| line |
true |
false |
branch |
|
120
|
0 |
2 |
if defined $genome_is_first |
|
138
|
0 |
38 |
if ($method and not $method =~ /est2genome/i) |
|
172
|
1 |
1 |
if $return_gene |
|
178
|
1 |
15 |
if (/Note Best alignment is between (reversed|forward) est and (reversed|forward) genome, (but|and) splice\s+sites imply\s+(forward gene|REVERSED GENE)/) { } |
|
|
4 |
11 |
elsif (/^Exon/) { } |
|
|
3 |
8 |
elsif (/^([\-\+\?])(Intron)/) { } |
|
|
1 |
7 |
elsif (/^Span/) { } |
|
|
5 |
2 |
elsif (/^Segment/) { } |
|
|
2 |
0 |
elsif (/^\s+$/) { } |
|
179
|
0 |
1 |
if ($seensegment) |
|
181
|
0 |
0 |
wantarray ? : |
|
183
|
0 |
1 |
if $1 eq 'reversed' |
|
184
|
0 |
1 |
if $4 eq 'REVERSED GENE' |
|
241
|
0 |
1 |
unless @features |
|
242
|
0 |
1 |
wantarray ? : |
|
256
|
1 |
15 |
if (/Note Best alignment is between (reversed|forward) est and (reversed|forward) genome, (but|and) splice\s+sites imply\s+(forward gene|REVERSED GENE)/) { } |
|
|
4 |
11 |
elsif (/^Exon/) { } |
|
|
3 |
8 |
elsif (/^([\-\+\?])(Intron)/) { } |
|
|
1 |
7 |
elsif (/^Span/) { } |
|
|
5 |
2 |
elsif (/^Segment/) { } |
|
|
2 |
0 |
elsif (/^\s+$/) { } |
|
257
|
0 |
1 |
if ($seensegment) |
|
261
|
0 |
1 |
if $1 eq 'reversed' |
|
262
|
0 |
1 |
if $4 eq 'REVERSED GENE' |
|
280
|
1 |
3 |
unless $transcript->seq_id |
|
324
|
0 |
1 |
unless $#exon >= 0 |
|
328
|
5 |
15 |
if ($sf->overlaps($e)) |