open OUT, ">", "$filename.counts";
foreach $chr (keys %chrsize){
    $size = $chrsize{$chr};  # chr, size, index work (print statements show reasonable values)
    foreach $index (0..$size) {
       $piRNA{$chr}{$index}=0 if (!exists $piRNA{$chr}{$index});       
        print OUT "$chr\t$index\t$piRNA{$chr}{$index}\n";
     }
}