ori wasnt set right in Exon.

External Gene get repaired now.

modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm

@@ -247,6 +247,9 @@ sub _new_Exon_from_hashRef {
    $exon->attach_seq($self->{rchash}{$hashRef->{'contig_id'}}->primary_seq);
    $exon->contig( $self->{rchash}{$hashRef->{'contig_id'}} );
    $exon->seqname($hashRef->{'cid'});
+   $exon->ori_start( $exon->start );
+   $exon->ori_end( $exon->end );
+   $exon->ori_strand( $exon->strand );
 
    # maybe we should cache this.
    

modules/Bio/EnsEMBL/DBSQL/ExternalWrapper.pm

@@ -197,13 +197,13 @@ sub get_Ensembl_Genes_contig_list{
        }
 
        foreach my $gene (@genes) {
-	 if (my $contig = $gc{$gene->id}) {
+	 if (my $contig = $gc{$gene->dbID}) {
 	   push(@{$cg{$contig}},$gene);
 	 }
        }
        $self->cg(\%cg);
        
-       print STDERR "Returning ".scalar(@genes)." $genes[0] genes...\n";
+       # print STDERR "Returning ".scalar(@genes)." $genes[0] genes...\n";
        return @genes;
    }
 }