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memory leak, where the Resource Pool was releasing based on the value and not the key, resulting in the resourceAssignments map growing with each additional shard 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1880 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-10-20 00:39:42 +00:00
parent 761a730758
commit d21b582b18
2 changed files with 6 additions and 6 deletions
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5
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java
View File

@ -79,8 +79,11 @@ abstract class ResourcePool <T,I extends Iterator> {
synchronized(this) {
// Find and remove the resource from the list of allocated resources.
T resource = resourceAssignments.get( iterator );
resourceAssignments.remove(resource);
Object obj = resourceAssignments.remove(iterator);
// make sure we actually removed the assignment
if (obj == null)
throw new StingException("Failed to remove resource assignment; target key had no associated value in the resource assignment map");
// Return the resource to the pool.
if( !allResources.contains(resource) )
throw new StingException("Iterator does not belong to the given pool.");

7
java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
View File

@ -2,8 +2,8 @@ package org.broadinstitute.sting.gatk.traversals;
import net.sf.samtools.SAMRecord;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.WalkerManager;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView;
import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
@ -16,7 +16,6 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.ArrayList;
import java.util.Arrays;
/*
@ -53,9 +52,7 @@ import java.util.Arrays;
* <p/>
* This class handles traversing by reads in the new shardable style
*/
public class TraverseReads extends TraversalEngine {
final ArrayList<String> x = new ArrayList<String>();
public class TraverseReads extends TraversalEngine {
/** our log, which we want to capture anything from this class */
protected static Logger logger = Logger.getLogger(TraverseReads.class);