| line |
true |
false |
branch |
|
51
|
1 |
6 |
if (@{$args;} != 1) |
|
58
|
0 |
6 |
if lc $_ eq 'stdin' |
|
59
|
1 |
5 |
unless (Path::Tiny::path($_)->is_file) |
|
64
|
0 |
5 |
unless (exists $opt->{'outfile'}) |
|
68
|
5 |
0 |
if ($opt->{'colors'}) |
|
78
|
0 |
5 |
if (lc $args->[0] eq 'stdin') { } |
|
97
|
5 |
135 |
if $in_fh->eof and $content eq '' |
|
99
|
135 |
0 |
unless ($in_fh->eof) |
|
102
|
0 |
135 |
if substr($line, 0, 1) eq '#' |
|
104
|
15 |
120 |
if ($line eq '' || $line =~ /^\s+$/ and $content ne '') { } |
|
116
|
15 |
0 |
if ($opt->{'length'}) |
|
117
|
1 |
14 |
if length $$info_of{$full_names[0]}{'seq'} < $opt->{'length'} |
|
253
|
2 |
12 |
if ($opt->{'outgroup'}) |
|
258
|
0 |
14 |
if ($seq_count < 2) |
|
263
|
2 |
12 |
if ($opt->{'outgroup'}) |
|
268
|
2 |
12 |
if ($opt->{'outgroup'}) |
|
274
|
2 |
25 |
if ($opt->{'nocomplex'} and $site->{'indel_freq'} == -1) |
|
278
|
4 |
21 |
if ($opt->{'nosingle'} and $site->{'indel_freq'} <= 1) |
|
282
|
6 |
15 |
if ($opt->{'noindel'}) |
|
291
|
7 |
361 |
if ($opt->{'nocomplex'} and $site->{'snp_freq'} == -1) |
|
295
|
63 |
298 |
if ($opt->{'nosingle'} and $site->{'snp_freq'} <= 1) |
|
324
|
2 |
12 |
if $opt->{'outgroup'} |
|
331
|
298 |
15 |
if ($var->{'var_type'} eq 'snp') |
|
342
|
80 |
1064 |
$var->{'snp_occured'} eq 'unknown' ? : |
|
344
|
691 |
453 |
if ($occ eq '1') { } |
|
358
|
48 |
250 |
if ($opt->{'outgroup'}) |
|
373
|
15 |
298 |
if ($var->{'var_type'} eq 'indel') |
|
379
|
0 |
15 |
if ($col_cursor + $col_taken > $opt->{'wrap'}) |
|
388
|
12 |
3 |
if ($var->{'indel_occured'} ne 'unknown') |
|
394
|
11 |
46 |
if ($var->{'indel_occured'} eq 'unknown') { } |
|
399
|
28 |
18 |
if ($occ eq '1') |
|
404
|
39 |
18 |
if ($flag) |
|
405
|
33 |
6 |
if ($col_taken == 1) { } |
|
|
6 |
0 |
elsif ($col_taken == 2) { } |
|
463
|
2 |
311 |
if ($col_cursor > $opt->{'wrap'}) |