Bio::Graphics::FeatureDir -- A directory of feature files and conf files

       Lincoln Stein <lincoln.stein@gmail.com>.

       Copyright (c) 2009 Ontario Institute for Cancer Research

       This  package  and  its accompanying libraries is free software; you can redistribute it and/or modify it
       under the terms of the GPL (either version 1, or at your option,  any  later  version)  or  the  Artistic
       License  2.0.   Refer  to  LICENSE  for the full license text. In addition, please see DISCLAIMER.txt for
       disclaimers of warranty.

       This class implements most of the methods of Bio::Graphics::FeatureFile, but stores the data files and
       features in a directory indexed by the Bio::DB::SeqFeature::Store::berkeleydb adaptor. Therefore it is
       fast.

   Methods
       $fd = Bio::Graphics::FeatureDir->new('/path/to/dir');
       $fd = Bio::Graphics::FeatureDir->new(-dir => '/path/to/dir');
           Create  a  new  FeatureDir,  based  in  the  indicated  directory.  In addition to the -dir directory
           argument, it takes any of the options that can be passed to Bio::Graphics::FeatureFile except for the
           -file and -text arguments;

       $db->_init_featuredb
           Internal method. Initializes the underlying feature database.

       $db->_init_conf
           Internal method -- initialize the configuration file(s)

       $created = $db->_maybe_create_dir($dir)
           Create $dir and its parents if it doesn't exist. Return true if the directory was created. Throws  an
           exception on filesystem errors.

       $dir = $db->dir
           Returns the base directory.

       $conf = $db->conf
           Returns the underlying Bio::Graphics::FeatureFile object

       $db = $db->db
           Returns the underlying Bio::DB::SeqFeature::Store object

       $db->add_file($file)
           Add the file to the directory. Can add files of type .fa, .gff, .gff3, .conf and .ff.

       $db->add_fh(\*FILEHANDLE [,'name'])
           Add the contents of the indicated filehandle to repository.  Name is optional; if provided it will be
           used as the base for all files created.

       Bio::Graphics::FeatureDir -- A directory of feature files and conf files

       Hey! Theabovedocumenthadsomecodingerrors,whichareexplainedbelow:

       Around line 160:
           '=item' outside of any '=over'

       Around line 272:
           =cut found outside a pod block.  Skipping to next block.

       Around line 274:
           You forgot a '=back' before '=head1'

perl v5.30.0                                       2019-11-25                     Bio::Graphics::FeatureDir(3pm)

       Bio::Graphics::Feature, Bio::Graphics::FeatureFile

        my $fd = Bio::Graphics::FeatureDir->new('/path/to/dir');
        $fd->add_file('tracks.conf');
        $fd->add_file('foo.gff3');
        $fd->add_file('foo.wig');
        $fd->add_fh(\*STDIN);

        my $option   = $fd->setting('EST' => 'bgcolor');
        my @features = $fd->get_features_by_name('M101');