f4643a54760ba12d889e9fc39944d6387e3c072b,public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java,ContextCovariate,recordValues,#GATKSAMRecord#ReadCovariates#,69

Before Change



        final int readLength = clippedRead.getReadLength();
        for (int i = 0; i < readLength; i++) {
            values.addCovariate(contextWith(bases, i, mismatchesContextSize), contextWith(bases, i, insertionsContextSize), contextWith(bases, i, deletionsContextSize), (negativeStrand ? readLength - i - 1 : i));
        }
    }

After Change



        final int readLength = clippedRead.getReadLength();
        for (int i = 0; i < readLength; i++) {
            final long indelKey = contextWith(bases, i, indelsContextSize);
            values.addCovariate(contextWith(bases, i, mismatchesContextSize), indelKey, indelKey, (negativeStrand ? readLength - i - 1 : i));
        }
    }