Branch Coverage

blib/lib/Bio/ToolBox/Data/Feature.pm

Criterion	Covered	Total	%
branch	139	490	28.3

line	true	false	branch
1028	0	0	unless defined $column
1034	0	24	if @_
1040	0	65	if @_
1046	0	0	if @_
1047	0	0	if (exists $self->{'data'}{'line_count'}) { }
	0	0	elsif (exists $self->{'data'}{'header_line_count'}) { }
1060	0	196	if @_
1063	118	78	wantarray ? :
1068	0	341	unless defined $column
1071	85	256	if (defined $value)
1076	340	1	CORE::length $v ? :
1081	1	20	if ($_[0])
1084	1	0	if (defined $i) { }
	0	0	elsif (exists $self->{'feature'}) { }
1097	15	6	if exists $self->{'seqid'}
1103	6	0	if (defined $i) { }
	0	0	elsif (exists $self->{'feature'}) { }
	0	0	elsif (defined $j) { }
	0	0	elsif ($self->feature_type eq 'named') { }
1117	0	0	if ($f)
1121	6	0	if defined $c
1127	5	114	if ($_[0])
1130	5	0	$_[0] =~ /^\d+$/ ? :
1131	1	4	if (defined $i and $d) { }
	0	4	elsif (not $d) { }
	4	0	elsif (exists $self->{'feature'}) { }
1132	1	0	if ($self->{'data'}->interbase) { }
1154	27	92	if exists $self->{'start'}
1160	87	5	if (defined $i) { }
	5	0	elsif (exists $self->{'feature'}) { }
	0	0	elsif (defined $j) { }
	0	0	elsif ($self->feature_type eq 'named') { }
1163	6	81	if ($self->{'data'}->interbase)
1178	0	0	if ($f)
1182	92	0	if defined $s
1189	2	36	if ($_[0])
1192	2	0	$_[0] =~ /^\d+$/ ? :
1193	2	0	if (defined $i and $d) { }
	0	0	elsif (not $d) { }
	0	0	elsif (exists $self->{'feature'}) { }
1209	27	11	if exists $self->{'end'}
1215	10	1	if (defined $i) { }
	1	0	elsif (exists $self->{'feature'}) { }
	0	0	elsif (defined $j) { }
	0	0	elsif ($self->feature_type eq 'named') { }
1229	0	0	if ($f)
1233	11	0	if defined $e
1239	1	28	if ($_[0])
1242	0	1	if (defined $i) { }
	0	1	elsif (exists $self->{'feature'}) { }
1255	22	7	if exists $self->{'strand'}
1259	2	5	if (my $i = $self->{'data'}->strand_column) { }
	4	1	elsif (exists $self->{'feature'}) { }
	0	1	elsif ($self->feature_type eq 'named') { }
1269	0	0	if ($f)
1280	0	2	if ($str eq '1' or $str eq '-1' or $str eq '0') { }
	0	2	elsif ($str eq '+') { }
	2	0	elsif ($str eq '-') { }
	0	0	elsif ($str eq '.') { }
	0	0	elsif ($str eq '2') { }
	0	0	elsif ($str eq '*') { }
1308	0	0	unless exists $self->{'seqid'}
1309	0	0	unless exists $self->{'start'}
1311	0	0	unless exists $self->{'end'}
1312	0	0	if (defined $str and not exists $self->{'strand'})
1320	2	1	if ($self->{'data'}->format eq 'narrowPeak') { }
1321	1	1	if (exists $self->{'feature'} and $self->{'feature'}->has_tag('peak')) { }
1337	5	0	if ($s and $e) { }
1348	1	75	if ($_[0])
1351	1	0	if (defined $i) { }
	0	0	elsif (exists $self->{'feature'}) { }
1362	5	70	if (exists $self->{'feature'})
1367	70	0	if (defined $i) { }
	0	0	elsif (my $att = $self->gff_attributes) { }
1378	0	3	if @_
1384	0	0	exists $self->{'feature'} ? :
	3	0	defined $start_i ? :
1386	3	0	if $end
1387	3	0	CORE::length $coord > 2 ? :
1392	1	8	if ($_[0])
1395	0	1	if (defined $i) { }
	0	1	elsif (exists $self->{'feature'}) { }
1407	0	9	if (defined $i)
1411	4	5	if (exists $self->{'feature'})
1415	5	0	if ($self->{'data'}->feature)
1424	0	66	if @_
1426	66	0	if defined $i
1427	66	0	if (defined $v and $v ne ".")
1430	0	0	if exists $self->{'feature'}
1431	0	0	if (my $att = $self->gff_attributes)
1439	0	2	if @_
1440	0	2	if ($self->{'data'}->vcf)
1446	2	0	if (defined $s and defined $e) { }
	0	0	elsif (defined $s) { }
1460	0	0	defined $c ? :
1465	0	0	if $self->{'data'}->gff
1466	0	0	if $self->{'data'}->vcf
1472	0	1	unless $self->{'data'}->gff
1473	0	1	if exists $self->{'attributes'}
1477	0	3	unless $tag and $value
1488	0	0	unless $self->{'data'}->vcf
1489	0	0	if exists $self->{'attributes'}
1494	0	0	if ($self->{'data'}->name(7) eq "INFO")
1495	0	0	defined $_->[1] ? :
1504	0	0	if ($self->{'data'}->number_columns > 8)
1510	0	0	defined $sampleVals[$_] ? :
1521	0	0	if $self->{'data'}->gff
1522	0	0	if $self->{'data'}->vcf
1528	0	1	unless $self->{'data'}->gff
1529	0	1	unless exists $self->{'attributes'}
1531	1	0	if (exists $self->{'attributes'}{'ID'})
1535	1	0	if (exists $self->{'attributes'}{'Name'})
1541	1	2	if $key eq "ID"
1542	1	1	if $key eq "Name"
1554	0	0	unless $self->{'data'}->vcf
1555	0	0	unless exists $self->{'attributes'}
1561	0	0	defined $self->{'attributes'}{'INFO'}{$_} ? :
1571	0	0	if exists $self->{'attributes'}{'9'}{'GT'}
1573	0	0	if $key eq "GT"
1576	0	0	if (@order) { }
1585	0	0	if (@order) { }
1603	0	4	if @_
1604	0	4	if exists $self->{'feature'}
1607	4	0	unless $self->feature_type eq "named" or $force
1611	0	0	if ($f)
1617	0	0	unless $self->{'data'}->database
1624	0	0	unless $f
1631	0	1	if @_
1632	0	1	unless $self->{'data'}->database
1633	1	0	if ($self->feature_type eq 'coordinate') { }
	0	0	elsif ($self->feature_type eq 'named') { }
1638	1	0	$db ? :
1642	0	0	$f ? :
1653	0	0	unless defined $db
1654	0	0	unless $db->can("features")
1674	0	0	if ($self->feature_type eq "named" and $args{'subfeature'})
1684	0	0	if (exists $args{'strand'})
1686	0	0	$args{'strand'} =~ /\-|r/i ? :
1688	0	0	if (exists $args{'extend'} and $args{'extend'})
1690	0	0	if $start <= 0
1693	0	0	unless defined $seqid and defined $start and defined $stop
1697	0	0	if ($strand == -1)
1709	0	0	unless (@$subfeatures)
1720	0	0	unless $Bio::ToolBox::Data::Feature::a->[1] <=> $Bio::ToolBox::Data::Feature::b->[1]
1732	0	0	if ($self->strand == -1)
1744	0	0	unless ($GENETOOL_LOADED)
1747	0	0	if ($@) { }
1757	0	0	unless $feature
1761	0	0	if ($subf eq 'exon') { }
	0	0	elsif ($subf eq 'cds') { }
	0	0	elsif ($subf eq '5p_utr') { }
	0	0	elsif ($subf eq '3p_utr') { }
	0	0	elsif ($subf eq 'intron') { }
1790	0	7	unless ($args{'dataset'})
1796	0	0	if ($self->feature_type eq "named" and $args{'subfeature'})
1805	7	0	if ($self->feature_type eq 'coordinate') { }
	0	0	elsif ($self->feature_type eq 'named') { }
1811	0	7	exists $args{'strand'} && defined $args{'strand'} ? :
1816	0	0	unless $f
1821	0	0	exists $args{'strand'} && defined $args{'strand'} ? :
1828	0	0	if (exists $args{'extend'} and $args{'extend'})
1834	0	7	if $params[1] <= 0
1835	0	7	if ($params[2] < $params[1])
1837	0	0	if $params[2] <= 0
1843	0	7	unless $params[0] and defined $params[1]
1863	0	0	unless (@$subfeatures)
1867	0	0	if exists $args->{'exon'}
1878	0	0	defined $args->{'strand'} ? :
1886	0	0	if defined $exon_scores
1900	0	1	unless ($args{'dataset'})
1910	0	1	unless ($args{'extend'})
1913	0	1	unless $args{'db'} or $self->{'data'}->open_meta_database
1916	1	0	unless defined $args{'coordinate'}
1922	0	1	if $params[1] < 1
1924	0	1	defined $args{'strand'} ? :
1935	0	1	if ($args{'avoid'})
1940	0	1	if ($args{'absolute'}) { }
1942	0	0	wantarray ? :
1958	0	4	unless ($args{'dataset'})
1967	0	4	unless $args{'db'} or $self->{'data'}->open_meta_database
1971	0	0	if ($self->feature_type eq "named" and $args{'subfeature'})
1983	0	4	defined $args{'strand'} ? :
1984	0	4	if ($args{'extend'})
1987	0	0	if $params[1] < 1
1999	0	4	if ($args{'avoid'})
2004	0	4	if ($args{'absolute'}) { }
2006	0	0	wantarray ? :
2010	4	0	unless defined $args{'coordinate'}
2021	0	0	unless (@$subfeatures)
2025	0	0	if exists $args->{'exon'}
2043	0	0	defined $args->{'strand'} ? :
2070	0	0	if ($args->{'extend'})
2102	0	0	if ($args->{'absolute'}) { }
2104	0	0	wantarray ? :
2119	0	9	defined $args->{'strand'} ? :
2120	6	3	if ($args->{'position'} == 5) { }
	1	2	elsif ($args->{'position'} == 3) { }
	2	0	elsif ($args->{'position'} == 4) { }
	0	0	elsif ($args->{'position'} == 9) { }
2121	1	5	if ($strand >= 0) { }
2129	1	0	if ($strand >= 0) { }
2139	1	1	if (exists $args->{'practical_start'}) { }
2161	0	0	if (ref $args->{'avoid'} eq 'ARRAY') { }
	0	0	elsif ($args->{'avoid'} eq '1') { }
	0	0	elsif ($args->{'avoid'} =~ /w+/i) { }
2166	0	0	if (defined $args->{'type'}) { }
2190	0	0	if (@overlap_features)
2199	0	0	if $feat->primary_id eq $primary
2206	0	0	if ($position >= $start and $position <= $stop)
2221	0	5	if ($strand >= 0) { }
	5	0	elsif ($strand < 0) { }
2231	5	0	wantarray ? :
2239	0	0	if ($method eq 'ncount') { }
2242	0	0	unless $p >= $start and $p <= $end
2244	0	0	if (exists $namecheck->{$n}) { }
2260	0	0	unless $p >= $start and $p <= $end
2275	0	0	unless ($args{'db'})
2278	0	0	unless ($args{'data'} and ref $args{'data'} eq "HASH")
2281	0	0	unless ($args{'callback'})
2287	0	0	if ($self->feature_type eq 'named' and $args{'subfeature'}) { }
2292	0	0	if (@$subfeatures) { }
2319	0	0	unless defined $tid
2348	0	0	unless $args{'bed'} =~ /^\d+$/
2349	0	0	unless $args{'bed'} >= 3
2357	0	0	if ($chr eq "." or not CORE::length $chr or $start eq "." or not CORE::length $start)
2361	0	0	if ($start > $stop)
2372	0	0	if ($args{'bed'} >= 4)
2376	0	0	if ($args{'bed'} >= 5)
2377	0	0	exists $args{'score'} ? :
2378	0	0	unless defined $score
2381	0	0	if ($args{'bed'} >= 6)
2383	0	0	if (exists $args{'strand'} and defined $args{'strand'}) { }
2389	0	0	$s == -1 ? :
2408	0	0	if ($chr eq "." or not CORE::length $chr or $start eq "." or not CORE::length $start)
2412	0	0	if ($start > $stop)
2420	0	0	if (exists $args{'strand'} and defined $args{'strand'}) { }
2426	0	0	$strand == 1 ? :
	0	0	$strand == -1 ? :
2431	0	0	if (defined $type and $type =~ /:/)
2434	0	0	unless ($source)
2437	0	0	unless ($primary_tag)
2438	0	0	$args{'primary_tag'} || defined $type ? :
2442	0	0	exists $args{'score'} ? :
2443	0	0	unless defined $score
2451	0	0	if (exists $args{'attributes'} and ref $args{'attributes'} eq "ARRAY")