| line |
true |
false |
branch |
|
53
|
1 |
7 |
if (@{$args;} != 1) |
|
60
|
0 |
7 |
if lc $_ eq 'stdin' |
|
61
|
1 |
6 |
unless (Path::Tiny::path($_)->is_file) |
|
66
|
0 |
6 |
unless (exists $opt->{'outfile'}) |
|
70
|
6 |
0 |
if ($opt->{'colors'}) |
|
80
|
0 |
6 |
if (lc $args->[0] eq 'stdin') { } |
|
99
|
6 |
162 |
if $in_fh->eof and $content eq '' |
|
101
|
162 |
0 |
unless ($in_fh->eof) |
|
104
|
0 |
162 |
if substr($line, 0, 1) eq '#' |
|
106
|
18 |
144 |
if ($line eq '' || $line =~ /^\s+$/ and $content ne '') { } |
|
118
|
18 |
0 |
if ($opt->{'length'}) |
|
119
|
1 |
17 |
if length $$info_of{$full_names[0]}{'seq'} < $opt->{'length'} |
|
255
|
2 |
15 |
if ($opt->{'outgroup'}) |
|
260
|
0 |
17 |
if ($seq_count < 2) |
|
265
|
2 |
15 |
if ($opt->{'outgroup'}) |
|
270
|
2 |
15 |
if ($opt->{'outgroup'}) |
|
276
|
2 |
31 |
if ($opt->{'nocomplex'} and $site->{'indel_freq'} == -1) |
|
280
|
4 |
27 |
if ($opt->{'nosingle'} and $site->{'indel_freq'} <= 1) |
|
284
|
6 |
21 |
if ($opt->{'noindel'}) |
|
288
|
4 |
17 |
if (defined $opt->{'min'} and $site->{'indel_freq'} / $seq_count < $opt->{'min'}) |
|
291
|
0 |
17 |
if (defined $opt->{'max'} and $site->{'indel_freq'} / $seq_count > $opt->{'max'}) |
|
300
|
7 |
441 |
if ($opt->{'nocomplex'} and $site->{'snp_freq'} == -1) |
|
304
|
63 |
378 |
if ($opt->{'nosingle'} and $site->{'snp_freq'} <= 1) |
|
308
|
63 |
315 |
if (defined $opt->{'min'} and $site->{'snp_freq'} / $seq_count < $opt->{'min'}) |
|
311
|
0 |
315 |
if (defined $opt->{'max'} and $site->{'snp_freq'} / $seq_count > $opt->{'max'}) |
|
340
|
2 |
15 |
if $opt->{'outgroup'} |
|
347
|
315 |
17 |
if ($var->{'var_type'} eq 'snp') |
|
358
|
80 |
1132 |
$var->{'snp_occured'} eq 'unknown' ? : |
|
360
|
725 |
487 |
if ($occ eq '1') { } |
|
374
|
48 |
267 |
if ($opt->{'outgroup'}) |
|
389
|
17 |
315 |
if ($var->{'var_type'} eq 'indel') |
|
395
|
0 |
17 |
if ($col_cursor + $col_taken > $opt->{'wrap'}) |
|
404
|
14 |
3 |
if ($var->{'indel_occured'} ne 'unknown') |
|
410
|
11 |
54 |
if ($var->{'indel_occured'} eq 'unknown') { } |
|
415
|
32 |
22 |
if ($occ eq '1') |
|
420
|
43 |
22 |
if ($flag) |
|
421
|
37 |
6 |
if ($col_taken == 1) { } |
|
|
6 |
0 |
elsif ($col_taken == 2) { } |
|
479
|
2 |
330 |
if ($col_cursor > $opt->{'wrap'}) |