| line |
true |
false |
branch |
|
40
|
1 |
8 |
unless $accepted_parameters{$parameter} |
|
53
|
2 |
0 |
if (defined $self->{'logfile'}) { } |
|
71
|
2 |
0 |
if (ref $_[0] eq "FASTX::ScriptHelper") |
|
76
|
0 |
2 |
unless defined $seq |
|
78
|
0 |
2 |
if (defined $comment) |
|
83
|
2 |
0 |
if ($self) { } |
|
94
|
0 |
0 |
if (ref $_[0] eq "FASTX::ScriptHelper") |
|
99
|
0 |
0 |
if (defined $comment) |
|
102
|
0 |
0 |
unless defined $qual |
|
104
|
0 |
0 |
if ($self) { } |
|
115
|
1 |
0 |
if (ref $_[0] eq "FASTX::ScriptHelper") |
|
119
|
1 |
0 |
if (is_seq($sequence)) |
|
128
|
0 |
1 |
if (ref $_[0] eq "FASTX::ScriptHelper") |
|
132
|
0 |
1 |
if ($string =~ /[^ACGTRYSWKMBDHVN]/iu) { } |
|
142
|
2 |
0 |
if (ref $_[0] eq "FASTX::ScriptHelper") |
|
146
|
0 |
2 |
unless $input_string |
|
150
|
0 |
2 |
unless $line_width |
|
161
|
2 |
0 |
if (ref $_[0] eq "FASTX::ScriptHelper") |
|
165
|
0 |
2 |
if ($remainder[0]) { } |
|
|
0 |
4 |
elsif (defined $reference and &reftype($reference) eq undef) { } |
|
172
|
0 |
0 |
if (defined $reference_name) |
|
181
|
2 |
0 |
if (defined $self and $self->{'verbose'} or defined $main::opt_verbose and $main::opt_verbose) { } |
|
183
|
0 |
2 |
if (defined $self->{'do_log'}) |
|
187
|
0 |
2 |
if defined $reference |
|
200
|
3 |
0 |
if (ref $_[0] eq "FASTX::ScriptHelper") |
|
208
|
0 |
3 |
if defined $reference |
|
219
|
0 |
0 |
if (ref $_[0] eq "FASTX::ScriptHelper") |
|
224
|
0 |
0 |
if (defined $self->{'do_log'}) |
|
230
|
0 |
0 |
unless my $file_path = $downloader->fetch("to", $destination) |
|
241
|
1 |
0 |
if (ref $_[0] eq "FASTX::ScriptHelper") |
|
252
|
1 |
0 |
if (defined $self) |
|
258
|
0 |
1 |
if ($cmd->{'exit'}) |
|
260
|
0 |
0 |
unless ($options->{'candie'}) |
|
267
|
1 |
0 |
if (defined $self) |
|
268
|
0 |
1 |
if ($options->{'logall'}) |
|
283
|
1 |
0 |
if ($^O =~ /linux/iu) { } |
|
|
0 |
0 |
elsif ($^O =~ /darwin/iu) { } |
|
285
|
1 |
0 |
if $num =~ /^(\d+)/u |
|
289
|
0 |
0 |
if $num =~ /.*Cores: (\d+)/u |
|
307
|
0 |
1 |
unless defined do {
$hash_ref
}->{$attr} |
|
312
|
0 |
1 |
if (ref $_[0] eq "FASTX::ScriptHelper") |