192       my ($first_site, $last_site) = $use_filtered ? @{$thresholds->{$dye}{'indices'}} : (0, $nchar-1);

##</code><code>##

188       my $nchar = ${$tax_sample->{'NChar'}}[0];

##</code><code>##

186 my $tax_sample = $data->{$taxon_label}{'Samples'}{$dye};

##</code><code>##

158 my ($thresholds, $data, $comments);
159 {
160   if (@ARGV) {
161     my $gtr_fname = canonpath $ARGV[0];
162     open GTR_IN, $gtr_fname or die "Cannot open `$gtr_fname' for reading: $!";
163   } else {
164     print STDERR "Reading data from standard input ...\n";
165     *GTR_IN = *STDIN;
166   }
167   ($thresholds, $data, $comments) = readGTR *GTR_IN;
168   close GTR_IN;
169 }

##</code><code>##

34 use genotyping_utilities qw( &canonpath &openForWriting &readGTR &getRepsTable &transpose &isReal &getReplicateGroups );