| line |
!l |
l&&!r |
l&&r |
condition |
|
77
|
0 |
0 |
52 |
defined $self->{'data_table'} and ref $self->{'data_table'} eq 'ARRAY' |
|
185
|
0 |
6 |
0 |
exists $self->{'0'} and not $self->{'0'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i |
|
194
|
0 |
6 |
0 |
exists $self->{'3'} and not $self->{'3'}{'name'} =~ /start|pos|position/i |
|
202
|
0 |
6 |
0 |
exists $self->{'4'} and not $self->{'4'}{'name'} =~ /stop|end|pos|position/i |
|
210
|
0 |
6 |
0 |
exists $self->{'6'} and not $self->{'6'}{'name'} =~ /strand/i |
|
262
|
0 |
21 |
0 |
exists $self->{'0'} and not $self->{'0'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i |
|
270
|
0 |
21 |
0 |
exists $self->{'1'} and not $self->{'1'}{'name'} =~ /start|pos|position/i |
|
277
|
0 |
21 |
0 |
exists $self->{'2'} and not $self->{'2'}{'name'} =~ /stop|end|pos|position/i |
|
284
|
6 |
15 |
0 |
exists $self->{'5'} and not $self->{'5'}{'name'} =~ /strand/i |
|
291
|
10 |
4 |
7 |
exists $self->{'6'} and not $self->{'format'} =~ /narrow|broad/i |
|
|
14 |
7 |
0 |
exists $self->{'6'} and not $self->{'format'} =~ /narrow|broad/i and not $self->{'6'}{'name'} =~ /start|thick|cds/i |
|
299
|
10 |
4 |
7 |
exists $self->{'7'} and not $self->{'format'} =~ /narrow|broad/i |
|
|
14 |
7 |
0 |
exists $self->{'7'} and not $self->{'format'} =~ /narrow|broad/i and not $self->{'7'}{'name'} =~ /end|stop|thick|cds/i |
|
307
|
10 |
4 |
7 |
exists $self->{'8'} and not $self->{'format'} =~ /narrow|broad/i |
|
|
14 |
7 |
0 |
exists $self->{'8'} and not $self->{'format'} =~ /narrow|broad/i and not $self->{'8'}{'name'} =~ /item|rgb|color/i |
|
315
|
10 |
4 |
7 |
exists $self->{'9'} and not $self->{'format'} =~ /narrow|broad/i |
|
|
14 |
7 |
0 |
exists $self->{'9'} and not $self->{'format'} =~ /narrow|broad/i and not $self->{'9'}{'name'} =~ /count|number|block|exon/i |
|
323
|
14 |
7 |
0 |
exists $self->{'10'} and not $self->{'10'}{'name'} =~ /size|length|block|exon/i |
|
330
|
14 |
7 |
0 |
exists $self->{'11'} and not $self->{'11'}{'name'} =~ /start|block|exon/i |
|
357
|
3 |
14 |
4 |
$self->{'format'} and $self->{'format'} =~ /narrow|broad/i |
|
375
|
17 |
0 |
4 |
$self->{'number_columns'} == 15 and $self->{'format'} =~ /gapped/i |
|
395
|
3 |
14 |
4 |
$self->{'format'} and $self->{'format'} =~ /narrowpeak/i |
|
|
17 |
4 |
0 |
$self->{'format'} and $self->{'format'} =~ /narrowpeak/i and $self->{'number_columns'} != 10 |
|
402
|
3 |
18 |
0 |
$self->{'format'} and $self->{'format'} =~ /broadpeak/i |
|
|
21 |
0 |
0 |
$self->{'format'} and $self->{'format'} =~ /broadpeak/i and $self->{'number_columns'} != 9 |
|
409
|
3 |
14 |
4 |
$self->{'format'} and $self->{'format'} =~ /gappedpeak/i |
|
|
17 |
4 |
0 |
$self->{'format'} and $self->{'format'} =~ /gappedpeak/i and $self->{'number_columns'} != 15 |
|
648
|
0 |
0 |
0 |
exists $self->{'1'} and not $self->{'1'}{'name'} =~ /^pos|start/i |
|
684
|
0 |
7 |
45 |
exists $self->{'extension'} and defined $self->{'extension'} |
|
|
7 |
45 |
0 |
exists $self->{'extension'} and defined $self->{'extension'} and $self->{'extension'} =~ /sgr/i |
|
729
|
5 |
18 |
0 |
$self->{'extension'} and $self->{'extension'} =~ /sgr/i |
|
|
0 |
0 |
23 |
$self->{'bed'} == 0 and $self->{'gff'} == 0 |
|
|
0 |
0 |
23 |
$self->{'bed'} == 0 and $self->{'gff'} == 0 and $self->{'ucsc'} == 0 |
|
|
5 |
0 |
18 |
$self->{'extension'} and not $self->{'extension'} =~ /sgr/i |
|
|
0 |
23 |
0 |
$self->{'bed'} == 0 and $self->{'gff'} == 0 and $self->{'ucsc'} == 0 and ($self->{'extension'} and not $self->{'extension'} =~ /sgr/i) |
|
1000
|
5 |
0 |
7 |
defined $self->chromo_column and defined $self->start_column |
|
|
0 |
0 |
0 |
defined $self->type_column and defined $self->name_column |
|
|
0 |
0 |
0 |
defined $self->feature and defined $self->name_column |
|
1028
|
19 |
0 |
0 |
exists $self->{'db_connection'} and $self->{'db_connection'} |
|
1055
|
86 |
0 |
5 |
defined $_[0] and $_[0] =~ /^(?:0|1|2|2\.[2|5]|3)$/ |
|
1073
|
91 |
0 |
43 |
defined $_[0] and $_[0] =~ /^\d+$/ |
|
1081
|
53 |
0 |
3 |
defined $_[0] and $_[0] =~ /^\d+$/ |
|
1089
|
39 |
0 |
0 |
defined $_[0] and $_[0] =~ /^[\d\.]+$/ |
|
1273
|
21 |
1 |
2 |
$key and $key eq 'name' |
|
1276
|
21 |
0 |
1 |
$key and defined $value |
|
|
21 |
0 |
0 |
$key and not defined $value |
|
1319
|
0 |
0 |
2 |
exists $self->{$source}{'name'} and exists $self->{$target}{'name'} |
|
1457
|
0 |
0 |
13 |
$row and $row <= $self->{'last_row'} |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
448
|
0 |
0 |
0 |
$colnumber == 15 or $colnumber == 12 |
|
729
|
21 |
5 |
26 |
$self->{'bed'} or $self->{'gff'} |
|
|
5 |
3 |
23 |
$self->{'bed'} or $self->{'gff'} or $self->{'ucsc'} |
|
|
3 |
0 |
23 |
$self->{'bed'} or $self->{'gff'} or $self->{'ucsc'} or $self->{'extension'} and $self->{'extension'} =~ /sgr/i |
|
820
|
0 |
0 |
0 |
$_[0] eq '0' or $_[0] eq '1' |
|
870
|
1 |
0 |
0 |
$database ||= $self->open_meta_database |
|
974
|
1 |
0 |
2 |
$self->gff or $self->bed |
|
|
1 |
0 |
2 |
$self->gff or $self->bed or $self->ucsc |
|
|
0 |
0 |
2 |
$self->gff or $self->bed or $self->ucsc or $self->vcf |
|
1000
|
5 |
0 |
0 |
defined $self->id_column or defined $self->type_column and defined $self->name_column |
|
|
0 |
0 |
0 |
defined $self->id_column or defined $self->type_column and defined $self->name_column or defined $self->feature and defined $self->name_column |
|
1057
|
0 |
0 |
5 |
$_[0] eq '2.2' or $_[0] eq '2.5' |