From abb91cf26b50b246896cc82d1b84d3135027fc5b Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Mon, 30 Jan 2012 15:36:12 -0500
Subject: [PATCH] Increasing the size of the active regions that are produced
 by the active probability integrator, more context is needed to call more
 complex events

---
 .../sting/gatk/traversals/TraverseActiveRegions.java        | 6 +++---
 .../genotyper/IndelGenotypeLikelihoodsCalculationModel.java | 2 +-
 .../varianteval/evaluators/IndelLengthHistogram.java        | 2 +-
 3 files 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 562a6d1d0..769bec720 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
@@ -216,7 +216,7 @@ 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 ) {
 
-        final double ACTIVE_PROB_THRESHOLD = 0.2;
+        final double ACTIVE_PROB_THRESHOLD = 0.2; // BUGBUG: needs to be set-able by the walker author
         final ArrayList<ActiveRegion> returnList = new ArrayList<ActiveRegion>();
         if( activeList.size() == 0 ) {
             return returnList;
@@ -227,8 +227,8 @@ 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 = 10;
-            final int MAX_ACTIVE_REGION = 200;
+            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
             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++ ) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 9126c0495..0422fbf03 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -335,7 +335,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
         if (ref.getWindow().getStop() < loc.getStop() + HAPLOTYPE_SIZE)
             return null;
         if (!(priors instanceof DiploidIndelGenotypePriors))
-            throw new StingException("Only diploid-based Indel priors are supported in the DINDEL GL model");
+            throw new StingException("Only diploid-based Indel priors are supported in the INDEL GL model");
 
         if (alleleList.isEmpty())
             return null;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
index ccec9af12..6cf8b7c2c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
@@ -15,7 +15,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
  * @Author chartl
  * @Date May 26, 2010
  */
-@Analysis(name = "Indel length histograms", description = "Shows the distrbution of insertion/deletion event lengths (negative for deletion, positive for insertion)")
+@Analysis(name = "Indel length histograms", description = "Shows the distribution of insertion/deletion event lengths (negative for deletion, positive for insertion)")
 public class IndelLengthHistogram extends VariantEvaluator {
     private static final int SIZE_LIMIT = 100;
     @DataPoint(description="Histogram of indel lengths")