICustomReaderFactory
DataReader
DataReaderFactory
DataReaderFactory.DataReaderWithStats
DataSeries
DataSeriesMap
DataSeriesType
DataWriter
DataWriterFactory
DateParser
DateParser.InvalidDateException
DefaultBitInputStream
DefaultBitOutputStream
Defaults
DefaultSAMRecordFactory
DeflaterFactory
DelegatingIterator
Deletion
DiploidGenotype
DiskBackedQueue
DiskBasedBAMFileIndex
DownsamplingIterator
DownsamplingIteratorFactory
DownsamplingIteratorFactory.Strategy
DuplicateReadFilter
DuplicateScoringStrategy
DuplicateScoringStrategy.ScoringStrategy
DuplicateSet
DuplicateSetIterator
DynamicIndexCreator
EnaRefService
EnaRefService.GaveUpException
Encoding
EncodingFactory
EncodingID
EncodingKey
EncodingParams
ExampleBinaryCodec
ExampleSamUsage
ExposedByteArrayOutputStream
ExternalByteArrayEncoding
ExternalByteEncoding
ExternalCompression
ExternalCompressor
ExternalIntegerEncoding
ExternalLongEncoding
FailsVendorReadQualityFilter
FastaSequenceFile
FastaSequenceIndex
FastGenotype
FastLineReader
FastqConstants
FastqConstants.FastqExtensions
FastqQualityFormat
FastqReader
FastqRecord
FastqWriter
FastqWriterFactory
Feature
FeatureCodec
FeatureCodecHeader
FeatureReader
FileAppendStreamLRUCache
FileTruncatedException
FilteringIterator
FilteringIterator
FilteringSamIterator
FilteringVariantContextIterator
FixBAMFile
FormatUtil
FTPClient
FTPHelper
FTPReply
FTPStream
FTPUtils
FullBEDFeature
GammaIntegerEncoding
GeliTextCodec
GeliTextFeature
GeneralUtils
GenomicIndexUtil
Genotype
GenotypeBuilder
GenotypeJEXLContext
GenotypeLikelihoods
GenotypeLikelihoods.GenotypeLikelihoodsAllelePair
GenotypeQualityFilter
GenotypesContext
GenotypeType
GolombIntegerEncoding
GolombLongEncoding
GolombRiceIntegerEncoding
HardClip
HardyWeinbergCalculation
Header
HeterozygosityFilter
Histogram
Histogram.Bin
HTTPHelper
HttpUtils
HuffmanByteEncoding
HuffmanCode
HuffmanIntegerEncoding
HuffmanTree
Index
IndexCreator
IndexedFastaSequenceFile
IndexFactory
IndexFactory.IndexBalanceApproach
IndexFactory.IndexType
IndexToTable
IndicesAreEqual
InputStreamUtils
InsertBase
Insertion
InsertSizeFilter
Interval
Interval
IntervalFilter
IntervalIndexCreator
IntervalKeepPairFilter
IntervalList
IntervalListReferenceSequenceMask
IntervalTree
IntervalTree
IntervalTree.Node
IntervalTree.ValuesIterator
IntervalTreeIndex
IntervalTreeIndex.ChrIndex
IntervalTreeMap
IntervalUtil
IntGenotypeFieldAccessors
IntGenotypeFieldAccessors.Accessor
IntGenotypeFieldAccessors.ADAccessor
IntGenotypeFieldAccessors.DPAccessor
IntGenotypeFieldAccessors.GQAccessor
IntGenotypeFieldAccessors.PLAccessor
IntHashMap
IOUtil
ISeekableStreamFactory
Iso8601Date
IterableAdapter
IterableOnceIterator
Iterables
ITF8
JavascriptSamRecordFilter
JavascriptVariantFilter
Lazy
Lazy.LazyInitializer
LazyGenotypesContext
LazyGenotypesContext.LazyData
LazyGenotypesContext.LazyParser
LiftOver
LiftOver.PartialLiftover
LinearIndex
LinearIndex
LinearIndex.ChrIndex
LinearIndexCreator
LineIterator
LineIteratorImpl
LineReader
LineReader
LineReaderUtil
LineReaderUtil.LineReaderOption
ListMap
LittleEndianInputStream
LittleEndianOutputStream
Locatable
LocationAware
Locus
LocusComparator
LocusImpl
Log
Log.LogLevel
LongLineBufferedReader
LTF8
MappingQualityFilter
MathUtils
MathUtils.RunningStat
Md5CalculatingInputStream
Md5CalculatingOutputStream
MergingIterator
MergingSamRecordIterator
MetricBase
MetricsFile
Murmur3
MutableIndex
MutableInt
NameAwareCodec
NotPrimaryAlignmentFilter
NotPrimarySkippingIterator
NullEncoding
Options
OverclippedReadFilter
OverlapDetector
Padding
ParsingUtils
PassingVariantFilter
PeekableIterator
PeekIterator
Positional
PositionalBufferedStream
PreservationPolicy
PrintReadsExample
PrintVariantsExample
ProcessExecutor
ProcessExecutor.ExitStatusAndOutput
ProfileIndexReading
ProgressLogger
ProgressLoggerInterface
QualityEncodingDetector
QualityEncodingDetector.FileContext
QualityScorePreservation
QualityScoreTreatment
QualityScoreTreatmentType
QualityUtil
QueryInterval
RANS
RANS.ORDER
ReadBase
ReadCategory
ReadCategoryType
ReadFeature
ReadNameFilter
ReadTag
ReferenceCache
ReferenceSequence
ReferenceSequenceFile
ReferenceSequenceFileFactory
ReferenceSequenceFileWalker
ReferenceSequenceMask
ReferenceSource
ReferenceTracks
RefSeqIdReader
RefSkip
RelativeIso8601Date
RemoteURLHelper
ReservedTagConstants
ResourceLimitedMap
ResourceLimitedMapFunctor
RuntimeEOFException
RuntimeIOException
RuntimeScriptException
Sam2CramRecordFactory
SAMBinaryTagAndUnsignedArrayValue
SAMBinaryTagAndValue
SAMException
SAMFileHeader
SAMFileHeader.GroupOrder
SAMFileHeader.PgIdGenerator
SAMFileHeader.SortOrder
SamFileHeaderMerger
SAMFileReader
SamFiles
SAMFileSource
SAMFileSpan
SAMFileTruncatedReader
SamFileValidator
SamFileValidator.ValidationMetrics
SAMFileWriter
SAMFileWriterFactory
SAMFileWriterImpl
SAMFlag
SamFlagField
SAMFormatException
SAMHeaderRecordComparator
SamIndexes
SamInputResource
SAMLineParser
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
SAMRecordUtil
SamRecordWithOrdinal
SAMSequenceDictionary
SAMSequenceDictionaryExtractor
SAMSequenceRecord
SAMSortOrderChecker
SamStreams
SAMTag
SAMTagUtil
SAMTestUtil
SAMTestUtil.SanityCheckFailedException
SAMTextHeaderCodec
SAMTextWriter
SAMTools
SAMUtils
SAMValidationError
SAMValidationError.Severity
SAMValidationError.Type
Scores
SecondaryAlignmentFilter
SecondaryOrSupplementaryFilter
SecondaryOrSupplementarySkippingIterator
SeekableBufferedStream
SeekableFileStream
SeekableFTPStream
SeekableFTPStreamHelper
SeekableHTTPStream
SeekableMemoryStream
SeekablePathStream
SeekableStream
SeekableStreamFactory
SequenceUtil
SequenceUtil.SequenceListsDifferException
SimpleBEDFeature
SimpleFeature
Slice
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
StringHeader
StringLineReader
StringUtil
SubexponentialIntegerEncoding
Substitution
SubstitutionMatrix
SynchronousLineReader
TabixFeatureReader
TabixFormat
TabixIndex
TabixIndexCreator
TabixIteratorLineReader
TabixReader
TabixReader.Iterator
TabixReader.TIndex
TabixReader.TPair64
TabixUtils
TabixUtils.TIndex
TabixUtils.TIntv
TabixUtils.TPair64
TagFilter
TagValueAndUnsignedArrayFlag
TempStreamFactory
TestUtil
TextCigarCodec
TextTagCodec
TimeChannel
TimeRandomAccessFile
Tribble
TribbleException
TribbleException.FeatureFileDoesntExist
TribbleException.InternalCodecException
TribbleException.InvalidDecodeLine
TribbleException.InvalidHeader
TribbleException.MalformedFeatureFile
TribbleException.TabixReaderFailure
TribbleException.UnableToCreateCorrectIndexType
TribbleException.UnableToReadIndexFile
TribbleIndexCreator
TribbleIndexedFeatureReader
TrimmingUtil
Tuple
UnsortedFileException
URLHelper
UserPasswordInput
Utils
ValidationStringency
VariantContext
VariantContext.Type
VariantContext.Validation
VariantContextBuilder
VariantContextComparator
VariantContextFilter
VariantContextUtils
VariantContextUtils.JexlVCMatchExp
VariantContextWriter
VariantContextWriterBuilder
VariantContextWriterBuilder.OutputType
VariantContextWriterFactory
VCF3Codec
VCFCodec
VCFCompoundHeaderLine
VCFCompoundHeaderLine.SupportedHeaderLineType
VCFConstants
VCFContigHeaderLine
VCFEncoder
VCFFileReader
VCFFilterHeaderLine
VCFFormatHeaderLine
VCFHeader
VCFHeader.HEADER_FIELDS
VCFHeaderLine
VCFHeaderLineCount
VCFHeaderLineTranslator
VCFHeaderLineType
VCFHeaderVersion
VCFIDHeaderLine
VCFInfoHeaderLine
VCFRecordCodec
VCFSimpleHeaderLine
VCFStandardHeaderLines
VCFUtils
Version
VersionHeader
WholeGenomeReferenceSequenceMask
WholeReadClippedFilter
Writer