| line |
true |
false |
branch |
|
25
|
0 |
1 |
unless defined $mode |
|
27
|
0 |
1 |
unless (defined $gff_file) |
|
61
|
1 |
0 |
if defined $candidate->{'gene'} |
|
76
|
5 |
0 |
if (defined $candi1->{'gene'}) |
|
81
|
5 |
0 |
if (defined $candi2->{'gene'}) |
|
87
|
2 |
0 |
if ($gene_id eq $_) |
|
92
|
2 |
1 |
if $found_same_gene == 1 |
|
101
|
1 |
0 |
if (@{$best_candidates;}) { } |
|
113
|
1 |
0 |
unless (defined $prioritySub or defined $compareSub) |
|
114
|
1 |
0 |
unless defined $prioritySub |
|
115
|
1 |
0 |
unless defined $compareSub |
|
123
|
1 |
0 |
if defined $prioritySub |
|
124
|
1 |
0 |
if (defined $priority and $priority != -1) |
|
125
|
1 |
0 |
if (not defined $best_priority) { } |
|
|
0 |
0 |
elsif ($priority < $best_priority) { } |
|
|
0 |
0 |
elsif (not defined $priority or $priority == $best_priority) { } |
|
139
|
0 |
0 |
if defined $compareSub |
|
141
|
0 |
0 |
if (not defined $candidate_chosen) { } |
|
|
0 |
0 |
elsif ($candidate_chosen == $candi) { } |
|
158
|
0 |
0 |
unless $found_better_candidate |
|
221
|
2 |
0 |
if (defined $mRNA) |
|
222
|
2 |
0 |
if (defined $mRNA->attribute('type') and $mRNA->attribute('type') =~ /protein_coding/i) { } |
|
223
|
0 |
2 |
if (defined $exon) { } |
|
224
|
0 |
0 |
if ($exon->start <= $pos_start and $exon->end >= $pos_end) { } |
|
226
|
0 |
0 |
if (defined $candidate->{'three'}) { } |
|
|
0 |
0 |
elsif (defined $candidate->{'five'}) { } |
|
244
|
0 |
0 |
if (defined $exon) |
|
245
|
0 |
0 |
if ($exon->start <= $pos_start and $exon->end >= $pos_end) |
|
258
|
0 |
0 |
if ($candidate1->{'exon'} and $candidate2->{'exon'}) |
|
261
|
0 |
0 |
if ($dist1 > $dist2) { } |
|
|
0 |
0 |
elsif ($dist1 < $dist2) { } |
|
269
|
0 |
0 |
if (defined $mRNA1 and defined $mRNA1->attribute('ID') and defined $mRNA2 and defined $mRNA2->attribute('ID')) |
|
270
|
0 |
0 |
if ($mRNA1->attribute('ID') lt $mRNA2->attribute('ID')) { } |
|
286
|
1 |
0 |
if ($self->mode eq 'fast') { } |
|
312
|
19 |
47 |
unless defined $candidate->{'leaf_feature'} |
|
315
|
0 |
66 |
unless (defined $annot_hash->{$annot_id}) |
|
320
|
42 |
24 |
if (@$parents) { } |
|
324
|
0 |
47 |
if ($parent eq $annot_id) { } |
|
|
0 |
47 |
elsif (not defined $annot_hash->{$parent}) { } |
|
|
10 |
37 |
elsif (defined $$candidate{$annot_hash->{$parent}->feature}) { } |
|
363
|
46 |
0 |
if ($self->mode eq 'fast') { } |
|
376
|
27 |
13 |
unless defined $hash_leaves{$parent} |
|
381
|
19 |
27 |
unless (defined $hash_leaves{$annot_id}) |