Sequence retrieved from the database is now uppercased. This is so that...

Sequence retrieved from the database is now uppercased.  This is so that softmasking can still be performed correctly when mixed/lower case sequence is stored in the database.

modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm

@@ -245,7 +245,8 @@ sub _fetch_seq {
         $sth->fetch();
         $sth->finish();
 
-        $entire_seq .= $tmp_seq;
+        # always give back uppercased sequence so it can be properly softmasked
+        $entire_seq .= uc($tmp_seq);
         $cache->{"$seq_region_id:$i"} = $tmp_seq;
       }
     }
@@ -270,6 +271,9 @@ sub _fetch_seq {
     $sth->fetch();
     $sth->finish();
 
+    # always give back uppercased sequence so it can be properly softmasked
+    $tmp_seq = uc($tmp_seq);
+
     return \$tmp_seq;
   }
 }