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Trivial change to allow GenerateVariantClusters to be run on indels - not that VQSR now works on indels, far from it, but at least it's a first step and it allows us to generate cluster plots to see how well known/novel sites differentiate in their covariates (short answer: no difference/separation :( ). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4902 348d0f76-0448-11de-a6fe-93d51630548a
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delangel 2010-12-22 22:39:09 +00:00
parent a61f0047f0
commit 376bc563d4
1 changed files with 1 additions and 1 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
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@ -179,7 +179,7 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
final double annotationValues[] = new double[annotationKeys.size()];
for( final VariantContext vc : tracker.getVariantContexts(ref, inputNames, null, context.getLocation(), false, false) ) {
if( vc != null && vc.isSNP() ) {
if( vc != null ) {
if( !vc.isFiltered() || IGNORE_ALL_INPUT_FILTERS || (ignoreInputFilterSet != null && ignoreInputFilterSet.containsAll(vc.getFilters())) ) {
int iii = 0;
for( final String key : annotationKeys ) {