use Data::Dumper;
$Data::Dumper::Sortkeys = 1;

##</code><code>##

my ($cnt00, $cnt01, $cnt10, $cnt11) = (0) x 4;
# add two lines
print Dumper $data;
die "missing \$nchar\n" if not $nchar;
my ($first_site, $last_site) = $use_filtered ? @{$thresholds->{$dye}{'indices'}} : (0, $nchar-1);