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Minor performance enhancement. Checkpoint commit before major performance 

overhaul.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3504 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-06-08 21:39:39 +00:00
parent 5ed2818ffb
commit c2858c8988
1 changed files with 4 additions and 4 deletions
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8
java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java
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@ -406,9 +406,10 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
ArrayList<PileupElement> pile = new ArrayList<PileupElement>(readStates.size());
// todo -- performance problem -- should be lazy, really
GenomeLoc location = getLocation();
for ( SAMRecordState state : readStates ) {
if ( state.getCurrentCigarOperator() != CigarOperator.D && state.getCurrentCigarOperator() != CigarOperator.N ) {
if ( filterRead(state.getRead(), getLocation().getStart(), filters ) ) {
if ( filterRead(state.getRead(), location.getStart(), filters ) ) {
discarded_bases++;
//printStatus("Adaptor bases", discarded_adaptor_bases);
continue;
@ -429,10 +430,9 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
}
}
GenomeLoc loc = getLocation();
updateReadStates(); // critical - must be called after we get the current state offsets and location
// if we got reads with non-D/N over the current position, we are done
if ( pile.size() != 0 ) nextAlignmentContext = new AlignmentContext(loc, new ReadBackedPileup(loc, pile, size, nDeletions, nMQ0Reads));
if ( pile.size() != 0 ) nextAlignmentContext = new AlignmentContext(location, new ReadBackedPileup(location, pile, size, nDeletions, nMQ0Reads));
}
}
}
@ -751,7 +751,7 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
List<SAMRecordState> readStatesBySample = new LinkedList<SAMRecordState>();
int readCount = 0;
for(SAMRecord read: reads) {
if(readCount < maxReads) {
if(readCount <= maxReads) {
SAMRecordState state = new SAMRecordState(read, readInfo.generateExtendedEvents());
state.stepForwardOnGenome();
readStatesBySample.add(state);