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Another trivial change to make VQSR work with indels 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5073 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2011-01-25 19:05:31 +00:00
parent b22f82d5dd
commit db2e2cb0ff
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
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@ -142,8 +142,8 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
return 1; return 1;
} }
for( VariantContext vc : tracker.getVariantContexts(ref, inputNames, null, context.getLocation(), false, false) ) { for( VariantContext vc : tracker.getVariantContexts(ref, inputNames, null, context.getLocation(), true, false) ) {
if( vc != null && vc.isSNP() ) { if( vc != null ) {
String filterString = null; String filterString = null;
if( !vc.isFiltered() ) { if( !vc.isFiltered() ) {
try { try {