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 Detail

      • 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.