From 0545664f9173b823c30dbee1e1f3057d3c6c98ce Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 24 Aug 2012 13:45:48 -0400
Subject: [PATCH] Fix ClassCastException seen in Tableau errors

---
 .../gatk/walkers/annotator/VariantAnnotatorEngine.java      | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
index a1bd8dcbd..22ec5468f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@@ -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);
             }