From 517f27f331160d50c07a3f7f8cc8f7e9108bc4d8 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 8 May 2009 21:55:10 +0000
Subject: [PATCH] Added sharding strat. code that picks the right kind of
 shard, based on the traversal engine

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@644 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/executive/MicroScheduler.java        | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
index 2c4713e1d..f76f6d859 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
@@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
 import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource;
 import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
-import org.broadinstitute.sting.gatk.traversals.TraverseByReads;
+import org.broadinstitute.sting.gatk.traversals.TraverseReads;
 import org.broadinstitute.sting.gatk.traversals.TraverseLociByReference;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.Walker;
@@ -69,7 +69,7 @@ public abstract class MicroScheduler {
      */
     protected MicroScheduler( Walker walker, List<File> reads, File refFile, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods ) {
         if (walker instanceof ReadWalker) {
-            traversalEngine = new TraverseByReads(reads, refFile, rods);
+            traversalEngine = new TraverseReads(reads, refFile, rods);
         } else {
             traversalEngine = new TraverseLociByReference(reads, refFile, rods);
         }
@@ -102,13 +102,16 @@ public abstract class MicroScheduler {
      */
     protected ShardStrategy getShardStrategy( ReferenceSequenceFile drivingDataSource, List<GenomeLoc> intervals ) {
         ShardStrategy shardStrategy = null;
-        if( intervals != null )
-            shardStrategy = ShardStrategyFactory.shatter( ShardStrategyFactory.SHATTER_STRATEGY.LINEAR,
+        ShardStrategyFactory.SHATTER_STRATEGY shardType = (traversalEngine instanceof TraverseReads) ?
+                ShardStrategyFactory.SHATTER_STRATEGY.READS : ShardStrategyFactory.SHATTER_STRATEGY.LINEAR;
+        
+        if( intervals != null && shardType != ShardStrategyFactory.SHATTER_STRATEGY.READS)
+            shardStrategy = ShardStrategyFactory.shatter( shardType,
                                                           drivingDataSource.getSequenceDictionary(),
                                                           SHARD_SIZE,
                                                           intervals );
         else
-            shardStrategy = ShardStrategyFactory.shatter( ShardStrategyFactory.SHATTER_STRATEGY.LINEAR,
+            shardStrategy = ShardStrategyFactory.shatter( shardType,
                                                           drivingDataSource.getSequenceDictionary(),
                                                           SHARD_SIZE );