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Added option to be able to write out the active regions to an interval list file

This commit is contained in:
Ryan Poplin 2012-01-25 09:47:06 -05:00
parent 9818c69df6
commit bbefe4a272
2 changed files with 11 additions and 2 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
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@ -128,7 +128,16 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
// add these blocks of work to the work queue
final ArrayList<ActiveRegion> activeRegions = integrateActiveList( isActiveList );
logger.debug("Integrated " + isActiveList.size() + " isActive calls into " + activeRegions.size() + " regions." );
workQueue.addAll( activeRegions );
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() );
}
}
}
// Since we've sufficiently past this point (or this contig!) in the workQueue we can unload those regions and process them
if( !workQueue.isEmpty() ) {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
View File

@ -40,7 +40,7 @@ import java.util.List;
public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
@Output(fullName="activeRegionOut", shortName="ARO", doc="Output the active region to this interval list file", required = false)
protected PrintStream activeRegionOutStream = null;
public PrintStream activeRegionOutStream = null;
@Input(fullName="activeRegionIn", shortName="AR", doc="Use this interval list file as the active regions to process", required = false)
protected List<IntervalBinding<Feature>> activeRegionBindings = null;