From 165dc6d3b066ce706822f51e822d5ed5650ce4c3 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 20 Aug 2010 19:16:14 +0000
Subject: [PATCH] Ryan, what did you decide about supporting this tool? Is it
 still useful?

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4073 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/variantoptimizer/AnnotationDataManager.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
index 8c8ecf599..bcedfc156 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
@@ -61,7 +61,7 @@ public class AnnotationDataManager {
         } // else, process all samples
 
         // Loop over each annotation in the vcf record
-        final Map<String,Object> infoField = vc.getAttributes();
+        final Map<String,Object> infoField = new HashMap<String, Object>(vc.getAttributes());
         infoField.put("QUAL", ((Double)vc.getPhredScaledQual()).toString() ); // add QUAL field to annotations
         for( Map.Entry<String, Object> annotation : infoField.entrySet() ) {