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package BioX::Map;
use Modern::Perl;
use IO::All;
use Moo;
use Carp qw/confess/;
use Types::Standard qw/Str Int Enum Bool/;
use File::Which;
use Cwd;
use IPC::Run qw/run timeout/;
use Parallel::ForkManager;
use File::ShareDir ":ALL";

our $VERSION = '0.0.12'; # VERSION
# ABSTRACT: map read to genome with bwa and soap



has infile => (
  is      => "ro",
  isa     => Str,
  default => '',
);


has indir => (
  is      => 'ro',
  isa     => Str,
);


has outfile => (
  is      => 'lazy',
  isa     => Str,
);


has outdir => (
  is        => 'lazy',
  isa       => Str,
  default   => "./",
);


has force_index => (
  is      => 'lazy',
  isa     => Bool,
  default => 0,
);


has mismatch => (
  is      => 'lazy',
  isa     => Int,
  default => 2,
);


has genome => (
  is      => 'ro',
  isa     => Str,
);