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 SoftClip.operator: final SoftClip softClip = (SoftClip) variation; for (int i = 0; i < softClip.getSequence().length; i++) bases[posInRead++ - 1] = softClip.getSequence()[i]; break; case Deletion.operator:
case SoftClip.operator: cigarOperator = CigarOperator.SOFT_CLIP; readFeatureLength = ((SoftClip) feature).getSequence().length; break; case HardClip.operator:
case SoftClip.operator: cigarOperator = CigarOperator.SOFT_CLIP; readFeatureLength = ((SoftClip) feature).getSequence().length; break; case HardClip.operator:
case SoftClip.operator: final SoftClip softClip = (SoftClip) variation; for (int i = 0; i < softClip.getSequence().length; i++) bases[posInRead++ - 1] = softClip.getSequence()[i]; break; case Deletion.operator:
case SoftClip.operator: final SoftClip softClip = (SoftClip) variation; for (int i = 0; i < softClip.getSequence().length; i++) bases[posInRead++ - 1] = softClip.getSequence()[i]; break; case Deletion.operator:
case SoftClip.operator: final SoftClip fv = (SoftClip) f; softClipCodec.writeData(fv.getSequence()); break; case HardClip.operator:
case SoftClip.operator: final SoftClip fv = (SoftClip) f; softClipCodec.writeData(fv.getSequence()); break; case HardClip.operator: