| line |
true |
false |
branch |
|
667
|
0 |
1 |
if $seq |
|
668
|
0 |
1 |
if $group_tag |
|
675
|
0 |
1 |
if $self->{'_reported_problems'} |
|
676
|
0 |
1 |
if $self->{'_ignore_problems'} |
|
678
|
0 |
1 |
if (not $self->{'_problems_reported'} and scalar @probs) |
|
707
|
1 |
11 |
if @_ |
|
747
|
0 |
9 |
if @_ |
|
769
|
14 |
28849 |
if @_ |
|
770
|
1 |
28848 |
unless ($self->{'partonomy'}) |
|
868
|
11 |
11 |
if @_ |
|
896
|
2 |
0 |
if exists $self->{'_problems'} |
|
924
|
1 |
5 |
unless exists $self->{'_problems'} |
|
925
|
0 |
6 |
if ($self->verbose > 0) |
|
936
|
6 |
0 |
if (@sfs) |
|
943
|
12 |
12 |
$sf->has_tag($_) ? : |
|
949
|
0 |
6 |
if ($severity > $thresh) |
|
972
|
0 |
0 |
unless ($fh) |
|
1033
|
1 |
6 |
if @_ |
|
1045
|
2725 |
12298 |
if (grep {$_ eq $type;} @roots) |
|
1051
|
192 |
12106 |
unless ($ctype) |
|
1125
|
1 |
10 |
unless ($self->seq) |
|
1131
|
0 |
11 |
if ($partonomy and defined $structure_type) |
|
1139
|
2 |
9 |
if defined $partonomy |
|
1143
|
0 |
11 |
if defined $structure_type |
|
1151
|
0 |
11 |
if (@all_seq_features > @flat_seq_features) |
|
1154
|
0 |
11 |
if (@all_seq_features < @flat_seq_features) |
|
1161
|
7 |
4 |
if ($use_magic) |
|
1174
|
1 |
6 |
if (@sfs_with_locus_tag) |
|
1177
|
0 |
1 |
if ($group_tag and $group_tag ne 'locus_tag') |
|
1188
|
0 |
1 |
if ($self->verbose > 0) |
|
1196
|
1 |
0 |
if (@sfs_with_locus_tag == 0 and @sfs_with_gene_tag == 0 and @sfs_with_product_tag > 0 and not $group_tag) |
|
1201
|
0 |
1 |
if ($self->verbose > 0) |
|
1207
|
7 |
4 |
unless ($group_tag) |
|
1247
|
64 |
6269 |
if (not $sf->has_tag($group_tag)) { } |
|
1256
|
0 |
6269 |
if (@group_tagvals > 1) |
|
1265
|
0 |
6269 |
unless $gtv |
|
1269
|
4253 |
2016 |
if ($group) { } |
|
1308
|
899 |
5434 |
if ($sf->has_tag('pseudo')) |
|
1312
|
101 |
798 |
if ($type eq 'misc_RNA' or $type eq 'mRNA') { } |
|
1330
|
7 |
4 |
if ($use_magic) |
|
1331
|
0 |
7 |
if (defined $structure_type) |
|
1341
|
1540 |
4480 |
if $_->primary_tag eq 'mRNA' |
|
1348
|
6 |
1 |
if ($n_cdss > 0) { } |
|
1354
|
1 |
5 |
if ($n_mrnas == 0) { } |
|
|
0 |
5 |
elsif ($n_mrnas_attached_to_gene == 0) { } |
|
1372
|
0 |
0 |
if ($self->verbose) |
|
1374
|
0 |
0 |
if $_->primary_tag eq 'mRNA' |
|
1384
|
0 |
0 |
if ($_->primary_tag eq 'mRNA') |
|
1404
|
1 |
0 |
if ($n_rnas > 0) |
|
1409
|
0 |
7 |
if $noinfer |
|
1411
|
7 |
0 |
if ($need_to_infer_exons) |
|
1419
|
130 |
5879 |
if ($type eq 'exon') |
|
1424
|
5879 |
130 |
if $type ne 'exon' |
|
1434
|
0 |
11 |
if (grep {not scalar @$_;} @groups) |
|
1439
|
0 |
11 |
if ($self->verbose > 0) |
|
1453
|
1 |
10 |
if ($structure_type) |
|
1454
|
1 |
0 |
if ($structure_type == 1) { } |
|
1468
|
7 |
4 |
if ($use_magic) |
|
1470
|
2 |
6018 |
if ($sf->has_tag('derived_from')) |
|
1476
|
7 |
4 |
if ($use_magic) |
|
1483
|
1384 |
547 |
if (@sfs > 1) |
|
1486
|
1238 |
3989 |
if $type eq 'gene' |
|
1488
|
9 |
3980 |
unless ($container_type) |
|
1530
|
1 |
10 |
if ($need_to_infer_mRNAs) |
|
1531
|
0 |
1 |
if ($self->verbose > 0) |
|
1538
|
7 |
4 |
if ($need_to_infer_exons) |
|
1558
|
2 |
5 |
if (@removed_exons) |
|
1582
|
130 |
0 |
if ($inferred_exons) { } |
|
1587
|
4 |
130 |
if $exons_done{$exon} |
|
1594
|
0 |
284 |
unless ($exon->can('add_tag_value')) |
|
1617
|
0 |
2 |
if (keys %exon_h) |
|
1627
|
0 |
2 |
if (@problems) |
|
1630
|
0 |
0 |
if (@bad_problems) |
|
1668
|
0 |
2080 |
if (@ranges == 0) { } |
|
|
2077 |
3 |
elsif (@ranges == 1) { } |
|
1678
|
0 |
3 |
if ($self->verbose > 0) |
|
1689
|
0 |
3 |
if ($self->verbose > 0) |
|
1709
|
11 |
2072 |
if (@genes > 1) |
|
1729
|
0 |
11 |
if ($self->verbose > 0) |
|
1736
|
10 |
12 |
if ($loc->isa('Bio::Location::SplitLocationI')) { } |
|
1738
|
10 |
0 |
if (@locs > 1) { } |
|
1750
|
1 |
10 |
if (@genes > 1) |
|
1754
|
11 |
0 |
if (@genes) |
|
1755
|
0 |
11 |
unless @genes == 1 |
|
1846
|
0 |
2078 |
if ($self->verbose > 0) |
|
1854
|
570 |
1508 |
if @sfs == 1 |
|
1876
|
1 |
1507 |
if ($resolver_tag) { } |
|
1883
|
2 |
0 |
if ($sf->has_tag($resolver_tag)) { } |
|
1891
|
0 |
4 |
if $self->verbose > 0 |
|
1893
|
6 |
4 |
if ($_->has_tag($tag)) |
|
1896
|
2 |
4 |
if (grep {$_ eq $resolver_tagval;} @vals) |
|
1914
|
0 |
1507 |
if $resolver_tag |
|
1931
|
0 |
1508 |
if (@top_sfs > 1) |
|
1986
|
4155 |
1362 |
if ($container_type) { } |
|
1989
|
249 |
3906 |
unless $sfs_by_type{$container_type} |
|
1994
|
249 |
3906 |
if (not @possible_container_sfs) { } |
|
1998
|
2934 |
972 |
if (@possible_container_sfs == 1) { } |
|
2010
|
0 |
972 |
unless @possible_container_sfs > 1 |
|
2019
|
0 |
972 |
if ($sf->primary_tag ne 'CDS') |
|
2028
|
0 |
972 |
unless $resolver_method |
|
2041
|
6 |
966 |
unless (%container_sfh) |
|
2105
|
0 |
0 |
if ($self->verbose > 0 and scalar keys %unresolved) |
|
2130
|
322 |
1186 |
if (%unresolved) |
|
2133
|
0 |
322 |
unless ($new_pairs) |
|
2141
|
0 |
966 |
if ($self->verbose > 0) |
|
2150
|
0 |
1508 |
if (%unresolved) |
|
2151
|
0 |
0 |
unless $unresolved_problem_reported |
|
2160
|
3906 |
1611 |
if ($container_sf) { } |
|
2164
|
3906 |
0 |
if ($container_sf->contains($sf)) { } |
|
2227
|
0 |
1288 |
if ($verbose > 0) |
|
2239
|
0 |
4604 |
if ($verbose > 0) |
|
2242
|
2302 |
2302 |
if ($selected_children{$_}) { } |
|
2258
|
322 |
966 |
unless scalar keys %unresolved_parents |
|
2262
|
0 |
966 |
unless scalar @I |
|
2294
|
0 |
1336 |
unless (grep {$_->[0] ne $psf;} @{$unresolved{$sf};}) |
|
2300
|
966 |
0 |
unless ($bad) |
|
2304
|
966 |
0 |
if ($set) |
|
2311
|
966 |
0 |
if $successful_pairs |
|
2328
|
0 |
0 |
if ($f->has_tag($group_tag)) |
|
2331
|
0 |
0 |
if ($self->verbose > 0) |
|
2358
|
0 |
0 |
unless shift() |
|
2360
|
0 |
0 |
if ($self->verbose > 0) |
|
2363
|
0 |
0 |
if ($sf->has_tag('product')) |
|
2395
|
1742 |
1864 |
if ($inside) |
|
2397
|
20 |
1722 |
if ($_->start > $start or $_->end < $end) |
|
2405
|
22 |
3584 |
if (not $inside and $sf->has_tag('ribosomal_slippage')) |
|
2406
|
0 |
22 |
if ($self->verbose > 0) |
|
2426
|
16 |
6 |
if (not scalar @transcript_splice_sites or $transcript_splice_sites[0] == $cds_splice_sites[0]) { } |
|
2436
|
14 |
22 |
if (not @transcript_splice_sites) { } |
|
|
20 |
2 |
elsif ($cds_splice_sites[0] == $transcript_splice_sites[0]) { } |
|
2453
|
0 |
14 |
if ($self->verbose > 0) |
|
2466
|
2 |
0 |
if ($cds_splice_sites[0] < $transcript_splice_sites[0]) { } |
|
2475
|
0 |
2 |
if ($self->verbose > 0) |
|
2488
|
16 |
0 |
if ($inside) |
|
2491
|
0 |
16 |
if (@slips > 1) |
|
2496
|
0 |
16 |
if (grep {$_ > 2;} @slips) |
|
2505
|
0 |
3606 |
if ($self->verbose > 0) |
|
2508
|
1738 |
1868 |
if ($inside) |
|
2524
|
4467 |
101 |
if ($sf->location->isa('Bio::Location::SplitLocationI')) |
|
2572
|
1 |
2034 |
unless $sfs |
|
2573
|
0 |
2035 |
if $sf |
|
2574
|
1 |
2034 |
if ($seq) |
|
2575
|
0 |
1 |
unless $seq->isa('Bio::SeqI') |
|
2579
|
0 |
2035 |
if (@exons) |
|
2590
|
0 |
5856 |
unless $sf->isa('Bio::SeqFeatureI') |
|
2591
|
0 |
5856 |
unless $sf->isa('Bio::FeatureHolderI') |
|
2594
|
3865 |
1991 |
unless $type eq 'mRNA' or $type =~ /RNA/ |
|
2600
|
1762 |
229 |
if ($sf->location->isa('Bio::Location::SplitLocationI')) |
|
2604
|
0 |
1991 |
unless (@locs) |
|
2616
|
18260 |
0 |
if $sf->seq_id |
|
2617
|
18260 |
0 |
if $sf->source_tag |
|
2630
|
7266 |
10994 |
if ($loc_h{$locstr}) { } |
|
2649
|
0 |
1991 |
unless ($sf->location->strand) |
|
2723
|
1 |
0 |
if ($seq) |
|
2724
|
0 |
1 |
unless $seq->isa('Bio::SeqI') |
|
2730
|
0 |
52 |
unless $sf->isa('Bio::SeqFeatureI') |
|
2731
|
0 |
52 |
unless $sf->isa('Bio::FeatureHolderI') |
|
2732
|
0 |
52 |
if ($self->verbose > 0) |
|
2736
|
0 |
52 |
if ($sf->primary_tag eq 'mRNA') |
|
2742
|
24 |
28 |
if (@cdsl) |
|
2749
|
0 |
24 |
if ($self->verbose > 0) |
|
2762
|
0 |
24 |
if ($noinfer) { } |
|
2772
|
24 |
0 |
if $cds->seq_id |
|
2773
|
24 |
0 |
if $cds->source_tag |
|
2828
|
0 |
0 |
unless $seq->isa('Bio::SeqI') |
|
2860
|
0 |
2039 |
unless @ranges |
|
2865
|
0 |
16469 |
if ($ranges[$i]->strand != $strand) |
|
2878
|
0 |
16469 |
if ($rangeP->start > $range->end) |
|
2879
|
0 |
0 |
if ($self->seq->is_circular) { } |
|
2894
|
0 |
2039 |
unless ($pass) |
|
2902
|
0 |
0 |
if ($rangeP->end < $range->start) |
|
2937
|
0 |
0 |
unless (defined $score) |