From ae4d4482ac7a176191fb3c1711e085f427723687 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 14 Aug 2012 22:10:07 -0400
Subject: [PATCH] Parallel combine variants!

-- CombineVariants is now TreeReducible!
-- Integration tests running in parallel all pass except one (will fix) due to incorrect use of db=0 flag on input from old VCF format
---
 .../sting/gatk/walkers/variantutils/CombineVariants.java  | 8 +++++++-
 .../variantutils/CombineVariantsIntegrationTest.java      | 2 +-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index d7dff030f..d6504e841 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts;
 import org.broadinstitute.sting.utils.SampleUtils;
@@ -99,7 +100,7 @@ import java.util.*;
  */
 @DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
 @Reference(window=@Window(start=-50,stop=50))
-public class CombineVariants extends RodWalker<Integer, Integer> {
+public class CombineVariants extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
     /**
      * The VCF files to merge together
      *
@@ -313,5 +314,10 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
         return counter + sum;
     }
 
+    @Override
+    public Integer treeReduce(Integer lhs, Integer rhs) {
+        return reduce(lhs, rhs);
+    }
+
     public void onTraversalDone(Integer sum) {}
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
index c8551657a..2f28a6dbc 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
@@ -50,7 +50,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
 
     private void cvExecuteTest(final String name, final WalkerTestSpec spec) {
         spec.disableShadowBCF();
-        executeTest(name, spec);
+        executeTestParallel(name, spec);
     }
 
     public void test1InOut(String file, String md5) {