| line |
true |
false |
branch |
|
74
|
0 |
0 |
unless defined $locigroup
|
|
76
|
0 |
0 |
unless defined $primers
|
|
77
|
0 |
0 |
unless UNIVERSAL::can($primers, 'isa') and $primers->isa('Bio::Polloc::Polloc::IO')
|
|
79
|
0 |
0 |
unless defined $primers->file
|
|
82
|
0 |
0 |
unless defined $locigroup->genomes->[$g]->file
|
|
89
|
0 |
0 |
if ($ln =~ /^Amplimer (\d+)/) { }
|
|
|
0 |
0 |
elsif ($ln =~ /^\s*Sequence: ([^\s]*)\s*/) { }
|
|
|
0 |
0 |
elsif ($ln =~ /^\s*\S+ hits forward strand at (\d+) with (\d+) mismatches/) { }
|
|
|
0 |
0 |
elsif ($ln =~ /^\s*\S+ hits reverse strand at \[(\d+)\] with (\d+) mismatches/) { }
|
|
|
0 |
0 |
elsif ($ln =~ /^\s*Amplimer length: (\d+) bp/) { }
|
|
143
|
0 |
0 |
unless defined $locigroup
|
|
146
|
0 |
0 |
unless my $left_aln = $locigroup->align_context(-1, $self->flanking_size, 0)
|
|
147
|
0 |
0 |
unless my $right_aln = $locigroup->align_context(1, $self->flanking_size, 0)
|
|
155
|
0 |
0 |
unless length $left_cons == $len and length $right_cons == $len
|
|
173
|
2 |
1 |
if defined $value
|
|
174
|
0 |
3 |
unless defined $$self{'_primer_conservation'}
|
|
186
|
2 |
1 |
if defined $value
|
|
187
|
0 |
3 |
unless defined $$self{'_primer_size'}
|
|
200
|
0 |
2 |
if defined $value
|
|
201
|
2 |
0 |
unless defined $$self{'_flanking_size'}
|
|
214
|
0 |
2 |
if defined $value
|