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
1155 4 0 1 defined $i and $d
1217 0 0 2 defined $i and $d
1336 0 0 0 defined $str and not exists $self->{'strand'}
1345 1 0 2 exists $self->{'feature'} and $self->{'feature'}->has_tag("peak")
1361 0 0 5 $s and $e
1451 0 0 66 defined $v and $v ne "."
1470 0 0 2 defined $s and defined $e
1501 0 0 3 $tag and $value
1698 0 0 0 $self->feature_type eq "named" and $args{'subfeature'}
1712 0 0 0 exists $args{'extend'} and $args{'extend'}
1717 0 0 0 defined $seqid and defined $start
0 0 0 defined $seqid and defined $start and defined $stop
1820 7 0 0 $self->feature_type eq "named" and $args{'subfeature'}
1835 7 0 0 exists $args{'strand'} && defined $args{'strand'}
1845 0 0 0 exists $args{'strand'} && defined $args{'strand'}
1852 7 0 0 exists $args{'extend'} and $args{'extend'}
1867 0 0 7 $params[0] and defined $params[1]
1997 4 0 0 $self->feature_type eq "named" and $args{'subfeature'}
2258 0 0 0 $position >= $start and $position <= $stop
2294 0 0 0 $p >= $start and $p <= $end
2312 0 0 0 $p >= $start and $p <= $end
2330 0 0 0 $args{'data'} and ref $args{'data'} eq "HASH"
2339 0 0 0 $self->feature_type eq "named" and $args{'subfeature'}
2435 0 0 0 exists $args{'strand'} and defined $args{'strand'}
2472 0 0 0 exists $args{'strand'} and defined $args{'strand'}
2483 0 0 0 defined $type and $type =~ /:/
2503 0 0 0 exists $args{'attributes'} and ref $args{'attributes'} eq "ARRAY"

or 2 conditions

line l !l condition
1396 0 0 $att->{'Name'} || $att->{'ID'} || $att->{'transcript_name'} || $att->{'gene_name'} || undef
1590 0 0 $info ||= "."
1626 0 4 shift() || 0
1647 0 0 $self->id || undef
0 0 $self->name || undef
1676 0 0 $args{'db'} || $self->{'data'}->open_meta_database || undef
1693 0 0 $args{'db'} || $args{'database'} || $self->{'data'}->open_meta_database || undef
1697 0 0 $args{'subfeature'} ||= undef
1812 7 0 $args{'ddb'} || $args{'db'} || $self->{'data'}->open_meta_database || undef
1819 0 7 $args{'subfeature'} ||= ""
1870 7 0 $args{'method'} || 'mean'
1871 3 4 $args{'strandedness'} || $args{'stranded'} || 'all'
1903 0 0 $args->{'strandedness'} || $args->{'stranded'} || 'all'
1904 0 0 $args->{'method'} || 'mean'
1929 1 0 $args{'stranded'} || 'all'
1930 1 0 $args{'position'} ||= 5
1931 0 1 $args{'coordinate'} ||= undef
1932 0 1 $args{'avoid'} ||= undef
1933 0 1 $args{'method'} ||= "mean"
1989 4 0 $args{'stranded'} || 'all'
1990 0 4 $args{'extend'} ||= 0
1991 0 4 $args{'position'} ||= 5
1992 3 1 $args{'method'} ||= "mean"
1996 0 4 $args{'subfeature'} ||= ""
2303 0 0 $pos2data->{$a} ||= []
2321 0 0 $args{'dataset'} || undef
2322 0 0 $args{'data'} ||= undef
2323 0 0 $args{'callback'} ||= undef
2324 0 0 $args{'subfeature'} ||= ""
2399 0 0 $args{'bed'} ||= 6
2481 0 0 $args{'type'} || $self->type || undef
2487 0 0 $args{'source'} || '.'

or 3 conditions

line l !l&&r !l&&!r condition
1304 0 0 2 $str eq 1 or $str eq -1
0 0 2 $str eq 1 or $str eq -1 or $str eq 0
1456 0 0 0 $att->{'ID'} || $att->{'Name'} || $att->{'transcript_id'}
1631 0 0 4 $self->feature_type eq "named" or $force
1647 0 0 0 $self->type || $self->{'data'}->feature
1660 1 0 0 $self->end || $start
1682 0 0 0 $args{'chromo'} || $self->seq_id
1683 0 0 0 $args{'start'} || $self->start
1684 0 0 0 $args{'end'} || $self->end
1685 0 0 0 $args{'type'} || $self->type
1704 0 0 0 $args{'seq_id'} || $args{'chromo'} || $self->seq_id
1705 0 0 0 $args{'start'} || $self->start
1706 0 0 0 $args{'stop'} || $args{'end'} || $self->end
1831 0 7 0 $args{'seq_id'} || $self->seq_id
1832 0 7 0 $args{'start'} || $self->start
1833 0 7 0 $args{'stop'} || $args{'end'} || $self->end
1841 0 0 0 $args{'seq_id'} || $f->seq_id
1842 0 0 0 $args{'start'} || $f->start
1843 0 0 0 $args{'stop'} || $args{'end'} || $f->end
1922 0 1 0 $args{'ddb'} || $args{'db'} || $self->{'data'}->open_meta_database
1929 0 1 0 $args{'strandedness'} ||= $args{'stranded'} || 'all'
1937 0 1 0 $args{'db'} or $self->{'data'}->open_meta_database
1982 0 4 0 $args{'ddb'} || $args{'db'} || $self->{'data'}->open_meta_database
1989 0 4 0 $args{'strandedness'} ||= $args{'stranded'} || 'all'
1993 0 4 0 $args{'db'} or $self->{'data'}->open_meta_database
2005 0 4 0 $self->seqfeature || $self
2006 0 4 0 $args{'chromo'} || $args{'seq_id'} || $feature->seq_id
2007 0 4 0 $args{'start'} || $feature->start
2008 0 4 0 $args{'stop'} || $args{'end'} || $feature->end
2173 0 1 0 $args->{'practical_start'} || $self->start
2176 0 5 0 $args->{'practical_stop'} || $self->end
2181 0 1 0 $args->{'practical_stop'} || $self->end
2184 0 0 0 $args->{'practical_start'} || $self->start
2233 0 0 0 $args->{'db'} || $self->{'data'}->open_meta_database
2321 0 0 0 $args{'db'} ||= $args{'dataset'} || undef
2356 0 0 0 $args{'start'} || $self->start
0 0 0 $args{'stop'} || $args{'end'} || $self->end
2364 0 0 0 $args{'start'} || $self->start
0 0 0 $args{'stop'} || $args{'end'} || $self->end
2405 0 0 0 $args{'chromo'} || $args{'seq_id'} || $self->seq_id
2406 0 0 0 $args{'start'} || $self->start
2407 0 0 0 $args{'stop'} || $args{'end'} || $self->stop || $start + $self->length - 1 || $start
2409 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
2425 0 0 0 $args{'name'} || $self->name || 'Feature_' . $self->line_number
2456 0 0 0 $args{'chromo'} || $args{'seq_id'} || $self->seq_id
2457 0 0 0 $args{'start'} || $self->start
2458 0 0 0 $args{'stop'} || $args{'end'} || $self->stop || $start + $self->length - 1 || $start
2460 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
2490 0 0 0 $args{'primary_tag'} || defined $type
2499 0 0 0 $args{'name'} || $self->name || 'Feature_' . $self->line_number
2501 0 0 0 $args{'id'} || sprintf('%08d', $self->line_number)