Branch Coverage

lib/Sanger/CGP/Vagrent/Annotators/ComplexIndelAnnotator.pm
Criterion Covered Total %
branch 88 102 86.2


line true false branch
44 0 230 unless (defined $var and $var->isa('Sanger::CGP::Vagrent::Data::ComplexIndel'))
50 0 230 unless ($var->isValid)
57 3 227 unless (defined $trans[0])
66 218 9 if (defined $g)
70 9 218 unless (scalar @groups > 0 and defined $groups[0])
83 9 218 unless (defined $rAnnot)
94 197 21 if ($tran->isProteinCoding) { }
95 76 121 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)) { }
111 0 121 unless (defined $cAnnot)
118 0 121 unless (defined $pAnnot)
138 0 227 unless (defined $mrnaMin and defined $mrnaMinOffset and defined $mrnaMax and defined $mrnaMaxOffset)
144 0 227 unless ($self->_safetyCheck($var, $tran, $mrnaMin, $mrnaMinOffset, $mrnaMax, $mrnaMaxOffset))
156 221 6 if (defined $upstream) { }
157 16 205 if ($upstream)
165 202 3 if (defined $downstream) { }
166 20 182 if ($downstream)
174 1 181 if ($mrnaMin == 0 and $mrnaMinOffset <= 0)
178 1 181 if ($mrnaMax == 0 and $mrnaMaxOffset >= 0)
183 161 21 if ($tran->isProteinCoding)
184 99 18 if ($mrnaMax > $tran->getCdsMinPos || $mrnaMax == $tran->getCdsMinPos && $mrnaMaxOffset >= 0 and $mrnaMin < $tran->getCdsMaxPos || $mrnaMin == $tran->getCdsMaxPos && $mrnaMinOffset <= 0)
190 45 116 if ($mrnaMin < $tran->getCdsMinPos or $mrnaMin == $tran->getCdsMinPos and $mrnaMinOffset < 0)
194 44 1 unless $self->_arrayHasString($self->getCDSClass, @groupClasses)
196 19 142 if ($mrnaMax > $tran->getCdsMaxPos or $mrnaMax == $tran->getCdsMaxPos and $mrnaMaxOffset > 0)
200 18 1 unless $self->_arrayHasString($self->getCDSClass, @groupClasses)
206 46 136 if (scalar keys %$tmpGroupClassesHash == 1 and defined $$tmpGroupClassesHash{$self->getIntronClass})
214 68 68 if ($tran->getStrand == 1) { }
223 0 136 if ($mrnaMin == 1 and $mrnaMax == length $tran->getcDNASeq) { }
231 0 136 if ($mrnaMin == 0 and $mrnaMax == 0) { }
38 98 elsif ($mrnaMinOffset == 0 and $mrnaMaxOffset == 0) { }
255 15 121 if (defined $$tmpGroupClassesHash{$self->getExonClass} and defined $$tmpGroupClassesHash{$self->getEssentialSpliceSiteClass}) { }
258 0 15 unless ($tran->isProteinCoding)
263 48 73 if (defined $$tmpGroupClassesHash{$self->getSpliceRegionClass})
266 43 78 if (defined $$tmpGroupClassesHash{$self->getEssentialSpliceSiteClass})
269 8 113 if (defined $$tmpGroupClassesHash{$self->getIntronClass})
272 38 83 if (defined $$tmpGroupClassesHash{$self->getExonClass})
273 34 4 if ($tran->isProteinCoding) { }
274 18 16 if ($self->_arrayHasString($self->getCDSClass, @groupClasses))
275 0 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)) { }
279 14 4 if (abs(length($wt) - length($mt)) % 3 == 0) { }
307 0 79 if ($mutStart == 1 and $mutEnd == length $tran->getCdsSeq) { }
326 93 122 if ($mutStart == $mutEnd and $mutStartOffset == $mutEndOffset) { }
328 41 52 if ($mutStartOffset > 0) { }
32 20 elsif ($mutStartOffset < 0) { }
20 0 elsif ($mutStartOffset == 0) { }
339 32 90 if ($mutStartOffset > 0) { }
40 50 elsif ($mutStartOffset < 0) { }
50 0 elsif ($mutStartOffset == 0) { }
347 48 74 if ($mutEndOffset > 0) { }
24 50 elsif ($mutEndOffset < 0) { }
50 0 elsif ($mutEndOffset == 0) { }
355 10 112 if (length $wt > 15) { }