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lib/Bio/DB/HTS.pm  view on Meta::CPAN

sub tam_fh {
    my $self = shift;
    return $self->features( -fh => 1 );
}

sub max_pileup_cnt {
    my $self = shift;
    return Bio::DB::HTSfile->max_pileup_cnt(@_);
}

# return a fragment of code that will be placed in the eval "" filter
# to eliminate alignments that don't match by name
sub _filter_by_name {
    my $self = shift;
    my $name = shift;

    my $frag = "my \$name=\$a->qname; defined \$name or return; ";

    if ( my $regexp = $self->_glob_match($name) ) {
        $frag .= "return unless \$name =~ /^$regexp\$/i;\n";
    }
    else {
        $frag .= "return unless lc \$name eq '$name';\n";
    }
}

# return a fragment of code that will be placed in the eval "" filter
# to eliminate alignments that don't match by attribute
sub _filter_by_attribute {
    my $self       = shift;
    my $attributes = shift;
    my $result;
    for my $tag ( keys %$attributes ) {
        $result .= "my \$value = lc \$a->get_tag_values('$tag');\n";
        $result .= "return unless defined \$value;\n";
        my @comps =
          ref $attributes->{$tag} eq 'ARRAY' ? @{ $attributes->{$tag} } :