From 2cc040aa1c7221066b58a8af5036891a3814291b Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 17 Mar 2010 03:32:45 +0000
Subject: [PATCH] New sharding system is live.  Disable with -ds.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3016 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/GenomeAnalysisEngine.java   | 8 ++++----
 .../sting/gatk/arguments/GATKArgumentCollection.java      | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index b4c0febec..15d7b8216 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -681,19 +681,19 @@ public class GenomeAnalysisEngine {
                         ShardStrategyFactory.SHATTER_STRATEGY.LINEAR;
                 shardStrategy = ShardStrategyFactory.shatter(readsDataSource,
                         referenceDataSource,
-                        argCollection.experimentalSharding ? ShardStrategyFactory.SHATTER_STRATEGY.LOCUS_EXPERIMENTAL : shardType,
+                        !argCollection.disableExperimentalSharding ? ShardStrategyFactory.SHATTER_STRATEGY.LOCUS_EXPERIMENTAL : shardType,
                         drivingDataSource.getSequenceDictionary(),
                         SHARD_SIZE,
                         intervals, maxIterations);
             } else
                 shardStrategy = ShardStrategyFactory.shatter(readsDataSource,
                         referenceDataSource,
-                        argCollection.experimentalSharding ? ShardStrategyFactory.SHATTER_STRATEGY.LOCUS_EXPERIMENTAL : ShardStrategyFactory.SHATTER_STRATEGY.LINEAR,
+                        !argCollection.disableExperimentalSharding ? ShardStrategyFactory.SHATTER_STRATEGY.LOCUS_EXPERIMENTAL : ShardStrategyFactory.SHATTER_STRATEGY.LINEAR,
                         drivingDataSource.getSequenceDictionary(),
                         SHARD_SIZE, maxIterations);
         } else if (walker instanceof ReadWalker ||
                 walker instanceof DuplicateWalker) {
-            if(argCollection.experimentalSharding)
+            if(!argCollection.disableExperimentalSharding)
                 shardType = ShardStrategyFactory.SHATTER_STRATEGY.READS_EXPERIMENTAL;
             else
                 shardType = ShardStrategyFactory.SHATTER_STRATEGY.READS;
@@ -740,7 +740,7 @@ public class GenomeAnalysisEngine {
             return null;
 
         SAMDataSource dataSource = null;
-        if(argCollection.experimentalSharding)
+        if(!argCollection.disableExperimentalSharding)
             dataSource = new BlockDrivenSAMDataSource(reads);
         else
             dataSource = new IndexDrivenSAMDataSource(reads);
diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index af18171a9..f742901f1 100755
--- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -155,8 +155,8 @@ public class GATKArgumentCollection {
 //    public boolean enableRodWalkers = false;
 
     @Element(required = false)
-    @Argument(fullName = "experimental_sharding",shortName="es", doc="Use the experimental sharding strategy.  Will not work for all traversal types.", required = false)
-    public boolean experimentalSharding = false;
+    @Argument(fullName = "disable_experimental_sharding",shortName="ds", doc="Disable the experimental sharding strategy.", required = false)
+    public boolean disableExperimentalSharding = false;
 
     /**
      * marshal the data out to a object