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Add Mongo switch

This commit is contained in:
Joel Thibault 2012-04-12 13:35:20 -04:00
parent 1b609e9075
commit b101b9c30b
1 changed files with 3 additions and 2 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -352,6 +352,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
private Set<String> IDsToKeep = null; private Set<String> IDsToKeep = null;
private final static boolean mongoOn = false;
/** /**
* Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher * Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher
*/ */
@ -466,8 +468,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
if ( tracker == null ) if ( tracker == null )
return 0; return 0;
//Collection<VariantContext> vcs = tracker.getValues(variantCollection.variants, context.getLocation()); Collection<VariantContext> vcs = mongoOn ? getMongoVariants(ref, context.getLocation()) : tracker.getValues(variantCollection.variants, context.getLocation());
Collection<VariantContext> vcs = getMongoVariants(ref, context.getLocation());
if ( vcs == null || vcs.size() == 0) { if ( vcs == null || vcs.size() == 0) {
return 0; return 0;