26e3bea76e1376ceef6c283b2a0d4731baeea893,java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java,ConstrainedMateFixingManager,addRead,#SAMRecord#,167

Before Change



        // 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() + " from " + waitingReads.peek().getReferenceName())) + " at " + newRead.getAlignmentStart());

            while ( getNReadsInQueue() > 1 ) {

After Change



        // 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().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 ) {