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lib/Bio/MUST/Drivers/Cap3.pm  view on Meta::CPAN

package Bio::MUST::Drivers::Cap3;
# ABSTRACT: Bio::MUST driver for running the CAP3 assembly program
$Bio::MUST::Drivers::Cap3::VERSION = '0.252830';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

# use Smart::Comments;

use Carp;
use IPC::System::Simple qw(system);
use Module::Runtime qw(use_module);
use Path::Class qw(file);
use Tie::IxHash;

use Bio::MUST::Core;
extends 'Bio::MUST::Core::Ali::Temporary';

use Bio::MUST::Core::Constants qw(:files);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::SeqId';

use Bio::MUST::Drivers::Utils qw(stringify_args);


has 'cap3_args' => (
    is       => 'ro',
    isa      => 'HashRef',
    default  => sub { {} },
);

has '_contig_seq_ids' => (
    traits   => ['Hash'],
    is       => 'ro',
    isa      => 'HashRef[ArrayRef[Bio::MUST::Core::SeqId]]',
    init_arg => undef,
    writer   => '_set_contig_seq_ids',
    handles  => {
        all_contig_names   => 'keys',
        all_contig_seq_ids => 'values',
        seq_ids_for        => 'get',
    },
);

has '_contigs' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Ali',
    init_arg => undef,
    writer   => '_set_contigs',
    handles  => {
          all_contigs =>   'all_seqs',
        count_contigs => 'count_seqs',
    },
);

has '_singlets' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Ali',
    init_arg => undef,
    writer   => '_set_singlets',
    handles  => {
          all_singlets =>   'all_seqs',
        count_singlets => 'count_seqs',