line |
true |
false |
branch |
46
|
0 |
282 |
unless (defined $var and $var->isa('Sanger::CGP::Vagrent::Data::Deletion'))
|
52
|
0 |
282 |
unless ($var->isValid)
|
59
|
4 |
278 |
unless (defined $trans[0])
|
68
|
270 |
8 |
if (defined $g)
|
72
|
8 |
270 |
unless (scalar @groups > 0 and defined $groups[0])
|
85
|
8 |
270 |
unless (defined $rAnnot)
|
96
|
230 |
40 |
if ($tran->isProteinCoding) { }
|
97
|
79 |
151 |
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)) { }
|
113
|
0 |
151 |
unless (defined $cAnnot)
|
120
|
0 |
151 |
unless (defined $pAnnot)
|
140
|
0 |
278 |
unless (defined $mrnaMin and defined $mrnaMinOffset and defined $mrnaMax and defined $mrnaMaxOffset)
|
146
|
0 |
278 |
unless ($self->_safetyCheck($var, $tran, $mrnaMin, $mrnaMinOffset, $mrnaMax, $mrnaMaxOffset))
|
157
|
273 |
5 |
if (defined $upstream) { }
|
158
|
23 |
250 |
if ($upstream)
|
166
|
247 |
3 |
if (defined $downstream) { }
|
167
|
16 |
231 |
if ($downstream)
|
175
|
5 |
226 |
if ($mrnaMin == 0 and $mrnaMinOffset <= 0)
|
179
|
5 |
226 |
if ($mrnaMax == 0 and $mrnaMaxOffset >= 0)
|
184
|
191 |
40 |
if ($tran->isProteinCoding)
|
185
|
100 |
29 |
if ($mrnaMax > $tran->getCdsMinPos || $mrnaMax == $tran->getCdsMinPos && $mrnaMaxOffset >= 0 and $mrnaMin < $tran->getCdsMaxPos || $mrnaMin == $tran->getCdsMaxPos && $mrnaMinOffset <= 0)
|
191
|
71 |
120 |
if ($mrnaMin < $tran->getCdsMinPos or $mrnaMin == $tran->getCdsMinPos and $mrnaMinOffset < 0)
|
195
|
62 |
9 |
unless $self->_arrayHasString($self->getCDSClass, @groupClasses)
|
197
|
35 |
156 |
if ($mrnaMax > $tran->getCdsMaxPos or $mrnaMax == $tran->getCdsMaxPos and $mrnaMaxOffset > 0)
|
201
|
29 |
6 |
unless $self->_arrayHasString($self->getCDSClass, @groupClasses)
|
207
|
52 |
179 |
if (scalar keys %$tmpGroupClassesHash == 1 and defined $$tmpGroupClassesHash{$self->getIntronClass})
|
219
|
2 |
177 |
if ($mrnaMin == 1 and $mrnaMax == length $tran->getcDNASeq) { }
|
227
|
0 |
179 |
if ($mrnaMin == 0 and $mrnaMax == 0) { }
|
|
46 |
133 |
elsif ($mrnaMinOffset == 0 and $mrnaMaxOffset == 0) { }
|
251
|
26 |
153 |
if (defined $$tmpGroupClassesHash{$self->getExonClass} and defined $$tmpGroupClassesHash{$self->getEssentialSpliceSiteClass}) { }
|
254
|
2 |
24 |
unless ($tran->isProteinCoding)
|
259
|
62 |
91 |
if (defined $$tmpGroupClassesHash{$self->getSpliceRegionClass})
|
262
|
49 |
104 |
if (defined $$tmpGroupClassesHash{$self->getEssentialSpliceSiteClass})
|
265
|
1 |
152 |
if (defined $$tmpGroupClassesHash{$self->getIntronClass})
|
268
|
43 |
110 |
if (defined $$tmpGroupClassesHash{$self->getExonClass})
|
269
|
37 |
6 |
if ($tran->isProteinCoding) { }
|
270
|
27 |
10 |
if ($self->_arrayHasString($self->getCDSClass, @groupClasses))
|
271
|
9 |
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)) { }
|
275
|
7 |
11 |
if (length($wt) % 3 == 0) { }
|
298
|
449 |
56 |
if ($mrnaMin > 0 or $mrnaMin == 0 and $mrnaMinOffset >= 0) { }
|
|
56 |
0 |
elsif ($mrnaMin == 0 and $mrnaMinOffset < 0) { }
|
301
|
20 |
36 |
if ($self->_isWithin2KBUpstreamOffsetDistance($mrnaMinOffset)) { }
|
|
17 |
19 |
elsif ($self->_isWithin5KBOffsetDistance($mrnaMinOffset)) { }
|
307
|
455 |
50 |
if ($mrnaMax > 0 or $mrnaMax == 0 and $mrnaMaxOffset >= 0) { }
|
|
50 |
0 |
elsif ($mrnaMax == 0 and $mrnaMaxOffset < 0) { }
|
310
|
25 |
25 |
if ($self->_isWithin2KBUpstreamOffsetDistance($mrnaMaxOffset)) { }
|
|
14 |
11 |
elsif ($self->_isWithin5KBOffsetDistance($mrnaMaxOffset)) { }
|
316
|
0 |
505 |
if $self->_debug
|
317
|
11 |
494 |
if ($upStartScore == 0 and $upEndScore == 0)
|
324
|
25 |
494 |
if ($i == 1) { }
|
|
31 |
463 |
elsif ($i == 2) { }
|
330
|
39 |
455 |
if ($upEndScore < 3)
|
341
|
413 |
42 |
if ($mrnaMin > 0 or $mrnaMin == 0 and $mrnaMinOffset <= 0) { }
|
|
42 |
0 |
elsif ($mrnaMin == 0 and $mrnaMinOffset > 0) { }
|
344
|
24 |
18 |
if ($self->_isWithin500BPDownstreamOffsetDistance($mrnaMinOffset)) { }
|
|
12 |
6 |
elsif ($self->_isWithin5KBOffsetDistance($mrnaMinOffset)) { }
|
350
|
407 |
48 |
if ($mrnaMax > 0 or $mrnaMax == 0 and $mrnaMaxOffset <= 0) { }
|
|
48 |
0 |
elsif ($mrnaMax == 0 and $mrnaMaxOffset > 0) { }
|
353
|
15 |
33 |
if ($self->_isWithin500BPDownstreamOffsetDistance($mrnaMaxOffset)) { }
|
|
20 |
13 |
elsif ($self->_isWithin5KBOffsetDistance($mrnaMaxOffset)) { }
|
359
|
0 |
455 |
if $self->_debug
|
360
|
6 |
449 |
if ($downStartScore == 0 and $downEndScore == 0)
|
367
|
27 |
450 |
if ($i == 1) { }
|
|
30 |
420 |
elsif ($i == 2) { }
|
373
|
36 |
413 |
if ($downStartScore < 3)
|
385
|
0 |
413 |
if $self->_debug
|
388
|
1529 |
6240 |
if ($mrnaMin > $e->getRnaMaxPos)
|
392
|
5708 |
532 |
if ($mrnaMax < $e->getRnaMinPos)
|
399
|
241 |
141 |
if ($mrnaMin < $e->getRnaMaxPos || $mrnaMin == $e->getRnaMaxPos && $mrnaMinOffset == 0 and $mrnaMax > $e->getRnaMinPos || $mrnaMax == $e->getRnaMinPos && $mrnaMaxOffset == 0)
|
402
|
0 |
532 |
if $self->_debug
|
404
|
278 |
254 |
if ($mrnaMin < $e->getRnaMinPos or $mrnaMin == $e->getRnaMinPos and $mrnaMinOffset < 0)
|
406
|
182 |
96 |
if ($mrnaMin < $e->getRnaMinPos or $self->_isIntronicOffsetDistance($mrnaMinOffset)) { }
|
|
36 |
60 |
elsif ($mrnaMin == $e->getRnaMinPos and $mrnaMinOffset >= $self->_getConsesnsusSpliceBeforeBoundry) { }
|
408
|
126 |
56 |
if ($mrnaMax > $e->getRnaMinPos or $mrnaMax == $e->getRnaMinPos and $mrnaMaxOffset == 0) { }
|
|
52 |
4 |
elsif ($self->_isIntronicOffsetDistance($mrnaMaxOffset)) { }
|
|
0 |
4 |
elsif ($mrnaMaxOffset < 0 and $mrnaMaxOffset >= $self->_getConsesnsusSpliceBeforeBoundry) { }
|
431
|
5 |
55 |
if ($mrnaMax > $e->getRnaMinPos or $mrnaMax == $e->getRnaMinPos and $mrnaMaxOffset == 0) { }
|
|
4 |
51 |
elsif ($mrnaMaxOffset < 0 and $mrnaMaxOffset >= $self->_getConsesnsusSpliceBeforeBoundry) { }
|
447
|
290 |
242 |
if ($mrnaMax > $e->getRnaMaxPos or $mrnaMax == $e->getRnaMaxPos and $mrnaMaxOffset > 0)
|
449
|
179 |
111 |
if ($mrnaMax > $e->getRnaMaxPos or $self->_isIntronicOffsetDistance($mrnaMaxOffset)) { }
|
|
60 |
51 |
elsif ($mrnaMax == $e->getRnaMaxPos and $mrnaMaxOffset <= $self->_getConsesnsusSpliceAfterBoundry) { }
|
451
|
128 |
51 |
if ($mrnaMin < $e->getRnaMaxPos or $mrnaMin == $e->getRnaMaxPos and $mrnaMinOffset == 0) { }
|
|
46 |
5 |
elsif ($self->_isIntronicOffsetDistance($mrnaMinOffset)) { }
|
|
1 |
4 |
elsif ($mrnaMinOffset > 0 and $mrnaMinOffset <= $self->_getConsesnsusSpliceAfterBoundry) { }
|
474
|
5 |
46 |
if ($mrnaMin < $e->getRnaMaxPos or $mrnaMin == $e->getRnaMaxPos and $mrnaMinOffset == 0) { }
|
|
4 |
42 |
elsif ($mrnaMinOffset > 0 and $mrnaMinOffset <= $self->_getConsesnsusSpliceAfterBoundry) { }
|
489
|
0 |
413 |
if $self->_debug
|
496
|
3 |
83 |
if ($mutStart == 1 and $mutEnd == length $tran->getCdsSeq) { }
|
507
|
168 |
92 |
if ($mutStart == $mutEnd and $mutStartOffset == $mutEndOffset) { }
|
509
|
76 |
92 |
if ($mutStartOffset > 0) { }
|
|
74 |
18 |
elsif ($mutStartOffset < 0) { }
|
|
18 |
0 |
elsif ($mutStartOffset == 0) { }
|
518
|
1 |
91 |
if ($mutStartOffset > 0) { }
|
|
17 |
74 |
elsif ($mutStartOffset < 0) { }
|
|
74 |
0 |
elsif ($mutStartOffset == 0) { }
|
526
|
22 |
70 |
if ($mutEndOffset > 0) { }
|
|
1 |
69 |
elsif ($mutEndOffset < 0) { }
|
|
69 |
0 |
elsif ($mutEndOffset == 0) { }
|
534
|
3 |
89 |
if (length $wt > 15) { }
|
554
|
18218601 |
962741 |
if ($i > $e->getMaxPos) { }
|
|
79779 |
882962 |
elsif ($i >= $e->getMinPos and $i <= $e->getMaxPos) { }
|
|
882962 |
0 |
elsif ($i < $e->getMinPos) { }
|
555
|
21002 |
18197599 |
if ($ec == scalar @exons) { }
|
566
|
861960 |
21002 |
unless $ec == 1
|
570
|
42004 |
941739 |
unless $use == 1
|
571
|
79779 |
861960 |
if ($isExonic) { }
|
577
|
207 |
237 |
if ($tran->getStrand == -1)
|
586
|
36 |
129 |
if ($rAnnot->hasClassification($self->getInFrameVariantClass) or $rAnnot->hasClassification($self->getFrameShiftVariantClass)) { }
|
|
41 |
88 |
elsif ($rAnnot->hasClassification($self->getComplexChangeVariantClass)) { }
|
592
|
220 |
122 |
unless $i >= $e->getMinPos and $i <= $e->getMaxPos
|
593
|
69 |
53 |
if ($tran->getStrand == 1) { }
|
595
|
69 |
0 |
if ($pos >= $tran->getCdsMinPos and $pos <= $tran->getCdsMaxPos)
|
601
|
53 |
0 |
if ($pos >= $tran->getCdsMinPos and $pos <= $tran->getCdsMaxPos)
|
607
|
122 |
0 |
if ($isCod)
|
611
|
14 |
22 |
if ($tran->getStrand == -1)
|
615
|
14 |
27 |
if ($rAnnot->getMinPos <= $tran->getCdsMinPos or $rAnnot->getMaxPos >= $tran->getCdsMaxPos) { }
|
622
|
8 |
6 |
if ($var->getMinPos < $genomicCdsLow) { }
|
628
|
9 |
5 |
if ($var->getMaxPos > $genomicCdsHigh) { }
|
670
|
0 |
36 |
if ($cAnnot->getMinOffset > 0) { }
|
681
|
0 |
36 |
if ($cAnnot->getMaxOffset < 0) { }
|
692
|
0 |
505 |
unless (defined $tranString)
|
696
|
0 |
505 |
unless (defined $genoString)
|
699
|
0 |
505 |
if ($self->_debug)
|
704
|
383 |
122 |
if (length $tranString == 0 and length $genoString == 0) { }
|
|
122 |
0 |
elsif (uc $tranString eq uc $genoString) { }
|
718
|
0 |
505 |
if $self->_debug
|
719
|
42 |
463 |
if ($mrnaMin == 0 and $mrnaMinOffset > 0) { }
|
|
50 |
413 |
elsif ($mrnaMax == 0 and $mrnaMaxOffset < 0) { }
|
|
76 |
337 |
elsif ($mrnaMinOffset == 0 and $mrnaMaxOffset == 0) { }
|
731
|
150 |
187 |
if ($mrnaMinOffset > 0) { }
|
736
|
141 |
196 |
if ($mrnaMaxOffset < 0) { }
|
741
|
6 |
331 |
if $leftAnchor < 1
|
742
|
6 |
331 |
if $rightAnchor == 0
|
743
|
0 |
337 |
if $self->_debug
|
744
|
291 |
46 |
if ($leftAnchor > $rightAnchor)
|
752
|
0 |
122 |
if $self->_debug
|
765
|
2793 |
2708 |
if ($e->getMaxPos < $var->getMinPos)
|
767
|
0 |
2793 |
if $self->_debug
|
771
|
241 |
2467 |
if ($var->getMinPos <= $e->getMaxPos and $e->getMinPos <= $var->getMaxPos)
|
776
|
86 |
155 |
if $start < 1
|
777
|
87 |
154 |
if $end > length $var->getDeletedSequence
|
782
|
119 |
122 |
if (defined $substr) { }
|
787
|
0 |
241 |
if $self->_debug
|
789
|
2467 |
241 |
if ($var->getMaxPos < $e->getMinPos)
|
790
|
0 |
2467 |
if $self->_debug
|
792
|
340 |
2127 |
unless (defined $substr)
|
798
|
43 |
122 |
if ($duringC == 0)
|
802
|
47 |
75 |
if ($tran->getStrand == -1)
|