2fda7eb68e093b8792ba9623ff4bd3f340d3d3a4,public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java,AlignmentUtils,getNumAlignedBasesCountingSoftClips,#SAMRecord#,240

Before Change


        if (cigar == null) return 0;

        for (final CigarElement e : cigar.getCigarElements())
            if (e.getOperator() == CigarOperator.M || e.getOperator() == CigarOperator.S)
                n += e.getLength();

        return n;

After Change


        if (cigar == null) return 0;

        for (final CigarElement e : cigar.getCigarElements())
            if (ALIGNED_TO_GENOME_PLUS_SOFTCLIPS.contains(e.getOperator()))
                n += e.getLength();

        return n;