use FileUtil;

my $f = shift;
my $bedTopOut = shift;
my $bedBotOut = shift;
my $fh = FileUtil::openFileHandle($f);
while (<$fh>) {
  $l = $_;
	chomp;
	my @d = split /\t/;
	next if $d[4] < 20;
	if ($d[1] & 16) {
		$mm{$d[2]}[0][$d[3]]++;
		$m{$d[2]}[0][$d[3]]++;
	} else {
		$mm{$d[2]}[1][$d[3]]++;
		$m{$d[2]}[1][$d[3]]++;
	}
}
$fh->close();

my $bfho = new FileHandle("| perl /geode/projects/ln/BL-CGBI/G1//bin/drusch/minimizeBedGraph.pl - >$bedTopOut");
foreach my $i (keys %m) {
	my $max = @{$m{$i}[0]};
	for (my $j = 0; $j <= $max; $j++) {
		my $l = join "\t",$i,$j,$j+1,$mm{$i}[0][$j]+0;
		print $bfho $l,"\n";
	}
}
$bfho->close();

my $bfho = new FileHandle("| perl /geode/projects/ln/BL-CGBI/G1//bin/drusch/minimizeBedGraph.pl - >$bedBotOut");
foreach my $i (keys %m) {
	my $max = @{$m{$i}[1]};
	for (my $j = 0; $j <= $max; $j++) {
		my $l = join "\t",$i,$j,$j+1,$mm{$i}[1][$j]+0;
		print $bfho $l,"\n";
	}
}
$bfho->close();