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SelectVariants is actually *NOT* NanoSchedulable

This commit is contained in:
Mark DePristo 2012-10-18 10:42:20 -04:00
parent f20fa9d082
commit d3fc797cfe
1 changed files with 6 additions and 5 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgume
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
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.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts; import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts;
@ -189,7 +188,7 @@ import java.util.*;
* *
*/ */
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) @DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
public class SelectVariants extends RodWalker<Integer, Integer> implements TreeReducible<Integer>, NanoSchedulable { public class SelectVariants extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
/** /**
@ -543,9 +542,11 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
VariantContext sub = subsetRecord(vc, EXCLUDE_NON_VARIANTS); VariantContext sub = subsetRecord(vc, EXCLUDE_NON_VARIANTS);
if ( REGENOTYPE && sub.isPolymorphicInSamples() && hasPLs(sub) ) { if ( REGENOTYPE && sub.isPolymorphicInSamples() && hasPLs(sub) ) {
final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(sub)).filters(sub.getFiltersMaybeNull()); synchronized (UG_engine) {
addAnnotations(builder, sub); final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(sub)).filters(sub.getFiltersMaybeNull());
sub = builder.make(); addAnnotations(builder, sub);
sub = builder.make();
}
} }
if ( (!EXCLUDE_NON_VARIANTS || sub.isPolymorphicInSamples()) && (!EXCLUDE_FILTERED || !sub.isFiltered()) ) { if ( (!EXCLUDE_NON_VARIANTS || sub.isPolymorphicInSamples()) && (!EXCLUDE_FILTERED || !sub.isFiltered()) ) {