From b68d6e06b74232b4914b44286d2b6db74d40881a Mon Sep 17 00:00:00 2001 From: chartl Date: Wed, 18 Nov 2009 06:09:24 +0000 Subject: [PATCH] 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 --- .../sting/gatk/walkers/annotator/SecondBaseSkew.java | 2 +- .../sting/gatk/walkers/genotyper/UnifiedGenotyper.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java index 07b17bdc2..660d553c2 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java @@ -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."); } } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index 7b2cb063c..f8ba7d20a 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -167,7 +167,7 @@ public class UnifiedGenotyper extends LocusWalker, GenotypeL Pair, 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 annotations = VariantAnnotator.getAnnotations(refContext, fullContext, call.first); ((ArbitraryFieldsBacked)call.second).setFields(annotations); }