Branch Coverage

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

Criterion	Covered	Total	%
branch	144	494	29.1

line	true	false	branch
1052	0	0	unless defined $column
1058	0	24	if @_
1064	0	65	if @_
1070	0	0	if @_
1071	0	0	if (exists $self->{'data'}{'line_count'}) { }
	0	0	elsif (exists $self->{'data'}{'header_line_count'}) { }
1084	0	196	if @_
1087	118	78	wantarray ? :
1092	0	341	unless defined $column
1095	85	256	if (defined $value)
1100	340	1	CORE::length $v ? :
1105	1	20	if ($_[0])
1108	1	0	if (defined $i) { }
	0	0	elsif (exists $self->{'feature'}) { }
1121	15	6	if exists $self->{'seqid'}
1127	6	0	if (defined $i) { }
	0	0	elsif (exists $self->{'feature'}) { }
	0	0	elsif (defined $j) { }
	0	0	elsif ($self->feature_type eq 'named') { }
1141	0	0	if ($f)
1145	6	0	if defined $c
1151	5	114	if ($_[0])
1154	5	0	$_[0] =~ /^\d+$/ ? :
1155	1	4	if (defined $i and $d) { }
	0	4	elsif (not $d) { }
	4	0	elsif (exists $self->{'feature'}) { }
1156	1	0	if ($self->{'data'}->interbase) { }
1178	27	92	if exists $self->{'start'}
1184	87	5	if (defined $i) { }
	5	0	elsif (exists $self->{'feature'}) { }
	0	0	elsif (defined $j) { }
	0	0	elsif ($self->feature_type eq 'named') { }
1187	6	81	if ($self->{'data'}->interbase)
1202	0	0	if ($f)
1206	92	0	if defined $s
1213	2	36	if ($_[0])
1216	2	0	$_[0] =~ /^\d+$/ ? :
1217	2	0	if (defined $i and $d) { }
	0	0	elsif (not $d) { }
	0	0	elsif (exists $self->{'feature'}) { }
1233	27	11	if exists $self->{'end'}
1239	10	1	if (defined $i) { }
	1	0	elsif (exists $self->{'feature'}) { }
	0	0	elsif (defined $j) { }
	0	0	elsif ($self->feature_type eq 'named') { }
1253	0	0	if ($f)
1257	11	0	if defined $e
1263	1	29	if ($_[0])
1266	0	1	if (defined $i) { }
	0	1	elsif (exists $self->{'feature'}) { }
1279	22	8	if exists $self->{'strand'}
1283	2	6	if (my $i = $self->{'data'}->strand_column) { }
	5	1	elsif (exists $self->{'feature'}) { }
	0	1	elsif ($self->feature_type eq 'named') { }
1293	0	0	if ($f)
1304	0	2	if ($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 '*') { }
1332	0	0	unless exists $self->{'seqid'}
1333	0	0	unless exists $self->{'start'}
1335	0	0	unless exists $self->{'end'}
1336	0	0	if (defined $str and not exists $self->{'strand'})
1344	3	1	if ($self->{'data'}->format eq 'narrowPeak') { }
1345	2	1	if (exists $self->{'feature'} and $self->{'feature'}->has_tag('peak')) { }
1361	5	0	if ($s and $e) { }
1372	1	75	if ($_[0])
1375	1	0	if (defined $i) { }
	0	0	elsif (exists $self->{'feature'}) { }
1386	5	70	if (exists $self->{'feature'})
1391	70	0	if (defined $i) { }
	0	0	elsif (my $att = $self->gff_attributes) { }
1402	0	3	if @_
1408	0	0	exists $self->{'feature'} ? :
	3	0	defined $start_i ? :
1410	3	0	if $end
1411	3	0	CORE::length $coord > 2 ? :
1416	1	8	if ($_[0])
1419	0	1	if (defined $i) { }
	0	1	elsif (exists $self->{'feature'}) { }
1431	0	9	if (defined $i)
1435	4	5	if (exists $self->{'feature'})
1439	5	0	if ($self->{'data'}->feature)
1448	0	66	if @_
1450	66	0	if defined $i
1451	66	0	if (defined $v and $v ne ".")
1454	0	0	if exists $self->{'feature'}
1455	0	0	if (my $att = $self->gff_attributes)
1463	0	2	if @_
1464	0	2	if ($self->{'data'}->vcf)
1470	2	0	if (defined $s and defined $e) { }
	0	0	elsif (defined $s) { }
1484	0	0	defined $c ? :
1489	0	0	if $self->{'data'}->gff
1490	0	0	if $self->{'data'}->vcf
1496	0	1	unless $self->{'data'}->gff
1497	0	1	if exists $self->{'attributes'}
1501	0	3	unless $tag and $value
1512	0	0	unless $self->{'data'}->vcf
1513	0	0	if exists $self->{'attributes'}
1518	0	0	if ($self->{'data'}->name(7) eq "INFO")
1519	0	0	defined $_->[1] ? :
1528	0	0	if ($self->{'data'}->number_columns > 8)
1534	0	0	defined $sampleVals[$_] ? :
1545	0	0	if $self->{'data'}->gff
1546	0	0	if $self->{'data'}->vcf
1552	0	1	unless $self->{'data'}->gff
1553	0	1	unless exists $self->{'attributes'}
1555	1	0	if (exists $self->{'attributes'}{'ID'})
1559	1	0	if (exists $self->{'attributes'}{'Name'})
1565	1	2	if $key eq "ID"
1566	1	1	if $key eq "Name"
1578	0	0	unless $self->{'data'}->vcf
1579	0	0	unless exists $self->{'attributes'}
1585	0	0	defined $self->{'attributes'}{'INFO'}{$_} ? :
1595	0	0	if exists $self->{'attributes'}{'9'}{'GT'}
1597	0	0	if $key eq "GT"
1600	0	0	if (@order) { }
1609	0	0	if (@order) { }
1627	0	4	if @_
1628	0	4	if exists $self->{'feature'}
1631	4	0	unless $self->feature_type eq "named" or $force
1635	0	0	if ($f)
1641	0	0	unless $self->{'data'}->database
1648	0	0	unless $f
1655	0	1	if @_
1656	0	1	unless $self->{'data'}->database
1657	1	0	if ($self->feature_type eq 'coordinate') { }
	0	0	elsif ($self->feature_type eq 'named') { }
1662	1	0	$db ? :
1666	0	0	$f ? :
1677	0	0	unless defined $db
1678	0	0	unless $db->can("features")
1698	0	0	if ($self->feature_type eq "named" and $args{'subfeature'})
1708	0	0	if (exists $args{'strand'})
1710	0	0	$args{'strand'} =~ /\-|r/i ? :
1712	0	0	if (exists $args{'extend'} and $args{'extend'})
1714	0	0	if $start <= 0
1717	0	0	unless defined $seqid and defined $start and defined $stop
1721	0	0	if ($strand == -1)
1733	0	0	unless (@$subfeatures)
1744	0	0	unless $Bio::ToolBox::Data::Feature::a->[1] <=> $Bio::ToolBox::Data::Feature::b->[1]
1756	0	0	if ($self->strand == -1)
1768	0	0	unless ($GENETOOL_LOADED)
1771	0	0	if ($@) { }
1781	0	0	unless $feature
1785	0	0	if ($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') { }
1814	0	7	unless ($args{'dataset'})
1820	0	0	if ($self->feature_type eq "named" and $args{'subfeature'})
1829	7	0	if ($self->feature_type eq 'coordinate') { }
	0	0	elsif ($self->feature_type eq 'named') { }
1835	0	7	exists $args{'strand'} && defined $args{'strand'} ? :
1840	0	0	unless $f
1845	0	0	exists $args{'strand'} && defined $args{'strand'} ? :
1852	0	0	if (exists $args{'extend'} and $args{'extend'})
1858	0	7	if $params[1] <= 0
1859	0	7	if ($params[2] < $params[1])
1861	0	0	if $params[2] <= 0
1867	0	7	unless $params[0] and defined $params[1]
1887	0	0	unless (@$subfeatures)
1891	0	0	if exists $args->{'exon'}
1902	0	0	defined $args->{'strand'} ? :
1910	0	0	if defined $exon_scores
1924	0	1	unless ($args{'dataset'})
1934	0	1	unless ($args{'extend'})
1937	0	1	unless $args{'db'} or $self->{'data'}->open_meta_database
1940	1	0	unless (defined $args{'coordinate'})
1948	0	1	if $params[1] < 1
1950	0	1	defined $args{'strand'} ? :
1961	0	1	if ($args{'avoid'})
1966	0	1	if ($args{'absolute'}) { }
1968	0	0	wantarray ? :
1984	0	4	unless ($args{'dataset'})
1993	0	4	unless $args{'db'} or $self->{'data'}->open_meta_database
1997	0	0	if ($self->feature_type eq "named" and $args{'subfeature'})
2009	0	4	defined $args{'strand'} ? :
2010	0	4	if ($args{'extend'})
2013	0	0	if $params[1] < 1
2025	0	4	if ($args{'avoid'})
2030	0	4	if ($args{'absolute'}) { }
2032	0	0	wantarray ? :
2036	4	0	unless (defined $args{'coordinate'})
2049	0	0	unless (@$subfeatures)
2053	0	0	if exists $args->{'exon'}
2071	0	0	defined $args->{'strand'} ? :
2098	0	0	if ($args->{'extend'})
2130	0	0	if ($args->{'absolute'}) { }
2132	0	0	wantarray ? :
2151	10	0	if (scalar @_ == 1) { }
2153	6	4	if (ref $_[0] eq 'HASH') { }
2170	0	10	defined $args->{'strand'} ? :
2171	6	4	if ($args->{'position'} == 5) { }
	1	3	elsif ($args->{'position'} == 3) { }
	2	1	elsif ($args->{'position'} == 4) { }
	1	0	elsif ($args->{'position'} == 9) { }
2172	1	5	if ($strand >= 0) { }
2180	1	0	if ($strand >= 0) { }
2190	1	1	if (exists $args->{'practical_start'}) { }
2213	0	0	if (ref $args->{'avoid'} eq 'ARRAY') { }
	0	0	elsif ($args->{'avoid'} eq '1') { }
	0	0	elsif ($args->{'avoid'} =~ /w+/i) { }
2218	0	0	if (defined $args->{'type'}) { }
2242	0	0	if (@overlap_features)
2251	0	0	if $feat->primary_id eq $primary
2258	0	0	if ($position >= $start and $position <= $stop)
2273	0	5	if ($strand >= 0) { }
	5	0	elsif ($strand < 0) { }
2283	5	0	wantarray ? :
2291	0	0	if ($method eq 'ncount') { }
2294	0	0	unless $p >= $start and $p <= $end
2296	0	0	if (exists $namecheck->{$n}) { }
2312	0	0	unless $p >= $start and $p <= $end
2327	0	0	unless ($args{'db'})
2330	0	0	unless ($args{'data'} and ref $args{'data'} eq "HASH")
2333	0	0	unless ($args{'callback'})
2339	0	0	if ($self->feature_type eq 'named' and $args{'subfeature'}) { }
2344	0	0	if (@$subfeatures) { }
2371	0	0	unless defined $tid
2400	0	0	unless $args{'bed'} =~ /^\d+$/
2401	0	0	unless $args{'bed'} >= 3
2409	0	0	if ($chr eq "." or not CORE::length $chr or $start eq "." or not CORE::length $start)
2413	0	0	if ($start > $stop)
2424	0	0	if ($args{'bed'} >= 4)
2428	0	0	if ($args{'bed'} >= 5)
2429	0	0	exists $args{'score'} ? :
2430	0	0	unless defined $score
2433	0	0	if ($args{'bed'} >= 6)
2435	0	0	if (exists $args{'strand'} and defined $args{'strand'}) { }
2441	0	0	$s == -1 ? :
2460	0	0	if ($chr eq "." or not CORE::length $chr or $start eq "." or not CORE::length $start)
2464	0	0	if ($start > $stop)
2472	0	0	if (exists $args{'strand'} and defined $args{'strand'}) { }
2478	0	0	$strand == 1 ? :
	0	0	$strand == -1 ? :
2483	0	0	if (defined $type and $type =~ /:/)
2486	0	0	unless ($source)
2489	0	0	unless ($primary_tag)
2490	0	0	$args{'primary_tag'} || defined $type ? :
2494	0	0	exists $args{'score'} ? :
2495	0	0	unless defined $score
2503	0	0	if (exists $args{'attributes'} and ref $args{'attributes'} eq "ARRAY")