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lib/App/SimulateReads/Simulator.pm  view on Meta::CPAN

package App::SimulateReads::Simulator;
# ABSTRACT: Class responsible to make the simulation

use App::SimulateReads::Base 'class';
use App::SimulateReads::Fastq::SingleEnd;
use App::SimulateReads::Fastq::PairedEnd;
use App::SimulateReads::InterlaceProcesses;
use App::SimulateReads::WeightedRaffle;
use App::SimulateReads::DB::Handle::Expression;
use Scalar::Util 'looks_like_number';
use File::Cat 'cat';
use Parallel::ForkManager;

with qw/App::SimulateReads::Role::IO/;

our $VERSION = '0.16'; # VERSION

has 'seed' => (
	is        => 'ro',
	isa       => 'Int',
	required  => 1
);

has 'jobs' => (
	is         => 'ro',
	isa        => 'My:IntGt0',
	required   => 1
);

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

has 'output_gzip' => (
	is         => 'ro',
	isa        => 'Bool',
	required   => 1
);

has 'fasta_file' => (
	is         => 'ro',
	isa        => 'My:Fasta',
	required   => 1
);

has 'coverage' => (
	is         => 'ro',
	isa        => 'My:NumGt0',
	required   => 0
);

has 'number_of_reads' => (
	is         => 'ro',
	isa        => 'My:IntGt0',
	required   => 0
);

has 'count_loops_by' => (
	is         => 'ro',
	isa        => 'My:CountLoopBy',
	required   => 1
);

has 'strand_bias' => (
	is         => 'ro',
	isa        => 'My:StrandBias',
	required   => 1
);