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Clean up logic for adding reads to ART cache 

-- No longer has duplicate code
This commit is contained in:
Mark DePristo 2012-03-14 14:59:31 -04:00
parent 5bcb5c7433
commit e440c9be98
1 changed files with 30 additions and 22 deletions
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52
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
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@ -94,19 +94,12 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
if( !myReads.contains(read) ) {
myReads.add(read);
}
// If this is the last pileup for this shard calculate the minimum alignment start so that we know
// which active regions in the work queue are now safe to process
minStart = Math.min(minStart, read.getAlignmentStart());
}
// If this is the last pileup for this shard calculate the minimum alignment start so that we know
// which active regions in the work queue are now safe to process
if( !locusView.hasNext() ) {
for( final PileupElement p : locus.getBasePileup() ) {
final GATKSAMRecord read = p.getRead();
if( !myReads.contains(read) ) {
myReads.add(read);
}
if( read.getAlignmentStart() < minStart ) { minStart = read.getAlignmentStart(); }
}
}
prevLoc = location;
printProgress(dataProvider.getShard(), locus.getLocation());
@ -117,18 +110,10 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
// band-pass filter the list of isActive probabilities and turn into active regions
final ActivityProfile bandPassFiltered = profile.bandPassFilter();
final List<ActiveRegion> activeRegions = bandPassFiltered.createActiveRegions( activeRegionExtension );
logger.debug("Integrated " + profile.size() + " isActive calls into " + activeRegions.size() + " regions." );
// add to work queue
if( walker.activeRegionOutStream == null ) {
workQueue.addAll( activeRegions );
} else { // Just want to output the active regions to a file, not actually process them
for( final ActiveRegion activeRegion : activeRegions ) {
if( activeRegion.isActive ) {
walker.activeRegionOutStream.println( activeRegion.getLocation() );
}
}
}
// add active regions to queue of regions to process
workQueue.addAll( activeRegions );
logger.debug("Integrated " + profile.size() + " isActive calls into " + activeRegions.size() + " regions." );
// now go and process all of the active regions
sum = processActiveRegions(walker, sum, minStart, dataProvider.getLocus().getContig());
@ -170,6 +155,29 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
// --------------------------------------------------------------------------------
private T processActiveRegions( final ActiveRegionWalker<M,T> walker, T sum, final int minStart, final String currentContig ) {
if( walker.activeRegionOutStream != null ) {
writeActiveRegionsToStream(walker);
return sum;
} else {
return callWalkerMapOnActiveRegions(walker, sum, minStart, currentContig);
}
}
/**
* Write out each active region to the walker activeRegionOutStream
*
* @param walker
*/
private void writeActiveRegionsToStream( final ActiveRegionWalker<M,T> walker ) {
// Just want to output the active regions to a file, not actually process them
for( final ActiveRegion activeRegion : workQueue ) {
if( activeRegion.isActive ) {
walker.activeRegionOutStream.println( activeRegion.getLocation() );
}
}
}
private T callWalkerMapOnActiveRegions( final ActiveRegionWalker<M,T> walker, T sum, final int minStart, final String currentContig ) {
// Since we've traversed sufficiently past this point (or this contig!) in the workQueue we can unload those regions and process them
while( workQueue.peek() != null ) {
final GenomeLoc extendedLoc = workQueue.peek().getExtendedLoc();