@Ignore("Broken test.") @Test public void test4() { String line2 = "98738 1187 20 18 29 99M1S = 1000253 432 AGCGGGGATATATAAAGGCTCAAAATTACTTTTTATATGGACAACTCTCTACTGCTTTGAGATGACTGATACTCATATTGATGGAGCTTTATCAAGAAAT !\"#$%&'()*+-./0'''''''''''#'#'#'''''''#''''#'''''''''##''''#'#''#'''''#'''''''''##''''#''##''''''''?"; String seqName = "20"; List<String> lines = Arrays.asList(new String[] { line2 }); byte[] ref = "CTGGTCTTAGTTCCGCAAGTGGGTATATATAAAGGCTCAAAATCAATCTTTATATTGACATCTCTCTACTTATTTGTGTTGTCTGATGCTCATATTGTAGGAGATTCCTCAAGAAAGG" .getBytes(); ReferenceTracks tracks = new ReferenceTracks(0, seqName, ref); QualityScorePreservation p = new QualityScorePreservation("R40X10-N40-U40"); for (int i = 0; i < ref.length; i++) tracks.addCoverage(i + 1, 66); for (String line : lines) { SAMRecord record = buildSAMRecord(seqName, line); Sam2CramRecordFactory f = new Sam2CramRecordFactory(ref, record.getHeader(), CramVersions.CRAM_v3); CramCompressionRecord cramRecord = f.createCramRecord(record); p.addQualityScores(record, cramRecord, tracks); if (!cramRecord.isForcePreserveQualityScores()) { CramNormalizer.restoreQualityScores((byte) 30, Collections.singletonList(cramRecord)); } StringBuffer sb = new StringBuffer(); sb.append(record.getBaseQualityString()); sb.append("\n"); sb.append(SAMUtils.phredToFastq(cramRecord.qualityScores)); assertArrayEquals(sb.toString(), record.getBaseQualities(), cramRecord.qualityScores); } }
private static void updateTracks(final List<SAMRecord> samRecords, final ReferenceTracks tracks) { for (final SAMRecord samRecord : samRecords) { if (samRecord.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START) { int refPos = samRecord.getAlignmentStart(); int readPos = 0; for (final CigarElement cigarElement : samRecord.getCigar().getCigarElements()) { if (cigarElement.getOperator().consumesReferenceBases()) { for (int elementIndex = 0; elementIndex < cigarElement.getLength(); elementIndex++) tracks.addCoverage(refPos + elementIndex, 1); } switch (cigarElement.getOperator()) { case M: case X: case EQ: for (int pos = readPos; pos < cigarElement.getLength(); pos++) { final byte readBase = samRecord.getReadBases()[readPos + pos]; final byte refBase = tracks.baseAt(refPos + pos); if (readBase != refBase) tracks.addMismatches(refPos + pos, 1); } break; default: break; } readPos += cigarElement.getOperator().consumesReadBases() ? cigarElement.getLength() : 0; refPos += cigarElement.getOperator().consumesReferenceBases() ? cigarElement.getLength() : 0; } } } }
private static void updateTracks(final List<SAMRecord> samRecords, final ReferenceTracks tracks) { for (final SAMRecord samRecord : samRecords) { if (samRecord.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START) { int refPos = samRecord.getAlignmentStart(); int readPos = 0; for (final CigarElement cigarElement : samRecord.getCigar().getCigarElements()) { if (cigarElement.getOperator().consumesReferenceBases()) { for (int elementIndex = 0; elementIndex < cigarElement.getLength(); elementIndex++) tracks.addCoverage(refPos + elementIndex, 1); } switch (cigarElement.getOperator()) { case M: case X: case EQ: for (int pos = readPos; pos < cigarElement.getLength(); pos++) { final byte readBase = samRecord.getReadBases()[readPos + pos]; final byte refBase = tracks.baseAt(refPos + pos); if (readBase != refBase) tracks.addMismatches(refPos + pos, 1); } break; default: break; } readPos += cigarElement.getOperator().consumesReadBases() ? cigarElement.getLength() : 0; refPos += cigarElement.getOperator().consumesReferenceBases() ? cigarElement.getLength() : 0; } } } }
if (cigarElement.getOperator().consumesReferenceBases()) { for (int elementIndex = 0; elementIndex < cigarElement.getLength(); elementIndex++) tracks.addCoverage(refPos + elementIndex, 1);