#!/usr/bin/perl -w
#
# Author: Jue Ruan <ruanjue@gmail.com>
#
use Getopt::Std;
use strict;

our ($opt_h, $opt_t, $opt_o, $opt_f, $opt_L, $opt_p, $opt_S, $opt_e, $opt_X);

getopts("ht:o:fL:p:S:e:X:");

&usage if($opt_h or @ARGV == 0);

my ($op_t, $op_o, $op_f, $op_L, $op_p, $op_S, $op_e);

$op_t = $opt_t || 0;
$op_f = $opt_f || 0;
$op_L = defined($opt_L)? $opt_L : 5000;
$op_e = $opt_e || 3;

if($opt_X){
	if($opt_X eq 'rs2'){
		$op_p = 21;
		$op_S = 4;
	}
}

1;

sub usage {
	print
qq{Usage: $0 [options] <seq_file1> [seq_file2 ...]
Options:
 -t <int>    Number of threads, 0 to use all, [0]
 -o <string> Prefix of output, [dbg]
 -f          Force overwrite
 -L <int>    Reads length cutoff, [5000]
 -p <int>    HPC-kmer size, [21]
 -S <float>  Subsampling 1/\$S of HPC-kmers, [4.0]
 -e <int>    Edge coverage cutoff, [3]
 -X <string> Preset, will be overwrited by the aboves
             - rs2    : genome size <= 4 G, Pacbio RSII
			 - rs2x   : genome size > 4 G, PacBio RSII
			 - sequel : genome size <= 4 G, PacBio sequel
			 - sequelx: genome size > 4 G, PacBio sequel
			 - ont    : genome size <= 4 G, Nanopore
			 - ontx   : genome size > 4G, Nanopore
			 ** The preset may be not suitable for your genome assembly **

};
}