now removes supercontigs

misc-scripts/surgery/SeqStoreConverter/vega/DanioRerio.pm

@@ -66,9 +66,6 @@ sub copy_current_clone_info {
     $sth->finish();    
 }
 
-
-
-
 sub update_clone_info {
   my $self = shift;
   my $target_cs_name = shift;
@@ -124,8 +121,24 @@ sub update_clone_info {
 
 sub remove_supercontigs {
     my $self = shift;
+    
     my $target = $self->target();
-    $self->debug("Vega Danio specific - NO supercontigs removed from $target");
+    my $dbh    = $self->dbh();
+    $self->debug("Vega mouse specific - removing supercontigs from $target");
+
+    $dbh->do("DELETE FROM $target.meta ". 
+	     "WHERE meta_value like '%supercontig%'");
+
+    $dbh->do("DELETE FROM $target.coord_system ".
+	     "WHERE name like 'supercontig'");
+    
+    $dbh->do("DELETE $target.assembly ".
+	     "FROM $target.assembly a, $target.seq_region sr ". 
+	     "WHERE sr.coord_system_id = 2 ".
+	     "and a.asm_seq_region_id = sr.seq_region_id");
+
+    $dbh->do("DELETE FROM $target.seq_region ".
+	     "WHERE coord_system_id = 2");
 }
 
 1;