org.seqdoop.hadoop_bam

Interfaces

• LazyParsingGenotypesContext.HeaderDataCache

Classes

• AnySAMInputFormat
• AnySAMOutputFormat
• BAMInputFormat
• BAMOutputFormat
• BAMRecordReader
• BAMRecordWriter
• BAMSplitGuesser
• BCFRecordReader
• BCFRecordWriter
• BCFSplitGuesser
• CRAMInputFormat
• CRAMOutputFormat
• CRAMRecordReader
• CRAMRecordWriter
• FastaInputFormat
• FastaInputFormat.FastaRecordReader
• FastqInputFormat
• FastqInputFormat.FastqRecordReader
• FastqOutputFormat
• FastqOutputFormat.FastqRecordWriter
• FileVirtualSplit
• FormatConstants
• KeyIgnoringAnySAMOutputFormat
• KeyIgnoringBAMOutputFormat
• KeyIgnoringBAMRecordWriter
• KeyIgnoringBCFRecordWriter
• KeyIgnoringCRAMOutputFormat
• KeyIgnoringCRAMRecordWriter
• KeyIgnoringSAMRecordWriter
• KeyIgnoringVCFOutputFormat
• KeyIgnoringVCFRecordWriter
• LazyBAMRecordFactory
• LazyBCFGenotypesContext
• LazyBCFGenotypesContext.HeaderDataCache
• LazyBCFGenotypesContext.Parser
• LazyParsingGenotypesContext
• LazyParsingGenotypesContext.Parser
• LazyVCFGenotypesContext
• LazyVCFGenotypesContext.HeaderDataCache
• LazyVCFGenotypesContext.Parser
• LineReader
• QseqInputFormat
• QseqInputFormat.QseqRecordReader
• QseqOutputFormat
• QseqOutputFormat.QseqRecordWriter
• ReferenceFragment
• SAMInputFormat
• SAMRecordReader
• SAMRecordWritable
• SAMRecordWriter
• SequencedFragment
• SplittingBAMIndex
• SplittingBAMIndexer
• VariantContextCodec
• VariantContextWithHeader
• VariantContextWritable
• VCFInputFormat
• VCFOutputFormat
• VCFRecordReader
• VCFRecordWriter

Enums

• FormatConstants.BaseQualityEncoding
• SAMFormat
• VCFFormat

Exceptions

• FormatException