From 348f2db7fdf2e5a1d52dc6476c1c116e4064a8d4 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Wed, 9 Nov 2011 22:00:52 -0500
Subject: [PATCH] Fix for HMM optimization. If the two penalty arrays match
 exactly the function should return the end of the array instead of 0.

---
 .../sting/gatk/walkers/indels/PairHMMIndelErrorModel.java     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index ef1c14576..319f41d53 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -622,7 +622,7 @@ public class PairHMMIndelErrorModel {
             if ( b1[i]!= b2[i])
                 return i;
         }
-        return 0; // sanity check
+        return b1.length;
     }
 
     private int computeFirstDifferingPosition(double[] b1, double[] b2) {
@@ -633,7 +633,7 @@ public class PairHMMIndelErrorModel {
             if ( b1[i]!= b2[i])
                 return i;
         }
-        return 0; // sanity check
+        return b1.length;
     }
 
     private final static double[] getHaplotypeLikelihoods(final int numHaplotypes, final int readCounts[], final double readLikelihoods[][]) {