7cf9a54b6485ea7319c3eddf098a3b7106c499ad,java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounter.java,CovariateCounter,updateDataFromRead,#String#SAMRecord#number#char#,112

Before Change


        if (read.getReadNegativeStrandFlag()) {
            ref = (char)BaseUtils.simpleComplement(ref);
            base = (char)BaseUtils.simpleComplement(base);
            prevBase = (char)BaseUtils.simpleComplement((char)bases[offset+1]);
            cycle = read.getReadLength() - (offset + 1);
        }

After Change


        if (read.getReadNegativeStrandFlag()) {
            ref = BaseUtils.simpleComplement(ref);
            base = BaseUtils.simpleComplement(base);
            prevBase = BaseUtils.simpleComplement((char)bases[offset+1]);
            cycle = read.getReadLength() - (offset + 1);
        }