74751a8ed37c95b4fc700f6b1a5c5ba162d91f76,java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SNPGenotypeConcordance.java,SNPGenotypeConcordance,computeConcordance,#Map#ReferenceContext#,34

Before Change


        if (!(call1 instanceof VariantBackedByGenotype) || !(call2 instanceof VariantBackedByGenotype))
                    throw new StingException("Both ROD tracks must be backed by genotype data. Ensure that your rod(s) contain genotyping information");

        double bestVsRef1 = call1.getNegLog10PError();
        double bestVsRef2 = call2.getNegLog10PError();
        String genotype1 = ((VariantBackedByGenotype)call1).getCalledGenotype().getBases();
        String genotype2 = ((VariantBackedByGenotype)call2).getCalledGenotype().getBases();

After Change


            return null;
        }

        double confidence1 = 10.0 * call1.getNegLog10PError();
        double confidence2 = 10.0 * call2.getNegLog10PError();
        String genotype1 = call1.getBases();
        String genotype2 = call2.getBases();