Condition Coverage

blib/lib/Bio/ToolBox/Data.pm
Criterion Covered Total %
condition 59 168 35.1


and 3 conditions

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]

or 2 conditions

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

or 3 conditions

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'}