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Minor cleanup before push

This commit is contained in:
Joel Thibault 2012-05-01 14:15:44 -04:00
parent b101b9c30b
commit aa4d41cce0
2 changed files with 7 additions and 5 deletions
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2
ivy.xml
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@ -100,7 +100,7 @@
<!-- snpEff annotator for pipelines --> <!-- snpEff annotator for pipelines -->
<dependency org="net.sf.snpeff" name="snpeff" rev="2.0.5" /> <dependency org="net.sf.snpeff" name="snpeff" rev="2.0.5" />
<!-- mongoDB for Bjorn experiments --> <!-- MongoDB for Bjorn -->
<dependency org="org.mongodb" name="mongo-java-driver" rev="2.7.3"/> <dependency org="org.mongodb" name="mongo-java-driver" rev="2.7.3"/>
<!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. --> <!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->

10
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -660,11 +660,11 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
vcs.add(builder.make()); vcs.add(builder.make());
} }
return combineVariants(vcs); return combineMongoVariants(vcs);
} }
// Copied from CombineVariants // Copied from CombineVariants
private Collection<VariantContext> combineVariants(Collection<VariantContext> vcs) { private Collection<VariantContext> combineMongoVariants(Collection<VariantContext> vcs) {
if (vcs.size() < 2) if (vcs.size() < 2)
return vcs; return vcs;
@ -822,8 +822,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
} }
public void onTraversalDone(Integer result) { public void onTraversalDone(Integer result) {
MongoDB.close(); if (mongoOn) {
MongoDB.close();
}
logger.info(result + " records processed."); logger.info(result + " records processed.");
if (SELECT_RANDOM_NUMBER) { if (SELECT_RANDOM_NUMBER) {