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;