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) { }
|