i = -1; if (reachedEndOfRead) cigar = cleanupCigar ? cleanUpCigar(cigar) : cigar;
final Cigar readToRefCigarClean = cleanUpCigar(readToRefCigarRaw); final Cigar readToRefCigar = leftAlignIndel(readToRefCigarClean, refHaplotype.getBases(), originalRead.getReadBases(), swPairwiseAlignment.getAlignmentStart2wrt1(), 0, true);