my $tax_sample = $data->{$taxon_label}{'Samples'}{$dye};
			my $rep_sample = $data->{$rep_label}  {'Samples'}{$dye};
			my $nchar = ${$tax_sample->{'NChar'}}[0];
			# I don't set these row sum variables to zero, because I want them undefined ifthe row is empty.
			my ($row_sum, $row_sum_abs, $row_sum_sq);
			my ($cnt00, $cnt01, $cnt10, $cnt11) = (0) x 4;
			my ($first_site, $last_site) = $use_filtered ? @{$thresholds->{$dye}{'indices'}} : (0, $nchar-1);