use File::Basename;
my $filename=fileparse($ARGV[0]);

$win=1000; # window size 1kb
$L=`/scratch/xli91_lab/bin/rpyc/sumcol $ARGV[2] 2`; # total nt of genome excluding chrUext and chrM
$N=$L/$win;
$ratio=$ARGV[1]*0.01;

open IN,$ARGV[2]; 
while(<IN>)
{
    chomp(my $line= $_);
    my @array = split(/\t/, $line);
    print"$array[0]\n";
    #array[1] are numbers
    #array[2] are chr names
    $chrsize{$array[0]}=int($array[1]/$win);
}