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The UG engine can return a null VC if there are tons of alt alleles, causing Tim's merge jobs to fail. 

Pushing the null check up so that it doesn't error out in such cases.
This commit is contained in:
Eric Banks 2014-02-07 12:41:20 -05:00
parent 335483bb53
commit 67ed0d2403
1 changed files with 7 additions and 3 deletions
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10
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
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@ -207,11 +207,15 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
final Map<String,Object> originalAttributes = combinedVC.getAttributes();
// only re-genotype polymorphic sites
if ( combinedVC.isVariant() )
result = new VariantContextBuilder(genotypingEngine.calculateGenotypes(result)).attributes(originalAttributes).make();
if ( combinedVC.isVariant() ) {
final VariantContext regenotypedVC = genotypingEngine.calculateGenotypes(result);
if ( regenotypedVC == null )
return null;
result = new VariantContextBuilder(regenotypedVC).attributes(originalAttributes).make();
}
// if it turned monomorphic and we don't want such sites, quit
if ( result == null || (!INCLUDE_NON_VARIANTS && result.isMonomorphicInSamples()) )
if ( !INCLUDE_NON_VARIANTS && result.isMonomorphicInSamples() )
return null;
// re-annotate it