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HAC10188
Name    HAC1018
...
Size    100    100.5    101    102.1    102.6    103.3    104.1
NChar    297
Allele    0$0    0$0    1$1503    0$0    0$0    0$0

my $tax_sample = $data->{$taxon_label}{'Samples'}{$dye};
            my $rep_sample = $data->{$rep_label}  {'Samples'}{$dye};
            my $nchar = ${$tax_sample->{'NChar'}}[0];
...
            my ($row_sum, $row_sum_abs, $row_sum_sq);
            my ($cnt00, $cnt01, $cnt10, $cnt11) = (0) x 4;
            my ($first_site, $last_site) = $use_filtered ? @{$threshol
+ds->{$dye}{'indices'}} : (0, $nchar-1);

#!/usr/bin/perl

# AFLP Replicate Difference Calculator
...
#    print STDERR "Wrote `".$base_fname.'.reps-in-row.heights'.($file_
+number++).'.tab.txt'."'.";
#    }
#}

# Reads in GTR file.
# Takes a filehandle opened for reading.  Returns two hash references.
+  One contains information specific to
# particular dyes: the threshold values and indices (the threshold det
+ermine which sites get filtered out) and
...
    }
    return \%thresholds, \%data, \%comments, \@labels;
}