From 3d4f0e9dd76d1ab23a7e7fdecd61067b57b8e7d7 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 7 Jul 2011 17:21:15 -0400
Subject: [PATCH] Now supports the case where you have multiple AC values in
 the info field.

---
 .../gatk/walkers/varianteval/stratifications/AlleleCount.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
index ff59c9e29..2cbc66e31 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
@@ -43,9 +43,9 @@ public class AlleleCount extends VariantStratifier {
 
         if (eval != null) {
             int AC = -1;
-            if ( eval.hasAttribute("AC") )
+            if ( eval.hasAttribute("AC") && eval.getAttribute("AC") instanceof Integer ) {
                 AC = eval.getAttributeAsInt("AC");
-            else if ( eval.isVariant() ) {
+            } else if ( eval.isVariant() ) {
                 for (Allele allele : eval.getAlternateAlleles())
                     AC = Math.max(AC, eval.getChromosomeCount(allele));
             } else