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When processing Beagle output and creating new vcf, output the filtered records in the original input vcf as is, so that we don't lose the information on them when we run Beagle. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4276 348d0f76-0448-11de-a6fe-93d51630548a
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delangel 2010-09-14 19:18:45 +00:00
parent 7fa6b2135b
commit 6d07181dc9
1 changed files with 4 additions and 0 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
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@ -124,6 +124,10 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
if ( vc_input == null )
return 0;
if (vc_input.isFiltered()) {
vcfWriter.add(vc_input, ref.getBase());
return 1;
}
List<Object> r2rods = tracker.getReferenceMetaData(R2_ROD_NAME);
// ignore places where we don't have a variant