private void setMateRefIDForRecord(int record, int refId) { view.start = index[record]; view.setMateRefID(refId); }
view.setReadName(readNameCodec.readData()); view.setMateRefID(mateReferenceIdCodec.readData()); view.setMateAlStart(mateAlignmentStartCodec.readData()); view.setInsertSize(insertSizeCodec.readData());
view.setIndexBin(99); view.setFlags(555); view.setMateRefID(0); view.setMateAlStart(78); view.setInsertSize(133);
view.setMappingScore(SAMRecord.NO_MAPPING_QUALITY); view.setCigar(new Cigar()); view.setMateRefID(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX); view.setMateAlStart(SAMRecord.NO_ALIGNMENT_START); view.setInsertSize(0);
private int translate(SAMRecord record, BAMRecordView view) { view.setReadName(record.getReadName()); view.setFlags(record.getFlags()); view.setRefID(record.getReferenceIndex()); view.setAlignmentStart(record.getAlignmentStart()); view.setMappingScore(record.getMappingQuality()); view.setCigar(record.getCigar()); view.setMateRefID(record.getMateReferenceIndex()); view.setMateAlStart(record.getMateAlignmentStart()); view.setInsertSize(record.getInferredInsertSize()); view.setBases(record.getReadBases()); view.setQualityScores(record.getBaseQualities()); view.setTagData(new byte[0], 0, 0); return view.finish(); }