From 1c32deb108ab327ede4cf8768aa6103912aa0c41 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 15 Apr 2011 20:59:10 +0000 Subject: [PATCH] For some reason I wasn't allowing expressions to be used with the -all argument. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5652 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/annotator/VariantAnnotator.java | 3 ++- .../gatk/walkers/annotator/VariantAnnotatorEngine.java | 9 +++------ 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index 9f864c40b..0d9ccf738 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -137,7 +137,8 @@ public class VariantAnnotator extends RodWalker { if ( USE_ALL_ANNOTATIONS ) engine = new VariantAnnotatorEngine(getToolkit()); else - engine = new VariantAnnotatorEngine(getToolkit(), annotationGroupsToUse, annotationsToUse, expressionsToUse); + engine = new VariantAnnotatorEngine(getToolkit(), annotationGroupsToUse, annotationsToUse); + engine.initializeExpressions(expressionsToUse); // setup the header fields // note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index f890f9964..3eb60a54f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -96,17 +96,14 @@ public class VariantAnnotatorEngine { initializeDBs(engine); } - // use this constructor if you want to select specific annotations (and/or interfaces), but no expressions + // use this constructor if you want to select specific annotations (and/or interfaces) public VariantAnnotatorEngine(GenomeAnalysisEngine engine, List annotationGroupsToUse, List annotationsToUse) { initializeAnnotations(annotationGroupsToUse, annotationsToUse); initializeDBs(engine); } - // use this constructor if you want to select specific annotations (and/or interfaces) plus expressions - public VariantAnnotatorEngine(GenomeAnalysisEngine engine, List annotationGroupsToUse, List annotationsToUse, List expressionsToUse) { - initializeAnnotations(annotationGroupsToUse, annotationsToUse); - initializeDBs(engine); - + // select specific expressions to use + public void initializeExpressions(List expressionsToUse) { // set up the expressions for ( String expression : expressionsToUse ) requestedExpressions.add(new VAExpression(expression));