BioX-Map
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lib/BioX/Map/CLIS/Cmd/Compare.pm view on Meta::CPAN
package BioX::Map::CLIS::Cmd::Compare;
use Modern::Perl;
use IO::All;
use Carp "confess";
use Moo;
use MooX::Options prefer_commandline => 1, with_config_from_file => 1;
use MooX::Cmd;
use BioX::Map;
use Types::Standard qw(Int Str Bool Enum);
use Parallel::ForkManager;
our $VERSION = '0.0.12'; # VERSION:
# ABSTRACT: a wrapper for mapping software
around _build_config_identifier => sub { 'berry' };
around _build_config_prefix => sub { 'biox_map' };
option indir => (
is => 'ro',
format => 's',
short => 'i',
default => '',
doc => "path of one fastq file",
);
option soap_suffix => (
is => 'ro',
format => 's',
short => 's',
doc => "suffix of all samples' soap result",
default => 'soap',
);
option bwa_suffix => (
is => 'ro',
format => 's',
short => 'b',
doc => "suffix of all samples' bwa result",
default => 'bwa',
);
option process => (
is => 'ro',
format => 's',
short => 'p',
doc => 'number of process will be used',
default => 2,
);
option outfile => (
is => 'ro',
format => 's',
short => 'o',
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