if $locationOfRead == $location
    $chrHash->{$chr}->{$location}++
##</code><code>##

 
use POSIX qw(ceil floor);
use strict; 

my $binSize = $ARGV[0]; # size of each bin (default 1000)
my $readSize = $ARGV[1];
my @chromosomes = ("chr1","chr2","chr3");
while(<STDIN>) {} # parse through file once to get number of lines
my $maxCount = $.; # max count => all reads from the same locus => number of lines in SAM file
my @counts = (0..$maxCount);
my @countHash;
map { $countHash{$_} = "" } @counts; # ???
my %chrHash;
map { $chrHash{$_} = { %countHash } } @chromosomes;

# old version:

my @bins = (0..(250000000/$binSize); # chr1 ~ 250 mio bases
my @binHash;
my %chrHash;
map { $binHash{$_} = 0 } @bins;
# assume that all chromosomes are equal size and create a hash of hashes for counting
map { $chrHash{$_} = { %binHash } } @chromosomes;
# Read in SAM file and count reads per bin
while(<STDIN>) {
	chomp();
	my @line = split(/\t/,$_);
	if ($line[2] ~~ @chromosomes) {
		my $location = floor(ceil((2*$line[3]+$readSize)/2)/1000);
		$chrHash{$line[2]}{$location}++;
	}
}