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 3715d2d14..f531cadd4 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
@@ -619,10 +619,10 @@ public class PairHMMIndelErrorModel {
             return 0; // sanity check
 
         for (int i=0; i < b1.length; i++ ){
-            if ( b1[i]!= b2[i])
+            if ( b1[i]!= b2[i] )
                 return i;
         }
-        return 0; // sanity check
+        return b1.length;
     }
 
     private int computeFirstDifferingPosition(double[] b1, double[] b2) {
@@ -630,10 +630,10 @@ public class PairHMMIndelErrorModel {
             return 0; // sanity check
 
         for (int i=0; i < b1.length; i++ ){
-            if ( b1[i]!= b2[i])
+            if ( MathUtils.compareDoubles(b1[i], b2[i]) != 0 )
                 return i;
         }
-        return 0; // sanity check
+        return b1.length;
     }
 
     private final static double[] getHaplotypeLikelihoods(final int numHaplotypes, final int readCounts[], final double readLikelihoods[][]) {