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;