Branch Coverage

lib/Sanger/CGP/Vagrent/Annotators/SimpleSubstitutionAnnotator.pm
Criterion Covered Total %
branch 71 84 84.5


line true false branch
46 0 156 unless (defined $var and $var->isa('Sanger::CGP::Vagrent::Data::Substitution'))
52 0 156 unless ($var->isValid)
59 2 154 unless (defined $trans[0])
68 148 6 if (defined $g)
72 6 148 unless (scalar @groups > 0 and defined $groups[0])
84 6 148 unless (defined $rAnnot)
95 122 26 if ($tran->isProteinCoding) { }
96 52 70 if ($rAnnot->hasClassification($self->getIntronVariantClass) or $rAnnot->hasClassification($self->get5KBUpStreamVariantClass) or $rAnnot->hasClassification($self->get2KBUpStreamVariantClass) or $rAnnot->hasClassification($self->get5KBDownStreamVariantClass) or $rAnnot->hasClassification($self->get500BPDownStreamVariantClass)) { }
105 0 70 unless (defined $cAnnot)
112 0 70 unless (defined $pAnnot)
133 0 154 unless (defined $mrnaMin and defined $mrnaMinOffset and defined $mrnaMax and defined $mrnaMaxOffset)
139 0 154 unless ($mrnaMin == $mrnaMax and $mrnaMinOffset == $mrnaMaxOffset)
157 29 125 if ($pos == 0)
159 16 13 if ($offset < 0) { }
13 0 elsif ($offset > 0) { }
161 8 8 if ($self->_isWithin2KBUpstreamOffsetDistance($offset)) { }
4 4 elsif ($self->_isWithin5KBOffsetDistance($offset)) { }
174 6 7 if ($self->_isWithin500BPDownstreamOffsetDistance($offset)) { }
5 2 elsif ($self->_isWithin5KBOffsetDistance($offset)) { }
192 99 26 if ($tran->isProteinCoding)
193 66 33 if ($pos > $tran->getCdsMinPos || $pos == $tran->getCdsMinPos && $offset >= 0 and $pos < $tran->getCdsMaxPos || $pos == $tran->getCdsMaxPos && $offset <= 0) { }
19 14 elsif ($pos < $tran->getCdsMinPos or $pos == $tran->getCdsMinPos and $offset < 0) { }
14 0 elsif ($pos > $tran->getCdsMaxPos or $pos == $tran->getCdsMaxPos and $offset > 0) { }
211 41 84 if ($self->_isIntronicOffsetDistance($offset))
216 43 41 if ($tran->getStrand == 1) { }
225 18 66 if ($offset == 0) { }
231 0 18 if (lc $substr ne lc $wt)
237 16 2 if ($tran->isProteinCoding) { }
238 4 12 if ($self->_arrayHasString($self->get5PrimeUtrClass, @groupClasses)) { }
2 10 elsif ($self->_arrayHasString($self->get3PrimeUtrClass, @groupClasses)) { }
239 2 2 if ($self->_isStartGained($var, $tran, $pos, $pos, $wt, $mt)) { }
255 15 51 if ($self->_isOffsetAConsensusSpliceDistance($offset)) { }
262 6 60 if ($self->_arrayHasString($self->get5PrimeUtrClass, @groupClasses)) { }
4 56 elsif ($self->_arrayHasString($self->get3PrimeUtrClass, @groupClasses)) { }
271 18 66 if ($offset == 0) { }
32 34 elsif ($offset > 0) { }
319 10 46 if ($mutStartOffset == 0) { }
22 24 elsif ($mutStartOffset > 0) { }
351 0 4 if ($substrStart < 0) { }
369 2 2 if (scalar @mtPos > scalar @wtPos) { }
0 2 elsif (scalar @mtPos == scalar @wtPos and scalar @wtPos > 0) { }
375 0 0 if ($mtPos[$i] != $wtPos[$i])