From d1e70d6ec21a8015596ac7aa4c3163c6b4af28ef Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 6 Oct 2011 18:29:26 -0700
Subject: [PATCH] Removed Nx counting of reads in metrics with -nt > 1

---
 .../broadinstitute/sting/gatk/executive/ShardTraverser.java   | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
index 11e51d99b..badd39860 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
@@ -66,15 +66,13 @@ public class ShardTraverser implements Callable {
                     microScheduler.getReadIterator(shard),
                     shard.getGenomeLocs(),
                     microScheduler.engine.getSampleDB().getSampleNames()); // todo: microScheduler.engine is protected - is it okay to user it here?
-            ShardDataProvider dataProvider = null;
 
             for(WindowMaker.WindowMakerIterator iterator: windowMaker) {
-                dataProvider = new LocusShardDataProvider(shard,iterator.getSourceInfo(),microScheduler.getEngine().getGenomeLocParser(),iterator.getLocus(),iterator,microScheduler.reference,microScheduler.rods);
+                final ShardDataProvider dataProvider = new LocusShardDataProvider(shard,iterator.getSourceInfo(),microScheduler.getEngine().getGenomeLocParser(),iterator.getLocus(),iterator,microScheduler.reference,microScheduler.rods);
                 accumulator = traversalEngine.traverse( walker, dataProvider, accumulator );
                 dataProvider.close();
             }
 
-            if (dataProvider != null) dataProvider.close();
             windowMaker.close();
             outputMergeTask = outputTracker.closeStorage();