| line |
true |
false |
branch |
|
41
|
0 |
3 |
unless (@{$args;}) |
|
48
|
0 |
3 |
if lc $_ eq 'stdin' |
|
49
|
0 |
3 |
unless (Path::Tiny::path($_)->is_file) |
|
54
|
0 |
3 |
if (not exists $opt->{'outfile'}) |
|
68
|
1 |
2 |
if ($opt->{'replace'}) |
|
69
|
0 |
1 |
if $opt->{'verbose'} |
|
74
|
6 |
0 |
if (@parts == 2) |
|
83
|
0 |
3 |
if $opt->{'verbose'} |
|
94
|
9 |
126 |
if (exists $replace_of->{$part}) { } |
|
115
|
45 |
0 |
if (@new_parts == 3 or @new_parts == 2) |
|
119
|
45 |
0 |
if (App::RL::Common::info_is_valid($info_0) and App::RL::Common::info_is_valid($info_1)) |
|
124
|
45 |
0 |
if (@new_parts == 3) |
|
125
|
45 |
0 |
if ($new_parts[2] eq '+' or $new_parts[2] eq '-') |
|
131
|
45 |
0 |
if (@new_parts == 2) |
|
140
|
33 |
12 |
if (@strands == 1) { } |
|
165
|
45 |
0 |
if (@new_parts == 2) |
|
169
|
45 |
0 |
if (App::RL::Common::info_is_valid($info_0) and App::RL::Common::info_is_valid($info_1)) |
|
172
|
8 |
4 |
if ($info_0->{'chr'} eq $info_1->{'chr'} and $info_0->{'start'} == $info_1->{'start'} and $info_0->{'end'} == $info_1->{'end'}) |
|
195
|
0 |
6 |
if $opt->{'verbose'} |
|
220
|
5 |
16 |
if ($intspan0_i->superset($intspan0_j) and $intspan1_i->superset($intspan1_j)) { } |
|
|
0 |
28 |
elsif ($intspan0_j->superset($intspan0_i) and $intspan1_j->superset($intspan1_i)) { } |
|
240
|
1 |
2 |
if ($opt->{'bundle'}) |
|
241
|
0 |
1 |
if $opt->{'verbose'} |
|
263
|
3 |
0 |
unless ($graph->has_vertex($line_i)) |
|
266
|
3 |
0 |
unless ($graph->has_vertex($line_j)) |
|
276
|
1 |
2 |
if ($intspan0_i->overlap($intspan0_j) >= $opt->{'bundle'} and $intspan1_i->overlap($intspan1_j) >= $opt->{'bundle'}) |
|
288
|
0 |
1 |
if $opt->{'verbose'} |
|
315
|
0 |
1 |
if $opt->{'verbose'} |
|
328
|
1 |
2 |
if ($opt->{'replace'}) |
|
329
|
0 |
1 |
if $opt->{'verbose'} |
|
333
|
0 |
8 |
$info_of->{$r0}{'chr'} eq $info_of->{$r1}{'chr'} ? : |
|
343
|
0 |
0 |
if ($intspan_i->is_not_empty) |
|
344
|
0 |
0 |
if ($intspan_i->size / $intspan0->size > 0.5 and $intspan_i->size / $intspan1->size > 0.5) |
|
357
|
3 |
0 |
if (lc $opt->{'outfile'} eq 'stdout') { } |