Branch Coverage

blib/lib/CracTools/Annotator.pm
Criterion Covered Total %
branch 33 86 38.3


line true false branch
24 0 1 unless defined $mode
26 0 1 unless (defined $gff_file)
60 1 0 if defined $candidate->{'gene'}
75 5 0 if (defined $candi1->{'gene'})
80 5 0 if (defined $candi2->{'gene'})
86 2 0 if ($gene_id eq $_)
91 2 1 if $found_same_gene == 1
100 1 0 if (@{$best_candidates;}) { }
112 1 0 unless (defined $prioritySub or defined $compareSub)
113 1 0 unless defined $prioritySub
114 1 0 unless defined $compareSub
122 1 0 if defined $prioritySub
123 1 0 if (defined $priority and $priority != -1)
124 1 0 if (not defined $best_priority) { }
0 0 elsif ($priority < $best_priority) { }
0 0 elsif (not defined $priority or $priority == $best_priority) { }
138 0 0 if defined $compareSub
140 0 0 if (not defined $candidate_chosen) { }
0 0 elsif ($candidate_chosen == $candi) { }
157 0 0 unless $found_better_candidate
220 2 0 if (defined $mRNA)
221 2 0 if (defined $mRNA->attribute('type') and $mRNA->attribute('type') =~ /protein_coding/i) { }
222 0 2 if (defined $exon) { }
223 0 0 if ($exon->start <= $pos_start and $exon->end >= $pos_end) { }
225 0 0 if (defined $candidate->{'three'}) { }
0 0 elsif (defined $candidate->{'five'}) { }
243 0 0 if (defined $exon)
244 0 0 if ($exon->start <= $pos_start and $exon->end >= $pos_end)
257 0 0 if ($candidate1->{'exon'} and $candidate2->{'exon'})
260 0 0 if ($dist1 > $dist2) { }
0 0 elsif ($dist1 < $dist2) { }
268 0 0 if (defined $mRNA1 and defined $mRNA1->attribute('ID') and defined $mRNA2 and defined $mRNA2->attribute('ID'))
269 0 0 if ($mRNA1->attribute('ID') lt $mRNA2->attribute('ID')) { }
285 1 0 if ($self->mode eq 'fast') { }
311 19 47 unless defined $candidate->{'leaf_feature'}
314 0 66 unless (defined $annot_hash->{$annot_id})
319 42 24 if (@$parents) { }
323 0 47 if ($parent eq $annot_id) { }
0 47 elsif (not defined $annot_hash->{$parent}) { }
10 37 elsif (defined $$candidate{$annot_hash->{$parent}->feature}) { }
362 46 0 if ($self->mode eq 'fast') { }
375 27 13 unless defined $hash_leaves{$parent}
380 19 27 unless (defined $hash_leaves{$annot_id})