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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
This commit is contained in:
Mark DePristo 2012-08-14 22:10:07 -04:00
parent bd7ed0d028
commit ae4d4482ac
2 changed files with 8 additions and 2 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
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@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.RodWalker; 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.Window;
import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts; import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
@ -99,7 +100,7 @@ import java.util.*;
*/ */
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) @DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-50,stop=50)) @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 * The VCF files to merge together
* *
@ -313,5 +314,10 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
return counter + sum; return counter + sum;
} }
@Override
public Integer treeReduce(Integer lhs, Integer rhs) {
return reduce(lhs, rhs);
}
public void onTraversalDone(Integer sum) {} public void onTraversalDone(Integer sum) {}
} }

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
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@ -50,7 +50,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
private void cvExecuteTest(final String name, final WalkerTestSpec spec) { private void cvExecuteTest(final String name, final WalkerTestSpec spec) {
spec.disableShadowBCF(); spec.disableShadowBCF();
executeTest(name, spec); executeTestParallel(name, spec);
} }
public void test1InOut(String file, String md5) { public void test1InOut(String file, String md5) {