public void addQualityScores(final SAMRecord samRecord, final CramCompressionRecord cramRecord, final ReferenceTracks referenceTracks) { if (samRecord.getBaseQualities() == SAMRecord.NULL_QUALS) { cramRecord.qualityScores = SAMRecord.NULL_QUALS; cramRecord.setForcePreserveQualityScores(false); return; } final byte[] scores = new byte[samRecord.getReadLength()]; Arrays.fill(scores, (byte) -1); for (final PreservationPolicy preservationPolicy : policyList) addQS(samRecord, cramRecord, scores, referenceTracks, preservationPolicy); if (!cramRecord.isForcePreserveQualityScores()) { for (int i = 0; i < scores.length; i++) { if (scores[i] > -1) { if (cramRecord.readFeatures == null) cramRecord.readFeatures = new LinkedList<ReadFeature>(); cramRecord.readFeatures.add(new BaseQualityScore(i + 1, scores[i])); } } if (cramRecord.readFeatures != null) Collections.sort(cramRecord.readFeatures, readFeaturePositionComparator); } cramRecord.qualityScores = scores; }
case BaseQualityScore.operator: int pos = feature.getPosition(); scores[pos - 1] = ((BaseQualityScore) feature).getQualityScore(); star = false; break;
public void addQualityScores(final SAMRecord samRecord, final CramCompressionRecord cramRecord, final ReferenceTracks referenceTracks) { if (samRecord.getBaseQualities() == SAMRecord.NULL_QUALS) { cramRecord.qualityScores = SAMRecord.NULL_QUALS; cramRecord.setForcePreserveQualityScores(false); return; } final byte[] scores = new byte[samRecord.getReadLength()]; Arrays.fill(scores, (byte) -1); for (final PreservationPolicy preservationPolicy : policyList) addQS(samRecord, cramRecord, scores, referenceTracks, preservationPolicy); if (!cramRecord.isForcePreserveQualityScores()) { for (int i = 0; i < scores.length; i++) { if (scores[i] > -1) { if (cramRecord.readFeatures == null) cramRecord.readFeatures = new LinkedList<ReadFeature>(); cramRecord.readFeatures.add(new BaseQualityScore(i + 1, scores[i])); } } if (cramRecord.readFeatures != null) Collections.sort(cramRecord.readFeatures, readFeaturePositionComparator); } cramRecord.qualityScores = scores; }
case BaseQualityScore.operator: int pos = feature.getPosition(); scores[pos - 1] = ((BaseQualityScore) feature).getQualityScore(); star = false; break;
public void addQualityScores(final SAMRecord s, final CramCompressionRecord r, final ReferenceTracks t) { if (s.getBaseQualities() == SAMRecord.NULL_QUALS) { r.qualityScores = SAMRecord.NULL_QUALS; r.setForcePreserveQualityScores(false); return; } final byte[] scores = new byte[s.getReadLength()]; Arrays.fill(scores, (byte) -1); for (final PreservationPolicy p : policyList) addQS(s, r, scores, t, p); if (!r.isForcePreserveQualityScores()) { for (int i = 0; i < scores.length; i++) { if (scores[i] > -1) { if (r.readFeatures == null || r.readFeatures == Collections.EMPTY_LIST) r.readFeatures = new LinkedList<ReadFeature>(); r.readFeatures.add(new BaseQualityScore(i + 1, scores[i])); } } if (r.readFeatures != null) Collections.sort(r.readFeatures, readFeaturePositionComparator); } r.qualityScores = scores; }
case BaseQualityScore.operator: int pos = feature.getPosition(); scores[pos - 1] = ((BaseQualityScore) feature).getQualityScore(); star = false; break;
break; case BaseQualityScore.operator: final BaseQualityScore baseQualityScore = new BaseQualityScore(pos, qualityScoreCodec.readData()); readFeatures.add(baseQualityScore); break;
case BaseQualityScore.operator: final BaseQualityScore bqs = (BaseQualityScore) f; qualityScoreCodec.writeData(bqs.getQualityScore()); break; default:
break; case BaseQualityScore.operator: final BaseQualityScore baseQualityScore = new BaseQualityScore(pos, qualityScoreCodec.readData()); readFeatures.add(baseQualityScore); break;
case BaseQualityScore.operator: final BaseQualityScore bqs = (BaseQualityScore) f; qualityScoreCodec.writeData(bqs.getQualityScore()); break; default: