| line |
true |
false |
branch |
|
22
|
0 |
24 |
unless @_ |
|
23
|
12 |
12 |
unless @_ > 1 |
|
30
|
1637 |
375046 |
if &$f() |
|
38
|
1529 |
384264 |
unless &$f() |
|
47
|
13816 |
0 |
defined $_ ? : |
|
54
|
12 |
7 |
if &$f() |
|
66
|
5 |
0 |
if (@fields >= 1) |
|
80
|
0 |
115 |
if @lines % 2 |
|
93
|
376 |
173 |
if ($want_full or not defined $info_ref->{'name'}) { } |
|
109
|
0 |
10 |
if @lines % 2 |
|
133
|
0 |
9 |
if @lines % 2 |
|
158
|
0 |
6 |
if @lines != 3 |
|
164
|
3 |
3 |
if ($query_strand eq '-') |
|
165
|
1 |
2 |
if (defined $length_of and ref $length_of eq 'HASH') |
|
166
|
1 |
0 |
if (exists $length_of->{$second_chr}) |
|
198
|
0 |
4 |
unless @lines > 0 |
|
206
|
0 |
16 |
unless defined $chr_name |
|
213
|
4 |
12 |
if ($strand eq '-') |
|
261
|
2271 |
75906 |
if ($base eq '-') { } |
|
262
|
536 |
1735 |
if ($offset == 0) |
|
268
|
524 |
75382 |
if ($offset != 0) |
|
275
|
12 |
196 |
if ($offset != 0) |
|
303
|
0 |
0 |
if ($aln_bin =~ /clus/iu) { } |
|
|
0 |
0 |
elsif ($aln_bin =~ /musc/iu) { } |
|
|
0 |
0 |
elsif ($aln_bin =~ /maff/iu) { } |
|
306
|
0 |
0 |
if (IPC::Cmd::can_run($e)) |
|
315
|
0 |
0 |
if (IPC::Cmd::can_run($e)) |
|
324
|
0 |
0 |
if (IPC::Cmd::can_run($e)) |
|
331
|
0 |
0 |
unless (defined $bin) |
|
354
|
0 |
0 |
if ($aln_bin eq 'clustalw') { } |
|
|
0 |
0 |
elsif ($aln_bin eq 'muscle') { } |
|
|
0 |
0 |
elsif ($aln_bin eq 'mafft') { } |
|
374
|
0 |
0 |
unless ($ok) |
|
386
|
0 |
0 |
if ($aln_bin eq 'clustalw') |
|
403
|
0 |
0 |
unless (defined $aln_prog) |
|
406
|
0 |
0 |
unless (defined $indel_pad) |
|
409
|
0 |
0 |
unless (defined $indel_fill) |
|
458
|
0 |
10 |
unless $seq_length |
|
469
|
4 |
524 |
if (&all(sub {
$_ eq '-';
}
, @bases)) |
|
498
|
0 |
11 |
if $seq_count < 3 |
|
513
|
15 |
8 |
if ($intersect_set->superset($span)) |
|
549
|
0 |
6 |
if $seq_count < 3 |
|
576
|
3 |
1 |
if ($sub_union_set->superset("$seg_start-$seg_end")) |
|
598
|
0 |
5 |
if ($sub_union_set->larger_than($sub_out_set)) |
|
619
|
0 |
8 |
if ($line eq '' or substr($line, 0, 1) eq ' ') { } |
|
|
0 |
8 |
elsif (substr($line, 0, 1) eq '#') { } |
|
|
4 |
4 |
elsif (substr($line, 0, 1) eq '>') { } |
|
662
|
0 |
17 |
if ($four_count == 0) { } |
|
678
|
0 |
60 |
if ($seq_count != 2) |
|
690
|
4858 |
85 |
if ($base0 =~ /[atcg]/iu and $base1 =~ /[atcg]/iu) |
|
694
|
915 |
3943 |
if ($base0 ne $base1) |
|
700
|
0 |
60 |
if ($comparable_bases == 0) { } |
|
715
|
0 |
7 |
if ($seq_count != 3) |
|
722
|
0 |
7 |
if $length == 0 |
|
728
|
8 |
62 |
if ($base0 ne $base1) |
|
729
|
7 |
1 |
if ($base0 =~ /[atcg]/iu and $base1 =~ /[atcg]/iu and $base_og =~ /[atcg]/iu) { } |
|
733
|
3 |
4 |
if ($base1 eq $base_og) { } |
|
|
3 |
1 |
elsif ($base0 eq $base_og) { } |
|
760
|
0 |
11 |
if ($seq_count < 2) |
|
776
|
725 |
21 |
if (&all(sub {
$_ =~ /[agct]/iu;
}
, @bases)) { } |
|
|
20 |
1 |
elsif (&any(sub {
$_ eq '-';
}
, @bases)) { } |
|
778
|
514 |
211 |
if (&all(sub {
$_ eq $bases[0];
}
, @bases)) { } |
|
792
|
0 |
11 |
if ($comparable_bases == 0) |
|
828
|
39884 |
773 |
if (&all(sub {
$_ =~ /[agct]/iu;
}
, @bases)) |
|
829
|
1617 |
38267 |
if (&any(sub {
$_ ne $bases[0];
}
, @bases)) |
|
848
|
0 |
1617 |
if (scalar @class < 2) { } |
|
|
84 |
1533 |
elsif (scalar @class > 2) { } |
|
859
|
3619 |
6843 |
if ($target_base ne $_) { } |
|
901
|
188 |
383 |
if ($_ eq $nt) |
|
903
|
394 |
188 |
unless ($class_bool) |
|
910
|
0 |
195 |
if (scalar @class < 2) { } |
|
|
191 |
4 |
elsif (scalar @class == 2) { } |
|
915
|
255 |
315 |
if ($nt eq $outgroup_base) { } |
|
932
|
28 |
167 |
if ($snp_occured eq '1' x length($snp_occured)) |
|
979
|
0 |
52 |
if (scalar @uniq_indel_seqs < 2) { } |
|
|
14 |
38 |
elsif (scalar @uniq_indel_seqs > 2) { } |
|
|
0 |
38 |
elsif ($indel_seq =~ /-/u) { } |
|
994
|
27 |
11 |
if ($indel_seqs[0] eq $indel_seq) { } |
|
1004
|
14 |
38 |
if ($indel_type eq 'C') { } |
|
1012
|
84 |
54 |
if ($indel_seqs[0] eq $_) { } |
|
1066
|
0 |
5 |
if (scalar @uniq_indel_seqs < 2) { } |
|
|
1 |
4 |
elsif (scalar @uniq_indel_seqs > 2) { } |
|
|
0 |
4 |
elsif ($indel_seq =~ /-/u) { } |
|
1077
|
0 |
4 |
if (not $indel_outgroup_seq =~ /\-/u and $indel_seq ne $indel_outgroup_seq) { } |
|
|
3 |
1 |
elsif ($outgroup_indel_set->intersect($indel_set)->is_not_empty) { } |
|
|
1 |
0 |
elsif ($outgroup_indel_set->intersect($indel_set)->is_empty) { } |
|
1093
|
2 |
1 |
if ($island->equal($indel_set)) { } |
|
1124
|
2 |
3 |
if ($indel_type eq 'C') { } |
|
1130
|
3 |
5 |
if ($seq eq $indel_outgroup_seq) { } |
|
1158
|
0 |
8 |
if ($pos < $chr_start or $pos > $chr_end) |
|
1163
|
5 |
3 |
if ($chr_strand eq '+') { } |
|
1184
|
0 |
734 |
if ($pos < 1) |
|
1189
|
728 |
6 |
if ($intspan->contains($pos)) { } |
|
|
2 |
4 |
elsif ($pos < $intspan->min) { } |
|
|
2 |
2 |
elsif ($pos > $intspan->max) { } |
|
1202
|
2 |
2 |
if ($spans[$i][1] < $pos) { } |
|
1213
|
727 |
7 |
if ($chr_strand eq '+') { } |
|
1229
|
0 |
9 |
if ($size != length $strB) |
|
1235
|
0 |
18 |
if (/[^10]/u) |
|
1249
|
0 |
9 |
if (&any(sub {
$_ == 0;
}
, $fA, $fa, $fB, $fb)) |
|
1258
|
23 |
47 |
if ($ichar eq '1' and $schar eq '1') |
|
1269
|
1 |
8 |
if ($DAB < 0) { } |
|
1310
|
0 |
0 |
unless ($ok) |
|
1326
|
0 |
0 |
unless (defined $info_of) |
|
1333
|
0 |
0 |
unless App::RL::Common::info_is_valid($info) |
|
1335
|
0 |
0 |
unless (exists $info_of->{$part}) |
|
1351
|
0 |
0 |
if (IPC::Cmd::can_run($e)) |
|
1356
|
0 |
0 |
unless (defined $bin) |
|
1366
|
0 |
0 |
if ($line =~ /^[\w-]+/u) |