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 { +public class CombineVariants extends RodWalker implements TreeReducible { /** * The VCF files to merge together * @@ -313,5 +314,10 @@ public class CombineVariants extends RodWalker { 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) {