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Fix for == used to test object equality. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5499 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-03-23 18:15:19 +00:00
parent 401d1cb97f
commit 26e3bea76e
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
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@ -175,7 +175,7 @@ public class ConstrainedMateFixingManager {
// if the new read is on a different contig or we have too many reads, then we need to flush the queue and clear the map
boolean tooManyReads = getNReadsInQueue() >= MAX_RECORDS_IN_MEMORY;
if ( tooManyReads || (getNReadsInQueue() > 0 && waitingReads.peek().getReferenceIndex() != newRead.getReferenceIndex()) ) {
if ( tooManyReads || (getNReadsInQueue() > 0 && !waitingReads.peek().getReferenceIndex().equals(newRead.getReferenceIndex())) ) {
if ( DEBUG ) logger.warn("Flushing queue on " + (tooManyReads ? "too many reads" : ("move to new contig: " + newRead.getReferenceName() + " from " + waitingReads.peek().getReferenceName())) + " at " + newRead.getAlignmentStart());
while ( getNReadsInQueue() > 1 ) {