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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
This commit is contained in:
ebanks 2009-11-24 04:08:22 +00:00
parent 36d493e645
commit ec321abd7b
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -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);