zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
View File

@ -207,11 +207,15 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
final Map<String,Object> originalAttributes = combinedVC.getAttributes(); final Map<String,Object> originalAttributes = combinedVC.getAttributes();
// only re-genotype polymorphic sites // only re-genotype polymorphic sites
if ( combinedVC.isVariant() ) if ( combinedVC.isVariant() ) {
result = new VariantContextBuilder(genotypingEngine.calculateGenotypes(result)).attributes(originalAttributes).make(); 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 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; return null;
// re-annotate it // re-annotate it