use warnings;

my $OUT;
open $OUT, ">", "$filename.counts" or die "$filename.counts: $!";
foreach my $chr (keys %chrsize){
    my $size = $chrsize{$chr};  # chr, size, index work (print statements show reasonable values)
    foreach my $index (0..$size) {
        #if (exists $piRNA{$chr}{$index}) {
        #   print $OUT "$chr\t$index\t$piRNA{$chr}{$index}\n";}
        $piRNA{$chr}{$index}=0 if (!exists $piRNA{$chr}{$index});
        #print "$piRNA{$chr}{$index}\n" if (exists $piRNA{$chr}{$index});  # test code I've put in
        print $OUT "$chr\t$index\t$piRNA{$chr}{$index}\n";
     }
}