Minor fix/enhancement for VariantEval: if a vcf has symbolic alleles, program would crash ungracefully - now we'll just skip record without processing. This is a big issue since we can't process 1000G integration files with code as is.

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java

@@ -130,6 +130,10 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                     nVariantLoci++;
                     nMixed++;
                     break;
+                case SYMBOLIC:
+                    // ignore symbolic alleles, but don't fail
+                    // todo - consistent way of treating symbolic alleles thgoughout codebase?
+                    break;
                 default:
                     throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
             }