| line |
!l |
l&&!r |
l&&r |
condition |
|
78
|
0 |
0 |
52 |
defined $self->{'data_table'} and ref $self->{'data_table'} eq "ARRAY" |
|
186
|
0 |
6 |
0 |
exists $self->{'0'} and not $self->{'0'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i |
|
195
|
0 |
6 |
0 |
exists $self->{'3'} and not $self->{'3'}{'name'} =~ /start|pos|position/i |
|
203
|
0 |
6 |
0 |
exists $self->{'4'} and not $self->{'4'}{'name'} =~ /stop|end|pos|position/i |
|
211
|
0 |
6 |
0 |
exists $self->{'6'} and not $self->{'6'}{'name'} =~ /strand/i |
|
263
|
0 |
21 |
0 |
exists $self->{'0'} and not $self->{'0'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i |
|
271
|
0 |
21 |
0 |
exists $self->{'1'} and not $self->{'1'}{'name'} =~ /start|pos|position/i |
|
278
|
0 |
21 |
0 |
exists $self->{'2'} and not $self->{'2'}{'name'} =~ /stop|end|pos|position/i |
|
285
|
6 |
15 |
0 |
exists $self->{'5'} and not $self->{'5'}{'name'} =~ /strand/i |
|
292
|
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 |
|
300
|
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 |
|
308
|
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 |
|
316
|
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 |
|
324
|
14 |
7 |
0 |
exists $self->{'10'} and not $self->{'10'}{'name'} =~ /size|length|block|exon/i |
|
331
|
14 |
7 |
0 |
exists $self->{'11'} and not $self->{'11'}{'name'} =~ /start|block|exon/i |
|
358
|
3 |
14 |
4 |
$self->{'format'} and $self->{'format'} =~ /narrow|broad/i |
|
376
|
17 |
0 |
4 |
$self->{'number_columns'} == 15 and $self->{'format'} =~ /gapped/i |
|
396
|
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 |
|
403
|
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 |
|
410
|
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 |
|
649
|
0 |
0 |
0 |
exists $self->{'1'} and not $self->{'1'}{'name'} =~ /^pos|start/i |
|
685
|
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 |
|
730
|
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) |
|
1001
|
5 |
0 |
8 |
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 |
|
1029
|
20 |
0 |
0 |
exists $self->{'db_connection'} and $self->{'db_connection'} |
|
1056
|
97 |
0 |
5 |
defined $_[0] and $_[0] =~ /^(?:0|1|2|2\.[2|5]|3)$/ |
|
1064
|
94 |
0 |
43 |
defined $_[0] and $_[0] =~ /^\d+$/ |
|
1072
|
59 |
0 |
3 |
defined $_[0] and $_[0] =~ /^\d+$/ |
|
1080
|
44 |
0 |
0 |
defined $_[0] and $_[0] =~ /^[\d\.]+$/ |
|
1269
|
21 |
3 |
2 |
$key and $key eq "name" |
|
1272
|
21 |
0 |
3 |
$key and defined $value |
|
|
21 |
0 |
0 |
$key and not defined $value |
|
1315
|
0 |
0 |
2 |
exists $self->{$source}{'name'} and exists $self->{$target}{'name'} |
|
1372
|
0 |
0 |
12 |
defined $id and defined $self->{'data_table'}[1] |
|
1378
|
8 |
0 |
4 |
not defined $coord and defined $name |
|
|
8 |
0 |
4 |
not defined $coord and defined $name and defined defined $self->{'data_table'}[1] |
|
1390
|
6 |
12 |
6 |
$self->{'zerostart'} == 0 and defined $start |
|
|
18 |
5 |
1 |
$self->{'zerostart'} == 0 and defined $start and substr($self->name($start), -1) eq 0 |
|
1419
|
0 |
0 |
2 |
$_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'} |
|
1433
|
0 |
0 |
2 |
$_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'} |
|
1447
|
0 |
0 |
2 |
$_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'} |
|
1462
|
0 |
0 |
0 |
$_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'} |
|
1476
|
0 |
0 |
2 |
$_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'} |
|
1490
|
0 |
0 |
0 |
$_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'} |
|
1504
|
0 |
0 |
2 |
$_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'} |
|
1518
|
0 |
0 |
0 |
$_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'} |
|
1532
|
0 |
0 |
0 |
$_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'} |
|
1548
|
0 |
0 |
0 |
$_[0] eq 1 and $n =~ /^start$/i |
|
|
0 |
0 |
0 |
$_[0] eq 0 and $n =~ /^start0$/i |
|
1574
|
0 |
0 |
13 |
$row and $row <= $self->{'last_row'} |