| 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
|
119 |
1 |
if (exists $self->{'DNAMutation'}) { } |
|
407
|
18 |
66 |
if (defined $value) |
|
408
|
0 |
18 |
if (not $value->isa('Bio::Variation::AAChange')) { } |
|
416
|
80 |
4 |
if (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) { } |