Fixed problem with GenomeLoc logic -- optimization was causing assertion failure.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@138 348d0f76-0448-11de-a6fe-93d51630548a

core/java/src/org/broadinstitute/sting/utils/GenomeLoc.java

@@ -190,7 +190,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
     {
         if ( thisContig == thatContig )
         {
-            assert(false);
+            // Optimization.  If the pointers are equal, then the contigs are equal.
             return 0;
         }