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diff --git a/param.h b/param.h
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@@ -1,232 +0,0 @@
-/*
-	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 __PARAM_H__                
-#define __PARAM_H__
-
-#include <vector>
-#include <map>
-#include <set>
-#include "gsl/gsl_vector.h"
-#include "gsl/gsl_matrix.h"
-
-using namespace std;
-
-
-
-class SNPINFO {
-public:
-	string chr;
-	string rs_number;
-	double cM;
-	long int base_position;
-	string a_minor;
-	string a_major;
-	size_t n_miss;
-	double missingness;
-	double maf;	
-};
-
-//results for lmm
-class SUMSTAT {
-public:
-	double beta;				//REML estimator for beta
-	double se;				//SE for beta  
-	double lambda_remle;		//REML estimator for lambda
-	double lambda_mle;		//MLE estimator for lambda
-	double p_wald;			//p value from a Wald test
-	double p_lrt;				//p value from a likelihood ratio test
-	double p_score;			//p value from a score test
-};
-
-//results for mvlmm
-class MPHSUMSTAT {
-public:
-	vector<double> v_beta;	//REML estimator for beta
-	double p_wald;			//p value from a Wald test
-	double p_lrt;				//p value from a likelihood ratio test
-	double p_score;			//p value from a score test
-	vector<double> v_Vg;	//estimator for Vg, right half
-	vector<double> v_Ve;	//estimator for Ve, right half
-	vector<double> v_Vbeta;	//estimator for Vbeta, right half
-};
-
-
-//hyper-parameters for bslmm
-class HYPBSLMM {
-public:
-	double h;
-	double pve;
-	double rho;
-	double pge;
-	double logp;
-	
-	size_t n_gamma;
-};
-
-
-
-
-class PARAM {
-public:	
-	// IO related parameters
-	bool mode_silence;
-	int a_mode;				//analysis mode, 1/2/3/4 for Frequentist tests
-	int k_mode;				//kinship read mode: 1: n by n matrix, 2: id/id/k_value; 		
-	vector<size_t> p_column;			//which phenotype column needs analysis
-	size_t d_pace;		//display pace
-	
-	string file_bfile;
-	string file_geno;
-	string file_pheno;
-	string file_anno;		//optional
-	string file_cvt;		//optional
-	string file_kin;
-	string file_ku, file_kd;
-	string file_mk;
-	string file_out;
-	string path_out;
-	
-	string file_epm;		//estimated parameter file
-	string file_ebv;		//estimated breeding value file
-	string file_log;		//log file containing mean estimate
-	
-	string file_read;		//file containing total number of reads
-	string file_gene;		//gene expression file
-	
-	string file_snps;		//file containing analyzed snps or genes
-	
-	
-	
-	// QC related parameters	
-	double miss_level;
-	double maf_level;	
-	double hwe_level;
-	double r2_level;
-	
-	// LMM related parameters
-	double l_min;
-	double l_max;
-	size_t n_region;
-	double l_mle_null, l_remle_null;
-	double logl_mle_H0, logl_remle_H0;
-	double pve_null, pve_se_null;
-	double vg_remle_null, ve_remle_null, vg_mle_null, ve_mle_null;
-	vector<double> Vg_remle_null, Ve_remle_null, Vg_mle_null, Ve_mle_null;
-	vector<double> VVg_remle_null, VVe_remle_null, VVg_mle_null, VVe_mle_null;
-	vector<double> beta_remle_null, se_beta_remle_null, beta_mle_null, se_beta_mle_null;
-	double p_nr;	
-	double em_prec, nr_prec;
-	size_t em_iter, nr_iter;
-	size_t crt;
-	double pheno_mean;		//phenotype mean from bslmm fitting or for prediction
-
-	//for fitting multiple variance components
-	//the first three are of size n_vc, and the next two are of size n_vc+1
-	vector<double> v_traceG;
-	vector<double> v_pve;
-	vector<double> v_se_pve;
-
-	vector<double> v_sigma2;
-	vector<double> v_se_sigma2;	
-	vector<double> v_beta;
-	vector<double> v_se_beta;	
-	
-	// BSLMM MCMC related parameters
-	double h_min, h_max, h_scale;			//priors for h
-	double rho_min, rho_max, rho_scale;		//priors for rho
-	double logp_min, logp_max, logp_scale;		//priors for log(pi)
-	size_t s_min, s_max;			//minimum and maximum number of gammas
-	size_t w_step;					//number of warm up/burn in iterations
-	size_t s_step;					//number of sampling iterations
-	size_t r_pace;					//record pace
-	size_t w_pace;					//write pace
-	size_t n_accept;				//number of acceptance
-	size_t n_mh;					//number of MH steps within each iteration
-	double geo_mean;				//mean of the geometric distribution
-	long int randseed;
-	double trace_G;
-
-	HYPBSLMM cHyp_initial;
-		
-	// Summary statistics
-	bool error;
-	size_t ni_total, ni_test, ni_cvt;	//number of individuals
-	size_t np_obs, np_miss;		//number of observed and missing phenotypes
-	size_t ns_total, ns_test;	//number of snps
-	size_t ng_total, ng_test;	//number of genes
-	size_t ni_control, ni_case;	//number of controls and number of cases
-	size_t n_cvt;			//number of covariates
-	size_t n_ph;			//number of phenotypes
-	size_t n_vc;			//number of variance components (including the diagonal matrix)
-	double time_total;		//record total time
-	double time_G;			//time spent on reading files the second time and calculate K
-	double time_eigen;		//time spent on eigen-decomposition
-	double time_UtX;		//time spent on calculating UX and Uy
-	double time_UtZ;		//time spent on calculating UtZ, for probit BSLMM
-	double time_opt;		//time spent on optimization iterations/or mcmc
-	double time_Omega;		//time spent on calculating Omega
-	double time_hyp;		//time spent on sampling hyper-parameters, in PMM
-	double time_Proposal;  //time spend on constructing the proposal distribution (i.e. the initial lmm or lm analysis)
-
-	// Data
-	vector<vector<double> > pheno;			//a vector record all phenotypes, NA replaced with -9
-	vector<vector<double> > cvt;			//a vector record all covariates, NA replaced with -9	
-	vector<vector<int> > indicator_pheno;			//a matrix record when a phenotype is missing for an individual; 0 missing, 1 available
-	vector<int> indicator_idv;				//indicator for individuals (phenotypes), 0 missing, 1 available for analysis
-	vector<int> indicator_snp;				//sequence indicator for SNPs: 0 ignored because of (a) maf, (b) miss, (c) non-poly; 1 available for analysis
-	vector<int> indicator_cvt;				//indicator for covariates, 0 missing, 1 available for analysis
-	
-	vector<int> indicator_bv;				//indicator for estimated breeding value file, 0 missing, 1 available for analysis
-	vector<int> indicator_read;				//indicator for read file, 0 missing, 1 available for analysis
-	vector<double> vec_read;				//total number of reads
-	vector<double> vec_bv;					//breeding values
-	vector<size_t> est_column;
-	
-	map<string, int> mapID2num;		//map small ID number to number, from 0 to n-1
-	map<string, string> mapRS2chr;		//map rs# to chromosome location
-	map<string, long int> mapRS2bp;		//map rs# to base position
-	map<string, double> mapRS2cM;		//map rs# to cM
-	map<string, double> mapRS2est;			//map rs# to parameters
-	
-	vector<SNPINFO> snpInfo;		//record SNP information
-	set<string> setSnps;			//a set of snps for analysis
-	
-	//constructor
-	PARAM();
-	
-	//functions
-	void ReadFiles ();		
-	void CheckParam (); 
-	void CheckData ();	
-	void PrintSummary ();
-	void ReadGenotypes (gsl_matrix *UtX, gsl_matrix *K, const bool calc_K);	
-	void CheckCvt ();
-	void CopyCvt (gsl_matrix *W);
-	void ProcessCvtPhen();
-	void CopyCvtPhen (gsl_matrix *W, gsl_vector *y, size_t flag);
-	void CopyCvtPhen (gsl_matrix *W, gsl_matrix *Y, size_t flag);
-	void CalcKin (gsl_matrix *matrix_kin);
-	void WriteMatrix (const gsl_matrix *matrix_U, const string suffix);
-	void WriteVector (const gsl_vector *vector_D, const string suffix);
-	void CopyRead (gsl_vector *log_N);
-};
-
-
-#endif
-