void calculateAlignmentBoundaries() { if (isSegmentUnmapped()) { alignmentSpan = 0; alignmentEnd = SAMRecord.NO_ALIGNMENT_START; } else if (readFeatures == null || readFeatures.isEmpty()) { alignmentSpan = readLength; alignmentEnd = alignmentStart + alignmentSpan - 1; } else { alignmentSpan = readLength; for (final ReadFeature readFeature : readFeatures) { switch (readFeature.getOperator()) { case InsertBase.operator: alignmentSpan--; break; case Insertion.operator: alignmentSpan -= ((Insertion) readFeature).getSequence().length; break; case SoftClip.operator: alignmentSpan -= ((SoftClip) readFeature).getSequence().length; break; case Deletion.operator: alignmentSpan += ((Deletion) readFeature).getLength(); break; default: break; } } alignmentEnd = alignmentStart + alignmentSpan - 1; } }
void calculateAlignmentBoundaries() { if (isSegmentUnmapped()) { alignmentSpan = 0; alignmentEnd = SAMRecord.NO_ALIGNMENT_START; } else if (readFeatures == null || readFeatures.isEmpty()) { alignmentSpan = readLength; alignmentEnd = alignmentStart + alignmentSpan - 1; } else { alignmentSpan = readLength; for (final ReadFeature readFeature : readFeatures) { switch (readFeature.getOperator()) { case InsertBase.operator: alignmentSpan--; break; case Insertion.operator: alignmentSpan -= ((Insertion) readFeature).getSequence().length; break; case SoftClip.operator: alignmentSpan -= ((SoftClip) readFeature).getSequence().length; break; case Deletion.operator: alignmentSpan += ((Deletion) readFeature).getLength(); break; default: break; } } alignmentEnd = alignmentStart + alignmentSpan - 1; } }
case Deletion.operator: cigarOperator = CigarOperator.DELETION; readFeatureLength = ((Deletion) feature).getLength(); break; case RefSkip.operator:
case Deletion.operator: cigarOperator = CigarOperator.DELETION; readFeatureLength = ((Deletion) feature).getLength(); break; case RefSkip.operator:
case Deletion.operator: final Deletion deletion = (Deletion) variation; posInSeq += deletion.getLength(); break; case InsertBase.operator:
case Deletion.operator: final Deletion deletion = (Deletion) variation; posInSeq += deletion.getLength(); break; case InsertBase.operator:
case Deletion.operator: final Deletion deletion = (Deletion) variation; posInSeq += deletion.getLength(); break; case InsertBase.operator:
case Deletion.operator: final Deletion dv = (Deletion) f; deletionLengthCodec.writeData(dv.getLength()); break; case RefSkip.operator:
case Deletion.operator: final Deletion dv = (Deletion) f; deletionLengthCodec.writeData(dv.getLength()); break; case RefSkip.operator: