From 601e53d633567ee7411afb9cda84235577ec3e95 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Thu, 2 Feb 2012 16:34:26 -0500
Subject: [PATCH] Fix when specifying preset active regions with -AR argument

---
 .../sting/gatk/traversals/TraverseActiveRegions.java   | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

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 769bec720..ce8cb557b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
@@ -124,7 +124,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
 
             // Take the individual isActive calls and integrate them into contiguous active regions and
             // add these blocks of work to the work queue
-            final ArrayList<ActiveRegion> activeRegions = integrateActiveList( isActiveList, firstIsActiveStart, activeRegionExtension );
+            final ArrayList<ActiveRegion> activeRegions = integrateActiveList( isActiveList, firstIsActiveStart, activeRegionExtension, walker.presetActiveRegions != null );
             logger.debug("Integrated " + isActiveList.size() + " isActive calls into " + activeRegions.size() + " regions." );
             if( walker.activeRegionOutStream == null ) { 
                 workQueue.addAll( activeRegions ); 
@@ -214,7 +214,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
     }
 
     // band-pass filter the list of isActive probabilities and turn into active regions
-    private ArrayList<ActiveRegion> integrateActiveList( final ArrayList<Double> activeList, final GenomeLoc firstIsActiveStart, final int activeRegionExtension ) {
+    private ArrayList<ActiveRegion> integrateActiveList( final ArrayList<Double> activeList, final GenomeLoc firstIsActiveStart, final int activeRegionExtension, final boolean presetRegions ) {
 
         final double ACTIVE_PROB_THRESHOLD = 0.2; // BUGBUG: needs to be set-able by the walker author
         final ArrayList<ActiveRegion> returnList = new ArrayList<ActiveRegion>();
@@ -227,11 +227,11 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
         } else {
             final Double[] activeProbArray = activeList.toArray(new Double[activeList.size()]);
             final double[] filteredProbArray = new double[activeProbArray.length];
-            final int FILTER_SIZE = 50; // BUGBUG: needs to be set-able by the walker author
-            final int MAX_ACTIVE_REGION = 425; // BUGBUG: needs to be set-able by the walker author
+            final int FILTER_SIZE = ( presetRegions ? 0 : 50 ); // BUGBUG: needs to be set-able by the walker author
+            final int MAX_ACTIVE_REGION = ( presetRegions ? 16001 : 425 ); // BUGBUG: needs to be set-able by the walker author
             for( int iii = 0; iii < activeProbArray.length; iii++ ) {
                 double maxVal = 0;
-                for( int jjj = Math.max(0, iii-FILTER_SIZE); jjj < Math.min(activeList.size(), iii+FILTER_SIZE); jjj++ ) {
+                for( int jjj = Math.max(0, iii-FILTER_SIZE); jjj < Math.min(activeList.size(), iii+FILTER_SIZE+1); jjj++ ) {
                     if( activeProbArray[jjj] > maxVal ) { maxVal = activeProbArray[jjj]; }
                 }
                 filteredProbArray[iii] = maxVal;