@Override protected Double getElementForRead(final GATKSAMRecord read, final int refLoc) { return (double)AlignmentUtils.getNumHardClippedBases(read); } }
@Test(enabled = !DEBUG, dataProvider = "NumHardClipped") public void testNumHardClipped(final Cigar cigar, final int expected) { final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, cigar == null ? 10 : cigar.getReadLength()); read.setCigar(cigar); Assert.assertEquals(AlignmentUtils.getNumHardClippedBases(read), expected, "Cigar " + cigar + " failed num hard clips"); }