From 167cd49e710f8a37e37ba28528b93722f50e6253 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 28 Mar 2013 17:35:00 -0400
Subject: [PATCH] Added -forceActive argument to ActiveRegionWalkers

-- Causes the ART tool to treat all bases as active.   Useful for debugging
---
 .../sting/gatk/traversals/TraverseActiveRegions.java      | 1 +
 .../sting/gatk/walkers/ActiveRegionWalker.java            | 8 ++++++++
 2 files changed, 9 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
index 7b831db32..908755a24 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
@@ -487,6 +487,7 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
                                    final AlignmentContext locus) {
         // must be called, even if we won't use the result, to satisfy walker contract
         final ActivityProfileState state = walker.isActive( tracker, refContext, locus );
+        if ( walker.forceActive) state.isActiveProb = 1.0;
         if ( ! walkerHasPresetRegions ) {
             activityProfile.add(state);
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
index ebfc52d3f..9595b8f42 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
@@ -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)
     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
     @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;