Condition Coverage

blib/lib/Bio/ToolBox/Data/Feature.pm
Criterion Covered Total %
condition 51 310 16.4


and 3 conditions

line !l l&&!r l&&r condition
1131 4 0 1 defined $i and $d
1193 0 0 2 defined $i and $d
1312 0 0 0 defined $str and not exists $self->{'strand'}
1321 1 0 1 exists $self->{'feature'} and $self->{'feature'}->has_tag("peak")
1337 0 0 5 $s and $e
1427 0 0 66 defined $v and $v ne "."
1446 0 0 2 defined $s and defined $e
1477 0 0 3 $tag and $value
1674 0 0 0 $self->feature_type eq "named" and $args{'subfeature'}
1688 0 0 0 exists $args{'extend'} and $args{'extend'}
1693 0 0 0 defined $seqid and defined $start
0 0 0 defined $seqid and defined $start and defined $stop
1796 7 0 0 $self->feature_type eq "named" and $args{'subfeature'}
1811 7 0 0 exists $args{'strand'} && defined $args{'strand'}
1821 0 0 0 exists $args{'strand'} && defined $args{'strand'}
1828 7 0 0 exists $args{'extend'} and $args{'extend'}
1843 0 0 7 $params[0] and defined $params[1]
1971 4 0 0 $self->feature_type eq "named" and $args{'subfeature'}
2206 0 0 0 $position >= $start and $position <= $stop
2242 0 0 0 $p >= $start and $p <= $end
2260 0 0 0 $p >= $start and $p <= $end
2278 0 0 0 $args{'data'} and ref $args{'data'} eq "HASH"
2287 0 0 0 $self->feature_type eq "named" and $args{'subfeature'}
2383 0 0 0 exists $args{'strand'} and defined $args{'strand'}
2420 0 0 0 exists $args{'strand'} and defined $args{'strand'}
2431 0 0 0 defined $type and $type =~ /:/
2451 0 0 0 exists $args{'attributes'} and ref $args{'attributes'} eq "ARRAY"

or 2 conditions

line l !l condition
1372 0 0 $att->{'Name'} || $att->{'ID'} || $att->{'transcript_name'} || $att->{'gene_name'} || undef
1566 0 0 $info ||= "."
1602 0 4 shift() || 0
1623 0 0 $self->id || undef
0 0 $self->name || undef
1652 0 0 $args{'db'} || $self->{'data'}->open_meta_database || undef
1669 0 0 $args{'db'} || $args{'database'} || $self->{'data'}->open_meta_database || undef
1673 0 0 $args{'subfeature'} ||= undef
1788 7 0 $args{'ddb'} || $args{'db'} || $self->{'data'}->open_meta_database || undef
1795 0 7 $args{'subfeature'} ||= ""
1846 7 0 $args{'method'} || 'mean'
1847 3 4 $args{'strandedness'} || $args{'stranded'} || 'all'
1879 0 0 $args->{'strandedness'} || $args->{'stranded'} || 'all'
1880 0 0 $args->{'method'} || 'mean'
1905 1 0 $args{'stranded'} || 'all'
1906 1 0 $args{'position'} ||= 5
1907 0 1 $args{'coordinate'} ||= undef
1908 0 1 $args{'avoid'} ||= undef
1909 0 1 $args{'method'} ||= "mean"
1963 4 0 $args{'stranded'} || 'all'
1964 0 4 $args{'extend'} ||= 0
1965 0 4 $args{'position'} ||= 5
1966 3 1 $args{'method'} ||= "mean"
1970 0 4 $args{'subfeature'} ||= ""
2251 0 0 $pos2data->{$a} ||= []
2269 0 0 $args{'dataset'} || undef
2270 0 0 $args{'data'} ||= undef
2271 0 0 $args{'callback'} ||= undef
2272 0 0 $args{'subfeature'} ||= ""
2347 0 0 $args{'bed'} ||= 6
2429 0 0 $args{'type'} || $self->type || undef
2435 0 0 $args{'source'} || '.'

or 3 conditions

line l !l&&r !l&&!r condition
1280 0 0 2 $str eq 1 or $str eq -1
0 0 2 $str eq 1 or $str eq -1 or $str eq 0
1432 0 0 0 $att->{'ID'} || $att->{'Name'} || $att->{'transcript_id'}
1607 0 0 4 $self->feature_type eq "named" or $force
1623 0 0 0 $self->type || $self->{'data'}->feature
1636 1 0 0 $self->end || $start
1658 0 0 0 $args{'chromo'} || $self->seq_id
1659 0 0 0 $args{'start'} || $self->start
1660 0 0 0 $args{'end'} || $self->end
1661 0 0 0 $args{'type'} || $self->type
1680 0 0 0 $args{'seq_id'} || $args{'chromo'} || $self->seq_id
1681 0 0 0 $args{'start'} || $self->start
1682 0 0 0 $args{'stop'} || $args{'end'} || $self->end
1807 0 7 0 $args{'seq_id'} || $self->seq_id
1808 0 7 0 $args{'start'} || $self->start
1809 0 7 0 $args{'stop'} || $args{'end'} || $self->end
1817 0 0 0 $args{'seq_id'} || $f->seq_id
1818 0 0 0 $args{'start'} || $f->start
1819 0 0 0 $args{'stop'} || $args{'end'} || $f->end
1898 0 1 0 $args{'ddb'} || $args{'db'} || $self->{'data'}->open_meta_database
1905 0 1 0 $args{'strandedness'} ||= $args{'stranded'} || 'all'
1913 0 1 0 $args{'db'} or $self->{'data'}->open_meta_database
1956 0 4 0 $args{'ddb'} || $args{'db'} || $self->{'data'}->open_meta_database
1963 0 4 0 $args{'strandedness'} ||= $args{'stranded'} || 'all'
1967 0 4 0 $args{'db'} or $self->{'data'}->open_meta_database
1979 0 4 0 $self->seqfeature || $self
1980 0 4 0 $args{'chromo'} || $args{'seq_id'} || $feature->seq_id
1981 0 4 0 $args{'start'} || $feature->start
1982 0 4 0 $args{'stop'} || $args{'end'} || $feature->end
2122 0 1 0 $args->{'practical_start'} || $self->start
2125 0 5 0 $args->{'practical_stop'} || $self->end
2130 0 1 0 $args->{'practical_stop'} || $self->end
2133 0 0 0 $args->{'practical_start'} || $self->start
2181 0 0 0 $args->{'db'} || $self->{'data'}->open_meta_database
2269 0 0 0 $args{'db'} ||= $args{'dataset'} || undef
2304 0 0 0 $args{'start'} || $self->start
0 0 0 $args{'stop'} || $args{'end'} || $self->end
2312 0 0 0 $args{'start'} || $self->start
0 0 0 $args{'stop'} || $args{'end'} || $self->end
2353 0 0 0 $args{'chromo'} || $args{'seq_id'} || $self->seq_id
2354 0 0 0 $args{'start'} || $self->start
2355 0 0 0 $args{'stop'} || $args{'end'} || $self->stop || $start + $self->length - 1 || $start
2357 0 0 0 $chr eq "." or not CORE::length $chr
0 0 0 $chr eq "." or not CORE::length $chr or $start eq "."
0 0 0 $chr eq "." or not CORE::length $chr or $start eq "." or not CORE::length $start
2373 0 0 0 $args{'name'} || $self->name || 'Feature_' . $self->line_number
2404 0 0 0 $args{'chromo'} || $args{'seq_id'} || $self->seq_id
2405 0 0 0 $args{'start'} || $self->start
2406 0 0 0 $args{'stop'} || $args{'end'} || $self->stop || $start + $self->length - 1 || $start
2408 0 0 0 $chr eq "." or not CORE::length $chr
0 0 0 $chr eq "." or not CORE::length $chr or $start eq "."
0 0 0 $chr eq "." or not CORE::length $chr or $start eq "." or not CORE::length $start
2438 0 0 0 $args{'primary_tag'} || defined $type
2447 0 0 0 $args{'name'} || $self->name || 'Feature_' . $self->line_number
2449 0 0 0 $args{'id'} || sprintf('%08d', $self->line_number)