private static boolean isClippingOperator(final CigarOperator op) { return op !=null && op.isClipping(); }
private static boolean isClippingOperator(final CigarOperator op) { return op !=null && op.isClipping(); }
public static int getStartClipLength(List<CigarElement> elements) { if (elements == null) { return 0; } int clipLength = 0; for (int i = 0; i < elements.size() && elements.get(i).getOperator().isClipping(); i++) { clipLength += elements.get(i).getLength(); } return clipLength; }
public static int getEndClipLength(List<CigarElement> elements) { if (elements == null) { return 0; } int clipLength = 0; for (int i = elements.size() - 1; i >= 0 && elements.get(i).getOperator().isClipping(); i--) { clipLength += elements.get(i).getLength(); } return clipLength; }
public static int getEndSoftClipLength(List<CigarElement> elements) { if (elements == null) return 0; int i = elements.size() - 1; while (i >= 0 && elements.get(i).getOperator().isClipping()) { if (elements.get(i).getOperator() == CigarOperator.SOFT_CLIP) { return elements.get(i).getLength(); } i--; } return 0; }
public static int getStartSoftClipLength(List<CigarElement> elements) { if (elements == null) { return 0; } int i = 0; while (i < elements.size() && elements.get(i).getOperator().isClipping()) { if (elements.get(i).getOperator() == CigarOperator.SOFT_CLIP) { return elements.get(i).getLength(); } i++; } return 0; }
@Test(dataProvider = "opStatus") public void testIsSetOfOperations(final CigarOperator op, final boolean isClipping, final boolean isIndel,final boolean isSkip, final boolean isAlignment, final boolean isPadding) throws Exception { Assert.assertEquals(op.isClipping(), isClipping); Assert.assertEquals(op.isIndel(), isIndel); Assert.assertEquals(op.isIndelOrSkippedRegion(), isIndel || isSkip); Assert.assertEquals(op.isAlignment(), isAlignment); Assert.assertEquals(op.isPadding(), isPadding); } }