line |
true |
false |
branch |
74
|
0 |
862 |
if (exists $$self{'_only_bookmarked'} and $$self{'_only_bookmarked'})
|
77
|
0 |
0 |
if ($a->hasBookmark)
|
95
|
0 |
14766 |
if (exists $$self{'_debug'} and defined $$self{'_debug'} and $$self{'_debug'}) { }
|
104
|
1 |
0 |
if defined $$self{'_msg'}
|
114
|
0 |
862 |
if (exists $$self{'_bookmarkers'} and defined $$self{'_bookmarkers'})
|
127
|
862 |
0 |
if ($k eq 'transcriptSource' and $vars{'transcriptSource'}->isa('Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSource')) { }
|
|
0 |
0 |
elsif ($k eq 'bookmarker') { }
|
|
0 |
0 |
elsif ($k eq 'only_bookmarked') { }
|
|
0 |
0 |
elsif ($k eq 'debug' and $vars{'debug'}) { }
|
130
|
0 |
0 |
if (ref $vars{'bookmarker'} eq 'ARRAY') { }
|
|
0 |
0 |
elsif ($vars{'bookmarker'}->isa('Sanger::CGP::Vagrent::Bookmarkers::AbstractBookmarker')) { }
|
132
|
0 |
0 |
if ($tmp->isa('Sanger::CGP::Vagrent::Bookmarkers::AbstractBookmarker'))
|
155
|
0 |
16276 |
if ($e->getChr ne $mut->getChr)
|
162
|
4382 |
11894 |
if ($e->getMaxPos < $mut->getMinPos)
|
164
|
3380 |
1002 |
if ($tran->getStrand == 1) { }
|
169
|
344 |
658 |
unless (defined $exonAfterInTrans)
|
175
|
123 |
11771 |
if ($mut->getMinPos <= $e->getMinPos and $e->getMaxPos <= $mut->getMaxPos)
|
181
|
11584 |
187 |
if ($mut->getMaxPos < $e->getMinPos)
|
183
|
10538 |
1046 |
if ($tran->getStrand == 1) { }
|
185
|
419 |
10119 |
unless (defined $exonAfterInTrans)
|
194
|
157 |
30 |
if ($e->getMinPos <= $mut->getMinPos and $mut->getMinPos <= $e->getMaxPos)
|
196
|
93 |
64 |
if ($tran->getStrand == 1) { }
|
204
|
158 |
29 |
if ($e->getMinPos <= $mut->getMaxPos and $mut->getMaxPos <= $e->getMaxPos)
|
206
|
93 |
65 |
if ($tran->getStrand == 1) { }
|
216
|
0 |
852 |
if ($self->_debug)
|
230
|
92 |
760 |
if (not defined $exonBeforeInTrans || defined $exonContainingStartInTrans) { }
|
|
70 |
690 |
elsif (defined $exonBeforeInTrans and not defined $exonContainingStartInTrans and not defined $exonsDuringInTrans and not defined $exonContainingEndInTrans and not defined $exonAfterInTrans) { }
|
|
158 |
532 |
elsif (defined $exonContainingStartInTrans) { }
|
|
532 |
0 |
elsif (defined $exonBeforeInTrans) { }
|
234
|
3 |
89 |
if (defined $exonsDuringInTrans and defined $$exonsDuringInTrans[0]) { }
|
|
6 |
83 |
elsif (defined $exonContainingEndInTrans) { }
|
242
|
62 |
30 |
if ($tran->getStrand == 1) { }
|
254
|
45 |
25 |
if ($tran->getStrand == 1) { }
|
261
|
93 |
65 |
if ($tran->getStrand == 1) { }
|
270
|
0 |
158 |
if $self->_debug
|
277
|
2 |
530 |
if (defined $exonsDuringInTrans) { }
|
|
22 |
508 |
elsif (defined $exonContainingEndInTrans) { }
|
284
|
278 |
254 |
if ($tran->getStrand == 1) { }
|
303
|
0 |
532 |
if ($self->_debug)
|
307
|
1 |
531 |
if ($mut->isa('Sanger::CGP::Vagrent::Data::Insertion') and $$beforeBoundry{'off'} + $$afterBoundry{'off'} == 0 and $$beforeBoundry{'pos'} + 1 == $$afterBoundry{'pos'}) { }
|
313
|
275 |
256 |
if (abs $$beforeBoundry{'off'} > abs $$afterBoundry{'off'}) { }
|
327
|
83 |
769 |
if (not defined $exonBeforeInTrans || defined $exonContainingStartInTrans || defined $exonsDuringInTrans || defined $exonContainingEndInTrans and defined $exonAfterInTrans) { }
|
|
79 |
690 |
elsif (not defined $exonContainingEndInTrans || defined $exonAfterInTrans) { }
|
|
157 |
533 |
elsif (defined $exonContainingEndInTrans) { }
|
|
533 |
0 |
elsif (defined $exonAfterInTrans) { }
|
334
|
55 |
28 |
if ($tran->getStrand == 1) { }
|
343
|
3 |
76 |
if (defined $exonsDuringInTrans and defined $$exonsDuringInTrans[scalar(@$exonsDuringInTrans) - 1]) { }
|
|
6 |
70 |
elsif (defined $exonContainingStartInTrans) { }
|
351
|
52 |
27 |
if ($tran->getStrand == 1) { }
|
358
|
93 |
64 |
if ($tran->getStrand == 1) { }
|
367
|
0 |
157 |
if $self->_debug
|
374
|
2 |
531 |
if (defined $exonsDuringInTrans) { }
|
|
23 |
508 |
elsif (defined $exonContainingStartInTrans) { }
|
381
|
278 |
255 |
if ($tran->getStrand == 1) { }
|
400
|
0 |
533 |
if ($self->_debug)
|
404
|
1 |
532 |
if ($mut->isa('Sanger::CGP::Vagrent::Data::Insertion') and $$beforeBoundry{'off'} + $$afterBoundry{'off'} == 1 and $$beforeBoundry{'pos'} + 1 == $$afterBoundry{'pos'}) { }
|
410
|
252 |
280 |
if (abs $$beforeBoundry{'off'} > abs $$afterBoundry{'off'}) { }
|
424
|
0 |
852 |
if $self->_debug
|
434
|
374 |
67 |
unless ($self->_canAnnotateToProtein($tran, $cAnnot))
|
435
|
3 |
371 |
if ($cAnnot->hasClassification($self->getComplexChangeVariantClass) and $cAnnot->getDescription eq 'c.0')
|
446
|
7 |
364 |
if $self->_coversStartCodon($tran, $cAnnot)
|
447
|
4 |
367 |
if $self->_coversStopCodon($tran, $cAnnot)
|
448
|
7 |
364 |
if ($coversStart)
|
451
|
4 |
367 |
if ($coversEnd)
|
465
|
0 |
67 |
unless (defined $cdsMinPos and defined $cdsMaxPos)
|
473
|
2 |
65 |
if ($wtProt eq $mtProt) { }
|
|
26 |
39 |
elsif ($cAnnot->hasClassification($self->getFrameShiftVariantClass)) { }
|
479
|
2 |
0 |
if (length $wt == 1 and length $mt == 1 and $mutProtMin == $mutProtMax) { }
|
486
|
0 |
2 |
if ($wt eq '*') { }
|
493
|
0 |
26 |
if ($wtProt eq $maxMtProt or $self->_sequenceStartsWithSequence($maxMtProt, $wtProt))
|
500
|
6 |
20 |
if ($mutProtMin == 1)
|
522
|
31 |
8 |
if ($wt ne '') { }
|
|
8 |
0 |
elsif ($wt eq '' and $mt ne '' and length $mt > 0) { }
|
524
|
12 |
19 |
if ($mt ne '' and length $wt == length $mt and length $wt == 1) { }
|
|
14 |
5 |
elsif ($mt ne '' and length $wt > 1 || length $mt > 1) { }
|
|
5 |
0 |
elsif ($mt eq '') { }
|
532
|
0 |
12 |
if ($wt eq $mt) { }
|
535
|
0 |
0 |
if ($wt eq '*') { }
|
541
|
2 |
10 |
if ($mt eq '*') { }
|
|
2 |
8 |
elsif ($wt eq '*') { }
|
|
2 |
6 |
elsif ($wt eq 'M' and $mutProtMin == 1) { }
|
557
|
3 |
11 |
if ($mt =~ s/^(.*?\*).*$/$1/ or $mt eq '*') { }
|
564
|
6 |
8 |
if ($mutProtMin == $mutProtMax) { }
|
577
|
5 |
0 |
if ($mutProtMin == $mutProtMax) { }
|
590
|
2 |
6 |
if ($mt =~ s/^(.*?\*).*$/$1/) { }
|
593
|
2 |
0 |
if (length $mt > 1)
|
636
|
152 |
289 |
unless ($self->_canAnnotateToCDS($tran, $rAnnot))
|
643
|
10 |
279 |
if ($rAnnot->getMinPos < $tran->getCdsMinPos) { }
|
|
7 |
272 |
elsif ($rAnnot->getMinPos == $tran->getCdsMinPos and $rAnnot->getMinOffset < 0) { }
|
648
|
0 |
7 |
if ($self->_isIntronicOffsetDistance($rAnnot->getMinOffset)) { }
|
658
|
7 |
282 |
if ($rAnnot->getMaxPos > $tran->getCdsMaxPos) { }
|
|
0 |
282 |
elsif ($rAnnot->getMaxPos == $tran->getCdsMaxPos and $rAnnot->getMaxOffset > 0) { }
|
663
|
0 |
0 |
if ($self->_isIntronicOffsetDistance($rAnnot->getMaxOffset)) { }
|
673
|
0 |
289 |
if $self->_debug
|
696
|
9 |
600 |
if $rc eq $self->get5KBUpStreamVariantClass or $rc eq $self->get2KBUpStreamVariantClass or $rc eq $self->get5KBDownStreamVariantClass or $rc eq $self->get500BPDownStreamVariantClass
|
851
|
15 |
284 |
if ($offset == $cf)
|
868
|
306 |
386 |
if (abs $offset >= $INTRONIC_OFFSET_CUTOFF)
|
876
|
81 |
66 |
if (abs $offset <= $UPDOWNSTREAM_5KB_CUTOFF)
|
888
|
63 |
79 |
if ($offset < 0 and $offset >= $UPSTREAM_2KB_CUTOFF)
|
900
|
53 |
68 |
if ($offset > 0 and $offset <= $DOWNSTREAM_500BP_CUTOFF)
|
913
|
0 |
371 |
unless ($tran->isProteinCoding)
|
919
|
0 |
371 |
if ($anno->getContext eq Sanger::CGP::Vagrent::Data::Annotation::getmRNAAnnotationContext()) { }
|
|
371 |
0 |
elsif ($anno->getContext eq Sanger::CGP::Vagrent::Data::Annotation::getCDSAnnotationContext()) { }
|
930
|
47 |
324 |
if ($anno->hasClassification($self->getInsertionClass)) { }
|
932
|
0 |
47 |
if ($anno->getMinPos < $startMax and $anno->getMaxPos > $startMin)
|
937
|
7 |
156 |
if ($anno->getMinPos < $startMax || $anno->getMinPos == $startMax && $anno->getMinOffset == 0 and $anno->getMaxPos > $startMin || $anno->getMaxPos == $startMin && $anno->getMaxOffset == 0)
|
949
|
0 |
371 |
unless ($tran->isProteinCoding)
|
954
|
0 |
371 |
if ($anno->getContext eq Sanger::CGP::Vagrent::Data::Annotation::getmRNAAnnotationContext()) { }
|
|
371 |
0 |
elsif ($anno->getContext eq Sanger::CGP::Vagrent::Data::Annotation::getCDSAnnotationContext()) { }
|
965
|
47 |
324 |
if ($anno->hasClassification($self->getInsertionClass)) { }
|
967
|
0 |
47 |
if ($anno->getMinPos < $stopMax and $anno->getMaxPos > $stopMin)
|
972
|
4 |
320 |
if ($anno->getMinPos < $stopMax || $anno->getMinPos == $stopMax && $anno->getMinOffset == 0 and $anno->getMaxPos > $stopMin || $anno->getMaxPos == $stopMin && $anno->getMaxOffset == 0)
|
990
|
441 |
0 |
if ($tran->getCdsPhase == 0) { }
|
|
0 |
0 |
elsif ($tran->getCdsPhase > 0 and $tran->getCdsPhase < 3) { }
|
994
|
0 |
0 |
if ($tran->getCdsPhase == 1) { }
|
|
0 |
0 |
elsif ($tran->getCdsPhase == 2) { }
|
1006
|
441 |
0 |
if (length($prePad . $tran->getCdsSeq) % 3 == 0) { }
|
1021
|
0 |
441 |
unless ($tran->isProteinCoding)
|
1025
|
441 |
0 |
if ($anno->getContext eq Sanger::CGP::Vagrent::Data::Annotation::getmRNAAnnotationContext()) { }
|
1027
|
99 |
342 |
if ($anno->hasClassification($self->getInsertionClass)) { }
|
1031
|
0 |
99 |
if $self->_debug
|
1032
|
0 |
99 |
if $self->_debug
|
1034
|
24 |
75 |
if ($anno->getMaxPos < $tran->getCdsMinPos or $anno->getMinPos > $tran->getCdsMaxPos) { }
|
|
7 |
68 |
elsif ($anno->getMaxPos == $tran->getCdsMinPos) { }
|
1039
|
3 |
4 |
if ($anno->getMinPos == $anno->getMaxPos and $anno->getMinPos == $tran->getCdsMinPos and abs($anno->getMinOffset) + abs($anno->getMaxOffset) > 0) { }
|
1041
|
0 |
3 |
unless ($anno->getMaxOffset <= 0 and $self->_isIntronicOffsetDistance($anno->getMaxOffset) == 0)
|
1050
|
121 |
221 |
if ($anno->getMaxPos < $tran->getCdsMinPos or $anno->getMinPos > $tran->getCdsMaxPos)
|
1056
|
180 |
112 |
if ($anno->hasClassification($self->getSpliceRegionVariantClass) or $anno->hasClassification($self->getEssentialSpliceSiteVariantClass)) { }
|
|
41 |
71 |
elsif ($anno->hasClassification($self->getComplexChangeVariantClass)) { }
|
|
31 |
40 |
elsif ($anno->hasClassification($self->getInFrameVariantClass)) { }
|
|
26 |
14 |
elsif ($anno->hasClassification($self->getFrameShiftVariantClass)) { }
|
|
10 |
4 |
elsif ($anno->hasClassification($self->getCodonVariantClass)) { }
|
|
0 |
4 |
elsif ($anno->hasClassification($self->getIntronVariantClass)) { }
|
|
0 |
4 |
elsif ($anno->hasClassification($self->getUnknownVariantClass)) { }
|
|
1 |
3 |
elsif ($anno->hasClassification($self->getInsertionClass) and $anno->hasClassification($self->get5PrimeUtrVariantClass)) { }
|
1090
|
0 |
441 |
unless ($tran->isProteinCoding)
|
1094
|
441 |
0 |
if ($anno->getContext eq Sanger::CGP::Vagrent::Data::Annotation::getCDSAnnotationContext()) { }
|
1095
|
152 |
289 |
if ($anno->hasClassification($self->getUnknownVariantClass)) { }
|
|
63 |
226 |
elsif ($anno->hasClassification($self->getEssentialSpliceSiteVariantClass)) { }
|
|
117 |
109 |
elsif ($anno->hasClassification($self->getSpliceRegionVariantClass)) { }
|
|
41 |
68 |
elsif ($anno->hasClassification($self->getComplexChangeVariantClass)) { }
|
|
31 |
37 |
elsif ($anno->hasClassification($self->getInFrameVariantClass)) { }
|
|
26 |
11 |
elsif ($anno->hasClassification($self->getFrameShiftVariantClass)) { }
|
|
10 |
1 |
elsif ($anno->hasClassification($self->getCodonVariantClass)) { }
|
1135
|
0 |
26 |
if $self->_debug
|
1136
|
0 |
26 |
if (length $seqRef < length $seqCheck)
|
1137
|
0 |
0 |
if $self->_debug
|
1140
|
0 |
26 |
if $self->_debug
|
1141
|
0 |
26 |
if $self->_debug
|
1143
|
0 |
26 |
if (substr($seqRef, 0, length $seqCheck) eq $seqCheck)
|
1144
|
0 |
0 |
if $self->_debug
|
1147
|
0 |
26 |
if $self->_debug
|
1159
|
0 |
26 |
if $self->_debug
|
1161
|
0 |
1751 |
if $self->_debug
|
1162
|
26 |
1725 |
if (not defined $wt and substr($wtProt, $i, 1) ne substr($mtProt, $i, 1)) { }
|
|
0 |
1725 |
elsif (not defined $wt and length $mtProt == $i + 1 and length $wtProt > $i + 1 and substr($wtProt, $i, 1) eq substr($mtProt, $i, 1)) { }
|
|
0 |
1725 |
elsif (defined $wt and length $mtProt == $i + 1 and substr($mtProt, $i, 1) ne '*') { }
|
|
535 |
1190 |
elsif (defined $wt) { }
|
1167
|
1 |
25 |
if ($mt eq '*') { }
|
1191
|
25 |
510 |
if (substr($mtProt, $i, 1) eq '*')
|
1197
|
0 |
26 |
if $self->_debug
|
1207
|
380 |
24 |
if ($tran->getStrand == 1) { }
|
1208
|
20 |
360 |
unless (defined $genoCdsMin)
|
1209
|
10 |
10 |
if ($e->getRnaMinPos <= $tran->getCdsMinPos and $e->getRnaMaxPos >= $tran->getCdsMinPos)
|
1213
|
380 |
0 |
unless (defined $genoCdsMax)
|
1214
|
10 |
370 |
if ($e->getRnaMinPos <= $tran->getCdsMaxPos and $e->getRnaMaxPos >= $tran->getCdsMaxPos)
|
1219
|
4 |
20 |
unless (defined $genoCdsMin)
|
1220
|
4 |
0 |
if ($e->getRnaMinPos <= $tran->getCdsMaxPos and $e->getRnaMaxPos >= $tran->getCdsMaxPos)
|
1224
|
16 |
8 |
unless (defined $genoCdsMax)
|
1225
|
4 |
12 |
if ($e->getRnaMinPos <= $tran->getCdsMinPos and $e->getRnaMaxPos >= $tran->getCdsMinPos)
|
1237
|
108 |
1272 |
if $a eq $val
|
1247
|
0 |
0 |
if defined $a->getCCDS and length $a->getCCDS > 0
|
1248
|
0 |
0 |
if defined $b->getCCDS and length $b->getCCDS > 0
|
1250
|
0 |
0 |
if ($chk == 0)
|
1252
|
0 |
0 |
if ($chk == 0)
|