| line |
true |
false |
branch |
|
45
|
0 |
1 |
unless open my $fh, '>', $self->summary_output_filename
|
|
52
|
1 |
0 |
$self->gene_category_count->{'core'} ? :
|
|
53
|
1 |
0 |
$self->gene_category_count->{'soft_core'} ? :
|
|
54
|
1 |
0 |
$self->gene_category_count->{'shell'} ? :
|
|
55
|
1 |
0 |
$self->gene_category_count->{'cloud'} ? :
|
|
58
|
1 |
0 |
if $core_genes < 100
|
|
76
|
0 |
4 |
if ($self->_soft_core_percentage <= $self->_shell_percentage)
|
|
86
|
1695 |
1305 |
if defined $self->_genes_to_rows->{$gene_name}[$i] and $self->_genes_to_rows->{$gene_name}[$i] ne ''
|
|
89
|
12 |
128 |
if ($isolates_with_gene < $self->_cloud_percentage * $number_of_samples) { }
|
|
|
72 |
56 |
elsif ($isolates_with_gene < $self->_shell_percentage * $number_of_samples) { }
|
|
|
2 |
54 |
elsif ($isolates_with_gene < $self->_soft_core_percentage * $number_of_samples) { }
|
|
120
|
4 |
140 |
if not defined $row->[0] or $row->[0] eq ''
|
|
132
|
0 |
96 |
if not defined $row->[$i] or $row->[$i] eq ''
|
|
157
|
0 |
300 |
unless defined $sample_gene_id
|
|
159
|
300 |
0 |
if ($sample_gene_id =~ /_([\d]+)$/) { }
|
|
179
|
53 |
247 |
unless ($current_gene_id + $self->contiguous_window >= $gene_id and $current_gene_id - $self->contiguous_window <= $gene_id)
|
|
182
|
53 |
0 |
if ($block_size >= $largest_block_size)
|
|
192
|
3 |
3 |
if ($block_size > $largest_block_size)
|