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Can now specify active regions to process at the command line, mainly for debugging purposes

This commit is contained in:
Ryan Poplin 2012-01-25 09:32:52 -05:00
parent 22f0caccac
commit 9818c69df6
2 changed files with 34 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
View File

@ -92,7 +92,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
// Call the walkers isActive function for this locus and add them to the list to be integrated later // Call the walkers isActive function for this locus and add them to the list to be integrated later
if( initialIntervals.overlaps(location) ) { if( initialIntervals.overlaps(location) ) {
final boolean isActive = walker.isActive( tracker, refContext, locus ); final boolean isActive = ( walker.presetActiveRegions == null ? walker.isActive( tracker, refContext, locus ) : walker.presetActiveRegions.overlaps(location) );
isActiveList.add( new ActiveRegion(location, isActive, engine.getGenomeLocParser(), activeRegionExtension ) ); isActiveList.add( new ActiveRegion(location, isActive, engine.getGenomeLocParser(), activeRegionExtension ) );
} }
@ -109,7 +109,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
if( !locusView.hasNext() ) { if( !locusView.hasNext() ) {
// Call the walkers isActive function for this locus and add them to the list to be integrated later // Call the walkers isActive function for this locus and add them to the list to be integrated later
if( initialIntervals.overlaps(location) ) { if( initialIntervals.overlaps(location) ) {
final boolean isActive = walker.isActive( tracker, refContext, locus ); final boolean isActive = ( walker.presetActiveRegions == null ? walker.isActive( tracker, refContext, locus ) : walker.presetActiveRegions.overlaps(location) );
isActiveList.add( new ActiveRegion(location, isActive, engine.getGenomeLocParser(), activeRegionExtension ) ); isActiveList.add( new ActiveRegion(location, isActive, engine.getGenomeLocParser(), activeRegionExtension ) );
} }

32
public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
View File

@ -1,6 +1,11 @@
package org.broadinstitute.sting.gatk.walkers; package org.broadinstitute.sting.gatk.walkers;
import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.IntervalBinding;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.filters.DuplicateReadFilter; import org.broadinstitute.sting.gatk.filters.DuplicateReadFilter;
@ -14,8 +19,10 @@ 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.ActiveRegion;
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.IntervalUtils; import org.broadinstitute.sting.utils.interval.IntervalUtils;
import java.io.PrintStream;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
@ -32,6 +39,31 @@ import java.util.List;
@ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class}) @ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class})
public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> { 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;
@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;
public GenomeLocSortedSet presetActiveRegions = null;
@Override
public void initialize() {
if( activeRegionBindings == null ) { return; }
List<GenomeLoc> allIntervals = new ArrayList<GenomeLoc>(0);
for ( IntervalBinding intervalBinding : activeRegionBindings ) {
List<GenomeLoc> intervals = intervalBinding.getIntervals(this.getToolkit());
if ( intervals.isEmpty() ) {
logger.warn("The interval file " + intervalBinding.getSource() + " contains no intervals that could be parsed.");
}
allIntervals = IntervalUtils.mergeListsBySetOperator(intervals, allIntervals, IntervalSetRule.UNION);
}
presetActiveRegions = IntervalUtils.sortAndMergeIntervals(this.getToolkit().getGenomeLocParser(), allIntervals, IntervalMergingRule.ALL);
}
// Do we actually want to operate on the context? // Do we actually want to operate on the context?
public boolean filter(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { public boolean filter(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
return true; // We are keeping all the reads return true; // We are keeping all the reads