@Test public void test() { SAMFileHeader header = new SAMFileHeader(); SAMRecord r1 = new SAMRecord(header); r1.setReadName("readName"); r1.setFlags(4); r1.setReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX); r1.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START); r1.setMappingQuality(SAMRecord.NO_MAPPING_QUALITY); r1.setCigar(new Cigar()); r1.setMateReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX); r1.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START); r1.setReadBases("A".getBytes()); r1.setBaseQualityString("!"); BAMRecordView view = new BAMRecordView(new byte[1024]); translate(r1, view); r1.setReadName("2"); translate(r1, view); List<SAMRecord> list = toSAMRecord(view, header); assertEquals(2, list.size()); Iterator<SAMRecord> iterator = list.iterator(); SAMRecord r2 = iterator.next(); r1.setReadName("readName"); compare(r1, r2); r1.setReadName("2"); r2 = iterator.next(); compare(r1, r2); }