All Classes
AnySAMInputFormat
AnySAMOutputFormat
BAMInputFormat
BAMOutputFormat
BAMRecordReader
BAMRecordWriter
BAMSplitGuesser
BCFRecordReader
BCFRecordWriter
BCFSplitGuesser
BGZFBlockIndex
BGZFBlockIndexer
BGZFCodec
BGZFEnhancedGzipCodec
BGZFSplitFileInputFormat
BGZFSplitGuesser
ConfHelper
CRAMInputFormat
CRAMOutputFormat
CRAMRecordReader
CRAMRecordWriter
DataInputWrapper
DataOutputWrapper
FastaInputFormat
FastaInputFormat.FastaRecordReader
FastqInputFormat
FastqInputFormat.FastqRecordReader
FastqOutputFormat
FastqOutputFormat.FastqRecordWriter
FileVirtualSplit
FormatConstants
FormatConstants.BaseQualityEncoding
FormatException
GetSortedBAMHeader
KeyIgnoringAnySAMOutputFormat
KeyIgnoringBAMOutputFormat
KeyIgnoringBAMRecordWriter
KeyIgnoringBCFRecordWriter
KeyIgnoringCRAMOutputFormat
KeyIgnoringCRAMRecordWriter
KeyIgnoringSAMRecordWriter
KeyIgnoringVCFOutputFormat
KeyIgnoringVCFRecordWriter
LazyBAMRecordFactory
LazyBCFGenotypesContext
LazyBCFGenotypesContext.HeaderDataCache
LazyBCFGenotypesContext.Parser
LazyParsingGenotypesContext
LazyParsingGenotypesContext.HeaderDataCache
LazyParsingGenotypesContext.Parser
LazyVCFGenotypesContext
LazyVCFGenotypesContext.HeaderDataCache
LazyVCFGenotypesContext.Parser
LinearBAMIndex
LineReader
MurmurHash3
NIOFileUtil
Pair
QseqInputFormat
QseqInputFormat.QseqRecordReader
QseqOutputFormat
QseqOutputFormat.QseqRecordWriter
ReferenceFragment
SAMFileMerger
SAMFormat
SAMHeaderReader
SAMInputFormat
SAMOutputPreparer
SAMRecordReader
SAMRecordWritable
SAMRecordWriter
SeekableArrayStream
SequencedFragment
SplittingBAMIndex
SplittingBAMIndexer
Timer
VariantContextCodec
VariantContextWithHeader
VariantContextWritable
VCFFileMerger
VCFFormat
VCFHeaderReader
VCFInputFormat
VCFOutputFormat
VCFRecordReader
VCFRecordWriter
WrapSeekable