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Minor debugging output change. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5488 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-03-22 12:59:26 +00:00
parent b463faad92
commit af7f78e8ba
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
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@ -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