7532be7f5ae13bd1e4cea7295d1938f66d6ef13a,public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java,ReadUtils,getRefCoordSoftUnclippedStop,#SAMRecord#,672
Before Change
public static int getRefCoordSoftUnclippedStop(SAMRecord read) {
int stop = read.getAlignmentEnd();
List<CigarElement> cigarElementList = read.getCigar().getCigarElements();
CigarElement lastCigarElement = cigarElementList.get(cigarElementList.size()-1);
if (lastCigarElement.getOperator() == CigarOperator.SOFT_CLIP)
stop += lastCigarElement.getLength();
After Change
public static int getRefCoordSoftUnclippedEnd(SAMRecord read) {
int stop = read.getUnclippedStart();
int shift = 0;
for (CigarElement cigarElement : read.getCigar().getCigarElements())
if (cigarElement.getOperator().consumesReferenceBases() || cigarElement.getOperator() == CigarOperator.SOFT_CLIP)
shift += cigarElement.getLength();
return (shift == 0) ? stop : stop+shift-1;