private void addSoftClip(final List<ReadFeature> features, final int zeroBasedPositionInRead, final int cigarElementLength, final byte[] bases) { final byte[] insertedBases = Arrays.copyOfRange(bases, zeroBasedPositionInRead, zeroBasedPositionInRead + cigarElementLength); final SoftClip softClip = new SoftClip(zeroBasedPositionInRead + 1, insertedBases); features.add(softClip); }
private void addSoftClip(final List<ReadFeature> features, final int zeroBasedPositionInRead, final int cigarElementLength, final byte[] bases) { final byte[] insertedBases = Arrays.copyOfRange(bases, zeroBasedPositionInRead, zeroBasedPositionInRead + cigarElementLength); final SoftClip softClip = new SoftClip(zeroBasedPositionInRead + 1, insertedBases); features.add(softClip); }
@Test public void faultyEquality() { final Bases b1 = new Bases(0, new byte[] {}); final Bases b2 = new Bases(0, new byte[] {}); Assert.assertEquals(b1, b2); final Scores s1 = new Scores(0, new byte[] {}); final Scores s2 = new Scores(0, new byte[] {}); Assert.assertEquals(s1, s2); final SoftClip sc1 = new SoftClip(0, new byte[] {}); final SoftClip sc2 = new SoftClip(0, new byte[] {}); Assert.assertEquals(sc1, sc2); } }
r.readFeatures = new ArrayList<>(); String softClip = "AAA"; r.readFeatures.add(new SoftClip(1, softClip.getBytes())); Assert.assertEquals(r.getAlignmentEnd(), r.readLength + r.alignmentStart - 1 - softClip.length());
break; case SoftClip.operator: final SoftClip softClip = new SoftClip(pos, softClipCodec.readData()); readFeatures.add(softClip); break;
break; case SoftClip.operator: final SoftClip softClip = new SoftClip(pos, softClipCodec.readData()); readFeatures.add(softClip); break;