private static boolean containsLargeIndel(List<CigarElement> cigar, int minsize) { for (CigarElement ce : cigar) { if (ce.getLength() >= minsize && ce.getOperator().isIndelOrSkippedRegion()) { return true; } } return false; }
int indelSize = 0; while (indelStartOffset < cl.size()) { if (cl.get(indelStartOffset).getOperator().isIndelOrSkippedRegion() && !cl.get(indelStartOffset - 1).getOperator().isIndelOrSkippedRegion()) { int indelEndOffset = indelStartOffset; while (indelEndOffset < cl.size() && cl.get(indelEndOffset).getOperator().isIndelOrSkippedRegion()) { indelSize += cl.get(indelEndOffset).getLength(); indelEndOffset++;
@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); } }
public static IndelEvidence create(SAMEvidenceSource source, SAMRecord record, int indelCigarElementOffset) { List<CigarElement> cl = record.getCigar().getCigarElements(); int indelEndOffset = indelCigarElementOffset; // exclusive end offset while (cl.get(indelEndOffset).getOperator().isIndelOrSkippedRegion() && indelEndOffset < cl.size()) { indelEndOffset++; assert(indelCigarElementOffset > 0); assert(indelEndOffset < cl.size()); assert(!cl.get(indelCigarElementOffset - 1).getOperator().isIndelOrSkippedRegion()); List<CigarElement> pre = cl.subList(0, indelCigarElementOffset); List<CigarElement> indel = cl.subList(indelCigarElementOffset, indelEndOffset);