From 635bfd860481fca5db76e0c23379b5e97d4b939c Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 23 Apr 2009 21:07:11 +0000
Subject: [PATCH] Added a little bit of hack to get the header back to the
 walker by initialization time, which was before sharding in the last version.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@516 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/executive/MicroManager.java            | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java b/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
index 26a817441..36cdb09aa 100644
--- a/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
@@ -103,8 +103,8 @@ public class MicroManager {
             throw new RuntimeException( ex );
         }
 
-        walker.initialize();
-        Object accumulator = ((LocusWalker<?,?>)walker).reduceInit();
+        boolean walkerInitialized = false;
+        Object accumulator = null;
 
         for(Shard shard: shardStrategy) {
             // CloseableIterator<SAMRecord> readShard = null;
@@ -121,6 +121,13 @@ public class MicroManager {
 
             // set the sam header of the traversal engine
             traversalEngine.setSAMHeader(readShard.getMergedHeader());
+
+            if (!walkerInitialized) {
+                walker.initialize();
+                accumulator = ((LocusWalker<?,?>)walker).reduceInit();
+                walkerInitialized = true;
+            }
+
             System.err.println(traversalEngine.getSAMHeader().getSequenceDictionary().toString());
             accumulator = traversalEngine.traverse( walker, shard, referenceProvider, locusProvider, accumulator );
             readShard.close();