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();