include scaffolds for mapping

misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm

@@ -201,7 +201,7 @@ sub run_script {
 
   my $sa = $core_dba->get_SliceAdaptor();
   my $sa_of = $otherf_dba->get_SliceAdaptor();
-  my $chromosomes_of = $sa_of->fetch_all('chromosome', undef, 1);
+  my $chromosomes_of = $sa_of->fetch_all('toplevel', undef, 1);
 
 # Fetch analysis object for refseq
   my $aa_of = $otherf_dba->get_AnalysisAdaptor();
@@ -250,7 +250,7 @@ sub run_script {
         }
 
 # Fetch slice in core database which overlaps refseq transcript
-        my $chromosome = $sa->fetch_by_region('chromosome', $chr_name, $transcript_of->seq_region_start, $transcript_of->seq_region_end);
+        my $chromosome = $sa->fetch_by_region('toplevel', $chr_name, $transcript_of->seq_region_start, $transcript_of->seq_region_end);
         my $transcripts = $chromosome->get_all_Transcripts(1);
 
 # Create a range registry for all the exons of the ensembl transcript