Package htsjdk.samtools
Interface SAMRecordFactory
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- All Known Implementing Classes:
DefaultSAMRecordFactory
public interface SAMRecordFactory
Factory interface which allows plugging in of different classes for generating instances of SAMRecord and BAMRecord when reading from SAM/BAM files.
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Method Summary
All Methods Instance Methods Abstract 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 in
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Method Detail
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createSAMRecord
SAMRecord createSAMRecord(SAMFileHeader header)
Create a new SAMRecord to be filled in
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createBAMRecord
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.
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