my $self = shift if (defined(caller(1)));

  my $source_id = shift;
  my $species_id = shift;
  my $files       = shift;
  my $release_file   = shift;
  my $verbose       = shift;

  my $file = @{$files}[0];

	open (INFILE, "<$file");
	my $i=0; my $type = "transcript";
	while (my $ln = <INFILE>) {
#	# parse GFF line:
		chomp($ln); $i++;
		my ($seqid, $source, $type, $start, $end, $score, $strand, $phase, $attributes) = split("\t",$ln);
		if ($strand eq ".")		{$strand = 0;}
		elsif ($strand eq "?")	{$strand = 0;}	# nb should more properly be NULL;
		my %attributes;
		unless ($attributes eq ".") {
			my @attributes = split(";",$attributes);
			foreach my $pair ( @attributes ){
				my ($key, $value) = split("=",$pair);

				if ($value =~ m/,/i ) {
					my @values = split(",",$value);
					foreach my $splitval (@values) {
						$splitval =~ s/%59/;/;
						$splitval =~ s/%44/,/;
						$splitval =~ s/%61/=/;			
						push (@{$attributes{uc($key)}},$splitval);
						}
					}
				else {
					$value =~ s/%59/;/;
					$value =~ s/%44/,/;
					$value =~ s/%61/=/;			
					push(@{$attributes{uc($key)}},$value);
					}								
				}
			}


#		# assess and build oligo_feature
		if (($seqid eq ".") || ($start eq ".") || ($end eq ".")) {
#				_parse_error(\%attributes,"incomplete location (".$seqid.":".$start."-".$end.")");
			}
		else {
    		foreach my $name (@{$attributes{"NAME"}}) {
				my %xref = ( 'accession'  => $name,
                			 'chromosome' => $seqid,
                			 'strand'     => $strand,
                			 'txStart'    => $start,
                			 'txEnd'      => $end,
                			 'cdsStart'   => $start,
                			 'cdsEnd'     => $end,
                			 'exonStarts' => $start,
                			 'exonEnds'   => $end );
				print STDERR "$name, $start, $end\n" if($verbose);
    			$self->add_xref( $source_id, $species_id,\% xref );
				}
			}
		}
	print STDERR $i." VB GFF3 xrefs succesfully parsed\n" if($verbose);
	close(INFILE);

  return 0;
} ## end sub run


#sub _parse_error {
#	my ($attributes, $errortext) = @_;
#	my %attributes = %{$attributes};
#	print STDERR "A:". $attributes{"ARRAY"}->[0].
#				 "\tS:". ($attributes{"PROBESET"}->[0] || ""). 
#				 "\tP:". $attributes{"NAME"}->[0].
#				 "\t".$errortext."\n";	
#	}


1;