| line |
true |
false |
branch |
|
47
|
1 |
8 |
if (@{$args;} != 1) |
|
54
|
0 |
8 |
if lc $_ eq 'stdin' |
|
55
|
1 |
7 |
unless (Path::Tiny::path($_)->is_file) |
|
60
|
1 |
6 |
if (exists $opt->{'annotation'}) |
|
61
|
0 |
1 |
unless (Path::Tiny::path($opt->{'annotation'})->is_file) |
|
66
|
0 |
7 |
if (not exists $opt->{'outfile'}) |
|
76
|
0 |
7 |
if (lc $args->[0] eq 'stdin') { } |
|
84
|
7 |
0 |
if (lc $opt->{'outfile'} eq 'stdout') { } |
|
93
|
1 |
6 |
if ($opt->{'annotation'}) |
|
95
|
0 |
1 |
unless defined $anno->{'cds'} |
|
96
|
0 |
1 |
unless defined $anno->{'repeat'} |
|
103
|
7 |
498 |
if $in_fh->eof and $content eq '' |
|
105
|
498 |
0 |
unless ($in_fh->eof) |
|
108
|
0 |
498 |
if substr($line, 0, 1) eq '#' |
|
110
|
34 |
464 |
if ($line eq '' || $line =~ /^\s+$/ and $content ne '') { } |
|
122
|
34 |
0 |
if ($opt->{'length'}) |
|
123
|
15 |
19 |
if length $$info_of{$full_names[0]}{'seq'} < $opt->{'length'} |
|
146
|
439 |
275 |
if ($opt->{'annotation'}) |
|
147
|
439 |
0 |
if (defined $cds_set_of->{$chr_name}) |
|
150
|
439 |
0 |
if (defined $repeat_set_of->{$chr_name}) |
|
190
|
9 |
10 |
if ($opt->{'outgroup'}) |
|
195
|
0 |
19 |
if ($seq_count < 2) |
|
202
|
9 |
10 |
if ($opt->{'outgroup'}) |
|
207
|
39 |
1124 |
if ($opt->{'nocomplex'} and $site->{'snp_freq'} == -1) |
|
210
|
410 |
714 |
if ($opt->{'nosingle'} and $site->{'snp_freq'} <= 1) |