| blib/lib/Bio/ToolBox/db_helper.pm | |||
|---|---|---|---|
| Criterion | Covered | Total | % |
| condition | 20 | 117 | 17.0 |
| line | !l | l&&!r | l&&r | condition |
|---|---|---|---|---|
| 922 | 1 | 0 | 4 | exists $OPENED_DB{$database} and not $no_cache |
| 1771 | 0 | 0 | 0 | defined $chr_exclude and $feature->seq_id =~ /$chr_exclude/ |
| 1877 | 0 | 0 | 0 | $name and $name eq '.' |
| 1878 | 0 | 0 | 0 | $args{'id'} and $args{'id'} eq '.' |
| 1879 | 0 | 0 | 0 | $args{'type'} and $args{'type'} eq '.' |
| 1882 | 0 | 0 | 0 | defined $args{'id'} and $db->can('fetch') |
| 1890 | 0 | 0 | 0 | defined $name and $feature->display_name ne $name |
| 1891 | 0 | 0 | 0 | defined $args{'type'} and $feature->type ne $args{'type'} |
| 1924 | 0 | 0 | 0 | @features and $name =~ /[;,\|]/ |
| 1991 | 0 | 9 | 3 | $_[7] and not ref $_[7] |
| 2137 | 0 | 0 | 0 | defined $chr_exclude and $chr =~ /$chr_exclude/i |
| 2161 | 0 | 0 | 0 | defined $chr_exclude and $_->[0] =~ /$chr_exclude/i |
| 2171 | 0 | 0 | 0 | defined $chr_exclude and $chr =~ /$chr_exclude/ |
| 2194 | 0 | 0 | 0 | defined $chr_exclude and $chr =~ /$chr_exclude/ |
| 2205 | 0 | 0 | 0 | defined $chr_exclude and $chr =~ /$chr_exclude/ |
| 2218 | 0 | 0 | 0 | defined $chr_exclude and $chr =~ /$chr_exclude/ |
| 2234 | 1 | 0 | 0 | defined $chr_exclude and $chr =~ /$chr_exclude/ |
| line | l | !l | condition |
|---|---|---|---|
| 892 | 0 | 0 | shift() || undef |
| 899 | 0 | 0 | shift() || undef |
| 907 | 0 | 6 | shift() || 0 |
| 1156 | 0 | 0 | $BAM_ADAPTER ||= 'hts' |
| 1376 | 0 | 1 | $args{'single'} ||= 0 |
| 1380 | 1 | 0 | $args{'feature'} ||= undef |
| 1393 | 0 | 1 | $args{'limit'} ||= undef |
| 1397 | 1 | 0 | $args{'db'} ||= undef |
| 1559 | 0 | 0 | $args{'prompt'} ||= undef |
| 1713 | 0 | 0 | $args{'data'} || undef |
| 1724 | 0 | 0 | $args{'db'} ||= undef |
| 1739 | 0 | 0 | $args{'feature'} || $args{'features'} || undef |
| 1747 | 0 | 0 | $args{'chrskip'} || undef |
| 1799 | 0 | 0 | $args{'data'} || undef |
| 1810 | 0 | 0 | $args{'db'} ||= undef |
| 1818 | 0 | 0 | $args{'win'} ||= 500 |
| 1830 | 0 | 0 | $args{'skip'} || $args{'chrskip'} || undef |
| 1864 | 0 | 0 | $args{'db'} ||= undef |
| 1872 | 0 | 0 | $args{'name'} || undef |
| 1876 | 0 | 0 | $args{'type'} ||= undef |
| 1885 | 0 | 0 | $db->fetch($args{'id'}) || undef |
| 2034 | 7 | 0 | $scores ||= [] |
| 2038 | 1 | 0 | scalar @$scores || 1 |
| 2101 | 0 | 1 | shift() || undef |
| line | l | !l&&r | !l&&!r | condition |
|---|---|---|---|---|
| 1351 | 0 | 0 | 0 | $type || $primary || $name |
| 1819 | 0 | 0 | 0 | $args{'step'} ||= $args{'win'} |
| 2001 | 3 | 9 | 0 | $DB_METHODS{$_[5]}{$_[6]}{$_[7]}{$_[8]} || _lookup_db_method(\@_) |
| 2037 | 1 | 1 | 1 | $method eq 'count' or $method eq 'pcount' |
| 2133 | 0 | 0 | 1 | $type eq 'Bio::DB::BigWig' or $type eq 'Bio::DB::BigBed' |
| 0 | 0 | 1 | $type eq 'Bio::DB::Sam' or $type eq 'Bio::DB::HTS' |