From e1b0aefb29b80f434c45bc39ec13995474767f6d Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 27 May 2010 22:16:14 +0000
Subject: [PATCH] fix for parallelism bug

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3451 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/executive/ShardTraverser.java   | 2 +-
 .../org/broadinstitute/sting/gatk/executive/WindowMaker.java  | 4 ----
 2 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
index 4baaa33ca..ad316d398 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
@@ -59,7 +59,7 @@ public class ShardTraverser implements Callable {
         long startTime = System.currentTimeMillis(); 
 
         Object accumulator = walker.reduceInit();
-        WindowMaker windowMaker = new WindowMaker(microScheduler.getReadIterator(shard),shard.getGenomeLocs());
+        WindowMaker windowMaker = new WindowMaker(microScheduler.getReadIterator(shard),shard.getGenomeLocs(),walker.getMandatoryReadFilters());
         ShardDataProvider dataProvider = null;
         try {
             for(WindowMaker.WindowMakerIterator iterator: windowMaker) {
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java b/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
index 280bb5275..55833be09 100644
--- a/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
@@ -55,10 +55,6 @@ public class WindowMaker implements Iterable<WindowMaker.WindowMakerIterator>, I
      */
     private boolean shardGenerated = false;
 
-    public WindowMaker(StingSAMIterator iterator, List<GenomeLoc> intervals) {
-        this(iterator, intervals, new ArrayList<SamRecordFilter>());
-    }
-
     /**
      * Create a new window maker with the given iterator as a data source, covering
      * the given intervals.