private void addHardClip(final List<ReadFeature> features, final int zeroBasedPositionInRead, final int cigarElementLength, final byte[] bases) { final byte[] insertedBases = Arrays.copyOfRange(bases, zeroBasedPositionInRead, zeroBasedPositionInRead + cigarElementLength); final HardClip hardClip = new HardClip(zeroBasedPositionInRead + 1, insertedBases.length); features.add(hardClip); }
case HardClip.operator: cigarOperator = CigarOperator.HARD_CLIP; readFeatureLength = ((HardClip) feature).getLength(); break; case InsertBase.operator:
case HardClip.operator: cigarOperator = CigarOperator.HARD_CLIP; readFeatureLength = ((HardClip) feature).getLength(); break; case InsertBase.operator:
private void addHardClip(final List<ReadFeature> features, final int zeroBasedPositionInRead, final int cigarElementLength, final byte[] bases) { final byte[] insertedBases = Arrays.copyOfRange(bases, zeroBasedPositionInRead, zeroBasedPositionInRead + cigarElementLength); final HardClip hardClip = new HardClip(zeroBasedPositionInRead + 1, insertedBases.length); features.add(hardClip); }
case HardClip.operator: final HardClip hv = (HardClip) f; hardClipCodec.writeData(hv.getLength()); break; case Padding.operator:
break; case H: features.add(new HardClip(zeroBasedPositionInRead + 1, cigarElementLength)); break; case S:
case HardClip.operator: final HardClip hv = (HardClip) f; hardClipCodec.writeData(hv.getLength()); break; case Padding.operator:
break; case H: features.add(new HardClip(zeroBasedPositionInRead + 1, cigarElementLength)); break; case S:
break; case HardClip.operator: final HardClip hardCLip = new HardClip(pos, hardClipCodec.readData()); readFeatures.add(hardCLip); break;
break; case HardClip.operator: final HardClip hardCLip = new HardClip(pos, hardClipCodec.readData()); readFeatures.add(hardCLip); break;