From 93f7e632bd2febd5f8af2e846bf054893997dee0 Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Thu, 6 Oct 2011 10:07:46 -0400
Subject: [PATCH] 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.

---
 .../gatk/walkers/varianteval/evaluators/CountVariants.java    | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
index 72058ba7b..e83434037 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/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());
             }