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])
|