Class DefaultSAMRecordFactory

    • Constructor Detail

      • DefaultSAMRecordFactory

        public DefaultSAMRecordFactory()
    • Method Detail

      • 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 interface SAMRecordFactory