version 0.95alpha

1 files changed, 0 insertions, 1928 deletions

diff --git a/bslmm.cpp b/bslmm.cpp
deleted file mode 100644
index 55a05ca..0000000
--- a/bslmm.cpp
+++ /dev/null
@@ -1,1928 +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/>.
- */
-
-#include <iostream>
-#include <fstream>
-#include <sstream>
-
-#include <iomanip>
-#include <cmath>
-#include <iostream>
-#include <stdio.h>
-#include <stdlib.h> 
-#include <ctime>
-#include <cstring>
-#include <algorithm>
-
-#include "gsl/gsl_vector.h"
-#include "gsl/gsl_matrix.h"
-#include "gsl/gsl_linalg.h"
-#include "gsl/gsl_blas.h"
-#include "gsl/gsl_eigen.h"
-#include "gsl/gsl_randist.h"
-#include "gsl/gsl_cdf.h"
-#include "gsl/gsl_roots.h"
-
-
-
-
-#include "lapack.h"
-
-#ifdef FORCE_FLOAT
-#include "param_float.h"
-#include "bslmm_float.h"
-#include "lmm_float.h"  //for class FUNC_PARAM and MatrixCalcLR
-#include "lm_float.h"
-#include "mathfunc_float.h"  //for function CenterVector
-#else
-#include "param.h"
-#include "bslmm.h"
-#include "lmm.h"
-#include "lm.h"
-#include "mathfunc.h"
-#endif
-
-using namespace std;
-
-
-
-
-void BSLMM::CopyFromParam (PARAM &cPar) 
-{
-	a_mode=cPar.a_mode;
-	d_pace=cPar.d_pace;
-	
-	file_bfile=cPar.file_bfile;
-	file_geno=cPar.file_geno;
-	file_out=cPar.file_out;
-	path_out=cPar.path_out;
-	
-	l_min=cPar.h_min;	
-	l_max=cPar.h_max;  
-	n_region=cPar.n_region;	
-	pve_null=cPar.pve_null;
-	pheno_mean=cPar.pheno_mean;
-	
-	time_UtZ=0.0;
-	time_Omega=0.0;
-	n_accept=0;
-	
-	h_min=cPar.h_min;	
-	h_max=cPar.h_max;  
-	h_scale=cPar.h_scale;
-	rho_min=cPar.rho_min;	
-	rho_max=cPar.rho_max;  
-	rho_scale=cPar.rho_scale;
-	logp_min=cPar.logp_min;	
-	logp_max=cPar.logp_max;  
-	logp_scale=cPar.logp_scale;
-	
-	s_min=cPar.s_min;
-	s_max=cPar.s_max;
-	w_step=cPar.w_step;
-	s_step=cPar.s_step;
-	r_pace=cPar.r_pace;
-	w_pace=cPar.w_pace;
-	n_mh=cPar.n_mh;
-	geo_mean=cPar.geo_mean;
-	randseed=cPar.randseed;
-	trace_G=cPar.trace_G;
-	
-	ni_total=cPar.ni_total;
-	ns_total=cPar.ns_total;
-	ni_test=cPar.ni_test;
-	ns_test=cPar.ns_test;
-	n_cvt=cPar.n_cvt;
-	
-	indicator_idv=cPar.indicator_idv;
-	indicator_snp=cPar.indicator_snp;
-	snpInfo=cPar.snpInfo;
-	
-	return;
-}
-
-
-void BSLMM::CopyToParam (PARAM &cPar) 
-{
-	cPar.time_UtZ=time_UtZ;
-	cPar.time_Omega=time_Omega;
-	cPar.time_Proposal=time_Proposal;
-	cPar.cHyp_initial=cHyp_initial;
-	cPar.n_accept=n_accept;
-	cPar.pheno_mean=pheno_mean;
-	cPar.randseed=randseed;
-	
-	return;
-}
-
-
-
-void BSLMM::WriteBV (const gsl_vector *bv) 
-{
-	string file_str;
-	file_str=path_out+"/"+file_out;
-	file_str+=".bv.txt";
-
-	ofstream outfile (file_str.c_str(), ofstream::out);
-	if (!outfile) {cout<<"error writing file: "<<file_str.c_str()<<endl; return;}
-	
-	size_t t=0;
-	for (size_t i=0; i<ni_total; ++i) {
-		if (indicator_idv[i]==0) {
-			outfile<<"NA"<<endl;
-		}		
-		else {
-			outfile<<scientific<<setprecision(6)<<gsl_vector_get(bv, t)<<endl;
-			t++;
-		}
-	}		
-	
-	outfile.clear();	
-	outfile.close();	
-	return;
-}
-
-
-
-
-void BSLMM::WriteParam (vector<pair<double, double> > &beta_g, const gsl_vector *alpha, const size_t w) 
-{
-	string file_str;
-	file_str=path_out+"/"+file_out;
-	file_str+=".param.txt";
-
-	ofstream outfile (file_str.c_str(), ofstream::out);
-	if (!outfile) {cout<<"error writing file: "<<file_str.c_str()<<endl; return;}
-	
-	outfile<<"chr"<<"\t"<<"rs"<<"\t"
-			<<"ps"<<"\t"<<"n_miss"<<"\t"<<"alpha"<<"\t"
-			<<"beta"<<"\t"<<"gamma"<<endl;
-	
-	size_t t=0;
-	for (size_t i=0; i<ns_total; ++i) {
-		if (indicator_snp[i]==0) {continue;}		
-		
-		outfile<<snpInfo[i].chr<<"\t"<<snpInfo[i].rs_number<<"\t"
-		<<snpInfo[i].base_position<<"\t"<<snpInfo[i].n_miss<<"\t";	
-				
-		outfile<<scientific<<setprecision(6)<<gsl_vector_get(alpha, t)<<"\t";
-		if (beta_g[t].second!=0) {
-			outfile<<beta_g[t].first/beta_g[t].second<<"\t"<<beta_g[t].second/(double)w<<endl;
-		}
-		else {
-			outfile<<0.0<<"\t"<<0.0<<endl;
-		}
-		t++;
-	}		
-	
-	outfile.clear();	
-	outfile.close();	
-	return;
-}
-
-
-void BSLMM::WriteParam (const gsl_vector *alpha) 
-{
-	string file_str;
-	file_str=path_out+"/"+file_out;
-	file_str+=".param.txt";
-
-	ofstream outfile (file_str.c_str(), ofstream::out);
-	if (!outfile) {cout<<"error writing file: "<<file_str.c_str()<<endl; return;}
-	
-	outfile<<"chr"<<"\t"<<"rs"<<"\t"
-			<<"ps"<<"\t"<<"n_miss"<<"\t"<<"alpha"<<"\t"
-			<<"beta"<<"\t"<<"gamma"<<endl;
-	
-	size_t t=0;
-	for (size_t i=0; i<ns_total; ++i) {
-		if (indicator_snp[i]==0) {continue;}		
-
-		outfile<<snpInfo[i].chr<<"\t"<<snpInfo[i].rs_number<<"\t"
-				<<snpInfo[i].base_position<<"\t"<<snpInfo[i].n_miss<<"\t";				
-		outfile<<scientific<<setprecision(6)<<gsl_vector_get(alpha, t)<<"\t";
-		outfile<<0.0<<"\t"<<0.0<<endl;
-		t++;
-	}		
-	
-	outfile.clear();	
-	outfile.close();	
-	return;
-}
-
-
-void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp, const gsl_matrix *Result_gamma, const size_t w_col) 
-{
-	string file_gamma, file_hyp;
-	file_gamma=path_out+"/"+file_out;
-	file_gamma+=".gamma.txt";
-	file_hyp=path_out+"/"+file_out;
-	file_hyp+=".hyp.txt";
-
-	ofstream outfile_gamma, outfile_hyp;
-		
-	if (flag==0) {
-		outfile_gamma.open (file_gamma.c_str(), ofstream::out);
-		outfile_hyp.open (file_hyp.c_str(), ofstream::out);
-		if (!outfile_gamma) {cout<<"error writing file: "<<file_gamma<<endl; return;}
-		if (!outfile_hyp) {cout<<"error writing file: "<<file_hyp<<endl; return;}
-		
-		outfile_hyp<<"h \t pve \t rho \t pge \t pi \t n_gamma"<<endl;
-		
-		for (size_t i=0; i<s_max; ++i) {
-			outfile_gamma<<"s"<<i<<"\t";
-		}
-		outfile_gamma<<endl;
-	}
-	else {
-		outfile_gamma.open (file_gamma.c_str(), ofstream::app);
-		outfile_hyp.open (file_hyp.c_str(), ofstream::app);
-		if (!outfile_gamma) {cout<<"error writing file: "<<file_gamma<<endl; return;}
-		if (!outfile_hyp) {cout<<"error writing file: "<<file_hyp<<endl; return;}
-		
-		size_t w;
-		if (w_col==0) {w=w_pace;}
-		else {w=w_col;}
-		
-		for (size_t i=0; i<w; ++i) {
-			outfile_hyp<<scientific;
-			for (size_t j=0; j<4; ++j) {
-				outfile_hyp<<setprecision(6)<<gsl_matrix_get (Result_hyp, i, j)<<"\t";
-			}
-			outfile_hyp<<setprecision(6)<<exp(gsl_matrix_get (Result_hyp, i, 4))<<"\t";
-			outfile_hyp<<(int)gsl_matrix_get (Result_hyp, i, 5)<<"\t";
-			outfile_hyp<<endl;
-		}
-		
-		for (size_t i=0; i<w; ++i) {
-			for (size_t j=0; j<s_max; ++j) {
-				outfile_gamma<<(int)gsl_matrix_get (Result_gamma, i, j)<<"\t";
-			}
-			outfile_gamma<<endl;
-		}
-		
-	}
-	
-	outfile_hyp.close();
-	outfile_hyp.clear();
-	outfile_gamma.close();
-	outfile_gamma.clear();	
-	return;
-}
-
-
-
-void BSLMM::CalcPgamma (double *p_gamma)
-{
-	double p, s=0.0;
-	for (size_t i=0; i<ns_test; ++i) {
-		p=0.7*gsl_ran_geometric_pdf (i+1, 1.0/geo_mean)+0.3/(double)ns_test;
-		p_gamma[i]=p;
-		s+=p;
-	}
-	for (size_t i=0; i<ns_test; ++i) {
-		p=p_gamma[i];
-		p_gamma[i]=p/s;
-	}
-	return;
-}
-
-
-
-void BSLMM::SetXgamma (gsl_matrix *Xgamma, const gsl_matrix *X, vector<size_t> &rank)
-{
-	size_t pos;
-	for (size_t i=0; i<rank.size(); ++i) {
-		pos=mapRank2pos[rank[i]];
-		gsl_vector_view Xgamma_col=gsl_matrix_column (Xgamma, i);
-		gsl_vector_const_view X_col=gsl_matrix_const_column (X, pos);
-		gsl_vector_memcpy (&Xgamma_col.vector, &X_col.vector);
-	}
-	
-	return;
-}
-
-
-
-double BSLMM::CalcPveLM (const gsl_matrix *UtXgamma, const gsl_vector *Uty, const double sigma_a2) 
-{
-	double pve, var_y;	
-	
-	gsl_matrix *Omega=gsl_matrix_alloc (UtXgamma->size2, UtXgamma->size2);
-	gsl_vector *Xty=gsl_vector_alloc (UtXgamma->size2);
-	gsl_vector *OiXty=gsl_vector_alloc (UtXgamma->size2);
-
-	gsl_matrix_set_identity (Omega);
-	gsl_matrix_scale (Omega, 1.0/sigma_a2); 
-
-#ifdef WITH_LAPACK
-	lapack_dgemm ((char *)"T", (char *)"N", 1.0, UtXgamma, UtXgamma, 1.0, Omega);
-#else
-	gsl_blas_dgemm (CblasTrans, CblasNoTrans, 1.0, UtXgamma, UtXgamma, 1.0, Omega);	
-#endif
-	gsl_blas_dgemv (CblasTrans, 1.0, UtXgamma, Uty, 0.0, Xty);
-
-	CholeskySolve(Omega, Xty, OiXty);
-	
-	gsl_blas_ddot (Xty, OiXty, &pve);
-	gsl_blas_ddot (Uty, Uty, &var_y);
-	
-	pve/=var_y;
-	
-	gsl_matrix_free (Omega);
-	gsl_vector_free (Xty);
-	gsl_vector_free (OiXty);
-
-	return pve;
-}
-
-
-void BSLMM::InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty, vector<size_t> &rank, class HYPBSLMM &cHyp, vector<pair<size_t, double> > &pos_loglr)
-{
-	double q_genome=gsl_cdf_chisq_Qinv(0.05/(double)ns_test, 1);
-	
-	cHyp.n_gamma=0;
-	for (size_t i=0; i<pos_loglr.size(); ++i) {
-		if (2.0*pos_loglr[i].second>q_genome) {cHyp.n_gamma++;}
-	}
-	if (cHyp.n_gamma<10) {cHyp.n_gamma=10;}
-	
-	if (cHyp.n_gamma>s_max) {cHyp.n_gamma=s_max;}
-	if (cHyp.n_gamma<s_min) {cHyp.n_gamma=s_min;}	
-	
-	rank.clear();
-	for (size_t i=0; i<cHyp.n_gamma; ++i) {
-		rank.push_back(i);
-	}
-	
-	cHyp.logp=log((double)cHyp.n_gamma/(double)ns_test);
-	cHyp.h=pve_null; 
-	
-	if (cHyp.logp==0) {cHyp.logp=-0.000001;}
-	if (cHyp.h==0) {cHyp.h=0.1;}
-
-	gsl_matrix *UtXgamma=gsl_matrix_alloc (ni_test, cHyp.n_gamma);
-	SetXgamma (UtXgamma, UtX, rank);
-	double sigma_a2;
-	if (trace_G!=0) {
-	  sigma_a2=cHyp.h*1.0/(trace_G*(1-cHyp.h)*exp(cHyp.logp)*(double)ns_test);
-	} else {
-	  sigma_a2=cHyp.h*1.0/( (1-cHyp.h)*exp(cHyp.logp)*(double)ns_test);
-	}
-	if (sigma_a2==0) {sigma_a2=0.025;}	
-	cHyp.rho=CalcPveLM (UtXgamma, Uty, sigma_a2)/cHyp.h;
-	gsl_matrix_free (UtXgamma);
-	
-	if (cHyp.rho>1.0) {cHyp.rho=1.0;}
-	
-	if (cHyp.h<h_min) {cHyp.h=h_min;}
-	if (cHyp.h>h_max) {cHyp.h=h_max;}
-	if (cHyp.rho<rho_min) {cHyp.rho=rho_min;}
-	if (cHyp.rho>rho_max) {cHyp.rho=rho_max;}
-	if (cHyp.logp<logp_min) {cHyp.logp=logp_min;}
-	if (cHyp.logp>logp_max) {cHyp.logp=logp_max;}
-	
-	
-//	if (fix_sigma>=0) {
-//		fix_sigma=cHyp.h;
-//		rho_max=1-cHyp.h;
-//		cHyp.rho=rho_max/2.0;
-//	}
-	
-	//Initial for grid sampling:
-//	cHyp.h=0.225;
-//	cHyp.rho=1.0;
-//	cHyp.logp=-4.835429;
-	
-	cout<<"initial value of h = "<<cHyp.h<<endl;
-	cout<<"initial value of rho = "<<cHyp.rho<<endl;
-	cout<<"initial value of pi = "<<exp(cHyp.logp)<<endl;
-	cout<<"initial value of |gamma| = "<<cHyp.n_gamma<<endl;
-	
-	return;
-}
-
-
-
-double BSLMM::CalcPosterior (const gsl_vector *Uty, const gsl_vector *K_eval, gsl_vector *Utu, gsl_vector *alpha_prime, class HYPBSLMM &cHyp)
-{
-	double sigma_b2=cHyp.h*(1.0-cHyp.rho)/(trace_G*(1-cHyp.h));
-	
-	gsl_vector *Utu_rand=gsl_vector_alloc (Uty->size);	
-	gsl_vector *weight_Hi=gsl_vector_alloc (Uty->size);
-	
-	double logpost=0.0;
-	double d, ds, uy, Hi_yy=0, logdet_H=0.0;
-	for (size_t i=0; i<ni_test; ++i) {
-		d=gsl_vector_get (K_eval, i)*sigma_b2;
-		ds=d/(d+1.0);
-		d=1.0/(d+1.0);		
-		gsl_vector_set (weight_Hi, i, d);
-		
-		logdet_H-=log(d);
-		uy=gsl_vector_get (Uty, i);
-		Hi_yy+=d*uy*uy;
-		
-		gsl_vector_set (Utu_rand, i, gsl_ran_gaussian(gsl_r, 1)*sqrt(ds));
-	}
-	
-	//sample tau
-	double tau=1.0;
-	if (a_mode==11) {tau = gsl_ran_gamma (gsl_r, (double)ni_test/2.0,  2.0/Hi_yy); }
-	
-	//sample alpha
-	gsl_vector_memcpy (alpha_prime, Uty);
-	gsl_vector_mul (alpha_prime, weight_Hi);
-	gsl_vector_scale (alpha_prime, sigma_b2);
-	
-	//sample u
-	gsl_vector_memcpy (Utu, alpha_prime);
-	gsl_vector_mul (Utu, K_eval);
-	if (a_mode==11) {gsl_vector_scale (Utu_rand, sqrt(1.0/tau));}
-	gsl_vector_add (Utu, Utu_rand);	
-	
-	//for quantitative traits, calculate pve and ppe
-	if (a_mode==11) {
-		gsl_blas_ddot (Utu, Utu, &d);
-		cHyp.pve=d/(double)ni_test;	
-		cHyp.pve/=cHyp.pve+1.0/tau;
-		cHyp.pge=0.0;	
-	}
-
-	//calculate likelihood
-	logpost=-0.5*logdet_H;
-	if (a_mode==11) {logpost-=0.5*(double)ni_test*log(Hi_yy);}
-	else {logpost-=0.5*Hi_yy;}
-	
-	logpost+=((double)cHyp.n_gamma-1.0)*cHyp.logp+((double)ns_test-(double)cHyp.n_gamma)*log(1-exp(cHyp.logp));
-	
-	gsl_vector_free (Utu_rand);
-	gsl_vector_free (weight_Hi);
-	
-	return logpost;
-}
-
-
-double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty, const gsl_vector *K_eval, gsl_vector *UtXb, gsl_vector *Utu, gsl_vector *alpha_prime, gsl_vector *beta, class HYPBSLMM &cHyp)
-{
-	clock_t time_start;	
-	
-	double sigma_a2=cHyp.h*cHyp.rho/(trace_G*(1-cHyp.h)*exp(cHyp.logp)*(double)ns_test);
-	double sigma_b2=cHyp.h*(1.0-cHyp.rho)/(trace_G*(1-cHyp.h));
-	
-	double logpost=0.0;
-	double d, ds, uy, P_yy=0, logdet_O=0.0, logdet_H=0.0;
-	
-	gsl_matrix *UtXgamma_eval=gsl_matrix_alloc (UtXgamma->size1, UtXgamma->size2);	
-	gsl_matrix *Omega=gsl_matrix_alloc (UtXgamma->size2, UtXgamma->size2);
-	gsl_vector *XtHiy=gsl_vector_alloc (UtXgamma->size2);
-	gsl_vector *beta_hat=gsl_vector_alloc (UtXgamma->size2);
-	gsl_vector *Utu_rand=gsl_vector_alloc (UtXgamma->size1);	
-	gsl_vector *weight_Hi=gsl_vector_alloc (UtXgamma->size1);
-	
-	gsl_matrix_memcpy (UtXgamma_eval, UtXgamma);
-	
-	logdet_H=0.0; P_yy=0.0;
-	for (size_t i=0; i<ni_test; ++i) {
-		gsl_vector_view UtXgamma_row=gsl_matrix_row (UtXgamma_eval, i);
-		d=gsl_vector_get (K_eval, i)*sigma_b2;
-		ds=d/(d+1.0);
-		d=1.0/(d+1.0);
-		gsl_vector_set (weight_Hi, i, d);
-		
-		logdet_H-=log(d);
-		uy=gsl_vector_get (Uty, i);
-		P_yy+=d*uy*uy;
-		gsl_vector_scale (&UtXgamma_row.vector, d);
-		
-		gsl_vector_set (Utu_rand, i, gsl_ran_gaussian(gsl_r, 1)*sqrt(ds));
-	}
-	
-	//calculate Omega
-	gsl_matrix_set_identity (Omega);
-	
-	time_start=clock();
-#ifdef WITH_LAPACK
-	lapack_dgemm ((char *)"T", (char *)"N", sigma_a2, UtXgamma_eval, UtXgamma, 1.0, Omega);
-#else
-	gsl_blas_dgemm (CblasTrans, CblasNoTrans, sigma_a2, UtXgamma_eval, UtXgamma, 1.0, Omega);
-#endif	
-	time_Omega+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
-	
-	
-	//calculate beta_hat
-	gsl_blas_dgemv (CblasTrans, 1.0, UtXgamma_eval, Uty, 0.0, XtHiy);	
-
-	logdet_O=CholeskySolve(Omega, XtHiy, beta_hat);
-	
-	gsl_vector_scale (beta_hat, sigma_a2);
-
-	gsl_blas_ddot (XtHiy, beta_hat, &d);
-	P_yy-=d;
-	
-	//sample tau
-	double tau=1.0;
-	if (a_mode==11) {tau =gsl_ran_gamma (gsl_r, (double)ni_test/2.0,  2.0/P_yy); }
-
-	//sample beta
-	for (size_t i=0; i<beta->size; i++)
-	{
-		d=gsl_ran_gaussian(gsl_r, 1); 
-		gsl_vector_set(beta, i, d); 
-	}
-	gsl_blas_dtrsv(CblasUpper, CblasNoTrans, CblasNonUnit, Omega, beta); 
-	
-	
-	//it compuates inv(L^T(Omega)) %*% beta;  
-	gsl_vector_scale(beta, sqrt(sigma_a2/tau));
-	gsl_vector_add(beta, beta_hat); 
-	gsl_blas_dgemv (CblasNoTrans, 1.0, UtXgamma, beta, 0.0, UtXb);
-	
-	//sample alpha
-	gsl_vector_memcpy (alpha_prime, Uty);
-	gsl_vector_sub (alpha_prime, UtXb);
-	gsl_vector_mul (alpha_prime, weight_Hi);
-	gsl_vector_scale (alpha_prime, sigma_b2);
-	
-	//sample u
-	gsl_vector_memcpy (Utu, alpha_prime);
-	gsl_vector_mul (Utu, K_eval);
-	
-	if (a_mode==11) {gsl_vector_scale (Utu_rand, sqrt(1.0/tau));}
-	gsl_vector_add (Utu, Utu_rand);	
-	
-	
-	//for quantitative traits, calculate pve and pge
-	if (a_mode==11) {
-		gsl_blas_ddot (UtXb, UtXb, &d);
-		cHyp.pge=d/(double)ni_test;
-	
-		gsl_blas_ddot (Utu, Utu, &d);
-		cHyp.pve=cHyp.pge+d/(double)ni_test;
-		
-		if (cHyp.pve==0) {cHyp.pge=0.0;}
-		else {cHyp.pge/=cHyp.pve;}
-		cHyp.pve/=cHyp.pve+1.0/tau;	
-	}	
-	
-
-	gsl_matrix_free (UtXgamma_eval);
-	gsl_matrix_free (Omega);
-	gsl_vector_free (XtHiy);
-	gsl_vector_free (beta_hat);
-	gsl_vector_free (Utu_rand);	
-	gsl_vector_free (weight_Hi);
-	
-	logpost=-0.5*logdet_H-0.5*logdet_O;
-	if (a_mode==11) {logpost-=0.5*(double)ni_test*log(P_yy);}
-	else {logpost-=0.5*P_yy;}
-//	else {logpost+=-0.5*P_yy*tau+0.5*(double)ni_test*log(tau);}
-	logpost+=((double)cHyp.n_gamma-1.0)*cHyp.logp+((double)ns_test-(double)cHyp.n_gamma)*log(1.0-exp(cHyp.logp));
-	
-	return logpost;
-}
-
-
-
-//calculate pve and pge, and calculate z_hat for case-control data	
-void BSLMM::CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *Utu, gsl_vector *z_hat, class HYPBSLMM &cHyp) 
-{
-	double d;
-	
-	gsl_blas_ddot (Utu, Utu, &d);
-	cHyp.pve=d/(double)ni_test;	
-		
-	gsl_blas_dgemv (CblasNoTrans, 1.0, U, Utu, 0.0, z_hat);
-		
-	cHyp.pve/=cHyp.pve+1.0;
-	cHyp.pge=0.0;	
-	
-	return;
-}
-
-
-//calculate pve and pge, and calculate z_hat for case-control data	
-void BSLMM::CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *UtXb, const gsl_vector *Utu, gsl_vector *z_hat, class HYPBSLMM &cHyp) 
-{
-	double d;
-	gsl_vector *UtXbU=gsl_vector_alloc (Utu->size);
-	
-	gsl_blas_ddot (UtXb, UtXb, &d);
-	cHyp.pge=d/(double)ni_test;
-	
-	gsl_blas_ddot (Utu, Utu, &d);
-	cHyp.pve=cHyp.pge+d/(double)ni_test;
-	
-	gsl_vector_memcpy (UtXbU, Utu);
-	gsl_vector_add (UtXbU, UtXb);
-	gsl_blas_dgemv (CblasNoTrans, 1.0, U, UtXbU, 0.0, z_hat);	
-	
-	if (cHyp.pve==0) {cHyp.pge=0.0;}
-	else {cHyp.pge/=cHyp.pve;}
-	
-	cHyp.pve/=cHyp.pve+1.0;
-	
-	gsl_vector_free(UtXbU);
-	return;
-}
-
-
-
-
-void BSLMM::SampleZ (const gsl_vector *y, const gsl_vector *z_hat, gsl_vector *z)
-{	
-	double d1, d2, z_rand=0.0;
-	for (size_t i=0; i<z->size; ++i) {
-		d1=gsl_vector_get (y, i);
-		d2=gsl_vector_get (z_hat, i);
-		//y is centerred for case control studies
-		if (d1<=0.0) {
-			//control, right truncated
-			do {				
-				z_rand=d2+gsl_ran_gaussian(gsl_r, 1.0);
-			} while (z_rand>0.0);
-		}
-		else {
-			do {
-				z_rand=d2+gsl_ran_gaussian(gsl_r, 1.0);
-			} while (z_rand<0.0);
-		}
-		
-		gsl_vector_set (z, i, z_rand);
-	}
-
-	return;
-}
-
-
-
-
-
-double BSLMM::ProposeHnRho (const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_new, const size_t &repeat)
-{
-	
-	double h=cHyp_old.h, rho=cHyp_old.rho;
-	
-	double d_h=(h_max-h_min)*h_scale, d_rho=(rho_max-rho_min)*rho_scale;
-	
-	for (size_t i=0; i<repeat; ++i) {
-		h=h+(gsl_rng_uniform(gsl_r)-0.5)*d_h;
-		if (h<h_min) {h=2*h_min-h;}
-		if (h>h_max) {h=2*h_max-h;}
-		
-		rho=rho+(gsl_rng_uniform(gsl_r)-0.5)*d_rho;
-		if (rho<rho_min) {rho=2*rho_min-rho;}
-		if (rho>rho_max) {rho=2*rho_max-rho;}
-	}
-	/*
-	//Grid Sampling
-	for (size_t i=0; i<repeat; ++i) {
-		if (gsl_rng_uniform(gsl_r)<0.66) {continue;}
-		h=h+(gsl_rng_uniform_int(gsl_r, 2)-0.5)*0.1;
-		if (h<h_min) {h=h_max;}
-		if (h>h_max) {h=h_min;}
-	}
-	
-	for (size_t i=0; i<repeat; ++i) {
-		if (gsl_rng_uniform(gsl_r)<0.66) {continue;}
-		rho=rho+(gsl_rng_uniform_int(gsl_r, 2)-0.5)*0.1;
-		if (rho<rho_min) {rho=rho_max;}
-		if (rho>rho_max) {rho=rho_min;}
-	}
-	*/
-	cHyp_new.h=h;
-	cHyp_new.rho=rho;
-	return 0.0;
-}
-
-
-double BSLMM::ProposePi (const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_new, const size_t &repeat)
-{
-	double logp_old=cHyp_old.logp, logp_new=cHyp_old.logp;
-	double log_ratio=0.0;
-	
-	double d_logp=min(0.1, (logp_max-logp_min)*logp_scale);
-	
-	for (size_t i=0; i<repeat; ++i) {
-		logp_new=logp_old+(gsl_rng_uniform(gsl_r)-0.5)*d_logp;
-		if (logp_new<logp_min) {logp_new=2*logp_min-logp_new;}
-		if (logp_new>logp_max) {logp_new=2*logp_max-logp_new;}		
-		
-		log_ratio+=logp_new-logp_old;
-		logp_old=logp_new;
-	}
-	/*
-	//Grid Sampling
-	for (size_t i=0; i<repeat; ++i) {
-		if (gsl_rng_uniform(gsl_r)<0.66) {continue;}
-		logp_new=logp_old+(gsl_rng_uniform_int(gsl_r, 2)-0.5)*0.5*log(10.0);
-		if (logp_new<logp_min) {logp_new=logp_max;}
-		if (logp_new>logp_max) {logp_new=logp_min;}	
-		
-		log_ratio+=logp_new-logp_old;
-		logp_old=logp_new;
-	}
-	*/
-	cHyp_new.logp=logp_new;
-	
-	return log_ratio;
-}
-
-bool comp_vec (size_t a, size_t b)
-{
-	return (a < b); 
-}
-
-
-double BSLMM::ProposeGamma (const vector<size_t> &rank_old, vector<size_t> &rank_new, const double *p_gamma, const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_new, const size_t &repeat)
-{
-	map<size_t, int> mapRank2in;
-	size_t r;
-	double unif, logp=0.0;
-	int flag_gamma;
-	size_t r_add, r_remove, col_id;
-	
-	rank_new.clear();
-	if (cHyp_old.n_gamma!=rank_old.size()) {cout<<"size wrong"<<endl;}
-	
-	if (cHyp_old.n_gamma!=0) {
-		for (size_t i=0; i<rank_old.size(); ++i) {
-			r=rank_old[i];
-			rank_new.push_back(r);
-			mapRank2in[r]=1;
-		}
-	}
-	cHyp_new.n_gamma=cHyp_old.n_gamma;	
-	
-	for (size_t i=0; i<repeat; ++i) {
-		unif=gsl_rng_uniform(gsl_r); 
-	
-		if (unif < 0.40 && cHyp_new.n_gamma<s_max) {flag_gamma=1;}
-		else if (unif>=0.40 && unif < 0.80 && cHyp_new.n_gamma>s_min) {flag_gamma=2;}
-		else if (unif>=0.80 && cHyp_new.n_gamma>0 && cHyp_new.n_gamma<ns_test) {flag_gamma=3;}
-		else {flag_gamma=4;}
-	
-		if(flag_gamma==1)  {//add a snp; 
-			do {
-				r_add=gsl_ran_discrete (gsl_r, gsl_t);
-			} while (mapRank2in.count(r_add)!=0); 
-		
-			double prob_total=1.0;
-			for (size_t i=0; i<cHyp_new.n_gamma; ++i) {
-				r=rank_new[i];
-				prob_total-=p_gamma[r];
-			}
-
-			mapRank2in[r_add]=1;
-			rank_new.push_back(r_add);
-			cHyp_new.n_gamma++;
-			logp+=-log(p_gamma[r_add]/prob_total)-log((double)cHyp_new.n_gamma);
-		}
-		else if (flag_gamma==2) {//delete a snp;
-			col_id=gsl_rng_uniform_int(gsl_r, cHyp_new.n_gamma);		
-			r_remove=rank_new[col_id];
-		
-			double prob_total=1.0;
-			for (size_t i=0; i<cHyp_new.n_gamma; ++i) {
-				r=rank_new[i];
-				prob_total-=p_gamma[r];
-			}
-			prob_total+=p_gamma[r_remove];
-		
-			mapRank2in.erase(r_remove);
-			rank_new.erase(rank_new.begin()+col_id);
-			logp+=log(p_gamma[r_remove]/prob_total)+log((double)cHyp_new.n_gamma);
-			cHyp_new.n_gamma--;
-		}
-		else if (flag_gamma==3) {//switch a snp;
-			col_id=gsl_rng_uniform_int(gsl_r, cHyp_new.n_gamma);		
-			r_remove=rank_new[col_id];
-		//careful with the proposal
-			do {
-				r_add=gsl_ran_discrete (gsl_r, gsl_t);
-			} while (mapRank2in.count(r_add)!=0); 
-			
-			double prob_total=1.0;
-			for (size_t i=0; i<cHyp_new.n_gamma; ++i) {
-				r=rank_new[i];
-				prob_total-=p_gamma[r];
-			}
-			
-			logp+=log(p_gamma[r_remove]/(prob_total+p_gamma[r_remove]-p_gamma[r_add]) );
-			logp-=log(p_gamma[r_add]/prob_total);
-			
-			mapRank2in.erase(r_remove);
-			mapRank2in[r_add]=1;
-			rank_new.erase(rank_new.begin()+col_id);
-			rank_new.push_back(r_add);
-		}
-		else {logp+=0;}//do not change
-	}
-	
-	stable_sort (rank_new.begin(), rank_new.end(), comp_vec);
-
-	mapRank2in.clear();
-	return logp;
-}
-
-
-
-
-
-
-bool comp_lr (pair<size_t, double> a, pair<size_t, double> b)
-{
-	return (a.second > b.second); 
-}
-
-
-
-
-
-
-
-//if a_mode==13 then Uty==y
-void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *K_eval, const gsl_vector *y) {
-	clock_t time_start;	
-
-	class HYPBSLMM cHyp_old, cHyp_new;
-	
-	gsl_matrix *Result_hyp=gsl_matrix_alloc (w_pace, 6);
-	gsl_matrix *Result_gamma=gsl_matrix_alloc (w_pace, s_max);	
-	
-	gsl_vector *alpha_prime=gsl_vector_alloc (ni_test);		
-	gsl_vector *alpha_new=gsl_vector_alloc (ni_test);
-	gsl_vector *alpha_old=gsl_vector_alloc (ni_test);	
-	gsl_vector *Utu=gsl_vector_alloc (ni_test);
-	gsl_vector *Utu_new=gsl_vector_alloc (ni_test);
-	gsl_vector *Utu_old=gsl_vector_alloc (ni_test);
-	
-	gsl_vector *UtXb_new=gsl_vector_alloc (ni_test);
-	gsl_vector *UtXb_old=gsl_vector_alloc (ni_test);
-	
-	gsl_vector *z_hat=gsl_vector_alloc (ni_test);
-	gsl_vector *z=gsl_vector_alloc (ni_test);
-	gsl_vector *Utz=gsl_vector_alloc (ni_test);	
-
-	gsl_vector_memcpy (Utz, Uty);			
-	
-	double logPost_new, logPost_old;
-	double logMHratio;
-	double mean_z=0.0;	
-	
-	gsl_matrix_set_zero (Result_gamma);
-	gsl_vector_set_zero (Utu);
-	gsl_vector_set_zero (alpha_prime);
-	if (a_mode==13) {
-		pheno_mean=0.0;
-	}
-	
-	vector<pair<double, double> > beta_g;
-	for (size_t i=0; i<ns_test; i++) {
-		beta_g.push_back(make_pair(0.0, 0.0));
-	}
-	
-	vector<size_t> rank_new, rank_old;
-	vector<double> beta_new, beta_old;	
-
-	vector<pair<size_t, double> > pos_loglr;
-
-	time_start=clock();
-	MatrixCalcLR (U, UtX, Utz, K_eval, l_min, l_max, n_region, pos_loglr);
-	time_Proposal=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
-
-	stable_sort (pos_loglr.begin(), pos_loglr.end(), comp_lr);
-	for (size_t i=0; i<ns_test; ++i) {
-		mapRank2pos[i]=pos_loglr[i].first;
-	}
-	
-	//calculate proposal distribution for gamma (unnormalized), and set up gsl_r and gsl_t			
-	gsl_rng_env_setup();                
-	const gsl_rng_type * gslType;                                               
-	gslType = gsl_rng_default; 
-	if (randseed<0)
-	{
-		time_t rawtime;
-		time (&rawtime);
-		tm * ptm = gmtime (&rawtime);
-		
-		randseed = (unsigned) (ptm->tm_hour%24*3600+ptm->tm_min*60+ptm->tm_sec);
-	}
-	gsl_r = gsl_rng_alloc(gslType); 
-	gsl_rng_set(gsl_r, randseed);
-	
-	double *p_gamma = new double[ns_test]; 
-	CalcPgamma (p_gamma);
-	
-	gsl_t=gsl_ran_discrete_preproc (ns_test, p_gamma);
-	
-	//initial parameters
-	InitialMCMC (UtX, Utz, rank_old, cHyp_old, pos_loglr);
-//	if (fix_sigma>=0) {
-//		rho_max=1-fix_sigma;
-//		cHyp_old.h=fix_sigma/(1-cHyp_old.rho);
-//	}
-	
-	cHyp_initial=cHyp_old;
-	
-	if (cHyp_old.n_gamma==0 || cHyp_old.rho==0) {
-		logPost_old=CalcPosterior(Utz, K_eval, Utu_old, alpha_old, cHyp_old);
-
-		beta_old.clear();
-		for (size_t i=0; i<cHyp_old.n_gamma; ++i) {
-		  beta_old.push_back(0);
-		}	
-	}
-	else {
-		gsl_matrix *UtXgamma=gsl_matrix_alloc (ni_test, cHyp_old.n_gamma);
-		gsl_vector *beta=gsl_vector_alloc (cHyp_old.n_gamma);
-		SetXgamma (UtXgamma, UtX, rank_old);		
-		logPost_old=CalcPosterior(UtXgamma, Utz, K_eval, UtXb_old, Utu_old, alpha_old, beta, cHyp_old);
-	
-		beta_old.clear();
-		for (size_t i=0; i<beta->size; ++i) {
-			beta_old.push_back(gsl_vector_get(beta, i));
-		}	
-		gsl_matrix_free (UtXgamma);
-		gsl_vector_free (beta);
-	}	
-	
-	//calculate centered z_hat, and pve
-	if (a_mode==13) {
-		time_start=clock();
-		if (cHyp_old.n_gamma==0 || cHyp_old.rho==0) {
-			CalcCC_PVEnZ (U, Utu_old, z_hat, cHyp_old);
-		}
-		else {
-			CalcCC_PVEnZ (U, UtXb_old, Utu_old, z_hat, cHyp_old);
-		}
-		time_UtZ+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
-	}
-	
-	//start MCMC
-	int accept;
-	size_t total_step=w_step+s_step;
-	size_t w=0, w_col, pos;
-	size_t repeat=0;
-	
-	for (size_t t=0; t<total_step; ++t) {
-		if (t%d_pace==0 || t==total_step-1) {ProgressBar ("Running MCMC ", t, total_step-1, (double)n_accept/(double)(t*n_mh+1));}
-//		if (t>10) {break;}		
-
-		if (a_mode==13) {			
-			SampleZ (y, z_hat, z);		
-			mean_z=CenterVector (z);	
-			
-			time_start=clock();
-			gsl_blas_dgemv (CblasTrans, 1.0, U, z, 0.0, Utz);
-			time_UtZ+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
-		
-			//First proposal
-			if (cHyp_old.n_gamma==0 || cHyp_old.rho==0) {				
-				logPost_old=CalcPosterior(Utz, K_eval, Utu_old, alpha_old, cHyp_old);
-				beta_old.clear();
-				for (size_t i=0; i<cHyp_old.n_gamma; ++i) {
-				  beta_old.push_back(0);
-				}	
-			}
-			else {
-				gsl_matrix *UtXgamma=gsl_matrix_alloc (ni_test, cHyp_old.n_gamma);
-				gsl_vector *beta=gsl_vector_alloc (cHyp_old.n_gamma);
-				SetXgamma (UtXgamma, UtX, rank_old);
-				logPost_old=CalcPosterior(UtXgamma, Utz, K_eval, UtXb_old, Utu_old, alpha_old, beta, cHyp_old);
-				
-				beta_old.clear();
-				for (size_t i=0; i<beta->size; ++i) {
-					beta_old.push_back(gsl_vector_get(beta, i));
-				}
-				gsl_matrix_free (UtXgamma);
-				gsl_vector_free (beta);
-			}
-		}
-		
-		//MH steps
-		for (size_t i=0; i<n_mh; ++i) {
-			if (gsl_rng_uniform(gsl_r)<0.33) {repeat = 1+gsl_rng_uniform_int(gsl_r, 20);}
-			else {repeat=1;}
-			
-			logMHratio=0.0;
-			logMHratio+=ProposeHnRho(cHyp_old, cHyp_new, repeat);		
-			logMHratio+=ProposeGamma (rank_old, rank_new, p_gamma, cHyp_old, cHyp_new, repeat);	
-			logMHratio+=ProposePi(cHyp_old, cHyp_new, repeat);
-			
-//			if (fix_sigma>=0) {
-//				cHyp_new.h=fix_sigma/(1-cHyp_new.rho);
-//			}
-			
-			if (cHyp_new.n_gamma==0 || cHyp_new.rho==0) {
-				logPost_new=CalcPosterior(Utz, K_eval, Utu_new, alpha_new, cHyp_new);
-				beta_new.clear();
-				for (size_t i=0; i<cHyp_new.n_gamma; ++i) {
-				  beta_new.push_back(0);
-				}	
-			}
-			else {
-				gsl_matrix *UtXgamma=gsl_matrix_alloc (ni_test, cHyp_new.n_gamma);
-				gsl_vector *beta=gsl_vector_alloc (cHyp_new.n_gamma);
-				SetXgamma (UtXgamma, UtX, rank_new);
-				logPost_new=CalcPosterior(UtXgamma, Utz, K_eval, UtXb_new, Utu_new, alpha_new, beta, cHyp_new);
-				beta_new.clear();
-				for (size_t i=0; i<beta->size; ++i) {
-					beta_new.push_back(gsl_vector_get(beta, i));
-				}
-				gsl_matrix_free (UtXgamma);
-				gsl_vector_free (beta);
-			}	
-			
-			logMHratio+=logPost_new-logPost_old;		
-		
-			if (logMHratio>0 || log(gsl_rng_uniform(gsl_r))<logMHratio) {accept=1; n_accept++;}
-			else {accept=0;}
-
-			if (accept==1) {			
-				logPost_old=logPost_new;
-				rank_old.clear(); beta_old.clear();
-				if (rank_new.size()!=0) {
-					for (size_t i=0; i<rank_new.size(); ++i) {
-						rank_old.push_back(rank_new[i]);
-						beta_old.push_back(beta_new[i]);
-					}
-				}
-				cHyp_old=cHyp_new;
-				gsl_vector_memcpy (alpha_old, alpha_new);
-				gsl_vector_memcpy (UtXb_old, UtXb_new);
-				gsl_vector_memcpy (Utu_old, Utu_new);
-			}
-			else {cHyp_new=cHyp_old;}
-		}				
-		
-		//calculate z_hat, and pve
-		if (a_mode==13) {
-			time_start=clock();
-			if (cHyp_old.n_gamma==0 || cHyp_old.rho==0) {
-				CalcCC_PVEnZ (U, Utu_old, z_hat, cHyp_old);
-			}
-			else {
-				CalcCC_PVEnZ (U, UtXb_old, Utu_old, z_hat, cHyp_old);
-			}
-			
-			//sample mu and update z hat
-			gsl_vector_sub (z, z_hat);
-			mean_z+=CenterVector(z);
-			mean_z+=gsl_ran_gaussian(gsl_r, sqrt(1.0/(double) ni_test) );			
-			
-			gsl_vector_add_constant (z_hat, mean_z);
-			
-			time_UtZ+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
-		}
-		
-		//Save data
-		if (t<w_step) {continue;}
-		else {		
-			if (t%r_pace==0) {
-				w_col=w%w_pace;
-				if (w_col==0) {
-					if (w==0) {WriteResult (0, Result_hyp, Result_gamma, w_col);}					
-					else {
-						WriteResult (1, Result_hyp, Result_gamma, w_col);
-						gsl_matrix_set_zero (Result_hyp);
-						gsl_matrix_set_zero (Result_gamma);
-					}
-				}
-				
-				gsl_matrix_set (Result_hyp, w_col, 0, cHyp_old.h);
-				gsl_matrix_set (Result_hyp, w_col, 1, cHyp_old.pve);
-				gsl_matrix_set (Result_hyp, w_col, 2, cHyp_old.rho);
-				gsl_matrix_set (Result_hyp, w_col, 3, cHyp_old.pge);
-				gsl_matrix_set (Result_hyp, w_col, 4, cHyp_old.logp);
-				gsl_matrix_set (Result_hyp, w_col, 5, cHyp_old.n_gamma);
-				
-				for (size_t i=0; i<cHyp_old.n_gamma; ++i) {
-					pos=mapRank2pos[rank_old[i]]+1;
-
-					gsl_matrix_set (Result_gamma, w_col, i, pos);
-					
-					beta_g[pos-1].first+=beta_old[i];
-					beta_g[pos-1].second+=1.0;	
-				}
-				
-				gsl_vector_add (alpha_prime, alpha_old);
-				gsl_vector_add (Utu, Utu_old);
-				
-				if (a_mode==13) {
-					pheno_mean+=mean_z;
-				}
-				
-				w++;
-				
-			}
-			
-		}
-	}
-	cout<<endl;
-	
-	w_col=w%w_pace;
-	WriteResult (1, Result_hyp, Result_gamma, w_col);	
-	
-	gsl_matrix_free(Result_hyp);
-	gsl_matrix_free(Result_gamma);	
-	
-	gsl_vector_free(z_hat);
-	gsl_vector_free(z);
-	gsl_vector_free(Utz);	
-	gsl_vector_free(UtXb_new);	
-	gsl_vector_free(UtXb_old);
-	gsl_vector_free(alpha_new);	
-	gsl_vector_free(alpha_old);
-	gsl_vector_free(Utu_new);	
-	gsl_vector_free(Utu_old);	
-	
-	gsl_vector_scale (alpha_prime, 1.0/(double)w);	
-	gsl_vector_scale (Utu, 1.0/(double)w);	
-	if (a_mode==13) {
-		pheno_mean/=(double)w;
-	}
-	
-	gsl_vector *alpha=gsl_vector_alloc (ns_test);
-	gsl_blas_dgemv (CblasTrans, 1.0/(double)ns_test, UtX, alpha_prime, 0.0, alpha);	
-	WriteParam (beta_g, alpha, w);
-	gsl_vector_free(alpha);
-	
-	gsl_blas_dgemv (CblasNoTrans, 1.0, U, Utu, 0.0, alpha_prime);
-	WriteBV(alpha_prime);	
-	
-	gsl_vector_free(alpha_prime);				
-	gsl_vector_free(Utu);	
-		
-	delete [] p_gamma;
-	beta_g.clear();
-	
-	return;
-}
-
-
-
-void BSLMM::RidgeR(const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *eval, const double lambda)
-{
-	gsl_vector *beta=gsl_vector_alloc (UtX->size2);
-	gsl_vector *H_eval=gsl_vector_alloc (Uty->size);
-	gsl_vector *bv=gsl_vector_alloc (Uty->size);
-
-	gsl_vector_memcpy (H_eval, eval);
-	gsl_vector_scale (H_eval, lambda);
-	gsl_vector_add_constant (H_eval, 1.0);
-	
-	gsl_vector_memcpy (bv, Uty);
-	gsl_vector_div (bv, H_eval);	
-
-	gsl_blas_dgemv (CblasTrans, lambda/(double)UtX->size2, UtX, bv, 0.0, beta);
-	gsl_vector_add_constant (H_eval, -1.0);
-	gsl_vector_mul (H_eval, bv);
-	gsl_blas_dgemv (CblasNoTrans, 1.0, U, H_eval, 0.0, bv);
-
-	WriteParam (beta);
-	WriteBV(bv);
-	
-	gsl_vector_free (H_eval);
-	gsl_vector_free (beta);
-	gsl_vector_free (bv);
-	
-	return;
-}
- 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-//below fits MCMC for rho=1
-void BSLMM::CalcXtX (const gsl_matrix *X, const gsl_vector *y, const size_t s_size, gsl_matrix *XtX, gsl_vector *Xty)
-{
-  time_t time_start=clock();	
-  gsl_matrix_const_view X_sub=gsl_matrix_const_submatrix(X, 0, 0, X->size1, s_size);
-  gsl_matrix_view XtX_sub=gsl_matrix_submatrix(XtX, 0, 0, s_size, s_size);
-  gsl_vector_view Xty_sub=gsl_vector_subvector(Xty, 0, s_size);
-
-#ifdef WITH_LAPACK
-  lapack_dgemm ((char *)"T", (char *)"N", 1.0, &X_sub.matrix, &X_sub.matrix, 0.0, &XtX_sub.matrix);
-#else
-  gsl_blas_dgemm (CblasTrans, CblasNoTrans, 1.0, &X_sub.matrix, &X_sub.matrix, 0.0, &XtX_sub.matrix);
-#endif
-  gsl_blas_dgemv(CblasTrans, 1.0, &X_sub.matrix, y, 0.0, &Xty_sub.vector);
-
-  time_Omega+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
-
-  return;
-}
-
-
-void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old, const gsl_matrix *XtX_old, const gsl_vector *Xty_old, const gsl_vector *y, const vector<size_t> &rank_old, const vector<size_t> &rank_new, gsl_matrix *X_new, gsl_matrix *XtX_new, gsl_vector *Xty_new)
-{
-  double d;
-
-  //rank_old and rank_new are sorted already inside PorposeGamma
-  //calculate vectors rank_remove and rank_add
-  //  size_t v_size=max(rank_old.size(), rank_new.size());
-  //make sure that v_size is larger than repeat
-  size_t v_size=20;
-  vector<size_t> rank_remove(v_size), rank_add(v_size), rank_union(s_max+v_size);
-  vector<size_t>::iterator it;
-
-  it=set_difference (rank_old.begin(), rank_old.end(), rank_new.begin(), rank_new.end(), rank_remove.begin());
-  rank_remove.resize(it-rank_remove.begin());
-
-  it=set_difference (rank_new.begin(), rank_new.end(), rank_old.begin(), rank_old.end(), rank_add.begin());
-  rank_add.resize(it-rank_add.begin());
-
-  it=set_union (rank_new.begin(), rank_new.end(), rank_old.begin(), rank_old.end(), rank_union.begin());
-  rank_union.resize(it-rank_union.begin());
-
-  //map rank_remove and rank_add
-  map<size_t, int> mapRank2in_remove, mapRank2in_add;
-  for (size_t i=0; i<rank_remove.size(); i++) {
-    mapRank2in_remove[rank_remove[i]]=1;
-  }
-  for (size_t i=0; i<rank_add.size(); i++) {
-    mapRank2in_add[rank_add[i]]=1;
-  }
-
-  //obtain the subset of matrix/vector
-  gsl_matrix_const_view Xold_sub=gsl_matrix_const_submatrix(X_old, 0, 0, X_old->size1, rank_old.size());
-  gsl_matrix_const_view XtXold_sub=gsl_matrix_const_submatrix(XtX_old, 0, 0, rank_old.size(), rank_old.size());
-  gsl_vector_const_view Xtyold_sub=gsl_vector_const_subvector(Xty_old, 0, rank_old.size());
-
-  gsl_matrix_view Xnew_sub=gsl_matrix_submatrix(X_new, 0, 0, X_new->size1, rank_new.size());
-  gsl_matrix_view XtXnew_sub=gsl_matrix_submatrix(XtX_new, 0, 0, rank_new.size(), rank_new.size());
-  gsl_vector_view Xtynew_sub=gsl_vector_subvector(Xty_new, 0, rank_new.size());
-
-  //get X_new and calculate XtX_new
-  /*
-  if (rank_remove.size()==0 && rank_add.size()==0) {
-    gsl_matrix_memcpy(&Xnew_sub.matrix, &Xold_sub.matrix);
-    gsl_matrix_memcpy(&XtXnew_sub.matrix, &XtXold_sub.matrix);
-    gsl_vector_memcpy(&Xtynew_sub.vector, &Xtyold_sub.vector);
-  } else {
-    gsl_matrix *X_temp=gsl_matrix_alloc(X_old->size1, rank_old.size()-rank_remove.size() );
-    gsl_matrix *XtX_temp=gsl_matrix_alloc(X_temp->size2, X_temp->size2);
-    gsl_vector *Xty_temp=gsl_vector_alloc(X_temp->size2);
-    
-    if (rank_remove.size()==0) {
-      gsl_matrix_memcpy (X_temp, &Xold_sub.matrix);
-      gsl_matrix_memcpy (XtX_temp, &XtXold_sub.matrix);
-      gsl_vector_memcpy (Xty_temp, &Xtyold_sub.vector);
-    } else {
-      size_t i_temp=0, j_temp;
-      for (size_t i=0; i<rank_old.size(); i++) {
-	if (mapRank2in_remove.count(rank_old[i])!=0) {continue;}
-	gsl_vector_const_view Xold_col=gsl_matrix_const_column(X_old, i);	
-	gsl_vector_view Xtemp_col=gsl_matrix_column(X_temp, i_temp);
-	gsl_vector_memcpy (&Xtemp_col.vector, &Xold_col.vector);
-
-	d=gsl_vector_get (Xty_old, i);
-	gsl_vector_set (Xty_temp, i_temp, d);
-	
-	j_temp=i_temp;
-	for (size_t j=i; j<rank_old.size(); j++) {
-	  if (mapRank2in_remove.count(rank_old[j])!=0) {continue;}
-	  d=gsl_matrix_get (XtX_old, i, j);
-	  gsl_matrix_set (XtX_temp, i_temp, j_temp, d);
-	  if (i_temp!=j_temp) {gsl_matrix_set (XtX_temp, j_temp, i_temp, d);}
-	  j_temp++;
-	}
-	i_temp++;
-      }
-    }
-
-    if (rank_add.size()==0) {
-      gsl_matrix_memcpy (&Xnew_sub.matrix, X_temp);
-      gsl_matrix_memcpy (&XtXnew_sub.matrix, XtX_temp);
-      gsl_vector_memcpy (&Xtynew_sub.vector, Xty_temp);
-    } else {
-      gsl_matrix *X_add=gsl_matrix_alloc(X_old->size1, rank_add.size() );
-      gsl_matrix *XtX_aa=gsl_matrix_alloc(X_add->size2, X_add->size2);
-      gsl_matrix *XtX_at=gsl_matrix_alloc(X_add->size2, X_temp->size2);
-      gsl_vector *Xty_add=gsl_vector_alloc(X_add->size2);
-
-      //get X_add
-      SetXgamma (X_add, X, rank_add);
-
-      //get t(X_add)X_add and t(X_add)X_temp	
-      clock_t time_start=clock();
-      
-      //somehow the lapack_dgemm does not work here
-      //#ifdef WITH_LAPACK
-      //lapack_dgemm ((char *)"T", (char *)"N", 1.0, X_add, X_add, 0.0, XtX_aa);
-      //lapack_dgemm ((char *)"T", (char *)"N", 1.0, X_add, X_temp, 0.0, XtX_at);
-      
-      //#else
-      gsl_blas_dgemm (CblasTrans, CblasNoTrans, 1.0, X_add, X_add, 0.0, XtX_aa);
-      gsl_blas_dgemm (CblasTrans, CblasNoTrans, 1.0, X_add, X_temp, 0.0, XtX_at);
-      //#endif
-      gsl_blas_dgemv(CblasTrans, 1.0, X_add, y, 0.0, Xty_add);
-
-      time_Omega+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
-
-      //save to X_new, XtX_new and Xty_new
-      size_t i_temp=0, j_temp, i_flag=0, j_flag=0;
-      for (size_t i=0; i<rank_new.size(); i++) {
-	if (mapRank2in_add.count(rank_new[i])!=0) {i_flag=1;} else {i_flag=0;}
-	gsl_vector_view Xnew_col=gsl_matrix_column(X_new, i); 
-	if (i_flag==1) {
-	  gsl_vector_view Xcopy_col=gsl_matrix_column(X_add, i-i_temp);
-	  gsl_vector_memcpy (&Xnew_col.vector, &Xcopy_col.vector);
-	} else {
-	  gsl_vector_view Xcopy_col=gsl_matrix_column(X_temp, i_temp);	  
-	  gsl_vector_memcpy (&Xnew_col.vector, &Xcopy_col.vector);
-	}	
-
-	if (i_flag==1) {
-          d=gsl_vector_get (Xty_add, i-i_temp);
-        } else {
-          d=gsl_vector_get (Xty_temp, i_temp);
-        }
-	gsl_vector_set (Xty_new, i, d);
-
-	j_temp=i_temp;
-	for (size_t j=i; j<rank_new.size(); j++) {
-          if (mapRank2in_add.count(rank_new[j])!=0) {j_flag=1;} else {j_flag=0;}
-
-	  if (i_flag==1 && j_flag==1) {
-            d=gsl_matrix_get(XtX_aa, i-i_temp, j-j_temp);
-	  } else if (i_flag==1) {
-	    d=gsl_matrix_get(XtX_at, i-i_temp, j_temp);
-	  } else if (j_flag==1) {
-	    d=gsl_matrix_get(XtX_at, j-j_temp, i_temp);
-	  } else {
-	    d=gsl_matrix_get(XtX_temp, i_temp, j_temp);
-	  }
-
-	  gsl_matrix_set (XtX_new, i, j, d);
-	  if (i!=j) {gsl_matrix_set (XtX_new, j, i, d);}
-
-	  if (j_flag==0) {j_temp++;}
-        }
-	if (i_flag==0) {i_temp++;}
-      }
-
-      gsl_matrix_free(X_add);
-      gsl_matrix_free(XtX_aa);
-      gsl_matrix_free(XtX_at);
-      gsl_vector_free(Xty_add);
-    }
-
-    gsl_matrix_free(X_temp);
-    gsl_matrix_free(XtX_temp);
-    gsl_vector_free(Xty_temp);
-  }
-  */
-
-
-  if (rank_remove.size()==0 && rank_add.size()==0) {
-    gsl_matrix_memcpy(&Xnew_sub.matrix, &Xold_sub.matrix);
-    gsl_matrix_memcpy(&XtXnew_sub.matrix, &XtXold_sub.matrix);
-    gsl_vector_memcpy(&Xtynew_sub.vector, &Xtyold_sub.vector);
-  } else {
-    size_t i_old, j_old, i_new, j_new, i_add, j_add, i_flag, j_flag;
-    if (rank_add.size()==0) {
-      i_old=0; i_new=0;
-      for (size_t i=0; i<rank_union.size(); i++) {
-	if (mapRank2in_remove.count(rank_old[i_old])!=0) {i_old++; continue;}
-
-	gsl_vector_view Xnew_col=gsl_matrix_column(X_new, i_new); 
-	gsl_vector_const_view Xcopy_col=gsl_matrix_const_column(X_old, i_old);
-	gsl_vector_memcpy (&Xnew_col.vector, &Xcopy_col.vector);
-
-	d=gsl_vector_get (Xty_old, i_old);
-	gsl_vector_set (Xty_new, i_new, d);
-
-	j_old=i_old; j_new=i_new;
-	for (size_t j=i; j<rank_union.size(); j++) {
-          if (mapRank2in_remove.count(rank_old[j_old])!=0) {j_old++; continue;}
-
-	  d=gsl_matrix_get(XtX_old, i_old, j_old);
-
-	  gsl_matrix_set (XtX_new, i_new, j_new, d);
-	  if (i_new!=j_new) {gsl_matrix_set (XtX_new, j_new, i_new, d);}
-
-	  j_old++; j_new++;
-        }
-	i_old++; i_new++;
-      }	
-    } else {
-      gsl_matrix *X_add=gsl_matrix_alloc(X_old->size1, rank_add.size() );
-      gsl_matrix *XtX_aa=gsl_matrix_alloc(X_add->size2, X_add->size2);
-      gsl_matrix *XtX_ao=gsl_matrix_alloc(X_add->size2, X_old->size2);
-      gsl_vector *Xty_add=gsl_vector_alloc(X_add->size2);
-
-      //get X_add
-      SetXgamma (X_add, X, rank_add);
-
-      //get t(X_add)X_add and t(X_add)X_temp	
-      clock_t time_start=clock();
-      
-      //somehow the lapack_dgemm does not work here
-      //#ifdef WITH_LAPACK
-      //lapack_dgemm ((char *)"T", (char *)"N", 1.0, X_add, X_add, 0.0, XtX_aa);
-      //lapack_dgemm ((char *)"T", (char *)"N", 1.0, X_add, X_temp, 0.0, XtX_at);
-      
-      //#else
-      gsl_blas_dgemm (CblasTrans, CblasNoTrans, 1.0, X_add, X_add, 0.0, XtX_aa);
-      gsl_blas_dgemm (CblasTrans, CblasNoTrans, 1.0, X_add, X_old, 0.0, XtX_ao);
-      //#endif
-      gsl_blas_dgemv(CblasTrans, 1.0, X_add, y, 0.0, Xty_add);
-
-      time_Omega+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
-
-      //save to X_new, XtX_new and Xty_new
-      i_old=0; i_new=0; i_add=0;
-      for (size_t i=0; i<rank_union.size(); i++) {
-	if (mapRank2in_remove.count(rank_old[i_old])!=0) {i_old++; continue;}
-	if (mapRank2in_add.count(rank_new[i_new])!=0) {i_flag=1;} else {i_flag=0;}
-
-	gsl_vector_view Xnew_col=gsl_matrix_column(X_new, i_new); 
-	if (i_flag==1) {
-	  gsl_vector_view Xcopy_col=gsl_matrix_column(X_add, i_add);
-	  gsl_vector_memcpy (&Xnew_col.vector, &Xcopy_col.vector);
-	} else {
-	  gsl_vector_const_view Xcopy_col=gsl_matrix_const_column(X_old, i_old);	  
-	  gsl_vector_memcpy (&Xnew_col.vector, &Xcopy_col.vector);
-	}	
-
-	if (i_flag==1) {
-          d=gsl_vector_get (Xty_add, i_add);
-        } else {
-          d=gsl_vector_get (Xty_old, i_old);
-        }
-	gsl_vector_set (Xty_new, i_new, d);
-
-	j_old=i_old; j_new=i_new; j_add=i_add;
-	for (size_t j=i; j<rank_union.size(); j++) {
-	  if (mapRank2in_remove.count(rank_old[j_old])!=0) {j_old++; continue;}
-	  if (mapRank2in_add.count(rank_new[j_new])!=0) {j_flag=1;} else {j_flag=0;}
-
-	  if (i_flag==1 && j_flag==1) {
-            d=gsl_matrix_get(XtX_aa, i_add, j_add);
-	  } else if (i_flag==1) {
-	    d=gsl_matrix_get(XtX_ao, i_add, j_old);
-	  } else if (j_flag==1) {
-	    d=gsl_matrix_get(XtX_ao, j_add, i_old);
-	  } else {
-	    d=gsl_matrix_get(XtX_old, i_old, j_old);
-	  }
-
-	  gsl_matrix_set (XtX_new, i_new, j_new, d);
-	  if (i_new!=j_new) {gsl_matrix_set (XtX_new, j_new, i_new, d);}
-
-	  j_new++; if (j_flag==1) {j_add++;} else {j_old++;}
-        }
-	i_new++; if (i_flag==1) {i_add++;} else {i_old++;}
-      }
-
-      gsl_matrix_free(X_add);
-      gsl_matrix_free(XtX_aa);
-      gsl_matrix_free(XtX_ao);
-      gsl_vector_free(Xty_add);
-    }
-
-  }
-
-  rank_remove.clear();
-  rank_add.clear();
-  rank_union.clear();
-  mapRank2in_remove.clear();
-  mapRank2in_add.clear();
-	
-  return;
-}
-
-
-double BSLMM::CalcPosterior (const double yty, class HYPBSLMM &cHyp)
-{	
-	double logpost=0.0;
-	
-	//for quantitative traits, calculate pve and pge
-	//pve and pge for case/control data are calculted in CalcCC_PVEnZ
-	if (a_mode==11) {
-		cHyp.pve=0.0;
-		cHyp.pge=1.0;	
-	}
-
-	//calculate likelihood
-	if (a_mode==11) {logpost-=0.5*(double)ni_test*log(yty);}
-	else {logpost-=0.5*yty;}
-	
-	logpost+=((double)cHyp.n_gamma-1.0)*cHyp.logp+((double)ns_test-(double)cHyp.n_gamma)*log(1-exp(cHyp.logp));
-		
-	return logpost;
-}
-
-
-double BSLMM::CalcPosterior (const gsl_matrix *Xgamma, const gsl_matrix *XtX, const gsl_vector *Xty, const double yty, const size_t s_size, gsl_vector *Xb, gsl_vector *beta, class HYPBSLMM &cHyp)
-{	
-	double sigma_a2=cHyp.h/( (1-cHyp.h)*exp(cHyp.logp)*(double)ns_test);
-	double logpost=0.0;
-	double d, P_yy=yty, logdet_O=0.0;
-
-	gsl_matrix_const_view Xgamma_sub=gsl_matrix_const_submatrix (Xgamma, 0, 0, Xgamma->size1, s_size);
-	gsl_matrix_const_view XtX_sub=gsl_matrix_const_submatrix (XtX, 0, 0, s_size, s_size);
-	gsl_vector_const_view Xty_sub=gsl_vector_const_subvector (Xty, 0, s_size);
-	
-	gsl_matrix *Omega=gsl_matrix_alloc (s_size, s_size);
-	gsl_matrix *M_temp=gsl_matrix_alloc (s_size, s_size);
-	gsl_vector *beta_hat=gsl_vector_alloc (s_size);	
-	gsl_vector *Xty_temp=gsl_vector_alloc (s_size);
-
-	gsl_vector_memcpy (Xty_temp, &Xty_sub.vector);
-
-	//calculate Omega
-	gsl_matrix_memcpy (Omega, &XtX_sub.matrix);
-	gsl_matrix_scale (Omega, sigma_a2);
-	gsl_matrix_set_identity (M_temp);
-	gsl_matrix_add (Omega, M_temp);
-	
-	//calculate beta_hat
-	logdet_O=CholeskySolve(Omega, Xty_temp, beta_hat);	
-	gsl_vector_scale (beta_hat, sigma_a2);
-
-	gsl_blas_ddot (Xty_temp, beta_hat, &d);
-	P_yy-=d;
-
-	//sample tau
-	double tau=1.0;
-	if (a_mode==11) {tau =gsl_ran_gamma (gsl_r, (double)ni_test/2.0,  2.0/P_yy); }
-
-	//sample beta
-	for (size_t i=0; i<s_size; i++)
-	{
-		d=gsl_ran_gaussian(gsl_r, 1); 
-		gsl_vector_set(beta, i, d); 
-	}
-	gsl_vector_view beta_sub=gsl_vector_subvector(beta, 0, s_size);
-	gsl_blas_dtrsv(CblasUpper, CblasNoTrans, CblasNonUnit, Omega, &beta_sub.vector); 
-		
-	//it compuates inv(L^T(Omega)) %*% beta;  
-	gsl_vector_scale(&beta_sub.vector, sqrt(sigma_a2/tau));
-	gsl_vector_add(&beta_sub.vector, beta_hat); 
-	gsl_blas_dgemv (CblasNoTrans, 1.0, &Xgamma_sub.matrix, &beta_sub.vector, 0.0, Xb);		
-	
-	//for quantitative traits, calculate pve and pge
-	if (a_mode==11) {
-		gsl_blas_ddot (Xb, Xb, &d);
-		cHyp.pve=d/(double)ni_test;
-		cHyp.pve/=cHyp.pve+1.0/tau;
-		cHyp.pge=1.0;	
-	}	
-	
-	logpost=-0.5*logdet_O;
-	if (a_mode==11) {logpost-=0.5*(double)ni_test*log(P_yy);}
-	else {logpost-=0.5*P_yy;}
-
-	logpost+=((double)cHyp.n_gamma-1.0)*cHyp.logp+((double)ns_test-(double)cHyp.n_gamma)*log(1.0-exp(cHyp.logp));
-
-	gsl_matrix_free (Omega);
-	gsl_matrix_free (M_temp);
-	gsl_vector_free (beta_hat);
-	gsl_vector_free (Xty_temp);
-
-	return logpost;
-}
-
-
-
-//calculate pve and pge, and calculate z_hat for case-control data	
-void BSLMM::CalcCC_PVEnZ (gsl_vector *z_hat, class HYPBSLMM &cHyp) 
-{
-  gsl_vector_set_zero(z_hat);
-  cHyp.pve=0.0;
-  cHyp.pge=1.0;		
-  return;
-}
-
-
-//calculate pve and pge, and calculate z_hat for case-control data	
-void BSLMM::CalcCC_PVEnZ (const gsl_vector *Xb, gsl_vector *z_hat, class HYPBSLMM &cHyp) 
-{
-	double d;
-	
-	gsl_blas_ddot (Xb, Xb, &d);
-	cHyp.pve=d/(double)ni_test;
-	cHyp.pve/=cHyp.pve+1.0;
-	cHyp.pge=1.0;
-	
-	gsl_vector_memcpy (z_hat, Xb);
-
-	return;
-}
-
-
-
-//if a_mode==13, then run probit model
-void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
-	clock_t time_start;	
-	double time_set=0, time_post=0;
-
-	class HYPBSLMM cHyp_old, cHyp_new;
-	
-	gsl_matrix *Result_hyp=gsl_matrix_alloc (w_pace, 6);
-	gsl_matrix *Result_gamma=gsl_matrix_alloc (w_pace, s_max);	
-	
-	gsl_vector *Xb_new=gsl_vector_alloc (ni_test);
-	gsl_vector *Xb_old=gsl_vector_alloc (ni_test);	
-	gsl_vector *z_hat=gsl_vector_alloc (ni_test);
-	gsl_vector *z=gsl_vector_alloc (ni_test);
-
-	gsl_matrix *Xgamma_old=gsl_matrix_alloc (ni_test, s_max);
-	gsl_matrix *XtX_old=gsl_matrix_alloc (s_max, s_max);
-	gsl_vector *Xtz_old=gsl_vector_alloc (s_max);
-	gsl_vector *beta_old=gsl_vector_alloc (s_max);
-
-	gsl_matrix *Xgamma_new=gsl_matrix_alloc (ni_test, s_max);
-	gsl_matrix *XtX_new=gsl_matrix_alloc (s_max, s_max);
-	gsl_vector *Xtz_new=gsl_vector_alloc (s_max);
-	gsl_vector *beta_new=gsl_vector_alloc (s_max);
-
-	double ztz=0.0;
-	gsl_vector_memcpy (z, y);
-	//for quantitative traits, y is centered already in gemma.cpp, but just in case
-	double mean_z=CenterVector (z);				
-	gsl_blas_ddot(z, z, &ztz);
-
-	double logPost_new, logPost_old;
-	double logMHratio;
-	
-	gsl_matrix_set_zero (Result_gamma);
-	if (a_mode==13) {
-		pheno_mean=0.0;
-	}
-	
-	vector<pair<double, double> > beta_g;
-	for (size_t i=0; i<ns_test; i++) {
-		beta_g.push_back(make_pair(0.0, 0.0));
-	}
-	
-	vector<size_t> rank_new, rank_old;
-	vector<pair<size_t, double> > pos_loglr;
-	
-	time_start=clock();
-	MatrixCalcLmLR (X, z, pos_loglr);
-	time_Proposal=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
-
-	stable_sort (pos_loglr.begin(), pos_loglr.end(), comp_lr);
-	for (size_t i=0; i<ns_test; ++i) {
-		mapRank2pos[i]=pos_loglr[i].first;
-	}
-	
-	//calculate proposal distribution for gamma (unnormalized), and set up gsl_r and gsl_t		
-	gsl_rng_env_setup();                
-	const gsl_rng_type * gslType;                                               
-	gslType = gsl_rng_default; 
-	if (randseed<0)
-	{
-		time_t rawtime;
-		time (&rawtime);
-		tm * ptm = gmtime (&rawtime);
-		
-		randseed = (unsigned) (ptm->tm_hour%24*3600+ptm->tm_min*60+ptm->tm_sec);
-	}
-	gsl_r = gsl_rng_alloc(gslType); 
-	gsl_rng_set(gsl_r, randseed);
-	
-	double *p_gamma = new double[ns_test]; 
-	CalcPgamma (p_gamma);
-	
-	gsl_t=gsl_ran_discrete_preproc (ns_test, p_gamma);
-	
-	//initial parameters
-	InitialMCMC (X, z, rank_old, cHyp_old, pos_loglr);
-	
-	cHyp_initial=cHyp_old;
-
-	if (cHyp_old.n_gamma==0) {	  
-	    logPost_old=CalcPosterior (ztz, cHyp_old);
-	}
-	else {	  
-	  SetXgamma (Xgamma_old, X, rank_old);	  
-	  CalcXtX (Xgamma_old, z, rank_old.size(), XtX_old, Xtz_old);
-	  logPost_old=CalcPosterior (Xgamma_old, XtX_old, Xtz_old, ztz, rank_old.size(), Xb_old, beta_old, cHyp_old);
-	}	
-
-	//calculate centered z_hat, and pve
-	if (a_mode==13) {
-		if (cHyp_old.n_gamma==0) {
-			CalcCC_PVEnZ (z_hat, cHyp_old);
-		}
-		else {
-			CalcCC_PVEnZ (Xb_old, z_hat, cHyp_old);
-		}
-	}
-	
-	//start MCMC
-	int accept;
-	size_t total_step=w_step+s_step;
-	size_t w=0, w_col, pos;
-	size_t repeat=0;
-	
-	for (size_t t=0; t<total_step; ++t) {
-		if (t%d_pace==0 || t==total_step-1) {ProgressBar ("Running MCMC ", t, total_step-1, (double)n_accept/(double)(t*n_mh+1));}
-//		if (t>10) {break;}		
-		if (a_mode==13) {			
-			SampleZ (y, z_hat, z);		
-			mean_z=CenterVector (z);
-			gsl_blas_ddot(z,z,&ztz);
-					
-			//First proposal		
-			if (cHyp_old.n_gamma==0) {	  
-			  logPost_old=CalcPosterior (ztz, cHyp_old);
-			} else {	  
-			  gsl_matrix_view Xold_sub=gsl_matrix_submatrix(Xgamma_old, 0, 0, ni_test, rank_old.size());
-			  gsl_vector_view Xtz_sub=gsl_vector_subvector(Xtz_old, 0, rank_old.size());
-			  gsl_blas_dgemv (CblasTrans, 1.0, &Xold_sub.matrix, z, 0.0, &Xtz_sub.vector);
-			  logPost_old=CalcPosterior (Xgamma_old, XtX_old, Xtz_old, ztz, rank_old.size(), Xb_old, beta_old, cHyp_old);
-			}	
-		}
-
-		//MH steps
-		for (size_t i=0; i<n_mh; ++i) {
-			if (gsl_rng_uniform(gsl_r)<0.33) {repeat = 1+gsl_rng_uniform_int(gsl_r, 20);}
-			else {repeat=1;}
-
-			logMHratio=0.0;
-			logMHratio+=ProposeHnRho(cHyp_old, cHyp_new, repeat);	
-			logMHratio+=ProposeGamma (rank_old, rank_new, p_gamma, cHyp_old, cHyp_new, repeat);	
-			logMHratio+=ProposePi(cHyp_old, cHyp_new, repeat);
-			
-			if (cHyp_new.n_gamma==0) {
-				logPost_new=CalcPosterior (ztz, cHyp_new);
-			} else {
-			  //this if makes sure that rank_old.size()==rank_remove.size() does not happen
-			  if (cHyp_new.n_gamma<=20 || cHyp_old.n_gamma<=20) {
-			    time_start=clock();
-			    SetXgamma (Xgamma_new, X, rank_new);	  
-			    CalcXtX (Xgamma_new, z, rank_new.size(), XtX_new, Xtz_new);	
-			    time_set+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
-			  } else {
-			    time_start=clock();
-			    SetXgamma (X, Xgamma_old, XtX_old, Xtz_old, z, rank_old, rank_new, Xgamma_new, XtX_new, Xtz_new);
-			    time_set+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
-			  }
-			  time_start=clock();
-			  logPost_new=CalcPosterior (Xgamma_new, XtX_new, Xtz_new, ztz, rank_new.size(), Xb_new, beta_new, cHyp_new);
-			  time_post+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
-			}	
-			logMHratio+=logPost_new-logPost_old;	
-		
-			if (logMHratio>0 || log(gsl_rng_uniform(gsl_r))<logMHratio) {accept=1; n_accept++;}
-			else {accept=0;}
-			
-			//cout<<rank_new.size()<<"\t"<<rank_old.size()<<"\t"<<logPost_new<<"\t"<<logPost_old<<endl;
-			if (accept==1) {			
-				logPost_old=logPost_new;
-				cHyp_old=cHyp_new;
-				gsl_vector_memcpy (Xb_old, Xb_new);
-
-				rank_old.clear();
-				if (rank_new.size()!=0) {
-					for (size_t i=0; i<rank_new.size(); ++i) {
-						rank_old.push_back(rank_new[i]);
-					}
-								
-					gsl_matrix_view Xold_sub=gsl_matrix_submatrix(Xgamma_old, 0, 0, ni_test, rank_new.size());
-					gsl_matrix_view XtXold_sub=gsl_matrix_submatrix(XtX_old, 0, 0, rank_new.size(), rank_new.size());
-					gsl_vector_view Xtzold_sub=gsl_vector_subvector(Xtz_old, 0, rank_new.size());
-					gsl_vector_view betaold_sub=gsl_vector_subvector(beta_old, 0, rank_new.size());
-
-					gsl_matrix_view Xnew_sub=gsl_matrix_submatrix(Xgamma_new, 0, 0, ni_test, rank_new.size());
-					gsl_matrix_view XtXnew_sub=gsl_matrix_submatrix(XtX_new, 0, 0, rank_new.size(), rank_new.size());
-					gsl_vector_view Xtznew_sub=gsl_vector_subvector(Xtz_new, 0, rank_new.size());
-					gsl_vector_view betanew_sub=gsl_vector_subvector(beta_new, 0, rank_new.size());
-
-					gsl_matrix_memcpy(&Xold_sub.matrix, &Xnew_sub.matrix);
-					gsl_matrix_memcpy(&XtXold_sub.matrix, &XtXnew_sub.matrix);
-					gsl_vector_memcpy(&Xtzold_sub.vector, &Xtznew_sub.vector);
-					gsl_vector_memcpy(&betaold_sub.vector, &betanew_sub.vector);
-				}
-			} else {
-			  cHyp_new=cHyp_old;
-			}
-			
-		}				
-
-		//calculate z_hat, and pve
-		if (a_mode==13) {
-			if (cHyp_old.n_gamma==0) {
-				CalcCC_PVEnZ (z_hat, cHyp_old);
-			}
-			else {
-				CalcCC_PVEnZ (Xb_old, z_hat, cHyp_old);
-			}
-			
-			//sample mu and update z hat
-			gsl_vector_sub (z, z_hat);
-			mean_z+=CenterVector(z);
-			mean_z+=gsl_ran_gaussian(gsl_r, sqrt(1.0/(double) ni_test) );			
-			
-			gsl_vector_add_constant (z_hat, mean_z);
-		}
-		
-		//Save data
-		if (t<w_step) {continue;}
-		else {		
-			if (t%r_pace==0) {
-				w_col=w%w_pace;
-				if (w_col==0) {
-					if (w==0) {WriteResult (0, Result_hyp, Result_gamma, w_col);}					
-					else {
-						WriteResult (1, Result_hyp, Result_gamma, w_col);
-						gsl_matrix_set_zero (Result_hyp);
-						gsl_matrix_set_zero (Result_gamma);
-					}
-				}
-
-				gsl_matrix_set (Result_hyp, w_col, 0, cHyp_old.h);
-				gsl_matrix_set (Result_hyp, w_col, 1, cHyp_old.pve);
-				gsl_matrix_set (Result_hyp, w_col, 2, cHyp_old.rho);
-				gsl_matrix_set (Result_hyp, w_col, 3, cHyp_old.pge);
-				gsl_matrix_set (Result_hyp, w_col, 4, cHyp_old.logp);
-				gsl_matrix_set (Result_hyp, w_col, 5, cHyp_old.n_gamma);
-				
-				for (size_t i=0; i<cHyp_old.n_gamma; ++i) {
-					pos=mapRank2pos[rank_old[i]]+1;
-
-					gsl_matrix_set (Result_gamma, w_col, i, pos);
-					
-					beta_g[pos-1].first+=gsl_vector_get(beta_old, i);
-					beta_g[pos-1].second+=1.0;	
-				}
-				
-				if (a_mode==13) {
-					pheno_mean+=mean_z;
-				}
-				
-				w++;
-				
-			}
-			
-		}
-	}
-	cout<<endl;
-
-	cout<<"time on selecting Xgamma: "<<time_set<<endl;
-	cout<<"time on calculating posterior: "<<time_post<<endl;
-
-	w_col=w%w_pace;
-	WriteResult (1, Result_hyp, Result_gamma, w_col);	
-	
-	gsl_vector *alpha=gsl_vector_alloc (ns_test);
-	gsl_vector_set_zero (alpha);
-	WriteParam (beta_g, alpha, w);
-	gsl_vector_free(alpha);
-
-	gsl_matrix_free(Result_hyp);
-	gsl_matrix_free(Result_gamma);	
-	
-	gsl_vector_free(z_hat);
-	gsl_vector_free(z);
-	gsl_vector_free(Xb_new);	
-	gsl_vector_free(Xb_old);
-
-	gsl_matrix_free(Xgamma_old);
-	gsl_matrix_free(XtX_old);
-	gsl_vector_free(Xtz_old);
-	gsl_vector_free(beta_old);
-
-	gsl_matrix_free(Xgamma_new);
-	gsl_matrix_free(XtX_new);
-	gsl_vector_free(Xtz_new);
-	gsl_vector_free(beta_new);
-	
-	delete [] p_gamma;
-	beta_g.clear();
-	
-	return;
-}