Package org.seqdoop.hadoop_bam

Interface Summary

Interface	Description
LazyParsingGenotypesContext.HeaderDataCache

Class Summary

Class	Description
AnySAMInputFormat	An InputFormat for SAM, BAM, and CRAM files.
AnySAMOutputFormat<K>	An abstract OutputFormat for SAM and BAM files.
BAMInputFormat	An InputFormat for BAM files.
BAMOutputFormat<K>	Currently this only locks down the value type of the OutputFormat: contains no functionality.
BAMRecordReader	The key is the bitwise OR of the reference sequence ID in the upper 32 bits and the 0-based leftmost coordinate in the lower.
BAMRecordWriter<K>	A base RecordWriter for BAM records.
BAMSplitGuesser	A class for heuristically finding BAM record positions inside an area of a BAM file.
BCFRecordReader	See VCFRecordReader for the meaning of the key.
BCFRecordWriter<K>	A base RecordWriter for compressed BCF.
BCFSplitGuesser	A class for heuristically finding BCF record positions inside an area of a BCF file.
CRAMInputFormat
CRAMOutputFormat<K>	Currently this only locks down the value type of the OutputFormat: contains no functionality.
CRAMRecordReader
CRAMRecordWriter<K>	A base RecordWriter for CRAM records.
FastaInputFormat	Reads the FASTA reference sequence format.
FastaInputFormat.FastaRecordReader
FastqInputFormat
FastqInputFormat.FastqRecordReader
FastqOutputFormat	Output format for the fastq format.
FastqOutputFormat.FastqRecordWriter
FileVirtualSplit	Like a FileSplit, but uses BGZF virtual offsets to fit with BlockCompressedInputStream.
FormatConstants
KeyIgnoringAnySAMOutputFormat<K>	Writes only the SAM records, not the key.
KeyIgnoringBAMOutputFormat<K>	Writes only the BAM records, not the key.
KeyIgnoringBAMRecordWriter<K>	A convenience class that you can use as a RecordWriter for BAM files.
KeyIgnoringBCFRecordWriter<K>	A convenience class that you can use as a RecordWriter for BCF files.
KeyIgnoringCRAMOutputFormat<K>	Writes only the BAM records, not the key.
KeyIgnoringCRAMRecordWriter<K>	A convenience class that you can use as a RecordWriter for CRAM files.
KeyIgnoringSAMRecordWriter<K>	A convenience class that you can use as a RecordWriter for SAM files.
KeyIgnoringVCFOutputFormat<K>	Writes only the VCF records, not the key.
KeyIgnoringVCFRecordWriter<K>	A convenience class that you can use as a RecordWriter for VCF files.
LazyBAMRecordFactory	A factory for the kind of lazy BAMRecord used internally.
LazyBCFGenotypesContext
LazyBCFGenotypesContext.HeaderDataCache
LazyBCFGenotypesContext.Parser
LazyParsingGenotypesContext	You need to call getParser().setHeader() here before trying to decode() a GenotypesContext in any VariantContext that came about via VariantContextWritable.readFields().
LazyParsingGenotypesContext.Parser
LazyVCFGenotypesContext
LazyVCFGenotypesContext.HeaderDataCache
LazyVCFGenotypesContext.Parser
LineReader	A class that provides a line reader from an input stream.
QseqInputFormat	Reads the Illumina qseq sequence format.
QseqInputFormat.QseqRecordReader
QseqOutputFormat	Output format for Illumina qseq format.
QseqOutputFormat.QseqRecordWriter
ReferenceFragment
SAMInputFormat	An InputFormat for SAM files.
SAMRecordReader	See BAMRecordReader for the meaning of the key.
SAMRecordWritable	A Writable SAMRecord.
SAMRecordWriter<K>	A base RecordWriter for SAM records.
SequencedFragment
SplittingBAMIndex	An index into BAM files, for BAMInputFormat.
SplittingBAMIndexer	An indexing tool and API for BAM files, making them palatable to BAMInputFormat.
VariantContextCodec
VariantContextWithHeader
VariantContextWritable	VariantContexts read here have LazyGenotypesContexts, which need to have a header set before the genotype data in the VariantContexts can be decoded.
VCFInputFormat	An InputFormat for VCF files.
VCFOutputFormat<K>	An abstract OutputFormat for VCF and BCF files.
VCFRecordReader	The key is the bitwise OR of the chromosome index in the upper 32 bits and the 0-based leftmost coordinate in the lower.
VCFRecordWriter<K>	A base RecordWriter for VCF.

Enum Summary

Enum	Description
FormatConstants.BaseQualityEncoding	Encodings for base quality formats.
SAMFormat	Describes a SAM format.
VCFFormat	Describes a VCF format.

Exception Summary

Exception	Description
FormatException