From af7f78e8ba8cceb2f8f42efe232273799122e39c Mon Sep 17 00:00:00 2001 From: ebanks Date: Tue, 22 Mar 2011 12:59:26 +0000 Subject: [PATCH] Minor debugging output change. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5488 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/indels/ConstrainedMateFixingManager.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 da3a5b185..75ca976e8 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java @@ -160,7 +160,7 @@ public class ConstrainedMateFixingManager { try { writer.addAlignment(read); } catch (IllegalArgumentException e) { - throw new UserException("If the maximum allowable reads in memory is too small, it may cause reads to be written out of order when trying to write the BAM; please see the --maxReadsInMemory argument for details. " + e.getMessage(), e); + throw new UserException("If the maximum allowable reads in memory is too small, it may cause reads to be written out of order when trying to write the BAM; please see the --maxReadsInMemory argument for details. " + e.getMessage(), e); } } @@ -176,7 +176,7 @@ 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 ( DEBUG ) logger.warn("Flushing queue on " + (tooManyReads ? "too many reads" : ("move to new contig: " + newRead.getReferenceName())) + " at " + newRead.getAlignmentStart()); + 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 ) { // emit to disk