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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
This commit is contained in:
rpoplin 2010-11-04 19:27:23 +00:00
parent 816c86776e
commit 913db5d1ab
1 changed files with 10 additions and 9 deletions
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19
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -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"); 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)); classes.addAll(PackageUtils.getClassesImplementingInterface(interfaceClass));
} }
// get the specific classes provided }
for ( String annotation : annotationsToUse ) {
Class annotationClass = classMap.get(annotation); // get the specific classes provided
if ( annotationClass == null ) for ( String annotation : annotationsToUse ) {
annotationClass = classMap.get(annotation + "Annotation"); Class annotationClass = classMap.get(annotation);
if ( annotationClass == null ) if ( annotationClass == null )
throw new UserException.BadArgumentValue("annotation", "Class " + annotation + " is not found; please check that you have specified the class name correctly"); annotationClass = classMap.get(annotation + "Annotation");
classes.add(annotationClass); 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 // get the instances