@Test(dataProvider = "ReadOffsetFromCigarData", enabled = !DEBUG) public void testReadOffsetFromCigar(final String cigarString, final int startOnCigar, final int expectedOffset) { final Cigar cigar = TextCigarCodec.decode(cigarString); final int actualOffset = AlignmentUtils.calcFirstBaseMatchingReferenceInCigar(cigar, startOnCigar); Assert.assertEquals(actualOffset, expectedOffset); }
final int readStartOnHaplotype = calcFirstBaseMatchingReferenceInCigar(extendedHaplotypeCigar, swPairwiseAlignment.getAlignmentStart2wrt1()); final int readStartOnReference = referenceStart + haplotype.getAlignmentStartHapwrtRef() + readStartOnHaplotype; read.setAlignmentStart(readStartOnReference);