e4469a83ee37599da1430cc5f6df2a6cefaefce6,public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java,GenotypeAndValidateWalker,map,#RefMetaDataTracker#ReferenceContext#AlignmentContext#,351

Before Change


            call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
        } else if ( bamIsTruth ) {
            // assume it's a SNP if no variation is present; this is necessary so that we can test supposed monomorphic sites against the truth bam
            call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
        } else {
            logger.info("Not SNP or INDEL " + vcComp.getChr() + ":" + vcComp.getStart() + " " + vcComp.getAlleles());
            return counter;

After Change


            call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context).get(0);
        } else if ( bamIsTruth ) {
            // assume it's a SNP if no variation is present; this is necessary so that we can test supposed monomorphic sites against the truth bam
            call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context).get(0);
        } else {
            logger.info("Not SNP or INDEL " + vcComp.getChr() + ":" + vcComp.getStart() + " " + vcComp.getAlleles());
            return counter;