From 6804ab6d2f23afeb573e12f1238ebfc17c32fe33 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sat, 24 Sep 2011 09:25:29 -0400
Subject: [PATCH] Bug fix for NPE in very short GATK runs

-- Was already in unstable, but not stable...
---
 .../broadinstitute/sting/gatk/traversals/TraversalEngine.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
index 27fd173cb..c6321e2ad 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
@@ -358,7 +358,7 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
     public void printOnTraversalDone() {
         printProgress(null, null, true);
 
-        final double elapsed = timer.getElapsedTime();
+        final double elapsed = timer == null ? 0 : timer.getElapsedTime();
 
         ReadMetrics cumulativeMetrics = engine.getCumulativeMetrics();