From 913db5d1ab63f9e36a2ab0211429dbe1b94b5155 Mon Sep 17 00:00:00 2001 From: rpoplin Date: Thu, 4 Nov 2010 19:27:23 +0000 Subject: [PATCH] Unfortunately when annotating sites with the UG the -G None option was wiping out the single annotations added by -A options git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4625 348d0f76-0448-11de-a6fe-93d51630548a --- .../annotator/VariantAnnotatorEngine.java | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) 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 df892075e..65aca754b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -136,15 +136,16 @@ public class VariantAnnotatorEngine { throw new UserException.BadArgumentValue("group", "Class " + group + " is not found; please check that you have specified the class name correctly"); classes.addAll(PackageUtils.getClassesImplementingInterface(interfaceClass)); } - // get the specific classes provided - for ( String annotation : annotationsToUse ) { - Class annotationClass = classMap.get(annotation); - if ( annotationClass == null ) - annotationClass = classMap.get(annotation + "Annotation"); - if ( annotationClass == null ) - throw new UserException.BadArgumentValue("annotation", "Class " + annotation + " is not found; please check that you have specified the class name correctly"); - classes.add(annotationClass); - } + } + + // get the specific classes provided + for ( String annotation : annotationsToUse ) { + Class annotationClass = classMap.get(annotation); + if ( annotationClass == null ) + annotationClass = classMap.get(annotation + "Annotation"); + if ( annotationClass == null ) + throw new UserException.BadArgumentValue("annotation", "Class " + annotation + " is not found; please check that you have specified the class name correctly"); + classes.add(annotationClass); } // get the instances