Branch Coverage

lib/Sanger/CGP/Vagrent/Annotators/DeletionAnnotator.pm
Criterion Covered Total %
branch 258 294 87.7


line true false branch
46 0 282 unless (defined $var and $var->isa('Sanger::CGP::Vagrent::Data::Deletion'))
52 0 282 unless ($var->isValid)
59 4 278 unless (defined $trans[0])
68 270 8 if (defined $g)
72 8 270 unless (scalar @groups > 0 and defined $groups[0])
85 8 270 unless (defined $rAnnot)
96 230 40 if ($tran->isProteinCoding) { }
97 79 151 if ($rAnnot->hasClassification($self->getIntronVariantClass) || $rAnnot->hasClassification($self->get5KBUpStreamVariantClass) || $rAnnot->hasClassification($self->get2KBUpStreamVariantClass) || $rAnnot->hasClassification($self->get5KBDownStreamVariantClass) || $rAnnot->hasClassification($self->get500BPDownStreamVariantClass) and not $rAnnot->hasClassification($self->getEssentialSpliceSiteVariantClass) and not $rAnnot->hasClassification($self->getSpliceRegionVariantClass) and not $rAnnot->hasClassification($self->getFrameShiftVariantClass) and not $rAnnot->hasClassification($self->getInFrameVariantClass) and not $rAnnot->hasClassification($self->get5PrimeUtrVariantClass) and not $rAnnot->hasClassification($self->get3PrimeUtrVariantClass) and not $rAnnot->hasClassification($self->getComplexChangeVariantClass)) { }
113 0 151 unless (defined $cAnnot)
120 0 151 unless (defined $pAnnot)
140 0 278 unless (defined $mrnaMin and defined $mrnaMinOffset and defined $mrnaMax and defined $mrnaMaxOffset)
146 0 278 unless ($self->_safetyCheck($var, $tran, $mrnaMin, $mrnaMinOffset, $mrnaMax, $mrnaMaxOffset))
157 273 5 if (defined $upstream) { }
158 23 250 if ($upstream)
166 247 3 if (defined $downstream) { }
167 16 231 if ($downstream)
175 5 226 if ($mrnaMin == 0 and $mrnaMinOffset <= 0)
179 5 226 if ($mrnaMax == 0 and $mrnaMaxOffset >= 0)
184 191 40 if ($tran->isProteinCoding)
185 100 29 if ($mrnaMax > $tran->getCdsMinPos || $mrnaMax == $tran->getCdsMinPos && $mrnaMaxOffset >= 0 and $mrnaMin < $tran->getCdsMaxPos || $mrnaMin == $tran->getCdsMaxPos && $mrnaMinOffset <= 0)
191 71 120 if ($mrnaMin < $tran->getCdsMinPos or $mrnaMin == $tran->getCdsMinPos and $mrnaMinOffset < 0)
195 62 9 unless $self->_arrayHasString($self->getCDSClass, @groupClasses)
197 35 156 if ($mrnaMax > $tran->getCdsMaxPos or $mrnaMax == $tran->getCdsMaxPos and $mrnaMaxOffset > 0)
201 29 6 unless $self->_arrayHasString($self->getCDSClass, @groupClasses)
207 52 179 if (scalar keys %$tmpGroupClassesHash == 1 and defined $$tmpGroupClassesHash{$self->getIntronClass})
219 2 177 if ($mrnaMin == 1 and $mrnaMax == length $tran->getcDNASeq) { }
227 0 179 if ($mrnaMin == 0 and $mrnaMax == 0) { }
46 133 elsif ($mrnaMinOffset == 0 and $mrnaMaxOffset == 0) { }
251 26 153 if (defined $$tmpGroupClassesHash{$self->getExonClass} and defined $$tmpGroupClassesHash{$self->getEssentialSpliceSiteClass}) { }
254 2 24 unless ($tran->isProteinCoding)
259 62 91 if (defined $$tmpGroupClassesHash{$self->getSpliceRegionClass})
262 49 104 if (defined $$tmpGroupClassesHash{$self->getEssentialSpliceSiteClass})
265 1 152 if (defined $$tmpGroupClassesHash{$self->getIntronClass})
268 43 110 if (defined $$tmpGroupClassesHash{$self->getExonClass})
269 37 6 if ($tran->isProteinCoding) { }
270 27 10 if ($self->_arrayHasString($self->getCDSClass, @groupClasses))
271 9 18 if ($self->_arrayHasString($self->get2KBUpStreamVariantClass, @classes) or $self->_arrayHasString($self->get5PrimeUtrClass, @groupClasses) or $self->_arrayHasString($self->get3PrimeUtrClass, @groupClasses) or $self->_arrayHasString($self->get500BPDownStreamVariantClass, @classes)) { }
275 7 11 if (length($wt) % 3 == 0) { }
298 449 56 if ($mrnaMin > 0 or $mrnaMin == 0 and $mrnaMinOffset >= 0) { }
56 0 elsif ($mrnaMin == 0 and $mrnaMinOffset < 0) { }
301 20 36 if ($self->_isWithin2KBUpstreamOffsetDistance($mrnaMinOffset)) { }
17 19 elsif ($self->_isWithin5KBOffsetDistance($mrnaMinOffset)) { }
307 455 50 if ($mrnaMax > 0 or $mrnaMax == 0 and $mrnaMaxOffset >= 0) { }
50 0 elsif ($mrnaMax == 0 and $mrnaMaxOffset < 0) { }
310 25 25 if ($self->_isWithin2KBUpstreamOffsetDistance($mrnaMaxOffset)) { }
14 11 elsif ($self->_isWithin5KBOffsetDistance($mrnaMaxOffset)) { }
316 0 505 if $self->_debug
317 11 494 if ($upStartScore == 0 and $upEndScore == 0)
324 25 494 if ($i == 1) { }
31 463 elsif ($i == 2) { }
330 39 455 if ($upEndScore < 3)
341 413 42 if ($mrnaMin > 0 or $mrnaMin == 0 and $mrnaMinOffset <= 0) { }
42 0 elsif ($mrnaMin == 0 and $mrnaMinOffset > 0) { }
344 24 18 if ($self->_isWithin500BPDownstreamOffsetDistance($mrnaMinOffset)) { }
12 6 elsif ($self->_isWithin5KBOffsetDistance($mrnaMinOffset)) { }
350 407 48 if ($mrnaMax > 0 or $mrnaMax == 0 and $mrnaMaxOffset <= 0) { }
48 0 elsif ($mrnaMax == 0 and $mrnaMaxOffset > 0) { }
353 15 33 if ($self->_isWithin500BPDownstreamOffsetDistance($mrnaMaxOffset)) { }
20 13 elsif ($self->_isWithin5KBOffsetDistance($mrnaMaxOffset)) { }
359 0 455 if $self->_debug
360 6 449 if ($downStartScore == 0 and $downEndScore == 0)
367 27 450 if ($i == 1) { }
30 420 elsif ($i == 2) { }
373 36 413 if ($downStartScore < 3)
385 0 413 if $self->_debug
388 1529 6240 if ($mrnaMin > $e->getRnaMaxPos)
392 5708 532 if ($mrnaMax < $e->getRnaMinPos)
399 241 141 if ($mrnaMin < $e->getRnaMaxPos || $mrnaMin == $e->getRnaMaxPos && $mrnaMinOffset == 0 and $mrnaMax > $e->getRnaMinPos || $mrnaMax == $e->getRnaMinPos && $mrnaMaxOffset == 0)
402 0 532 if $self->_debug
404 278 254 if ($mrnaMin < $e->getRnaMinPos or $mrnaMin == $e->getRnaMinPos and $mrnaMinOffset < 0)
406 182 96 if ($mrnaMin < $e->getRnaMinPos or $self->_isIntronicOffsetDistance($mrnaMinOffset)) { }
36 60 elsif ($mrnaMin == $e->getRnaMinPos and $mrnaMinOffset >= $self->_getConsesnsusSpliceBeforeBoundry) { }
408 126 56 if ($mrnaMax > $e->getRnaMinPos or $mrnaMax == $e->getRnaMinPos and $mrnaMaxOffset == 0) { }
52 4 elsif ($self->_isIntronicOffsetDistance($mrnaMaxOffset)) { }
0 4 elsif ($mrnaMaxOffset < 0 and $mrnaMaxOffset >= $self->_getConsesnsusSpliceBeforeBoundry) { }
431 5 55 if ($mrnaMax > $e->getRnaMinPos or $mrnaMax == $e->getRnaMinPos and $mrnaMaxOffset == 0) { }
4 51 elsif ($mrnaMaxOffset < 0 and $mrnaMaxOffset >= $self->_getConsesnsusSpliceBeforeBoundry) { }
447 290 242 if ($mrnaMax > $e->getRnaMaxPos or $mrnaMax == $e->getRnaMaxPos and $mrnaMaxOffset > 0)
449 179 111 if ($mrnaMax > $e->getRnaMaxPos or $self->_isIntronicOffsetDistance($mrnaMaxOffset)) { }
60 51 elsif ($mrnaMax == $e->getRnaMaxPos and $mrnaMaxOffset <= $self->_getConsesnsusSpliceAfterBoundry) { }
451 128 51 if ($mrnaMin < $e->getRnaMaxPos or $mrnaMin == $e->getRnaMaxPos and $mrnaMinOffset == 0) { }
46 5 elsif ($self->_isIntronicOffsetDistance($mrnaMinOffset)) { }
1 4 elsif ($mrnaMinOffset > 0 and $mrnaMinOffset <= $self->_getConsesnsusSpliceAfterBoundry) { }
474 5 46 if ($mrnaMin < $e->getRnaMaxPos or $mrnaMin == $e->getRnaMaxPos and $mrnaMinOffset == 0) { }
4 42 elsif ($mrnaMinOffset > 0 and $mrnaMinOffset <= $self->_getConsesnsusSpliceAfterBoundry) { }
489 0 413 if $self->_debug
496 3 83 if ($mutStart == 1 and $mutEnd == length $tran->getCdsSeq) { }
507 168 92 if ($mutStart == $mutEnd and $mutStartOffset == $mutEndOffset) { }
509 76 92 if ($mutStartOffset > 0) { }
74 18 elsif ($mutStartOffset < 0) { }
18 0 elsif ($mutStartOffset == 0) { }
518 1 91 if ($mutStartOffset > 0) { }
17 74 elsif ($mutStartOffset < 0) { }
74 0 elsif ($mutStartOffset == 0) { }
526 22 70 if ($mutEndOffset > 0) { }
1 69 elsif ($mutEndOffset < 0) { }
69 0 elsif ($mutEndOffset == 0) { }
534 3 89 if (length $wt > 15) { }
554 18218601 962741 if ($i > $e->getMaxPos) { }
79779 882962 elsif ($i >= $e->getMinPos and $i <= $e->getMaxPos) { }
882962 0 elsif ($i < $e->getMinPos) { }
555 21002 18197599 if ($ec == scalar @exons) { }
566 861960 21002 unless $ec == 1
570 42004 941739 unless $use == 1
571 79779 861960 if ($isExonic) { }
577 207 237 if ($tran->getStrand == -1)
586 36 129 if ($rAnnot->hasClassification($self->getInFrameVariantClass) or $rAnnot->hasClassification($self->getFrameShiftVariantClass)) { }
41 88 elsif ($rAnnot->hasClassification($self->getComplexChangeVariantClass)) { }
592 220 122 unless $i >= $e->getMinPos and $i <= $e->getMaxPos
593 69 53 if ($tran->getStrand == 1) { }
595 69 0 if ($pos >= $tran->getCdsMinPos and $pos <= $tran->getCdsMaxPos)
601 53 0 if ($pos >= $tran->getCdsMinPos and $pos <= $tran->getCdsMaxPos)
607 122 0 if ($isCod)
611 14 22 if ($tran->getStrand == -1)
615 14 27 if ($rAnnot->getMinPos <= $tran->getCdsMinPos or $rAnnot->getMaxPos >= $tran->getCdsMaxPos) { }
622 8 6 if ($var->getMinPos < $genomicCdsLow) { }
628 9 5 if ($var->getMaxPos > $genomicCdsHigh) { }
670 0 36 if ($cAnnot->getMinOffset > 0) { }
681 0 36 if ($cAnnot->getMaxOffset < 0) { }
692 0 505 unless (defined $tranString)
696 0 505 unless (defined $genoString)
699 0 505 if ($self->_debug)
704 383 122 if (length $tranString == 0 and length $genoString == 0) { }
122 0 elsif (uc $tranString eq uc $genoString) { }
718 0 505 if $self->_debug
719 42 463 if ($mrnaMin == 0 and $mrnaMinOffset > 0) { }
50 413 elsif ($mrnaMax == 0 and $mrnaMaxOffset < 0) { }
76 337 elsif ($mrnaMinOffset == 0 and $mrnaMaxOffset == 0) { }
731 150 187 if ($mrnaMinOffset > 0) { }
736 141 196 if ($mrnaMaxOffset < 0) { }
741 6 331 if $leftAnchor < 1
742 6 331 if $rightAnchor == 0
743 0 337 if $self->_debug
744 291 46 if ($leftAnchor > $rightAnchor)
752 0 122 if $self->_debug
765 2793 2708 if ($e->getMaxPos < $var->getMinPos)
767 0 2793 if $self->_debug
771 241 2467 if ($var->getMinPos <= $e->getMaxPos and $e->getMinPos <= $var->getMaxPos)
776 86 155 if $start < 1
777 87 154 if $end > length $var->getDeletedSequence
782 119 122 if (defined $substr) { }
787 0 241 if $self->_debug
789 2467 241 if ($var->getMaxPos < $e->getMinPos)
790 0 2467 if $self->_debug
792 340 2127 unless (defined $substr)
798 43 122 if ($duringC == 0)
802 47 75 if ($tran->getStrand == -1)