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+/*
+	Genome-wide Efficient Mixed Model Association (GEMMA)
+    Copyright (C) 2011  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"
+
+
+#ifdef FORCE_FLOAT
+#include "param_float.h"
+#include "io_float.h"
+#else
+#include "param.h"
+#include "io.h"
+#endif
+
+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
+
+