Condition Coverage

blib/lib/Bio/ToolBox/Data/Feature.pm
Criterion Covered Total %
condition 48 319 15.0


and 3 conditions

line !l l&&!r l&&r condition
1101 4 0 1 defined $i and $d
1147 0 0 1 defined $i and $d
1309 0 0 65 defined $v and $v ne '.'
1328 0 0 0 defined $s and defined $e
1359 0 0 0 $tag and $value
1556 0 0 0 $self->feature_type eq 'named' and $args{'subfeature'}
1570 0 0 0 exists $args{'extend'} and $args{'extend'}
1575 0 0 0 defined $seqid and defined $start
0 0 0 defined $seqid and defined $start and defined $stop
1678 7 0 0 $self->feature_type eq 'named' and $args{'subfeature'}
1693 7 0 0 exists $args{'strand'} && defined $args{'strand'}
1703 0 0 0 exists $args{'strand'} && defined $args{'strand'}
1710 7 0 0 exists $args{'extend'} and $args{'extend'}
1725 0 0 7 $params[0] and defined $params[1]
1853 4 0 0 $self->feature_type eq 'named' and $args{'subfeature'}
2003 0 5 0 $args->{'position'} == 5 and $strand >= 0
5 0 0 $args->{'position'} == 3 and $strand >= 0
0 0 5 $args->{'position'} == 5 and $strand < 0
0 0 0 $args->{'position'} == 3 and $strand < 0
2074 0 0 0 $position >= $start and $position <= $stop
2110 0 0 0 $p >= $start and $p <= $end
2128 0 0 0 $p >= $start and $p <= $end
2146 0 0 0 $args{'data'} and ref $args{'data'} eq 'HASH'
2155 0 0 0 $self->feature_type eq 'named' and $args{'subfeature'}
2244 0 0 0 exists $args{'strand'} and defined $args{'strand'}
2274 0 0 0 exists $args{'strand'} and defined $args{'strand'}
2285 0 0 0 defined $type and $type =~ /:/
2305 0 0 0 exists $args{'attributes'} and ref $args{'attributes'} eq 'ARRAY'

or 2 conditions

line l !l condition
1254 0 0 $att->{'Name'} || $att->{'ID'} || $att->{'transcript_name'} || $att->{'gene_name'} || undef
1448 0 0 $info ||= '.'
1484 0 9 shift() || 0
1505 0 0 $self->id || undef
0 0 $self->name || undef
1534 0 0 $args{'db'} || $self->{'data'}->open_meta_database || undef
1551 0 0 $args{'db'} || $args{'database'} || $self->{'data'}->open_meta_database || undef
1555 0 0 $args{'subfeature'} ||= undef
1670 7 0 $args{'ddb'} || $args{'db'} || $self->{'data'}->open_meta_database || undef
1677 0 7 $args{'subfeature'} ||= ''
1728 7 0 $args{'method'} || 'mean'
1729 3 4 $args{'strandedness'} || $args{'stranded'} || 'all'
1761 0 0 $args->{'strandedness'} || $args->{'stranded'} || 'all'
1762 0 0 $args->{'method'} || 'mean'
1787 1 0 $args{'stranded'} || 'all'
1788 1 0 $args{'position'} ||= 5
1789 0 1 $args{'coordinate'} ||= undef
1790 0 1 $args{'avoid'} ||= undef
1791 0 1 $args{'method'} ||= 'mean'
1845 4 0 $args{'stranded'} || 'all'
1846 0 4 $args{'extend'} ||= 0
1847 0 4 $args{'position'} ||= 5
1848 3 1 $args{'method'} ||= 'mean'
1852 0 4 $args{'subfeature'} ||= ''
2119 0 0 $pos2data->{$a} ||= []
2137 0 0 $args{'dataset'} || undef
2138 0 0 $args{'data'} ||= undef
2139 0 0 $args{'callback'} ||= undef
2140 0 0 $args{'subfeature'} ||= ''
2215 0 0 $args{'bed'} ||= 6
2283 0 0 $args{'type'} || $self->type || undef
2289 0 0 $args{'source'} || '.'

or 3 conditions

line l !l&&r !l&&!r condition
1202 0 0 18 $str eq '1' or $str eq '-1'
0 0 18 $str eq '1' or $str eq '-1' or $str eq '0'
1314 0 0 0 $att->{'ID'} || $att->{'Name'} || $att->{'transcript_id'}
1489 0 0 9 $self->feature_type eq 'named' or $force
1505 0 0 0 $self->type || $self->{'data'}->feature
1518 1 0 0 $self->end || $start
1540 0 0 0 $args{'chromo'} || $self->seq_id
1541 0 0 0 $args{'start'} || $self->start
1542 0 0 0 $args{'end'} || $self->end
1543 0 0 0 $args{'type'} || $self->type
1562 0 0 0 $args{'seq_id'} || $args{'chromo'} || $self->seq_id
1563 0 0 0 $args{'start'} || $self->start
1564 0 0 0 $args{'stop'} || $args{'end'} || $self->end
1689 0 7 0 $args{'seq_id'} || $self->seq_id
1690 0 7 0 $args{'start'} || $self->start
1691 0 7 0 $args{'stop'} || $args{'end'} || $self->end
1699 0 0 0 $args{'seq_id'} || $f->seq_id
1700 0 0 0 $args{'start'} || $f->start
1701 0 0 0 $args{'stop'} || $args{'end'} || $f->end
1780 0 1 0 $args{'ddb'} || $args{'db'} || $self->{'data'}->open_meta_database
1787 0 1 0 $args{'strandedness'} ||= $args{'stranded'} || 'all'
1795 0 1 0 $args{'db'} or $self->{'data'}->open_meta_database
1838 0 4 0 $args{'ddb'} || $args{'db'} || $self->{'data'}->open_meta_database
1845 0 4 0 $args{'strandedness'} ||= $args{'stranded'} || 'all'
1849 0 4 0 $args{'db'} or $self->{'data'}->open_meta_database
1861 0 4 0 $self->seqfeature || $self
1862 0 4 0 $args{'chromo'} || $args{'seq_id'} || $feature->seq_id
1863 0 4 0 $args{'start'} || $feature->start
1864 0 4 0 $args{'stop'} || $args{'end'} || $feature->end
2001 0 5 0 $self->seqfeature || $self
2004 0 0 0 $args->{'practical_start'} || $feature->start
2007 0 0 0 $args->{'practical_stop'} || $feature->end
2010 0 5 0 $args->{'practical_stop'} || $feature->end
2013 0 0 0 $args->{'practical_start'} || $feature->start
2017 0 0 0 $args->{'practical_start'} || $feature->start
2049 0 0 0 $args->{'db'} || $self->{'data'}->open_meta_database
2137 0 0 0 $args{'db'} ||= $args{'dataset'} || undef
2172 0 0 0 $args{'start'} || $self->start
0 0 0 $args{'stop'} || $args{'end'} || $self->end
2180 0 0 0 $args{'start'} || $self->start
0 0 0 $args{'stop'} || $args{'end'} || $self->end
2221 0 0 0 $args{'chromo'} || $args{'seq_id'} || $self->seq_id
2222 0 0 0 $args{'start'} || $self->start
2223 0 0 0 $args{'stop'} || $args{'end'} || $self->stop || $start + $self->length - 1 || $start
2225 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
2234 0 0 0 $args{'name'} || $self->name || 'Feature_' . $self->line_number
2265 0 0 0 $args{'chromo'} || $args{'seq_id'} || $self->seq_id
2266 0 0 0 $args{'start'} || $self->start
2267 0 0 0 $args{'stop'} || $args{'end'} || $self->stop || $start + $self->length - 1 || $start
2269 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
2292 0 0 0 $args{'primary_tag'} || defined $type
2301 0 0 0 $args{'name'} || $self->name || 'Feature_' . $self->line_number
2303 0 0 0 $args{'id'} || sprintf('%08d', $self->line_number)