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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
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ebanks 2010-08-20 19:16:14 +00:00
parent 2ef2f1b24a
commit 165dc6d3b0
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
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@ -61,7 +61,7 @@ public class AnnotationDataManager {
} // else, process all samples } // else, process all samples
// Loop over each annotation in the vcf record // 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 infoField.put("QUAL", ((Double)vc.getPhredScaledQual()).toString() ); // add QUAL field to annotations
for( Map.Entry<String, Object> annotation : infoField.entrySet() ) { for( Map.Entry<String, Object> annotation : infoField.entrySet() ) {