<commit_before>package Transposome;

use 5.012;
use Moose;
use namespace::autoclean;
use Transposome::PairFinder;
use Transposome::Cluster;
use Transposome::SeqStore;
use Transpsome::Annotation;

with 'MooseX::Getopt';

=head1 NAME

Transposome - Explore the transposon strucuture of a genome through sequence reads.

=head1 VERSION

Version 0.01

=cut

our $VERSION = '0.01';

=head1 SYNOPSIS

    use Transposome;

    my $trans_obj = Transposome->new_from_options();
    ...

=head1 ATTRIBUTES

has 'config' => (isa => 'Str', is => 'ro', required => 1);

has 'context' => (
    isa     => 'HashRef',
    is      => 'rw',
    lazy    => 1,
    traits  => ['NoGetopt'],
    default => sub { LoadFile shift->config }
);
<commit_msg>update Transposome.pm for using a config role rather than cl opts<commit_after>package Transposome;

use 5.012;
use Moose;
use namespace::autoclean;

with 'MooseX::Getopt',
     'Transposome::Role::Config';

=head1 NAME

Transposome - Investigate the repeat strucuture of a genome through sequence reads.

=head1 VERSION

Version 0.01

=cut

our $VERSION = '0.01';

=head1 SYNOPSIS

    use Transposome;

    my $trans_obj = Transposome->new_with_config( configfile => 'transposome.yaml' );
    ...
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{'dir': 'git-commits-cleaned', 'id': '187746', 'n_tokens_mistral': 454, 'n_tokens_neox': 436, 'n_words': 121}