Package htsjdk.samtools
Class DefaultSAMRecordFactory
- java.lang.Object
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- htsjdk.samtools.DefaultSAMRecordFactory
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- All Implemented Interfaces:
SAMRecordFactory
public class DefaultSAMRecordFactory extends Object implements SAMRecordFactory
Default factory for creating SAM and BAM records used by theSamReader
classes.
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Constructor Summary
Constructors Constructor Description DefaultSAMRecordFactory()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description 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.SAMRecord
createSAMRecord(SAMFileHeader header)
Create a new SAMRecord to be filled instatic DefaultSAMRecordFactory
getInstance()
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Method Detail
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getInstance
public static DefaultSAMRecordFactory getInstance()
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createSAMRecord
public SAMRecord createSAMRecord(SAMFileHeader header)
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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