private void addInsertion(final List<ReadFeature> features, final int zeroBasedPositionInRead, final int cigarElementLength, final byte[] bases) { final byte[] insertedBases = Arrays.copyOfRange(bases, zeroBasedPositionInRead, zeroBasedPositionInRead + cigarElementLength); for (int i = 0; i < insertedBases.length; i++) { // single base insertion: final InsertBase insertBase = new InsertBase(); insertBase.setPosition(zeroBasedPositionInRead + 1 + i); insertBase.setBase(insertedBases[i]); features.add(insertBase); } }
case InsertBase.operator: final InsertBase insert = (InsertBase) variation; bases[posInRead++ - 1] = insert.getBase(); break; case RefSkip.operator:
r.setSegmentUnmapped(false); r.readFeatures = new ArrayList<>(); r.readFeatures.add(new InsertBase(1, (byte) 'A')); Assert.assertEquals(r.getAlignmentEnd(), r.readLength + r.alignmentStart - 1 - 1);
case InsertBase.operator: final InsertBase insert = (InsertBase) variation; bases[posInRead++ - 1] = insert.getBase(); break; case RefSkip.operator:
break; case InsertBase.operator: final InsertBase insertBase = new InsertBase(pos, baseCodec.readData()); readFeatures.add(insertBase); break;
private void addInsertion(final List<ReadFeature> features, final int zeroBasedPositionInRead, final int cigarElementLength, final byte[] bases) { final byte[] insertedBases = Arrays.copyOfRange(bases, zeroBasedPositionInRead, zeroBasedPositionInRead + cigarElementLength); for (int i = 0; i < insertedBases.length; i++) { // single base insertion: final InsertBase insertBase = new InsertBase(); insertBase.setPosition(zeroBasedPositionInRead + 1 + i); insertBase.setBase(insertedBases[i]); features.add(insertBase); } }
case InsertBase.operator: final InsertBase insert = (InsertBase) variation; bases[posInRead++ - 1] = insert.getBase(); break; case RefSkip.operator:
break; case InsertBase.operator: final InsertBase insertBase = new InsertBase(pos, baseCodec.readData()); readFeatures.add(insertBase); break;
case InsertBase.operator: final InsertBase ib = (InsertBase) f; baseCodec.writeData(ib.getBase()); break; case BaseQualityScore.operator:
case InsertBase.operator: final InsertBase ib = (InsertBase) f; baseCodec.writeData(ib.getBase()); break; case BaseQualityScore.operator: