my @file1 = ();
open(FILE, @ARGV[0]) || 
	die ("could not open file @ARGV[0]\n");

    while (my $line = <FILE>) {
	chomp $line;
	my ($chr, $start, $stop) = split(/\t/, $line);
        push @file1, [$chr, $start, $stop];
	}
close FILE;

open(FILE, @ARGV[1])||die ("could not open file @ARGV[1]\n");
	
	while(<FILE>){
		($Gene,$Chrom,$ModStart,$ModEnd,$Strand,$ExonCount,$SizeKB)= split;		
		foreach my $line (@file1){
			$Count = 0;
			my ($chr, $start, $stop) = @$line;
			if ($chr eq $Chrom && $start gt $ModStart && $end lt $ModEnd){
			$Count++;
			print ("$Gene\t$Chrom\t$ModStart\t$ModEnd\t$Strand\t$ExonCount\t$SizeKB\t$Count\n")
			}	
	}
}