use FileUtil;

my $gff = shift;      	### annotation information for genome(s)
my $bedList1 = shift; 	### top strand list of bed file(s)
my $bedList2 = shift; 	### bot strand list of bed file(s)
my $unique = shift;		### if true, then only determine the presence/absence of an insertion event, not the quantity of insertions

### NOTE: bed files specify the insertion points of tn-seq element(s). Because the tn-seq elements have a directionality,
### there is top/bottom strandedness to these insertions

my $gfh = FileUtil::openFileHandle($gff);
while (<$gfh>) {
	chomp;
	my @d = split /\t/;
	next unless $d[2] eq "exon" or $d[2] eq "CDS" or $d[2] eq "riboswitch";
	my ($id) = $d[8] =~ /ID=(.*?);/;
    print $id,"\n";
	if (exists($features{$id})) {
	
	} else {
		$features{$id} = \@d;
	}
	my $len = int(0.2*($d[4] - $d[3])); ### look at the 60% internal of gene
	$len = 0; ### set to 20 to look at the 60% internal of gene
	for (my $i = $d[3]-1+$len; $i < $d[4]-$len; $i++) {
		$m{$d[0]}[$i]{$id} = 1;
	}
}
$gfh->close();