/*
    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_vector.h"
#include "gsl/gsl_matrix.h"
#include "param.h"
#include "io.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