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No need to pass fields as parameters

This commit is contained in:
Joel Thibault 2012-12-14 17:37:29 -05:00
parent 47e620dfbc
commit ffbd4d85f2
1 changed files with 4 additions and 4 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
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@ -227,7 +227,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
final GenomeLoc extendedLoc = workQueue.peek().getExtendedLoc(); final GenomeLoc extendedLoc = workQueue.peek().getExtendedLoc();
if ( extendedLoc.getStop() < minStart || (currentContig != null && !workQueue.peek().getExtendedLoc().getContig().equals(currentContig))) { if ( extendedLoc.getStop() < minStart || (currentContig != null && !workQueue.peek().getExtendedLoc().getContig().equals(currentContig))) {
final ActiveRegion activeRegion = workQueue.remove(); final ActiveRegion activeRegion = workQueue.remove();
sum = processActiveRegion( activeRegion, myReads, workQueue, sum, walker ); sum = processActiveRegion( activeRegion, sum, walker );
} else { } else {
break; break;
} }
@ -236,9 +236,9 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
return sum; return sum;
} }
private T processActiveRegion( final ActiveRegion activeRegion, final LinkedHashSet<GATKSAMRecord> reads, final Queue<ActiveRegion> workQueue, final T sum, final ActiveRegionWalker<M,T> walker ) { private T processActiveRegion( final ActiveRegion activeRegion, final T sum, final ActiveRegionWalker<M,T> walker ) {
final ArrayList<GATKSAMRecord> placedReads = new ArrayList<GATKSAMRecord>(); final ArrayList<GATKSAMRecord> placedReads = new ArrayList<GATKSAMRecord>();
for( final GATKSAMRecord read : reads ) { for( final GATKSAMRecord read : myReads ) {
final GenomeLoc readLoc = this.engine.getGenomeLocParser().createGenomeLoc( read ); final GenomeLoc readLoc = this.engine.getGenomeLocParser().createGenomeLoc( read );
if( activeRegion.getLocation().overlapsP( readLoc ) ) { if( activeRegion.getLocation().overlapsP( readLoc ) ) {
// The region which the highest amount of overlap is chosen as the primary region for the read (tie breaking is done as right most region) // The region which the highest amount of overlap is chosen as the primary region for the read (tie breaking is done as right most region)
@ -278,7 +278,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
activeRegion.add( read ); activeRegion.add( read );
} }
} }
reads.removeAll( placedReads ); // remove all the reads which have been placed into their active region myReads.removeAll( placedReads ); // remove all the reads which have been placed into their active region
// WARNING: This hashset relies on reads being exactly equal when they are placed in the list as when they are removed. So the ActiveRegionWalker can't modify the reads in any way. // WARNING: This hashset relies on reads being exactly equal when they are placed in the list as when they are removed. So the ActiveRegionWalker can't modify the reads in any way.
logger.debug(">> Map call with " + activeRegion.getReads().size() + " " + (activeRegion.isActive ? "active" : "inactive") + " reads @ " + activeRegion.getLocation() + " with full extent: " + activeRegion.getReferenceLoc()); logger.debug(">> Map call with " + activeRegion.getReads().size() + " " + (activeRegion.isActive ? "active" : "inactive") + " reads @ " + activeRegion.getLocation() + " with full extent: " + activeRegion.getReferenceLoc());