From 0c9fabb06f6225fb7d8bb51ce28068cbb1d5888e Mon Sep 17 00:00:00 2001 From: rpoplin Date: Thu, 23 Sep 2010 19:48:44 +0000 Subject: [PATCH] Fix in AnalyzeAnnotations, somebody changed it look for ID in the vc's info field. This dinosaur desperately needs integration tests. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4338 348d0f76-0448-11de-a6fe-93d51630548a --- .../walkers/analyzeannotations/AnnotationDataManager.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java index d8a8267e4..8a2c54a9f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java @@ -1,6 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.analyzeannotations; import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -85,11 +86,11 @@ public class AnnotationDataManager { treeSet.add(datum); } - final boolean isNovelVariant = infoField.containsKey(VariantContext.ID_KEY); + final boolean isNovelVariant = !infoField.get(VariantContext.ID_KEY).toString().contains("rs"); // Decide if the variant is a transition or transversion if ( vc.isSNP() ) { - if( BaseUtils.isTransition( vc.getReference().getBases()[0], vc.getAlternateAllele(0).getBases()[0]) ) { + if( VariantContextUtils.getSNPSubstitutionType(vc).compareTo(BaseUtils.BaseSubstitutionType.TRANSITION) == 0 ) { datum.incrementTi( isNovelVariant, isInTruthSet, isTrueVariant ); } else { datum.incrementTv( isNovelVariant, isInTruthSet, isTrueVariant );