From 95f1be94c0289fb9a330444ae6c4071f5cf42ef6 Mon Sep 17 00:00:00 2001 From: chartl Date: Wed, 18 Nov 2009 05:56:31 +0000 Subject: [PATCH] Fix for the broken build: do **not** attempt to annotate if UnifiedGenotyper is called from another walker! Why this didn't break the build earlier I have no idea. Ultimately, there should be a better way of interfacing UG with another walker -- what if some other walker wants the annotations from UG? But since we're calling map directly -- and the annotations don't get returned directly from map -- this needs to be handled differently, while the map function should ultimately return the LOD score or quality under the GCM alone. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2066 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/genotyper/UnifiedGenotyper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 0beae9c8d..7b2cb063c 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) { + if ( call != null && call.second != null && call.second instanceof ArbitraryFieldsBacked && ! (VARIANTS_FILE == null && out == null) ) { Map annotations = VariantAnnotator.getAnnotations(refContext, fullContext, call.first); ((ArbitraryFieldsBacked)call.second).setFields(annotations); }