From 78af6d5a409ab91b0192c8ee3d44b2dffbecc1dd Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 25 Mar 2010 18:39:04 +0000
Subject: [PATCH] New sharding system is going live again for on-the-fly
 merging.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3076 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java   | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 6cbcaa5b5..775f43ce6 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -769,10 +769,6 @@ public class GenomeAnalysisEngine {
         if (reads.getReadsFiles().size() == 0)
             return null;
 
-        // Force dynamic merging to use original sharding method until memory usage is under control.
-        if (reads.getReadsFiles().size() > 1)
-            argCollection.disableExperimentalSharding = true;
-
         SAMDataSource dataSource = null;
         if(!argCollection.disableExperimentalSharding)
             dataSource = new BlockDrivenSAMDataSource(reads);