From ec321abd7b9f3bab81565ece5888e6050757745c Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 24 Nov 2009 04:08:22 +0000
Subject: [PATCH] Added ability to filter on the QUAL field

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2135 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/filters/VariantFiltrationWalker.java    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
index 982aef9cb..97ff0b63b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
@@ -119,7 +119,8 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
             addFilter(filterString, "SnpCluster");
 
         if ( filterExpression != null ) {
-            Map<String, String> infoMap = context.second.mCurrentRecord.getInfoValues();
+            Map<String, String> infoMap = new HashMap<String, String>(context.second.mCurrentRecord.getInfoValues());
+            infoMap.put("QUAL", String.valueOf(context.second.mCurrentRecord.getQual()));
 
             JexlContext jContext = JexlHelper.createContext();
             jContext.setVars(infoMap);