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

Minor fix/enhancement for VariantEval: if a vcf has symbolic alleles, program would crash ungracefully - now we'll just skip record without processing. This is a big issue since we can't process 1000G integration files with code as is.

This commit is contained in:
Guillermo del Angel 2011-10-06 10:07:46 -04:00
parent f75573dd54
commit 93f7e632bd
1 changed files with 4 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
View File

@ -130,6 +130,10 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
nVariantLoci++; nVariantLoci++;
nMixed++; nMixed++;
break; break;
case SYMBOLIC:
// ignore symbolic alleles, but don't fail
// todo - consistent way of treating symbolic alleles thgoughout codebase?
break;
default: default:
throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType()); throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
} }