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!
                    }