Branch Coverage

lib/Sanger/CGP/Vagrent/Annotators/InsertionAnnotator.pm
Criterion Covered Total %
branch 69 78 88.4


line true false branch
44 0 194 unless (defined $var and $var->isa('Sanger::CGP::Vagrent::Data::Insertion'))
50 0 194 unless ($var->isValid)
57 1 193 unless (defined $trans[0])
66 182 11 if (defined $g)
70 11 182 unless (scalar @groups > 0 and defined $groups[0])
83 11 182 unless (defined $rAnnot)
94 158 24 if ($tran->isProteinCoding) { }
95 59 99 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)) { }
104 0 99 unless (defined $cAnnot)
111 0 99 unless (defined $pAnnot)
137 16 5 if ($cAnnot->getMinOffset == 0) { }
5 0 elsif ($cAnnot->getMinOffset == -1) { }
157 0 193 unless (defined $mrnaMin and defined $mrnaMinOffset and defined $mrnaMax and defined $mrnaMaxOffset)
163 0 3 unless ($mrnaMax - $mrnaMin == 1 and $mrnaMinOffset == 0 and $mrnaMaxOffset == 0 or $mrnaMax == $mrnaMin and $mrnaMaxOffset - $mrnaMinOffset == 1 or $mrnaMin == 0 and $mrnaMax == 1 and $mrnaMinOffset == -1 and $mrnaMaxOffset == 0 or $mrnaMin == length $tran->getcDNASeq and $mrnaMax == 0 and $mrnaMinOffset == 0 and $mrnaMaxOffset == 1)
173 20 173 if ($mrnaMin == 0 and $mrnaMinOffset < 0) { }
18 310 elsif ($mrnaMax == 0 and $mrnaMaxOffset > 0) { }
174 10 10 if ($self->_isWithin2KBUpstreamOffsetDistance($mrnaMinOffset)) { }
4 6 elsif ($self->_isWithin5KBOffsetDistance($mrnaMinOffset)) { }
185 8 10 if ($self->_isWithin500BPDownstreamOffsetDistance($mrnaMaxOffset)) { }
5 5 elsif ($self->_isWithin5KBOffsetDistance($mrnaMaxOffset)) { }
198 86 69 if ($tran->getStrand == 1) { }
209 131 24 if ($tran->isProteinCoding)
210 80 51 if ($mrnaMax > $tran->getCdsMinPos and $mrnaMin < $tran->getCdsMaxPos) { }
28 23 elsif ($mrnaMax <= $tran->getCdsMinPos) { }
23 0 elsif ($mrnaMin >= $tran->getCdsMaxPos) { }
229 44 111 if ($mrnaMinOffset < 0 and $self->_isIntronicOffsetDistance($mrnaMinOffset) or $mrnaMaxOffset > 0 and $self->_isIntronicOffsetDistance($mrnaMaxOffset)) { }
45 66 elsif ($mrnaMinOffset == 0 and $mrnaMaxOffset == 0 or $mrnaMinOffset == -1 and $mrnaMaxOffset == 0 or $mrnaMinOffset == 0 and $mrnaMaxOffset == 1) { }
236 10 35 if ($mrnaMinOffset != $mrnaMaxOffset) { }
241 45 0 if ($tran->isProteinCoding) { }
242 21 24 if ($self->_arrayHasString($self->getCDSClass, @groupClasses))
243 10 11 if (length($mt) % 3 == 0) { }
253 39 6 if ($mrnaMinOffset == 0) { }
258 41 4 if ($mrnaMaxOffset == 0) { }
267 19 47 if ($mrnaMinOffset < 0 and $mrnaMinOffset >= $self->_getConsesnsusSpliceBeforeBoundry or $mrnaMinOffset > 0 and $mrnaMaxOffset <= $self->_getConsesnsusSpliceAfterBoundry) { }
276 34 32 if ($mrnaMinOffset < 0) { }
321 16 52 if ($mutStartOffset == 0) { }
22 30 elsif ($mutStartOffset > 0) { }
328 18 50 if ($mutEndOffset == 0) { }
26 24 elsif ($mutEndOffset > 0) { }