From 0fd55d91d25cf8da7344c4056df7e1156130c4a8 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 17 Mar 2009 15:28:04 +0000
Subject: [PATCH] Fixed bug in unsafe mode

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@78 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../src/org/broadinstitute/sting/gatk/TraversalEngine.java     | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/playground/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java b/playground/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
index aa434ae7f..2644524cd 100755
--- a/playground/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
+++ b/playground/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
@@ -526,7 +526,8 @@ public class TraversalEngine {
     protected <M,R> int traverseByRead(ReadWalker<M,R> walker) {
         if ( refFileName == null && ! walker.requiresOrderedReads() ) {
             System.out.println("STATUS: No reference file provided and unordered reads are tolerated, enabling out of order read processing.");
-            verifyingSamReadIter.setCheckOrderP(false);
+            if ( verifyingSamReadIter != null )
+                verifyingSamReadIter.setCheckOrderP(false);
         }
 
         verifySortOrder( refFileName != null || walker.requiresOrderedReads());