- { long => 'genome', short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
- { long => 'fast_map', short => 'f', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'occ', short => 'c', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'intron_max', short => 'i', type => 'uint', mandatory => 'no', default => 750000, allowed => undef, disallowed => undef },
- { long => 'tile_size', short => 't', type => 'uint', mandatory => 'no', default => 11, allowed => undef, disallowed => 0 },
- { long => 'step_size', short => 's', type => 'uint', mandatory => 'no', default => 11, allowed => undef, disallowed => 0 },
- { long => 'min_identity', short => 'm', type => 'uint', mandatory => 'no', default => 90, allowed => undef, disallowed => 0 },
- { long => 'min_score', short => 'M', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
- { long => 'one_off', short => 'o', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
+ { long => 'database', short => 'd', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'genome', short => 'g', type => 'genome', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'fast_map', short => 'f', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'occ', short => 'c', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'intron_max', short => 'i', type => 'uint', mandatory => 'no', default => 750000, allowed => undef, disallowed => undef },
+ { long => 'tile_size', short => 't', type => 'uint', mandatory => 'no', default => 11, allowed => undef, disallowed => 0 },
+ { long => 'step_size', short => 's', type => 'uint', mandatory => 'no', default => 11, allowed => undef, disallowed => 0 },
+ { long => 'min_identity', short => 'm', type => 'uint', mandatory => 'no', default => 90, allowed => undef, disallowed => 0 },
+ { long => 'min_score', short => 'M', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
+ { long => 'one_off', short => 'o', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
+ { long => 'allow_N_blocks', short => 'N', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },