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Added -forceActive argument to ActiveRegionWalkers 

-- Causes the ART tool to treat all bases as active.   Useful for debugging
This commit is contained in:
Mark DePristo 2013-03-28 17:35:00 -04:00
parent 8656bd5e29
commit 167cd49e71
2 changed files with 9 additions and 0 deletions
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1
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
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@ -487,6 +487,7 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
final AlignmentContext locus) { final AlignmentContext locus) {
// must be called, even if we won't use the result, to satisfy walker contract // must be called, even if we won't use the result, to satisfy walker contract
final ActivityProfileState state = walker.isActive( tracker, refContext, locus ); final ActivityProfileState state = walker.isActive( tracker, refContext, locus );
if ( walker.forceActive) state.isActiveProb = 1.0;
if ( ! walkerHasPresetRegions ) { if ( ! walkerHasPresetRegions ) {
activityProfile.add(state); activityProfile.add(state);
} }

8
public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
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@ -88,6 +88,14 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
@Argument(fullName="activeRegionExtension", shortName="activeRegionExtension", doc="The active region extension; if not provided defaults to Walker annotated default", required = false) @Argument(fullName="activeRegionExtension", shortName="activeRegionExtension", doc="The active region extension; if not provided defaults to Walker annotated default", required = false)
public Integer activeRegionExtension = null; public Integer activeRegionExtension = null;
/**
* For the active region walker to treat all bases as active. Useful for debugging when you want to force something like
* the HaplotypeCaller to process a specific interval you provide the GATK
*/
@Advanced
@Argument(fullName="forceActive", shortName="forceActive", doc="If provided, all bases will be tagged as active", required = false)
public boolean forceActive = false;
@Advanced @Advanced
@Argument(fullName="activeRegionMaxSize", shortName="activeRegionMaxSize", doc="The active region maximum size; if not provided defaults to Walker annotated default", required = false) @Argument(fullName="activeRegionMaxSize", shortName="activeRegionMaxSize", doc="The active region maximum size; if not provided defaults to Walker annotated default", required = false)
public Integer activeRegionMaxSize = null; public Integer activeRegionMaxSize = null;