79cb6d921d2c1aebb10a5b42b9805bf511ee03b8,src/main/java/picard/sam/AbstractAlignmentMerger.java,AbstractAlignmentMerger,clipForOverlappingReads,#SAMRecord#SAMRecord#,593
Before Change
if (posDiff > 0) {
CigarUtil.softClip3PrimeEndOfRead(pos, Math.min(pos.getReadLength(),
pos.getReadLength() - posDiff + 1));
removeNmMdAndUqTags(pos); // these tags are now invalid!
}
After Change
Collections.reverse(elems);
final int clipped = lengthOfSoftClipping(elems.iterator());
final int clipFrom = pos.getReadLength() - posDiff - clipped + 1;
CigarUtil.softClip3PrimeEndOfRead(pos, Math.min(pos.getReadLength(), clipFrom));
removeNmMdAndUqTags(pos); // these tags are now invalid!
}