| line |
true |
false |
branch |
|
152
|
4 |
92 |
if $aa eq '*' |
|
154
|
96 |
0 |
if defined $2 |
|
204
|
17 |
2 |
if $start |
|
205
|
12 |
7 |
if $end |
|
206
|
12 |
7 |
if $length |
|
207
|
0 |
19 |
if $strand |
|
208
|
0 |
19 |
if $primary |
|
209
|
0 |
19 |
if $source |
|
210
|
0 |
19 |
if $frame |
|
211
|
0 |
19 |
if $score |
|
212
|
0 |
19 |
if $gff_string |
|
214
|
0 |
19 |
if $allele_ori |
|
215
|
0 |
19 |
if $allele_mut |
|
216
|
0 |
19 |
if $upstreamseq |
|
217
|
0 |
19 |
if $dnstreamseq |
|
219
|
0 |
19 |
if $label |
|
220
|
0 |
19 |
if $status |
|
221
|
12 |
7 |
if $proof |
|
222
|
0 |
19 |
if $region |
|
223
|
0 |
19 |
if $region_value |
|
224
|
0 |
19 |
if $region_dist |
|
225
|
0 |
19 |
if $numbering |
|
226
|
12 |
7 |
if $mut_number |
|
227
|
0 |
19 |
if $ismutation |
|
245
|
18 |
48 |
if (defined $value) |
|
246
|
0 |
18 |
if (not $value->isa('Bio::Variation::RNAChange')) { } |
|
254
|
0 |
66 |
if (not exists $self->{'RNAChange'}) { } |
|
286
|
15 |
0 |
if $self->allele_ori and $self->allele_ori->seq |
|
287
|
14 |
1 |
if $self->allele_mut and $self->allele_mut->seq |
|
289
|
0 |
15 |
if ($self->start == 1) { } |
|
|
0 |
15 |
elsif ($o and substr($o, 0, 1) eq '*') { } |
|
|
0 |
15 |
elsif ($o and $m and $o eq $m) { } |
|
|
2 |
13 |
elsif ($m and $m eq '*') { } |
|
|
0 |
13 |
elsif ($o and $m and $o eq $m) { } |
|
|
1 |
12 |
elsif (not $m or $o and $m and length $o > length $m and substr($m, -1, 1) ne '*') { } |
|
|
1 |
11 |
elsif (not $o or $o and $m and length $o < length $m and substr($m, -1, 1) ne '*') { } |
|
|
8 |
3 |
elsif ($o and $m and $o ne $m and length $o == 1 and length $m == 1) { } |
|
290
|
0 |
0 |
if ($o and substr($o, 0, 1) ne substr($m, 0, 1)) { } |
|
|
0 |
0 |
elsif ($o and $m and $o eq $m) { } |
|
299
|
0 |
0 |
if ($m and substr($o, 0, 1) ne substr($m, 0, 1)) { } |
|
|
0 |
0 |
elsif ($m and $o eq $m) { } |
|
319
|
0 |
0 |
if ($o and $m and not $o =~ /$m/ and not $o =~ /$m/) |
|
327
|
1 |
0 |
if ($o and $m and not $o =~ /$m/ and not $o =~ /$m/) |
|
335
|
8 |
0 |
if (defined $value) |
|
336
|
2 |
6 |
$value < 0 ? : |
|
361
|
9 |
0 |
if $self->allele_ori and $self->allele_ori->seq |
|
362
|
9 |
0 |
if $self->allele_mut and $self->allele_mut->seq |
|
363
|
0 |
9 |
unless $o and $m and length $o == 1 and length $m == 1 |
|
364
|
0 |
9 |
unless $o =~ /[ARNDCQEGHILKMFPSTWYVBZX*]/i and $m =~ /[ARNDCQEGHILKMFPSTWYVBZX*]/i |
|
389
|
0 |
19 |
if (defined $value) { } |
|
394
|
19 |
0 |
if $self->allele_ori and $self->allele_ori->seq |
|
397
|
19 |
0 |
if $o |
|
401
|
17 |
2 |
if ($self->isMutation) { } |
|
407
|
2 |
17 |
if $sep eq '|' |
|
411
|
19 |
1 |
if $allele->seq |
|
416
|
19 |
1 |
if $m |
|
417
|
0 |
20 |
if ($self->RNAChange->label =~ /initiation codon/ and ($o and $m and $o ne $m)) { } |
|
|
15 |
5 |
elsif (length $o == 1 and length $m == 1) { } |
|
|
2 |
3 |
elsif ($self->RNAChange->label =~ /deletion/) { } |
|
|
2 |
1 |
elsif ($self->RNAChange->label =~ /insertion/) { } |
|
|
1 |
0 |
elsif ($self->RNAChange->label =~ /complex/) { } |
|
|
0 |
0 |
elsif ($self->label =~ /truncation/) { } |
|
427
|
1 |
1 |
if ($aamutterm eq '*') |
|
431
|
1 |
1 |
if ($self->RNAChange and $self->RNAChange->label =~ /inframe/) |
|
437
|
1 |
1 |
if ($aamutterm eq '*' and length($m) - 1 != 0) |
|
441
|
1 |
1 |
if ($self->RNAChange->label =~ /inframe/) |
|
447
|
1 |
0 |
if ($diff >= 0) { } |
|
452
|
1 |
0 |
if ($aamutterm eq '*' and length($m) - 1 != 0) |
|
456
|
0 |
1 |
if ($self->RNAChange->label =~ /inframe/) |
|
458
|
0 |
0 |
if ($diff >= 0) { } |