| blib/lib/Bio/ToolBox/db_helper.pm | |||
|---|---|---|---|
| Criterion | Covered | Total | % |
| condition | 26 | 125 | 20.8 |
| line | !l | l&&!r | l&&r | condition |
|---|---|---|---|---|
| 998 | 1 | 0 | 5 | exists $OPENED_DB{$database} and not $no_cache |
| 1831 | 0 | 0 | 0 | defined $chr_exclude and $feature->seq_id =~ /$chr_exclude/ |
| 1898 | 0 | 1 | 0 | exists $args{'exclude'} and defined $args{'exclude'} |
| 1937 | 122 | 0 | 0 | $Tree and scalar @{$Tree->fetch($start - 1, $end);} >= 1 |
| 1965 | 0 | 0 | 0 | $name and $name eq "." |
| 1966 | 0 | 0 | 0 | $args{'id'} and $args{'id'} eq "." |
| 1967 | 0 | 0 | 0 | $args{'type'} and $args{'type'} eq "." |
| 1970 | 0 | 0 | 0 | defined $args{'id'} and $db->can("fetch") |
| 1978 | 0 | 0 | 0 | defined $name and $feature->display_name ne $name |
| 1979 | 0 | 0 | 0 | defined $args{'type'} and $feature->type ne $args{'type'} |
| 2012 | 0 | 0 | 0 | @features and $name =~ /[;,\|]/ |
| 2079 | 0 | 9 | 3 | $_[7] and not ref $_[7] |
| 2172 | 0 | 0 | 0 | defined $chr_exclude and $chr =~ /$chr_exclude/i |
| 2192 | 0 | 0 | 0 | defined $chr_exclude and $_->{'name'} =~ /$chr_exclude/i |
| 2204 | 0 | 0 | 0 | defined $chr_exclude and $chr =~ /$chr_exclude/i |
| 2227 | 0 | 0 | 0 | defined $chr_exclude and $chr =~ /$chr_exclude/i |
| 2238 | 0 | 0 | 0 | defined $chr_exclude and $chr =~ /$chr_exclude/i |
| 2251 | 0 | 0 | 0 | defined $chr_exclude and $chr =~ /$chr_exclude/i |
| 2267 | 2 | 0 | 0 | defined $chr_exclude and $chr =~ /$chr_exclude/i |
| line | l | !l | condition |
|---|---|---|---|
| 968 | 0 | 0 | shift() || undef |
| 975 | 0 | 0 | shift() || undef |
| 983 | 0 | 8 | shift() || 0 |
| 1229 | 0 | 0 | $BAM_ADAPTER ||= "hts" |
| 1436 | 0 | 1 | $args{'single'} ||= 0 |
| 1440 | 1 | 0 | $args{'feature'} ||= undef |
| 1453 | 0 | 1 | $args{'limit'} ||= undef |
| 1457 | 1 | 0 | $args{'db'} ||= undef |
| 1619 | 0 | 0 | $args{'prompt'} ||= undef |
| 1773 | 0 | 0 | $args{'data'} || undef |
| 1784 | 0 | 0 | $args{'db'} ||= undef |
| 1799 | 0 | 0 | $args{'feature'} || $args{'features'} || undef |
| 1807 | 0 | 0 | $args{'chrskip'} || undef |
| 1859 | 1 | 0 | $args{'data'} || undef |
| 1868 | 1 | 0 | $args{'db'} ||= undef |
| 1876 | 1 | 0 | $args{'win'} ||= 500 |
| 1888 | 0 | 1 | $args{'skip'} || $args{'chrskip'} || undef |
| 1897 | 0 | 1 | $args{'blacklist'} || undef |
| 1927 | 0 | 1 | $exclusion_tree{$chr} || undef |
| 1952 | 0 | 0 | $args{'db'} ||= undef |
| 1960 | 0 | 0 | $args{'name'} || undef |
| 1964 | 0 | 0 | $args{'type'} ||= undef |
| 1973 | 0 | 0 | $db->fetch($args{'id'}) || undef |
| 2122 | 7 | 0 | $scores ||= [] |
| 2136 | 0 | 2 | shift() || undef |
| line | l | !l&&r | !l&&!r | condition |
|---|---|---|---|---|
| 1410 | 0 | 0 | 0 | $type || $primary || $name |
| 1877 | 0 | 1 | 0 | $args{'step'} ||= $args{'win'} |
| 1897 | 0 | 0 | 1 | $args{'exclude'} ||= $args{'blacklist'} || undef |
| 2089 | 3 | 9 | 0 | $DB_METHODS{$_[5]}{$_[6]}{$_[7]}{$_[8]} || _lookup_db_method(\@_) |
| 2168 | 0 | 0 | 2 | $type eq "Bio::DB::BigWig" or $type eq "Bio::DB::BigBed" |
| 0 | 0 | 2 | $type eq "Bio::DB::Sam" or $type eq "Bio::DB::HTS" |