public void setBases(byte[] bases) { setBases(bases, 0, bases.length); }
private void setFlagsForRecord(int record, int flags) { view.start = index[record]; view.setFlags(flags); }
private void setInsertSizeForRecord(int record, int insertSize) { view.start = index[record]; view.setInsertSize(insertSize); }
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(); }
private void setMateRefIDForRecord(int record, int refId) { view.start = index[record]; view.setMateRefID(refId); }
private void setMateAlignmentStartForRecord(int record, int astart) { view.start = index[record]; view.setMateAlStart(astart); }
public void read() throws IOException { index[recordCounter] = view.position(); view.setRefID(refIdCodec.readData()); else view.setRefID(refId); view.setAlignmentStart(prevAlStart); view.setReadName(readNameCodec.readData()); mateFlags = mateBitFlagCodec.readData(); if (!captureReadNames) view.setReadName(readNameCodec.readData()); view.setMateRefID(mateReferenceIdCodec.readData()); view.setMateAlStart(mateAlignmentStartCodec.readData()); view.setInsertSize(insertSizeCodec.readData()); detachedCount++; distances[recordCounter] = 0; view.setFlags(flags); if (!view.isReadNameSet()) { if (names[recordCounter] == 0) view.setReadName(String.valueOf(recordCounter).getBytes()); else view.setReadName(String.valueOf(names[recordCounter]).getBytes()); view.setMappingScore(mappingScoreCodec.readData());
@Test public void test1() { BAMRecordView view = new BAMRecordView(new byte[1024]); view.setReadName("readName"); view.setFlags(4); view.setRefID(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX); view.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START); 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); view.setBases("A".getBytes()); view.setQualityScores(new byte[] { 0 }); view.addTag(SAMTagUtil.getSingleton().AM, new byte[] { 'c', 0 }, 0, 1); view.finish();
@Test public void test() throws IOException { byte[] buf = new byte[1024]; BAMRecordView view = new BAMRecordView(buf); view.setRefID(0); view.setAlignmentStart(77); view.setMappingScore(44); view.setIndexBin(99); view.setFlags(555); view.setMateRefID(0); view.setMateAlStart(78); view.setInsertSize(133); view.setReadName("name1"); view.setCigar(TextCigarCodec.decode("10M")); view.setBases("AAAAAAAAAA".getBytes()); view.setQualityScores("BBBBBBBBBB".getBytes()); view.addTag(id, "Q".getBytes(), 0, 1); int len = view.finish();