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/*
Genome-wide Efficient Mixed Model Association (GEMMA)
Copyright © 2011-2017, Xiang Zhou
Copyright © 2017, Peter Carbonetto
Copyright © 2017, Pjotr Prins
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/>.
*/
#ifndef __GEMMA_H__
#define __GEMMA_H__
#include "param.h"
using namespace std;
// OPTIONS
// -------
// gk: 21-22
// gs: 25-26
// gq: 27-28
// eigen: 31-32
// lmm: 1-5
// bslmm: 11-15
// predict: 41-43
// lm: 51
// vc: 61
// ci: 66-67
// calccor: 71
// gw: 72
enum M_MODE { M_LMM1=1, M_LMM2=2, M_LMM3=3, M_LMM4=4, M_LMM5=5,
M_BSLMM5=15,
M_KIN=21, M_KIN2=22, M_EIGEN=31 };
class GEMMA {
public:
// Parameters.
string version;
string date;
string year;
// Constructor.
GEMMA(void);
// Functions.
void PrintHeader(void);
void PrintHelp(size_t option);
void PrintLicense(void);
void Assign(int argc, char **argv, PARAM &cPar);
void BatchRun(PARAM &cPar);
void WriteLog(int argc, char **argv, PARAM &cPar);
};
#endif
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