1 /*
2 Genome-wide Efficient Mixed Model Association (GEMMA)
3 Copyright (C) 2011-2017, Xiang Zhou
4
5 This program is free software: you can redistribute it and/or modify
6 it under the terms of the GNU General Public License as published by
7 the Free Software Foundation, either version 3 of the License, or
8 (at your option) any later version.
9
10 This program is distributed in the hope that it will be useful,
11 but WITHOUT ANY WARRANTY; without even the implied warranty of
12 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 GNU General Public License for more details.
14
15 You should have received a copy of the GNU General Public License
16 along with this program. If not, see <http://www.gnu.org/licenses/>.
17 */
18
19 #include "gemma.h"
20 #include <fstream>
21 #include <iostream>
22 #include <sstream>
23 #include <sys/stat.h>
24 #include <sys/types.h>
25
26 using namespace std;
27
main(int argc,char * argv[])28 int main(int argc, char *argv[]) {
29 GEMMA cGemma;
30 PARAM cPar;
31
32 gsl_set_error_handler (&gemma_gsl_error_handler);
33
34 if (argc <= 1) {
35 cGemma.PrintHeader();
36 cGemma.PrintHelp(0);
37 return EXIT_SUCCESS;
38 }
39 if (argc == 2 && argv[1][0] == '-' && argv[1][1] == 'h') {
40 cGemma.PrintHeader();
41 cGemma.PrintHelp(0);
42 return EXIT_SUCCESS;
43 }
44 if (argc == 3 && argv[1][0] == '-' && argv[1][1] == 'h') {
45 string str;
46 str.assign(argv[2]);
47 cGemma.PrintHeader();
48 cGemma.PrintHelp(atoi(str.c_str()));
49 return EXIT_SUCCESS;
50 }
51 if (argc == 2 && argv[1][0] == '-' && argv[1][1] == 'l') {
52 cGemma.PrintHeader();
53 cGemma.PrintLicense();
54 return EXIT_SUCCESS;
55 }
56
57 cGemma.Assign(argc, argv, cPar);
58
59 ifstream check_dir((cPar.path_out).c_str());
60 if (!check_dir) {
61 #ifdef WINDOWS
62 mkdir((cPar.path_out).c_str());
63 #else
64 mkdir((cPar.path_out).c_str(), S_IRWXU | S_IRGRP | S_IROTH);
65 #endif
66 }
67
68 if (!is_quiet_mode())
69 cGemma.PrintHeader();
70
71 if (cPar.error == true) {
72 return EXIT_FAILURE;
73 }
74
75 if (is_quiet_mode()) {
76 stringstream ss;
77 cout.rdbuf(ss.rdbuf());
78 }
79
80 cPar.CheckParam();
81
82 if (cPar.error == true) {
83 return EXIT_FAILURE;
84 }
85
86 cGemma.BatchRun(cPar);
87
88 if (cPar.error == true) {
89 return EXIT_FAILURE;
90 }
91
92 cGemma.WriteLog(argc, argv, cPar);
93
94 return EXIT_SUCCESS;
95 }
96