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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/>.
*/
#ifndef __VARCOV_H__
#define __VARCOV_H__
#include "gsl/gsl_matrix.h"
#include "gsl/gsl_vector.h"
#include "io.h"
#include "param.h"
using namespace std;
class VARCOV {
public:
// IO-related parameters.
string file_out;
string path_out;
string file_geno;
string file_bfile;
int d_pace;
vector<int> indicator_idv;
vector<int> indicator_snp;
vector<SNPINFO> snpInfo;
double time_opt;
// Class-specific parameters.
double window_cm;
size_t window_bp;
size_t window_ns;
// Main functions.
void CopyFromParam(PARAM &cPar);
void CopyToParam(PARAM &cPar);
void CalcNB(vector<SNPINFO> &snpInfo_sort);
void WriteCov(const int flag, const vector<SNPINFO> &snpInfo_sub,
const vector<vector<double>> &Cov_mat);
void AnalyzeBimbam();
void AnalyzePlink();
};
#endif
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