| line |
true |
false |
branch |
|
40
|
1 |
5 |
unless (@species_list)
|
|
72
|
5 |
1 |
unless $self->output_fasta_files or $self->output_phylip_files
|
|
88
|
0 |
5 |
@{$self->_species_list;} < $self->parallel_processes ? :
|
|
89
|
5 |
0 |
int $self->parallel_processes / @{$self->_species_list;} ? :
|
|
95
|
4 |
4 |
if $pm->start
|
|
99
|
0 |
4 |
if $self->verbose
|
|
120
|
0 |
1 |
if $self->verbose
|
|
133
|
0 |
2 |
unless open my $fh_out, '>' . $result_file
|
|
163
|
0 |
0 |
unless @row
|
|
165
|
0 |
0 |
if ($row[0] eq 'Isolate' and $row[1] eq 'ST')
|
|
175
|
0 |
0 |
if ($row[$i] ne 'U')
|
|
189
|
0 |
4 |
if ($self->report_all_mlst_db) { }
|
|
|
0 |
4 |
elsif (@positive_rows) { }
|
|
191
|
0 |
0 |
if @positive_rows || $previous_positive_result and $i > 1
|
|
196
|
0 |
0 |
if $previous_positive_result and $i > 1
|
|
200
|
0 |
4 |
if (@positive_rows)
|
|
208
|
0 |
4 |
scalar @positive_rows ? :
|
|
209
|
0 |
4 |
if scalar @positive_rows
|
|
211
|
0 |
4 |
if $self->verbose and $file_type eq 'allele'
|
|
215
|
2 |
0 |
unless ($self->report_all_mlst_db or $results_found_flag)
|
|
230
|
0 |
5 |
unless $self->_check_input_files_exist
|
|
231
|
0 |
5 |
unless $self->_check_fasta_phylip_options
|