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..1e41a084d 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
@@ -619,7 +619,7 @@ 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
@@ -630,7 +630,7 @@ 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