use strict;
use warnings;

my %chroms;

# Count frequency of start sited in the column-2.
while (<DATA>) {
    next if /^#/;    #ignore comments in the input file
    chomp(my $line = $_);
    my ($chr, $start, $end, $strand) = (split /\t/, $line)[0, 1, 2, 5];
    my $startPoint;

    if ($strand eq '+') {
        $startPoint = $start;
        $chroms{$chr}{startPoints_plusStrand}{$startPoint}++;
    } elsif ($strand eq '-') {
        $startPoint = $end;
        $chroms{$chr}{startPoints_minusStrand}{$startPoint}++;
    } else {
        die "Goofy BED Data on line $.:\n$_";
    }
}

print "#Plus Strand BedGraph:\n";

for my $chromKey (keys %chroms) {
    my $chrom = $chroms{$chromKey};

    print "--- $chromKey\n";
    for my $key (sort {$a <=> $b} keys %{$chrom->{startPoints_plusStrand}}) {
        print $key + 1, "\t", "+", "$chrom->{startPoints_plusStrand}{$key}\n";
    }
}

__DATA__
#chromosome	start	end	position	col-5	strand
chr7	127471196	127472363	Pos1	0	+
chr7	127471196	127472363	Pos1	0	+
chr7	127471196	127472363	Pos1	0	+
chr7	127471196	127472363	Pos1	0	+
chr7	127471196	127472363	Pos1	0	+
chr7	127472363	127473530	Pos2	0	+
chr7	127473530	127474697	Pos3	0	-
chr7	127474697	127475864	Pos4	0	-
chr8	40000	40500	Pos5	0	+
chr8	40000	40600	Pos5	0	+
chr8	40000	40650	Pos5	0	+
chr8	41000	41200	Pos6	0	-