/* preseq: to predict properties of genomic sequencing libraries

*

* Copyright (C) 2013-2024 University of Southern California and

* Andrew D. Smith and Timothy Daley

*

* Authors: Timothy Daley, Chao Deng, Victoria Helus, and Andrew Smith

*

* This program is free software: you can redistribute it and/or

* modify it under the terms of the GNU General Public License as

* published by the Free Software Foundation, either version 3 of the

* License, or (at your option) any later version.

*

* This program is distributed in the hope that it will be useful, but

* WITHOUT ANY WARRANTY; without even the implied warranty of

* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU

* General Public License for more details.

*

* You should have received a copy of the GNU General Public License

* along with this program. If not, see

* <http://www.gnu.org/licenses/>.

*/

#include <config.h>

#include "common.hpp"

// the preseq commands

#include "bound_pop.hpp"

#include "c_curve.hpp"

#include "gc_extrap.hpp"

#include "lc_extrap.hpp"

#include "pop_size.hpp"

#include <fstream>

#include <iomanip>

#include <iostream>

#include <string>

static std::string

usage_message() {

std::ostringstream oss;

oss << "preseq: a program for analyzing library complexity\n"

"Version: ";

oss << VERSION;

oss << "\n\n"

"Usage: preseq <command> [OPTIONS]\n\n"

"<command>: c_curve generate complexity curve for a library\n"

" lc_extrap predict the yield for future experiments\n"

" gc_extrap predict genome coverage low input\n"

" sequencing experiments\n"

" bound_pop lower bound on population size\n"

" pop_size estimate number of unique species\n";

return oss.str();

}

int

main(const int argc, const char *argv[]) {

if (argc < 2) {

std::cerr << usage_message() << std::endl;

return EXIT_SUCCESS;

}

static const std::string cmd = argv[1];

if (cmd == "lc_extrap")

return lc_extrap_main(argc, argv);

if (cmd == "c_curve")

return c_curve_main(argc, argv);

if (cmd == "gc_extrap")

return gc_extrap_main(argc, argv);

if (cmd == "bound_pop")

return bound_pop_main(argc, argv);

if (cmd == "pop_size")

return pop_size_main(argc, argv);

std::cerr << "Error: unrecognized command: " << argv[1] << std::endl

<< usage_message() << std::endl;

return EXIT_FAILURE;

}