Branch Coverage

blib/lib/Bio/ToolBox/db_helper.pm

Criterion	Covered	Total	%
branch	66	526	12.5

line	true	false	branch
969	0	0	if $a
976	0	0	if $a
984	0	8	unless ($database)
991	2	6	if ($db_ref =~ /DB|big::BigWigSet/)
998	5	1	if (exists $OPENED_DB{$database} and not $no_cache)
1006	0	1	if $database =~ /^Parsed:/
1020	0	1	if ($database =~ /^(?:https?|ftp)/i) { }
	1	0	elsif (-f $database) { }
	0	0	elsif (-d $database) { }
1023	0	0	if ($database =~ /\.bam$/i) { }
	0	0	elsif ($database =~ /\.(?:bb|bigbed)$/i) { }
	0	0	elsif ($database =~ /\.(?:bw|bigwig)$/i) { }
	0	0	elsif ($database =~ /\.useq$/) { }
	0	0	elsif ($database =~ /\.fa(?:sta)?$/i) { }
1025	0	0	unless $BAM_OK
1026	0	0	if ($BAM_OK) { }
1028	0	0	unless ($db)
1042	0	0	unless $BIGBED_OK
1043	0	0	if ($BIGBED_OK) { }
1045	0	0	unless ($db)
1059	0	0	unless $BIGWIG_OK
1060	0	0	if ($BIGWIG_OK) { }
1062	0	0	unless ($db)
1088	0	0	unless $BIGWIG_OK
1090	0	0	if ($BIGWIG_OK) { }
1092	0	0	unless ($db)
1109	0	1	if ($database =~ /\.bam$/i) { }
	0	1	elsif ($database =~ /\.(?:bb|bigbed)$/i) { }
	0	1	elsif ($database =~ /\.(?:bw|bigwig)$/i) { }
	1	0	elsif ($database =~ /\.useq$/i) { }
	0	0	elsif ($database =~ /\.fa(?:sta)?(?:\.gz)?$/i) { }
	0	0	elsif ($database =~ /\.(?:gff3?|gff3?\.gz|db|sqlite)$/) { }
	0	0	elsif ($database =~ /\.cram$/i) { }
1111	0	0	unless $BAM_OK
1112	0	0	if ($BAM_OK) { }
1115	0	0	unless ($db)
1129	0	0	unless $BIGBED_OK
1130	0	0	if ($BIGBED_OK) { }
1133	0	0	unless ($db)
1147	0	0	unless $BIGWIG_OK
1148	0	0	if ($BIGWIG_OK) { }
1151	0	0	unless ($db)
1165	1	0	unless $USEQ_OK
1167	1	0	if ($USEQ_OK) { }
1169	0	1	unless ($db)
1183	0	0	unless $BAM_OK
1184	0	0	if ($BAM_OK) { }
1186	0	0	unless ($db)
1192	0	0	unless $SEQFASTA_OK
1194	0	0	if ($SEQFASTA_OK) { }
1196	0	0	unless ($db)
1198	0	0	if (-e "$database.index")
1212	0	0	unless $SEQFASTA_OK
1214	0	0	if ($SEQFASTA_OK) { }
1216	0	0	unless ($db)
1230	0	0	if ($BAM_ADAPTER eq "sam")
1233	0	0	unless $BAM_OK
1234	0	0	if ($BAM_OK) { }
1237	0	0	unless ($db)
1257	0	0	unless $BIGWIG_OK
1258	0	0	if ($BIGWIG_OK) { }
1260	0	0	unless ($db)
1272	0	0	unless ($db)
1273	0	0	unless $SEQFASTA_OK
1275	0	0	if ($SEQFASTA_OK) { }
1277	0	0	unless ($db)
1294	0	0	unless $SEQFASTA_OK
1296	0	0	if ($SEQFASTA_OK) { }
1298	0	0	unless ($db)
1309	1	0	if ($db) { }
1311	1	0	unless $no_cache
1326	0	0	unless $db
1328	0	0	unless $db_ref
1330	0	0	if ($db_ref =~ /^Bio::DB::SeqFeature::Store/) { }
	0	0	elsif ($db_ref eq 'Bio::DB::Sam') { }
	0	0	elsif ($db_ref eq 'Bio::DB::HTS') { }
1363	0	0	unless ($db)
1373	0	0	if ($db_ref =~ /^Bio::DB::SeqFeature::Store/) { }
	0	0	elsif ($db_ref =~ /BigWigSet/i) { }
1379	0	0	unless $Bio::ToolBox::db_helper::a->[0] cmp $Bio::ToolBox::db_helper::b->[0]
1398	0	0	if ($attribute =~ /^type/i) { }
	0	0	elsif ($attribute =~ /name/i) { }
	0	0	elsif ($attribute =~ /^primary_tag|method$/i) { }
1441	0	1	if (ref $args{'feature'} eq 'ARRAY') { }
	1	0	elsif (defined $args{'feature'}) { }
1458	1	0	$args{'db'} ? :
1466	1	0	if (@datasets) { }
1471	0	1	if ($item =~ /,/) { }
1485	0	1	if ($dataset =~ /^(?: http | ftp) .+ \. (?: bam | bw | bb) $/xi) { }
	1	0	elsif ($dataset =~ /\.(?:bam|bw|bigwig|bb|bigbed|useq)$/i) { }
1501	1	0	if (-e $file) { }
1511	1	0	if (@files) { }
1524	0	0	unless (%db_features)
1525	0	0	if ($db) { }
1530	0	0	if ($source) { }
1540	0	0	unless (%db_features)
1558	0	0	if (exists $db_features{$d}) { }
1569	0	0	if ($check) { }
1585	0	0	if ($db) { }
1589	0	0	if ($limit)
1592	0	0	unless $p =~ /$limit/i
1599	0	0	unless (%db_features)
1620	0	0	if ($args{'prompt'}) { }
1626	0	0	if ($args{'single'}) { }
1641	0	0	if ($args{'single'})
1642	0	0	unless (scalar @answer_list == 1)
1651	0	0	if ($answer =~ /&/) { }
1658	0	0	unless (exists $db_features{$_})
1664	0	0	if ($check) { }
1677	0	0	if (exists $db_features{$answer}) { }
1688	0	1	if (@bad_datasets)
1696	0	1	if ($args{'single'}) { }
1716	0	0	if (exists $TOTAL_READ_NUMBER{$dataset}) { }
	0	0	elsif ($dataset =~ /\.bam$/) { }
	0	0	elsif ($dataset =~ /\.bb$/) { }
1725	0	0	unless $BAM_OK
1726	0	0	if ($BAM_OK) { }
1741	0	0	unless $BIGBED_OK
1743	0	0	if ($BIGBED_OK) { }
1774	0	0	unless ($data)
1778	0	0	unless (ref $data eq "Bio::ToolBox::Data")
1786	0	0	unless ($db)
1793	0	0	unless ($db_ref =~ /^Bio::DB::SeqFeature::Store/)
1800	0	0	unless ($searchFeature)
1816	0	0	scalar @classes ? :
1819	0	0	unless ($iterator)
1831	0	0	if defined $chr_exclude and $feature->seq_id =~ /$chr_exclude/
1860	0	1	unless ($data)
1863	0	1	unless (ref $data eq "Bio::ToolBox::Data")
1870	0	1	unless ($db)
1890	0	1	unless (@chromosomes)
1898	0	1	if (exists $args{'exclude'} and defined $args{'exclude'})
1899	0	0	if (ref $args{'exclude'} eq 'Bio::ToolBox::Data') { }
1900	0	0	if (_load_helper_module('Set::IntervalTree')) { }
1906	0	0	unless (exists $exclusion_tree{$row->seq_id})
1932	1	121	if ($end > $length)
1937	0	122	if $Tree and scalar @{$Tree->fetch($start - 1, $end);} >= 1
1953	0	0	unless ($args{'db'})
1963	0	0	exists $args{'id'} ? :
1965	0	0	if $name and $name eq "."
1966	0	0	if $args{'id'} and $args{'id'} eq "."
1967	0	0	if $args{'type'} and $args{'type'} eq "."
1970	0	0	if (defined $args{'id'} and $db->can("fetch"))
1976	0	0	$feature ? :
1977	0	0	if ($check)
1978	0	0	if defined $name and $feature->display_name ne $name
1979	0	0	if defined $args{'type'} and $feature->type ne $args{'type'}
1983	0	0	if ($check) { }
1988	0	0	unless ($PRIMARY_ID_WARNING)
1996	0	0	unless $name
2004	0	0	unless (@features)
2012	0	0	unless (@features and $name =~ /[;,\|]/)
2026	0	0	if (scalar @features > 1) { }
	0	0	elsif (not @features) { }
2031	0	0	if ($args{'name'} =~ /;/)
2040	0	0	if ($check eq $f_name)
2046	0	0	if (scalar @candidates == 1) { }
	0	0	elsif (scalar @candidates > 1) { }
2076	0	12	unless scalar @_ == 9
2079	3	9	if $_[7] and not ref $_[7]
2082	0	12	if ($_[8] =~ /&/)
2097	5	7	if ($_[6] > 0) { }
2106	7	0	if (ref $scores) { }
2110	0	0	unless (defined $scores)
2111	0	0	if $_[5] =~ /count|sum/
2123	7	0	if (exists $SCORE_CALCULATOR_SUB{$method}) { }
2140	0	2	unless ($db)
2147	0	2	if (ref($db) =~ /BigWigSet/)
2168	0	2	if ($type =~ /^Bio::DB::SeqFeature::Store/) { }
	0	2	elsif ($type eq 'Bio::DB::Big::File') { }
	0	2	elsif ($type eq 'Bio::DB::BigWig' or $type eq 'Bio::DB::BigBed') { }
	0	2	elsif ($type eq 'Bio::DB::Sam' or $type eq 'Bio::DB::HTS') { }
	0	2	elsif ($type eq 'Bio::DB::HTS::Faidx') { }
	0	2	elsif ($type eq 'Bio::DB::Fasta') { }
	2	0	elsif ($db->can('seq_ids')) { }
2172	0	0	if defined $chr_exclude and $chr =~ /$chr_exclude/i
2176	0	0	$seqf ? :
2192	0	0	if defined $chr_exclude and $_->{'name'} =~ /$chr_exclude/i
2204	0	0	if defined $chr_exclude and $chr =~ /$chr_exclude/i
2227	0	0	if defined $chr_exclude and $chr =~ /$chr_exclude/i
2238	0	0	if defined $chr_exclude and $chr =~ /$chr_exclude/i
2251	0	0	if defined $chr_exclude and $chr =~ /$chr_exclude/i
2255	0	0	$seq ? :
2267	0	2	if defined $chr_exclude and $chr =~ /$chr_exclude/i
2276	2	0	if $segment->seq_id eq $chr
2280	0	2	unless ($segment)
2299	0	2	unless (@chrom_lengths)
2308	0	0	unless scalar @_ == 6
2311	0	0	unless ($BAM_ADAPTER)
2312	0	0	ref($sam) =~ /hts/i ? :
2314	0	0	if ($BAM_ADAPTER eq 'hts') { }
	0	0	elsif ($BAM_ADAPTER eq 'sam') { }
2317	0	0	unless $index
2323	0	0	unless $index
2333	0	0	unless scalar @_ == 4
2336	0	0	unless ($BAM_ADAPTER)
2337	0	0	ref($sam) =~ /hts/i ? :
2339	0	0	if ($BAM_ADAPTER eq 'hts') { }
	0	0	elsif ($BAM_ADAPTER eq 'sam') { }
2342	0	0	unless $index
2348	0	0	unless $index
2358	0	0	unless scalar @_ == 4
2363	0	0	unless $type
2366	0	0	if ($type eq 'Bio::DB::HTS::Faidx') { }
	0	0	elsif ($type eq 'Bio::DB::Sam::Fai') { }
	0	0	elsif ($db->can('seq')) { }
2396	9	0	if ($param->[8] =~ /^file|http|ftp/) { }
	0	0	elsif (ref($param->[7]) =~ /BigWigSet/) { }
	0	0	elsif (ref($param->[7]) =~ /^Bio::DB/) { }
2400	0	9	if ($param->[8] =~ /\.(?:bw|bigwig)$/i) { }
	0	9	elsif ($param->[8] =~ /\.(?:bb|bigbed)$/i) { }
	0	9	elsif ($param->[8] =~ /\.bam$/i) { }
	9	0	elsif ($param->[8] =~ /\.useq$/i) { }
2406	0	0	unless $BIGWIG_OK
2407	0	0	if ($BIGWIG_OK) { }
2408	0	0	if ($param->[6] == 2) { }
	0	0	elsif ($param->[6] == 1) { }
	0	0	elsif ($param->[5] =~ /min|max|mean/) { }
	0	0	elsif ($param->[5] =~ /sum|count/) { }
2419	0	0	$BIG_ADAPTER eq 'ucsc' ? :
2438	0	0	unless $BIGBED_OK
2439	0	0	if ($BIGBED_OK) { }
2440	0	0	if ($param->[6] == 2) { }
2459	0	0	unless $BAM_OK
2460	0	0	if ($BAM_OK) { }
2476	0	9	unless $USEQ_OK
2478	9	0	if ($USEQ_OK) { }
2479	4	5	if ($param->[6] == 2) { }
2507	0	0	unless $BIGWIG_OK
2508	0	0	unless $BIGWIG_OK
2512	0	0	if ($param->[6] == 2) { }
	0	0	elsif ($param->[6] == 1) { }
	0	0	elsif ($param->[5] =~ /min|max|mean|sum|count/) { }
2522	0	0	$BIG_ADAPTER eq 'ucsc' ? :
2539	0	0	unless $SEQFASTA_OK
2541	0	0	if ($SEQFASTA_OK) { }
2544	0	0	unless ($param->[7]->can("get_seq_stream"))
2559	0	0	unless $param->[8]
2560	0	0	unless $param->[7]
2585	0	0	if ($BAM_ADAPTER) { }
2586	0	0	if ($BAM_ADAPTER =~ /sam/i) { }
	0	0	elsif ($BAM_ADAPTER =~ /hts/i) { }
	0	0	elsif ($BAM_ADAPTER =~ /none/i) { }
2602	0	0	unless ($BAM_OK)
2610	0	0	if ($BAM_OK) { }
2615	0	0	if $BAM_OK
2623	0	0	if ($BIG_ADAPTER) { }
2624	0	0	if ($BIG_ADAPTER =~ /ucsc|kent/i) { }
	0	0	elsif ($BIG_ADAPTER =~ /big/i) { }
	0	0	elsif ($BIG_ADAPTER =~ /none/i) { }
2641	0	0	unless ($BIGWIG_OK)
2649	0	0	if ($BIGWIG_OK) { }
2652	0	0	if $BIGWIG_OK
2656	0	0	if $BIGWIG_OK
2663	0	0	if ($BIG_ADAPTER) { }
2664	0	0	if ($BIG_ADAPTER =~ /ucsc|kent/i) { }
	0	0	elsif ($BIG_ADAPTER =~ /big/i) { }
	0	0	elsif ($BIG_ADAPTER =~ /none/i) { }
	0	0	elsif ($BAM_ADAPTER =~ /\w+/) { }
2681	0	0	unless ($BIGWIG_OK)
2689	0	0	if ($BIGBED_OK) { }
2692	0	0	if $BIGBED_OK
2696	0	0	if $BIGBED_OK