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Switch from PriorityQueue to TreeSet for better and more consistent performance. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5952 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
alecw 2011-06-06 20:41:30 +00:00
parent 78f5309656
commit 2901abf070
1 changed files with 14 additions and 8 deletions
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22
java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
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@ -111,7 +111,13 @@ public class ConstrainedMateFixingManager {
/** read.name -> records */ /** read.name -> records */
HashMap<String, SAMRecordHashObject> forMateMatching = new HashMap<String, SAMRecordHashObject>(); HashMap<String, SAMRecordHashObject> forMateMatching = new HashMap<String, SAMRecordHashObject>();
Queue<SAMRecord> waitingReads = new PriorityQueue<SAMRecord>(1000, comparer); TreeSet<SAMRecord> waitingReads = new TreeSet<SAMRecord>(comparer);
private <T> T remove(TreeSet<T> treeSet) {
final T first = treeSet.first();
treeSet.remove(first);
return first;
}
private class SAMRecordHashObject { private class SAMRecordHashObject {
public SAMRecord record; public SAMRecord record;
@ -186,15 +192,15 @@ 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 // 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; boolean tooManyReads = getNReadsInQueue() >= MAX_RECORDS_IN_MEMORY;
if ( canFlush && (tooManyReads || (getNReadsInQueue() > 0 && !waitingReads.peek().getReferenceIndex().equals(newRead.getReferenceIndex()))) ) { if ( canFlush && (tooManyReads || (getNReadsInQueue() > 0 && !waitingReads.first().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()); if ( DEBUG ) logger.warn("Flushing queue on " + (tooManyReads ? "too many reads" : ("move to new contig: " + newRead.getReferenceName() + " from " + waitingReads.first().getReferenceName())) + " at " + newRead.getAlignmentStart());
while ( getNReadsInQueue() > 1 ) { while ( getNReadsInQueue() > 1 ) {
// emit to disk // emit to disk
writeRead(waitingReads.remove()); writeRead(remove(waitingReads));
} }
SAMRecord lastRead = waitingReads.remove(); SAMRecord lastRead = remove(waitingReads);
lastLocFlushed = (lastRead.getReferenceIndex() == -1) ? null : genomeLocParser.createGenomeLoc(lastRead); lastLocFlushed = (lastRead.getReferenceIndex() == -1) ? null : genomeLocParser.createGenomeLoc(lastRead);
writeRead(lastRead); writeRead(lastRead);
@ -250,7 +256,7 @@ public class ConstrainedMateFixingManager {
if ( ++counter % EMIT_FREQUENCY == 0 ) { if ( ++counter % EMIT_FREQUENCY == 0 ) {
while ( ! waitingReads.isEmpty() ) { // there's something in the queue while ( ! waitingReads.isEmpty() ) { // there's something in the queue
SAMRecord read = waitingReads.peek(); SAMRecord read = waitingReads.first();
if ( noReadCanMoveBefore(read.getAlignmentStart(), newRead) && if ( noReadCanMoveBefore(read.getAlignmentStart(), newRead) &&
(!pairedReadIsMovable(read) // we won't try to move such a read (!pairedReadIsMovable(read) // we won't try to move such a read
@ -264,7 +270,7 @@ public class ConstrainedMateFixingManager {
newRead.getAlignmentStart(), read.getReadName(), read.getAlignmentStart(), newRead.getAlignmentStart(), read.getReadName(), read.getAlignmentStart(),
read.getInferredInsertSize(), read.getMateAlignmentStart(), read.getAttribute("OP"))); read.getInferredInsertSize(), read.getMateAlignmentStart(), read.getAttribute("OP")));
// emit to disk // emit to disk
writeRead(waitingReads.remove()); writeRead(remove(waitingReads));
} else { } else {
if ( DEBUG ) if ( DEBUG )
logger.warn(String.format("At %d: read %s at %d with isize %d couldn't be emited, mate start %d", logger.warn(String.format("At %d: read %s at %d with isize %d couldn't be emited, mate start %d",
@ -319,7 +325,7 @@ public class ConstrainedMateFixingManager {
public void close() { public void close() {
// write out all of the remaining reads // write out all of the remaining reads
while ( ! waitingReads.isEmpty() ) { // there's something in the queue while ( ! waitingReads.isEmpty() ) { // there's something in the queue
writeRead(waitingReads.remove()); writeRead(remove(waitingReads));
} }
} }
} }