From 391e5843e48c61adff02fc90400c0b7a464982e3 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 26 Mar 2010 20:52:21 +0000
Subject: [PATCH] If the annotation engine has not been supplied, don't try to
 annotate anything.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3081 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java   | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 6ef0626a6..9bd07494d 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -223,9 +223,10 @@ public class UnifiedGenotyperEngine {
             call = gcm.get().callLocus(tracker, ref, rawContext.getLocation(), stratifiedContexts, priors);
 
             // annotate the call, if possible
-            if ( call != null && call.vc != null ) {
+            if ( call != null && call.vc != null && annotationEngine != null ) {
                 // first off, we want to use the *unfiltered* context for the annotations
                 stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(rawContext.getBasePileup());
+
                 call.vc = annotationEngine.annotateContext(tracker, refContext, stratifiedContexts, call.vc);
             }
         }