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/*
Genome-wide Efficient Mixed Model Association (GEMMA)
Copyright (C) 2011-2017, Xiang Zhou
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 <iostream>
#include <fstream>
#include <sstream>
#include <sys/stat.h>
#include <sys/types.h>
#include "gemma.h"
using namespace std;
int main(int argc, char * argv[]) {
GEMMA cGemma;
PARAM cPar;
if (argc <= 1) {
cGemma.PrintHeader();
return EXIT_SUCCESS;
}
if (argc==2 && argv[1][0] == '-' && argv[1][1] == 'h') {
cGemma.PrintHelp(0);
return EXIT_SUCCESS;
}
if (argc==3 && argv[1][0] == '-' && argv[1][1] == 'h') {
string str;
str.assign(argv[2]);
cGemma.PrintHelp(atoi(str.c_str()));
return EXIT_SUCCESS;
}
if (argc==2 && argv[1][0] == '-' && argv[1][1] == 'l') {
cGemma.PrintLicense();
return EXIT_SUCCESS;
}
cGemma.Assign(argc, argv, cPar);
ifstream check_dir((cPar.path_out).c_str());
if (!check_dir) {
mkdir((cPar.path_out).c_str(), S_IRWXU|S_IRGRP|S_IROTH);
}
if (cPar.error==true) {return EXIT_FAILURE;}
if (cPar.mode_silence) {stringstream ss; cout.rdbuf (ss.rdbuf());}
cPar.CheckParam();
if (cPar.error==true) {return EXIT_FAILURE;}
cGemma.BatchRun(cPar);
if (cPar.error==true) {return EXIT_FAILURE;}
cGemma.WriteLog(argc, argv, cPar);
return EXIT_SUCCESS; }
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