main.cc 1.6 KB
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/* Spell-QTL  Software suite for the QTL analysis of modern datasets.
 * Copyright (C) 2016,2017  Damien Leroux <damien.leroux@inra.fr>, Sylvain Jasson <sylvain.jasson@inra.fr>
 *
 * 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/>.
 */

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#include "pedigree.h"
#include "pedigree_settings.h"

void print_usage();


int main(int argc, const char** argv)
{
    msg_handler_t::debug_enabled() = false;
    ped_settings_t* settings = ped_settings_t::from_args(argc, argv);
    if (!settings) {
        prg_name(basename(argv[0]));
        print_usage();
    } else {
        pedigree_type ped = read_pedigree(settings->pedigree_filename, settings->csv_sep, settings->max_states);
        std::string ped_output;
        if (settings->work_directory != "") {
            ped_output = settings->work_directory + "/" + basename(settings->pedigree_filename.c_str()) + ".ped-data";
        } else {
            ped_output = settings->pedigree_filename + ".ped-data";
        }
        ped.save(ped_output);
        delete settings;
    }
    return 0;
}