Branch Coverage

lib/Sanger/CGP/Vagrent/Annotators/AbstractAnnotator.pm
Criterion Covered Total %
branch 256 350 73.1


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)