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misc cleanup in active region traversal.

This commit is contained in:
Ryan Poplin 2012-08-30 11:01:01 -04:00
parent 76853806b0
commit 7b366d4049
2 changed files with 8 additions and 7 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
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@ -185,7 +185,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
*/ */
private void writeActiveRegionsToStream( final ActiveRegionWalker<M,T> walker ) { private void writeActiveRegionsToStream( final ActiveRegionWalker<M,T> walker ) {
// Just want to output the active regions to a file, not actually process them // Just want to output the active regions to a file, not actually process them
for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion : workQueue ) { for( final ActiveRegion activeRegion : workQueue ) {
if( activeRegion.isActive ) { if( activeRegion.isActive ) {
walker.activeRegionOutStream.println( activeRegion.getLocation() ); walker.activeRegionOutStream.println( activeRegion.getLocation() );
} }
@ -198,7 +198,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
while( workQueue.peek() != null ) { while( workQueue.peek() != null ) {
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 org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion = workQueue.remove(); final ActiveRegion activeRegion = workQueue.remove();
sum = processActiveRegion( activeRegion, myReads, workQueue, sum, walker ); sum = processActiveRegion( activeRegion, myReads, workQueue, sum, walker );
} else { } else {
break; break;
@ -208,15 +208,15 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
return sum; return sum;
} }
private T processActiveRegion( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final LinkedHashSet<GATKSAMRecord> reads, final Queue<org.broadinstitute.sting.utils.activeregion.ActiveRegion> workQueue, final T sum, final ActiveRegionWalker<M,T> walker ) { private T processActiveRegion( final ActiveRegion activeRegion, final LinkedHashSet<GATKSAMRecord> reads, final Queue<ActiveRegion> workQueue, 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 : reads ) {
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)
long maxOverlap = activeRegion.getLocation().sizeOfOverlap( readLoc ); long maxOverlap = activeRegion.getLocation().sizeOfOverlap( readLoc );
org.broadinstitute.sting.utils.activeregion.ActiveRegion bestRegion = activeRegion; ActiveRegion bestRegion = activeRegion;
for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion otherRegionToTest : workQueue ) { for( final ActiveRegion otherRegionToTest : workQueue ) {
if( otherRegionToTest.getLocation().sizeOfOverlap(readLoc) >= maxOverlap ) { if( otherRegionToTest.getLocation().sizeOfOverlap(readLoc) >= maxOverlap ) {
maxOverlap = otherRegionToTest.getLocation().sizeOfOverlap( readLoc ); maxOverlap = otherRegionToTest.getLocation().sizeOfOverlap( readLoc );
bestRegion = otherRegionToTest; bestRegion = otherRegionToTest;
@ -229,7 +229,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
if( !bestRegion.equals(activeRegion) ) { if( !bestRegion.equals(activeRegion) ) {
activeRegion.add( read ); activeRegion.add( read );
} }
for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion otherRegionToTest : workQueue ) { for( final ActiveRegion otherRegionToTest : workQueue ) {
if( !bestRegion.equals(otherRegionToTest) && otherRegionToTest.getExtendedLoc().overlapsP( readLoc ) ) { if( !bestRegion.equals(otherRegionToTest) && otherRegionToTest.getExtendedLoc().overlapsP( readLoc ) ) {
otherRegionToTest.add( read ); otherRegionToTest.add( read );
} }

3
public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
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@ -12,6 +12,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalSetRule; import org.broadinstitute.sting.utils.interval.IntervalSetRule;
@ -77,7 +78,7 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
public abstract ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context); public abstract ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context);
// Map over the ActiveRegion // Map over the ActiveRegion
public abstract MapType map(final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker); public abstract MapType map(final ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker);
public final GenomeLocSortedSet extendIntervals( final GenomeLocSortedSet intervals, final GenomeLocParser genomeLocParser, IndexedFastaSequenceFile reference ) { public final GenomeLocSortedSet extendIntervals( final GenomeLocSortedSet intervals, final GenomeLocParser genomeLocParser, IndexedFastaSequenceFile reference ) {
final int activeRegionExtension = this.getClass().getAnnotation(ActiveRegionExtension.class).extension(); final int activeRegionExtension = this.getClass().getAnnotation(ActiveRegionExtension.class).extension();