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Fix ClassCastException seen in Tableau errors

This commit is contained in:
Eric Banks 2012-08-24 13:45:48 -04:00
parent 740520c23b
commit 0545664f91
1 changed files with 4 additions and 2 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -34,7 +34,6 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.*;
import java.util.*;
@ -218,7 +217,10 @@ public class VariantAnnotatorEngine {
// go through all the requested info annotationTypes
for ( InfoFieldAnnotation annotationType : requestedInfoAnnotations ) {
Map<String, Object> annotationsFromCurrentType = ((ActiveRegionBasedAnnotation)annotationType).annotate(perReadAlleleLikelihoodMap, vc);
if ( !(annotationType instanceof ActiveRegionBasedAnnotation) )
continue;
Map<String, Object> annotationsFromCurrentType = annotationType.annotate(perReadAlleleLikelihoodMap, vc);
if ( annotationsFromCurrentType != null ) {
infoAnnotations.putAll(annotationsFromCurrentType);
}