| line |
true |
false |
branch |
|
150
|
0 |
8 |
if ($method and not $method =~ /Spidey/i) |
|
188
|
1 |
163 |
if (/^--SPIDEY\s+version\s+(\d+\.\d+)--/) { } |
|
|
1 |
162 |
elsif (/^Genomic:\s+(\S+)\s.*,\s+(\d+)\sbp$/) { } |
|
|
1 |
161 |
elsif (/^mRNA:\s+(\S+)\s.*,(?:\s+mRNA\s+sequence,)?\s(\d+)\sbp$/) { } |
|
|
1 |
160 |
elsif (/^Strand:/) { } |
|
|
1 |
159 |
elsif (/^Number of exons: (\d+)/) { } |
|
|
1 |
158 |
elsif (/^Number of splice sites:\s+(\d+)/) { } |
|
|
1 |
157 |
elsif (/^mRNA coverage:\s+(\d+)%/) { } |
|
|
1 |
156 |
elsif (/^overall percent identity:\s+([\d\.]+)%/) { } |
|
|
1 |
155 |
elsif (/^Missing mRNA ends:\s+(\w+)/) { } |
|
|
6 |
149 |
elsif (/^Exon (\d+): (\d+)-(\d+) \(gen\)\s+(\d+)-(\d+) \(mRNA\)/) { } |
|
|
0 |
149 |
elsif (/No alignment found/) { } |
|
189
|
0 |
1 |
if ($started) |
|
194
|
0 |
1 |
if ($version != 1.4) |
|
212
|
0 |
1 |
if (/plus/) { } |
|
229
|
6 |
0 |
if (defined($_ = $self->_readline)) { } |
|
232
|
6 |
0 |
if (/^Exon\s${ec}[\(\)-]*:\s(\d+)-(\d+)\s\(gen\)\s+(\d+)-(\d+)\s\(mRNA\)\s+id\s([\d\.inf-]+)%\s+mismatches\s(\d+)\s+gaps\s(\d+)\s+splice\ssite\s\(d\s+a\):\s(\d+)\s+(\d+)\s*(\w*)/) { } |
|
254
|
6 |
0 |
if ($exon->feature1->can('seqlength')) { } |
|
324
|
1 |
1 |
@exons ? : |
|
357
|
1 |
1 |
unless (defined $exons) |
|
361
|
0 |
1 |
if (@$exons == 0) |
|
424
|
1 |
1 |
if (@args) { } |
|
448
|
1 |
1 |
if (@args) { } |
|
472
|
1 |
1 |
if (@args) { } |
|
496
|
1 |
1 |
if (@args) { } |
|
520
|
1 |
1 |
if (@args) { } |