Branch Coverage

Bio/Variation/RNAChange.pm
Criterion Covered Total %
branch 116 162 71.6


line true false branch
164 22 4 if $start
165 22 4 if $end
166 17 9 if $length
167 0 26 if $strand
168 0 26 if $primary
169 0 26 if $source
170 0 26 if $frame
171 0 26 if $score
172 0 26 if $gff_string
174 0 26 if $allele_ori
175 0 26 if $allele_mut
176 17 9 if $upstreamseq
177 17 9 if $dnstreamseq
179 0 26 if $label
180 0 26 if $status
181 16 10 if $proof
182 0 26 if $region
183 0 26 if $region_value
184 0 26 if $region_dist
185 0 26 if $numbering
186 16 10 if $mut_number
187 3 23 if $isMutation
189 3 23 if $codon_ori
190 3 23 if $codon_mut
191 4 22 if $codon_pos
192 0 26 if $codon_table
193 1 25 if $cds_end
217 3 120 if (defined $value) { }
19 101 elsif (not $self->{'codon_ori'}) { }
218 0 3 if (length $value != 3)
226 19 0 if ($self->region eq 'coding' and $self->start and $self->start >= 1)
228 0 19 unless defined $self->codon_pos
230 0 19 unless defined $self->upStreamSeq
232 0 19 unless defined $self->dnStreamSeq
237 16 3 if $self->allele_ori and $self->allele_ori->seq
266 3 59 if (defined $value) { }
267 0 3 if (length $value != 3)
274 59 0 if ($self->allele_ori->seq and $self->allele_mut->seq and length $self->allele_ori->seq == 1 and length $self->allele_mut->seq == 1 and $self->region eq 'coding' and $self->start >= 1)
279 0 59 unless defined $self->codon_pos
281 0 59 unless defined $self->upStreamSeq
283 0 59 unless defined $self->dnStreamSeq
285 0 59 unless defined $self->allele_mut
290 59 0 if $self->allele_mut and $self->allele_mut->seq
319 23 173 if (defined $value)
320 0 23 unless ($value =~ /[123]/)
347 13 71 if (defined $value)
348 0 13 if (not $value =~ /^\d$/) { }
355 17 67 if (not exists $self->{'codon_table'}) { }
377 21 99 if (defined $value)
378 0 21 if (not $value->isa('Bio::Variation::DNAMutation')) { }
386 1 119 if (not exists $self->{'DNAMutation'}) { }
407 18 66 if (defined $value)
408 0 18 if (not $value->isa('Bio::Variation::AAChange')) { }
416 4 80 if (not exists $self->{'AAChange'}) { }
436 0 0 if (defined $value)
462 24 138 if (defined $value) { }
7 131 elsif (not defined $self->{'region'}) { }
467 0 7 if not defined $self->start and $self->verbose
469 0 7 if not defined $self->end and $self->verbose
471 0 7 if not defined $self->cds_end and $self->verbose
475 0 7 if ($self->end and $self->end < 0) { }
0 7 elsif ($self->start and $self->cds_end and $self->start > $self->cds_end) { }
506 2 22 if (defined $value) { }
507 0 2 unless $value =~ /^\d+$/
511 15 7 if $self->SeqDiff
539 42 13 if $self->allele_ori and $self->allele_ori->seq
540 44 11 if $self->allele_mut and $self->allele_mut->seq
543 28 27 if ($o and $m and length $o == 1 and length $m == 1) { }
544 24 4 if (defined $self->AAChange) { }
545 0 24 if ($self->start > 0 and $self->start < 4) { }
0 24 elsif ($self->codon_ori and $ct->is_ter_codon($self->codon_ori)) { }
5 19 elsif ($self->codon_mut and $ct->is_ter_codon($self->codon_mut)) { }
2 17 elsif ($o and $m and $o eq $m || $self->AAChange->allele_ori->seq eq $self->AAChange->allele_mut->seq) { }
568 14 13 if $o
569 16 11 if $m
570 12 15 if ($len % 3 == 0) { }
575 11 16 if (not $m) { }
10 6 elsif (not $o) { }
584 0 27 if ($self->codon_ori and $ct->is_ter_codon($self->codon_ori))
613 0 0 if ($cpos > 3) { }
0 0 elsif ($cpos < 1) { }