Coverage bed to csv file to be used in CeleraToGephi script

bedToCovCSV.pl

#!/usr/bin/perl


print "Name,MedianCoverage,ReferenceLength,MapsTo\n";

use List::Util qw(sum max);
open FBed, $ARGV[0];
open Fnuc, $ARGV[1];

while(<FBed>){
    if (!/^track/){
        chomp;
        split;
        $length{$_[0]} = $_[2];
        push(@{$coverageArray{$_[0]}},$_[4]);
    }
}

while(<Fnuc>){
    if(/^ +[0-9]+/){
        split;
        $contig = $_[12];
        $ref = $_[11];
        @out = split(/\|/,$_[12]);
        $map{$out[0]} = $_[11];
    }
}

foreach $contig (sort keys %length){
    $medianCov = median(@{$coverageArray{$contig}});
    print $contig.','.$medianCov.','.$length{$contig}.",".$map{$contig}."\n";
}

sub mean
{
    return sum(@_)/@_;;

}

sub median
{
    my @vals = sort {$a <=> $b} @_;
    my $len = @vals;
    if($len%2) #odd?
    {
        return $vals[int($len/2)];
    }
    else #even
    {
        return ($vals[int($len/2)-1] + $vals[int($len/2)])/2;
    }
}