htsjdk.samtools

Interface SAMRecordFactory

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.

Method Summary

Modifier and Type	Method and 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

Method Detail

createSAMRecord

SAMRecord createSAMRecord(SAMFileHeader header)

Create a new SAMRecord to be filled in

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.