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lib/Bio/MUST/Apps/Leel/RunProcessor.pm  view on Meta::CPAN

package Bio::MUST::Apps::Leel::RunProcessor;
# ABSTRACT: Internal class for leel tool
$Bio::MUST::Apps::Leel::RunProcessor::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments;                    # logging always enabled here

use Path::Class qw(dir);

use Parallel::Batch;

use aliased 'Bio::MUST::Apps::Leel::AliProcessor';

with 'Bio::MUST::Apps::Roles::RunProcable';


has '+out_suffix' => (
    default  => '-1331',
);


# blast_args


# trim_homologues

# trim_max_shift

# trim_extra_margin


has 'aligner_mode' => (
    is       => 'ro',
    isa      => 'Str',
    default  => 'exonerate',
);


has 'id_match_mode' => (
    is       => 'ro',
    isa      => 'Str',
    default  => 'enforce',
);


has 'round_trip_mode' => (
    is       => 'ro',
    isa      => 'Str',
    default  => 'off',
);


# bank_dir

# orgs

# infiles

# out_dir

# debug_mode