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>) #there was no $_[1]; it was undef/blank. After explicitly declaring/storing in @array, it worked
{
    chomp;
    split(/\t/);
    $chrsize{$_[0]}=int($_[1]/$win);
}