diff --git a/core/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/core/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index 0221662a5..196162168 100644
--- a/core/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/core/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -186,35 +186,51 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
     //
     // Comparison operations
     //
-    public static int compareContigs( final String thisContig, final String thatContig ) {
+    public static int compareContigs( final String thisContig, final String thatContig ) 
+    {
         if ( thisContig == thatContig )
+        {
+            assert(false);
             return 0;
+        }
 
-        if ( refContigOrdering != null ) {
-            if ( ! refContigOrdering.containsKey(thisContig) ) {
-                if ( ! refContigOrdering.containsKey(thatContig) ) {
+        assert refContigOrdering.containsKey(thisContig);// : this;
+        assert refContigOrdering.containsKey(thatContig);// : that;
+
+        if ( refContigOrdering != null ) 
+        {
+            if ( ! refContigOrdering.containsKey(thisContig) ) 
+            {
+                if ( ! refContigOrdering.containsKey(thatContig) ) 
+                {
                     // Use regular sorted order
                     return thisContig.compareTo(thatContig);
                 }
-                else {
+                else 
+                {
                     // this is always bigger if that is in the key set
                     return 1;
                 }
             }
             else if ( ! refContigOrdering.containsKey(thatContig) )
+            {
                 return -1;
-            else {
+            }
+            else 
+            {
                 assert refContigOrdering.containsKey(thisContig);// : this;
                 assert refContigOrdering.containsKey(thatContig);// : that;
 
                 final int thisO = refContigOrdering.get(thisContig);
                 final int thatO = refContigOrdering.get(thatContig);
+
                 if ( thisO < thatO ) return -1;
                 if ( thisO > thatO ) return 1;
                 return 0;
             }
         }
-        else {
+        else 
+        {
             return thisContig.compareTo(thatContig);
         }
     }
@@ -235,4 +251,4 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
         if ( this.getStop() > that.getStop() ) return 1;
         return 0;
     }
-}
\ No newline at end of file
+}