From 64446f0ddf784a4ecd644bdf6301db825f96d79a Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 8 Aug 2010 05:16:52 +0000
Subject: [PATCH] Avoid NaNs in the final output.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3973 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/variantutils/SelectVariants.java     | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 1173f6cef..66c905be9 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -212,7 +212,11 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
 
         attributes.put("AC", alleleCount);
         attributes.put("AN", numberOfAlleles);
-        attributes.put("AF", ((double) alleleCount) / ((double) numberOfAlleles));
+        if (numberOfAlleles == 0) {
+            attributes.put("AF", 0.0);
+        } else {
+            attributes.put("AF", ((double) alleleCount) / ((double) numberOfAlleles));
+        }
         attributes.put("DP", depth);
 
         sub = VariantContextUtils.modifyAttributes(sub, attributes);