From 99d4ebc26db3e6dc5d6e80e0f5d291a489a02cb1 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 15 May 2009 20:20:27 +0000
Subject: [PATCH] Added functionality to return the final accumulator of a
 traversal, so external tools can get the result of a walker.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@724 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/executive/HierarchicalMicroScheduler.java      | 4 +++-
 .../sting/gatk/executive/LinearMicroScheduler.java            | 4 +++-
 .../broadinstitute/sting/gatk/executive/MicroScheduler.java   | 3 ++-
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
index b98b30928..0c6560e31 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
@@ -65,7 +65,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
             throw new UnsupportedOperationException("Traversal engine supports only traverse loci by reference at this time.");
     }
 
-    public void execute( Walker walker, List<GenomeLoc> intervals ) {
+    public Object execute( Walker walker, List<GenomeLoc> intervals ) {
         // Fast fail for walkers not supporting TreeReducible interface.
         if( !(walker instanceof TreeReducible) )
             throw new IllegalArgumentException("Hierarchical microscheduler only works with TreeReducible walkers");
@@ -110,6 +110,8 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
         
         traversalEngine.printOnTraversalDone(result);
         walker.onTraversalDone(result);
+
+        return result;
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
index 3c12d2b57..8da7618c0 100644
--- a/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
@@ -30,7 +30,7 @@ public class LinearMicroScheduler extends MicroScheduler {
      * @param walker    Computation to perform over dataset.
      * @param locations Subset of the dataset over which to walk.
      */
-    public void execute(Walker walker, List<GenomeLoc> locations) {
+    public Object execute(Walker walker, List<GenomeLoc> locations) {
         ShardStrategy shardStrategy = getShardStrategy(reference, locations);
 
         walker.initialize();
@@ -45,6 +45,8 @@ public class LinearMicroScheduler extends MicroScheduler {
         traversalEngine.printOnTraversalDone(accumulator);
 
         walker.onTraversalDone(accumulator);
+
+        return accumulator;
     }
 
 
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
index f76f6d859..55b9b540b 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
@@ -91,8 +91,9 @@ public abstract class MicroScheduler {
      * Walks a walker over the given list of intervals.
      * @param walker Computation to perform over dataset.
      * @param intervals A list of intervals over which to walk.  Null for whole dataset.
+     * @return the return type of the walker
      */
-    public abstract void execute( Walker walker, List<GenomeLoc> intervals);
+    public abstract Object execute( Walker walker, List<GenomeLoc> intervals);
 
     /**
      * Get the sharding strategy given a driving data source.