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lib/Bio/DB/Sam.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::Bam->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}}