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lib/Bio/MUST/Apps/TwoScalp/Seq2Seq.pm  view on Meta::CPAN

package Bio::MUST::Apps::TwoScalp::Seq2Seq;
# ABSTRACT: internal class for two-scalp tool
$Bio::MUST::Apps::TwoScalp::Seq2Seq::VERSION = '0.243240';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments -ENV;

use List::AllUtils qw(part);

use Bio::MUST::Core;
use Bio::MUST::Core::Constants qw(:gaps);
use Bio::MUST::Core::Utils qw(secure_outfile);
use Bio::MUST::Drivers;
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::Ali::Temporary';
use aliased 'Bio::MUST::Core::Seq';
use aliased 'Bio::MUST::Core::SeqId';
use aliased 'Bio::MUST::Core::SeqMask';
use aliased 'Bio::MUST::Apps::SlaveAligner::Local';


has 'coverage_mul' => (
    is       => 'ro',
    isa      => 'Num',
    default  => 1.1,
);

has 'single_hsp' => (
    is       => 'ro',
    isa      => 'Bool',
    default  => 0,
);

has 'out_suffix' => (
    is       => 'ro',
    isa      => 'Maybe[Str]',
    default  => '-ts',
);

has 'ali' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Ali',
    required => 1,
    coerce   => 1,
);

has 'lookup' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::IdList',
    init_arg => undef,
    writer   => '_set_lookup',
);

has 'new_ali' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Ali',
    init_arg => undef,
    writer   => '_set_new_ali',
);

has 'integrator' => (