From aa4d41cce0e5ac3fab5b16b1741e6c624f941f02 Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Tue, 1 May 2012 14:15:44 -0400
Subject: [PATCH] Minor cleanup before push

---
 ivy.xml                                                |  2 +-
 .../gatk/walkers/variantutils/SelectVariants.java      | 10 ++++++----
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/ivy.xml b/ivy.xml
index 42de21738..270c1d074 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -100,7 +100,7 @@
     <!-- snpEff annotator for pipelines -->
     <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"/>
 
     <!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index b71ab1983..12c5d6728 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -660,11 +660,11 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             vcs.add(builder.make());
         }
 
-        return combineVariants(vcs);
+        return combineMongoVariants(vcs);
     }
 
     // Copied from CombineVariants
-    private Collection<VariantContext> combineVariants(Collection<VariantContext> vcs) {
+    private Collection<VariantContext> combineMongoVariants(Collection<VariantContext> vcs) {
         if (vcs.size() < 2)
             return vcs;
 
@@ -822,8 +822,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     }
 
     public void onTraversalDone(Integer result) {
-        MongoDB.close();
-
+        if (mongoOn) {
+            MongoDB.close();
+        }
+        
         logger.info(result + " records processed.");
 
         if (SELECT_RANDOM_NUMBER) {