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) { }
|