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This was busted because it assumed 1 (and only 1) record at each position. However it's possible to have 0 (which generated a NullPointer) or 2+ records (which dropped records). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5361 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-03-02 21:35:50 +00:00
parent 1e68259f5c
commit f0f4bc3363
1 changed files with 1 additions and 2 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
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@ -131,8 +131,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation());
if ( ASSUME_IDENTICAL_SAMPLES ) {
final VariantContext vc = vcs.iterator().next();
if( vc != null ) {
for ( final VariantContext vc : vcs ) {
vcfWriter.add( vc, ref.getBase() );
}