Package htsjdk.samtools
Class DefaultSAMRecordFactory
java.lang.Object
htsjdk.samtools.DefaultSAMRecordFactory
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SAMRecordFactory
Default factory for creating SAM and BAM records used by the
SamReader
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptioncreateBAMRecord
(SAMFileHeader header, int referenceSequenceIndex, int alignmentStart, short readNameLength, short mappingQuality, int indexingBin, int cigarLen, int flags, int readLen, int mateReferenceSequenceIndex, int mateAlignmentStart, int insertSize, byte[] variableLengthBlock) Create a new BAM Record.createSAMRecord
(SAMFileHeader header) Create a new SAMRecord to be filled instatic DefaultSAMRecordFactory
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Constructor Details
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DefaultSAMRecordFactory
public DefaultSAMRecordFactory()
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Method Details
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getInstance
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createSAMRecord
Create a new SAMRecord to be filled in- Specified by:
createSAMRecord
in interfaceSAMRecordFactory
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createBAMRecord
public BAMRecord createBAMRecord(SAMFileHeader header, int referenceSequenceIndex, int alignmentStart, short readNameLength, short mappingQuality, int indexingBin, int cigarLen, int flags, int readLen, int mateReferenceSequenceIndex, int mateAlignmentStart, int insertSize, byte[] variableLengthBlock) Create a new BAM Record. If the reference sequence index or mate reference sequence index are any value other than NO_ALIGNMENT_REFERENCE_INDEX, the values must be resolvable against the sequence dictionary in the header argument.- Specified by:
createBAMRecord
in interfaceSAMRecordFactory
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