From 26e3bea76e1376ceef6c283b2a0d4731baeea893 Mon Sep 17 00:00:00 2001 From: hanna Date: Wed, 23 Mar 2011 18:15:19 +0000 Subject: [PATCH] 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 --- .../sting/gatk/walkers/indels/ConstrainedMateFixingManager.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java index 75ca976e8..d3e61092c 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java @@ -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 ) {