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Rollback of the previous "fix" and implementation of the real fix. 

We totally *do* want to annotate the call if called by another walker. Totally boneheaded misenterpretation of what the code was doing -- Eric, please forgive me for being an idiot.

Instead, change the StingException to what it really should be -- an IllegalStateException, which is not coincidentally already handled by the calling function. 



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2067 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-11-18 06:09:24 +00:00
parent 95f1be94c0
commit b68d6e06b7
2 changed files with 2 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java
View File

@ -92,6 +92,6 @@ public class SecondBaseSkew implements VariantAnnotation{
}
}
throw new StingException("List of genotypes did not contain a variant.");
throw new IllegalStateException("List of genotypes did not contain a variant.");
}
}

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -167,7 +167,7 @@ public class UnifiedGenotyper extends LocusWalker<Pair<List<Genotype>, GenotypeL
Pair<List<Genotype>, GenotypeLocusData> call = gcm.calculateGenotype(tracker, ref, MQ0freeContext, priors);
// annotate the call, if possible
if ( call != null && call.second != null && call.second instanceof ArbitraryFieldsBacked && ! (VARIANTS_FILE == null && out == null) ) {
if ( call != null && call.second != null && call.second instanceof ArbitraryFieldsBacked ) {
Map<String, String> annotations = VariantAnnotator.getAnnotations(refContext, fullContext, call.first);
((ArbitraryFieldsBacked)call.second).setFields(annotations);
}