From c822b7c760245064741acf3c2221a299c89d21cb Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 4 Sep 2012 18:02:40 -0400
Subject: [PATCH] Fix long-standing NPE in LMS due to inappropriate timing of
 initialization

---
 .../sting/gatk/executive/LinearMicroScheduler.java             | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
index 5bcb16c94..740bcb566 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
@@ -60,11 +60,12 @@ public class LinearMicroScheduler extends MicroScheduler {
 
         boolean done = walker.isDone();
         int counter = 0;
+
+        traversalEngine.startTimersIfNecessary();
         for (Shard shard : shardStrategy ) {
             if ( done || shard == null ) // we ran out of shards that aren't owned
                 break;
 
-            traversalEngine.startTimersIfNecessary();
             if(shard.getShardType() == Shard.ShardType.LOCUS) {
                 WindowMaker windowMaker = new WindowMaker(shard, engine.getGenomeLocParser(),
                         getReadIterator(shard), shard.getGenomeLocs(), SampleUtils.getSAMFileSamples(engine));