Prepare reference sequences for JBrowse part1

jb-refseq-part1.pl

#!/usr/bin/env perl

use v5.10.1;
use strict;
use POSIX qw/floor/;
use autodie qw(:file);
use OptArgs;
use FindBin qw/$Bin/;
use Bio::DB::SeqFeature::Store;
use JSON;
use File::Spec::Functions;
use File::Path qw/make_path/;
use lib "$Bin/../../src/perl5";
use JsonGenerator;

opt out => (
    isa     => 'Str',
    default => sub {
        return "$Bin/../../data";
    },
    comment =>
        'output directory,  defaults to data under the jbrowse project folder'
);

arg conf => (
    isa      => 'Str',
    required => 1,
    comment  => 'JBrowse JSON config file'
);

opt reftype => (
    isa     => 'Str',
    comment => 'Reference feature type, default is region',
    default => 'region'
);

opt refnames => (
    isa => 'Str',
    comment =>
        'Comma separated list of unique name of the reference features,  take precedence over reftype option'
);