| line |
!l |
l&&!r |
l&&r |
condition |
|
1124
|
32 |
5 |
7 |
$args{'file'} and $args{'parse'} |
|
|
32 |
0 |
0 |
exists $args{'db'} and $args{'features'} |
|
1130
|
0 |
0 |
5 |
$self->database =~ /^Parsed:(.+)$/ and $self->feature_type eq 'named' |
|
1168
|
31 |
0 |
0 |
exists $args{'gff'} and $args{'gff'} |
|
|
31 |
0 |
0 |
exists $args{'bed'} and $args{'bed'} |
|
|
31 |
0 |
0 |
exists $args{'ucsc'} and $args{'ucsc'} |
|
1187
|
0 |
0 |
0 |
$args{'bed'} =~ /^\d{1,2}$/ and $args{'bed'} >= 3 |
|
1246
|
12 |
0 |
0 |
exists $args->{'simplify'} && defined $args->{'simplify'} |
|
1303
|
12 |
1 |
0 |
lc $feature eq 'mrna' and not $parser->typelist =~ /mrna/i |
|
|
13 |
0 |
0 |
lc $feature eq 'mrna' and not $parser->typelist =~ /mrna/i and not $self->last_row |
|
1355
|
7 |
0 |
0 |
$mrna_check and is_coding($f) |
|
1477
|
0 |
40 |
191 |
$_[0] and ref $_[0] eq 'ARRAY' |
|
|
0 |
0 |
40 |
$_[0] and ref $_[0] eq 'Bio::ToolBox::Data::Feature' |
|
|
0 |
0 |
0 |
$_[0] and $_[0] =~ /\t/ |
|
1509
|
1 |
0 |
4 |
exists $self->{'SeqFeatureObjects'} and defined $self->{'SeqFeatureObjects'}[$row_number] |
|
1540
|
0 |
0 |
508 |
defined $row and defined $column |
|
1570
|
0 |
0 |
178 |
defined $row_i and ref $seqfeature |
|
1733
|
0 |
0 |
1 |
defined $v and not $v =~ m[^(?:\.|n/?a|nan|\-?inf)$]i |
|
1944
|
0 |
0 |
1 |
$part and $total_parts |
|
2111
|
0 |
0 |
0 |
$args{'dataset'} and ref $args{'dataset'} eq 'ARRAY' |
|
|
0 |
0 |
0 |
$args{'dataset'} and ref $args{'dataset'} eq 'SCALAR' |
|
2118
|
0 |
0 |
0 |
$args{'startcolumn'} and ref $args{'startcolumn'} eq 'ARRAY' |
|
|
0 |
0 |
0 |
$args{'startcolumn'} and ref $args{'startcolumn'} eq 'SCALAR' |
|
2126
|
0 |
0 |
0 |
$args{'endcolumn'} and ref $args{'endcolumn'} eq 'ARRAY' |
|
|
0 |
0 |
0 |
$args{'endcolumn'} and ref $args{'endcolumn'} eq 'SCALAR' |
|
2243
|
0 |
0 |
0 |
$do_percentile and substr($self->name($column), -2) eq 'bp' |
|
2324
|
88 |
60 |
0 |
exists $self->{'data'}{'SeqFeatureObjects'} and defined $self->{'data'}{'SeqFeatureObjects'}[$i] |
| line |
l |
!l |
condition |
|
1107
|
2 |
43 |
$args{'feature'} || 'gene' |
|
1108
|
0 |
44 |
$args{'Stream'} || 0 |
|
1109
|
1 |
32 |
$args{'in'} || undef |
|
1110
|
7 |
38 |
$args{'parse'} ||= 0 |
|
1111
|
0 |
45 |
$args{'noheader'} ||= 0 |
|
1126
|
2 |
5 |
$args{'subfeature'} ||= '' |
|
1167
|
0 |
31 |
$args{'datasets'} || undef |
|
1242
|
12 |
0 |
$args->{'file'} || '' |
|
1243
|
7 |
5 |
$args->{'feature'} || '' |
|
1244
|
2 |
10 |
$args->{'subfeature'} || '' |
|
1346
|
0 |
2 |
$args->{'chrskip'} || undef |
|
1574
|
165 |
13 |
$self->{'SeqFeatureObjects'} ||= [] |
|
1620
|
0 |
0 |
$self->value($i, $name_i) || undef |
|
|
0 |
0 |
$self->value($i, $type_i) || undef |
|
|
0 |
0 |
$self->value($i, $id_i) || undef |
|
1636
|
0 |
0 |
shift() || 'exon' |
|
1693
|
0 |
0 |
$self->value($i, $name_i) || undef |
|
|
0 |
0 |
$self->value($i, $type_i) || undef |
|
|
0 |
0 |
$self->value($i, $id_i) || undef |
|
1717
|
1 |
0 |
shift() || 'i' |
|
2109
|
0 |
0 |
$args{'filename'} || undef |
|
2162
|
0 |
0 |
$self->metadata($i, 'dataset') || undef |
|
2165
|
0 |
0 |
$possibles{$d} ||= [] |
|
2256
|
0 |
0 |
$self->metadata($column, 'log2') || 0 |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
1107
|
0 |
45 |
0 |
$args{'features'} ||= $args{'feature'} || 'gene' |
|
1108
|
1 |
0 |
44 |
$args{'stream'} ||= $args{'Stream'} || 0 |
|
1109
|
12 |
1 |
32 |
$args{'file'} ||= $args{'in'} || undef |
|
1167
|
1 |
0 |
31 |
$args{'columns'} ||= $args{'datasets'} || undef |
|
1355
|
113 |
0 |
7 |
$f->type =~ /$feature/i or $mrna_check and is_coding($f) |
|
1453
|
0 |
0 |
28 |
$self->gff or $self->bed |
|
|
0 |
0 |
28 |
$self->gff or $self->bed or $self->ucsc |
|
|
0 |
0 |
28 |
$self->gff or $self->bed or $self->ucsc or $self->vcf |
|
1681
|
0 |
0 |
0 |
$length || $feature->length |
|
1700
|
0 |
0 |
0 |
$length || $feature->length |
|
1835
|
0 |
0 |
1 |
$direction eq 'i' or $direction eq 'I' |
|
|
1 |
0 |
0 |
$direction eq 'd' or $direction eq 'D' |
|
2125
|
0 |
0 |
0 |
$args{'endcolumn'} ||= $args{'stopcolumn'} |