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fixed a bug when the concordance track doesn't have the sample in the variant track. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5535 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-03-29 18:24:19 +00:00
parent c3f70cc5cb
commit 0f4ace0902
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -164,7 +164,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
// if the genotype of any of the samples we're looking it is HET or HomVar, we write this variant // if the genotype of any of the samples we're looking it is HET or HomVar, we write this variant
for (String sample : samples) { for (String sample : samples) {
Genotype g = compVC.getGenotype(sample); Genotype g = compVC.getGenotype(sample);
if ( g.isHet() || g.isHomVar() ) { if ( g != null && (g.isHet() || g.isHomVar()) ) {
vcfWriter.add(compVC, ref.getBase()); vcfWriter.add(compVC, ref.getBase());
return 1; return 1;
} }