All Classes
AnySAMInputFormat
AnySAMOutputFormat
BAMInputFormat
BAMOutputFormat
BAMRecordReader
BAMRecordWriter
BAMSplitGuesser
BCFRecordReader
BCFRecordWriter
BCFSplitGuesser
BGZFBlockIndex
BGZFBlockIndexer
BGZFSplitFileInputFormat
BGZFSplitGuesser
Cat
CLIMergingAnySAMOutputFormat
CLIMRBAMPlugin
CLIMRPlugin
CLIPlugin
CmdLineParser
CmdLineParser.IllegalOptionValueException
CmdLineParser.NotFlagException
CmdLineParser.Option
CmdLineParser.Option.BooleanOption
CmdLineParser.Option.DoubleOption
CmdLineParser.Option.IntegerOption
CmdLineParser.Option.LongOption
CmdLineParser.Option.StringOption
CmdLineParser.OptionException
CmdLineParser.UnknownOptionException
CmdLineParser.UnknownSuboptionException
ConfHelper
CRAMInputFormat
CRAMOutputFormat
CRAMRecordReader
CRAMRecordWriter
DataInputWrapper
DataOutputWrapper
FastaInputFormat
FastaInputFormat.FastaRecordReader
FastqInputFormat
FastqInputFormat.FastqRecordReader
FastqOutputFormat
FastqOutputFormat.FastqRecordWriter
FileVirtualSplit
FixMate
FormatConstants
FormatConstants.BaseQualityEncoding
FormatException
Frontend
GetSortedBAMHeader
Index
InputSampler
InputSampler.IntervalSampler
InputSampler.RandomSampler
InputSampler.Sampler
InputSampler.SplitSampler
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
LineReader
MultipleOutputs
MurmurHash3
Pair
QseqInputFormat
QseqInputFormat.QseqRecordReader
QseqOutputFormat
QseqOutputFormat.QseqRecordWriter
ReferenceFragment
SAMFormat
SAMHeaderReader
SAMInputFormat
SAMOutputPreparer
SAMRecordReader
SAMRecordWritable
SAMRecordWriter
SeekableArrayStream
SequencedFragment
Sort
SplittingBAMIndex
SplittingBAMIndexer
Summarize
SummarySort
Timer
TotalOrderPartitioner
Utils
VariantContextCodec
VariantContextWithHeader
VariantContextWritable
VCFFormat
VCFHeaderReader
VCFInputFormat
VCFOutputFormat
VCFRecordReader
VCFRecordWriter
VCFSort
View
WrapSeekable