| line |
true |
false |
branch |
|
59
|
1 |
5 |
if (@{$args;} != 1) |
|
66
|
0 |
5 |
if lc $_ eq 'stdin' |
|
67
|
1 |
4 |
unless (Path::Tiny::path($_)->is_file) |
|
72
|
0 |
4 |
if (not exists $opt->{'outfile'}) |
|
81
|
0 |
4 |
if (lc $args->[0] eq 'stdin') { } |
|
89
|
4 |
0 |
if (lc $opt->{'outfile'} eq 'stdout') { } |
|
99
|
4 |
88 |
if $in_fh->eof and $content eq '' |
|
101
|
87 |
1 |
unless ($in_fh->eof) |
|
104
|
10 |
78 |
if ($line eq '' || $line =~ /^\s+$/ and $content ne '') { } |
|
108
|
3 |
7 |
if ($opt->{'parallel'} >= 2) { } |
|
122
|
1 |
3 |
if ($opt->{'parallel'} >= 2) |
|
161
|
0 |
7 |
if ($opt->{'msa'} ne 'none') |
|
162
|
0 |
0 |
if ($opt->{'quick'}) { } |
|
176
|
0 |
7 |
if ($opt->{'outgroup'}) |
|
189
|
3 |
4 |
if ($opt->{'chop'}) |
|
216
|
3 |
0 |
defined $chop_length ? : |
|
221
|
0 |
3 |
if $chop_length * 2 >= $align_length |
|
231
|
2 |
1 |
if $indel_set->is_empty |
|
239
|
1 |
0 |
if ($head_indel_set->is_not_empty) |
|
243
|
11 |
1 |
if ($base ne '-') |
|
244
|
6 |
5 |
if ($info->{'strand'} eq '+') { } |
|
262
|
1 |
0 |
if ($tail_indel_set->is_not_empty) |
|
266
|
6 |
2 |
if ($base ne '-') |
|
267
|
4 |
2 |
if ($info->{'strand'} eq '+') { } |