Merge pull request #51 from genenetwork/spacing

Spacing fixes.

1 files changed, 390 insertions, 390 deletions

diff --git a/src/bslmm.cpp b/src/bslmm.cpp
index 563b743..d579802 100644
--- a/src/bslmm.cpp
+++ b/src/bslmm.cpp
@@ -1,17 +1,17 @@
 /*
  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/>.
 */
@@ -24,7 +24,7 @@
 #include <cmath>
 #include <iostream>
 #include <stdio.h>
-#include <stdlib.h> 
+#include <stdlib.h>
 #include <ctime>
 #include <cstring>
 #include <algorithm>
@@ -50,32 +50,32 @@ 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;	
+
+	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_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_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_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;
@@ -86,17 +86,17 @@ void BSLMM::CopyFromParam (PARAM &cPar) {
 	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;
 }
 
@@ -108,7 +108,7 @@ void BSLMM::CopyToParam (PARAM &cPar) {
 	cPar.n_accept=n_accept;
 	cPar.pheno_mean=pheno_mean;
 	cPar.randseed=randseed;
-	
+
 	return;
 }
 
@@ -119,28 +119,28 @@ void BSLMM::WriteBV (const gsl_vector *bv) {
 
 	ofstream outfile (file_str.c_str(), ofstream::out);
 	if (!outfile) {
-	  cout<<"error writing file: "<<file_str.c_str()<<endl; 
+	  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();	
+	}
+
+	outfile.clear();
+	outfile.close();
 	return;
 }
 
-void BSLMM::WriteParam (vector<pair<double, double> > &beta_g, 
+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;
@@ -148,20 +148,20 @@ void BSLMM::WriteParam (vector<pair<double, double> > &beta_g,
 
 	ofstream outfile (file_str.c_str(), ofstream::out);
 	if (!outfile) {
-	  cout<<"error writing file: "<<file_str.c_str()<<endl; 
+	  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;}		
-		
+		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) {
@@ -172,10 +172,10 @@ void BSLMM::WriteParam (vector<pair<double, double> > &beta_g,
 			outfile<<0.0<<"\t"<<0.0<<endl;
 		}
 		t++;
-	}		
-	
-	outfile.clear();	
-	outfile.close();	
+	}
+
+	outfile.clear();
+	outfile.close();
 	return;
 }
 
@@ -186,17 +186,17 @@ void BSLMM::WriteParam (const gsl_vector *alpha) {
 
 	ofstream outfile (file_str.c_str(), ofstream::out);
 	if (!outfile) {
-	  cout<<"error writing file: "<<file_str.c_str()<<endl; 
+	  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;}		
+		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";
@@ -204,14 +204,14 @@ void BSLMM::WriteParam (const gsl_vector *alpha) {
 		  gsl_vector_get(alpha, t)<<"\t";
 		outfile<<0.0<<"\t"<<0.0<<endl;
 		t++;
-	}		
-	
-	outfile.clear();	
-	outfile.close();	
+	}
+
+	outfile.clear();
+	outfile.close();
 	return;
 }
 
-void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp, 
+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;
@@ -220,21 +220,21 @@ void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp,
 	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; 
+		  cout<<"error writing file: "<<file_gamma<<endl;
 		  return;
 		}
 		if (!outfile_hyp) {
-		  cout<<"error writing file: "<<file_hyp<<endl; 
+		  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";
 		}
@@ -244,18 +244,18 @@ void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp,
 		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; 
+		  cout<<"error writing file: "<<file_gamma<<endl;
 		  return;
 		}
 		if (!outfile_hyp) {
-		  cout<<"error writing file: "<<file_hyp<<endl; 
+		  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) {
@@ -267,7 +267,7 @@ void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp,
 			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<<
@@ -275,13 +275,13 @@ void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp,
 			}
 			outfile_gamma<<endl;
 		}
-		
+
 	}
-	
+
 	outfile_hyp.close();
 	outfile_hyp.clear();
 	outfile_gamma.close();
-	outfile_gamma.clear();	
+	outfile_gamma.clear();
 	return;
 }
 
@@ -300,7 +300,7 @@ void BSLMM::CalcPgamma (double *p_gamma) {
 	return;
 }
 
-void BSLMM::SetXgamma (gsl_matrix *Xgamma, const gsl_matrix *X, 
+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) {
@@ -309,32 +309,32 @@ void BSLMM::SetXgamma (gsl_matrix *Xgamma, const gsl_matrix *X,
 		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, 
+double BSLMM::CalcPveLM (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
 			 const double sigma_a2) {
-	double pve, var_y;	
-	
+	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); 
+	gsl_matrix_scale (Omega, 1.0/sigma_a2);
 
 	lapack_dgemm ((char *)"T", (char *)"N", 1.0, UtXgamma, UtXgamma,
 		      1.0, Omega);
 	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);
@@ -342,28 +342,28 @@ double BSLMM::CalcPveLM (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
 	return pve;
 }
 
-void BSLMM::InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty, 
-			 vector<size_t> &rank, class HYPBSLMM &cHyp, 
+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;}	
-	
+	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; 
-	
+	cHyp.h=pve_null;
+
 	if (cHyp.logp==0) {cHyp.logp=-0.000001;}
 	if (cHyp.h==0) {cHyp.h=0.1;}
 
@@ -376,114 +376,114 @@ void BSLMM::InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty,
 	} else {
 	  sigma_a2=cHyp.h*1.0/( (1-cHyp.h)*exp(cHyp.logp)*(double)ns_test);
 	}
-	if (sigma_a2==0) {sigma_a2=0.025;}	
+	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;}
-	
+
 	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, 
+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 *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);		
+		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_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); 
+	  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);	
-	
+	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=d/(double)ni_test;
 		cHyp.pve/=cHyp.pve+1.0/tau;
-		cHyp.pge=0.0;	
+		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, 
+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;	
-	
+	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 *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 *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=
@@ -492,139 +492,139 @@ double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma,
 		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();
 	lapack_dgemm ((char *)"T", (char *)"N", sigma_a2, UtXgamma_eval,
 		      UtXgamma, 1.0, Omega);
 	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); 
+	  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); 
+		d=gsl_ran_gaussian(gsl_r, 1);
+		gsl_vector_set(beta, i, d);
 	}
-	gsl_blas_dtrsv(CblasUpper, CblasNoTrans, CblasNonUnit, Omega, beta); 
-	
+	gsl_blas_dtrsv(CblasUpper, CblasNoTrans, CblasNonUnit, Omega, beta);
+
 	// This computes inv(L^T(Omega)) %*% beta.
 	gsl_vector_scale(beta, sqrt(sigma_a2/tau));
-	gsl_vector_add(beta, beta_hat); 
+	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);	
-	
+	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;	
-	}	
+		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 (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;}
 	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, 
+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;	
-		
+	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;	
-	
+	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, 
+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);	
-	
+	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) {	
+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);
@@ -634,7 +634,7 @@ void BSLMM::SampleZ (const gsl_vector *y, const gsl_vector *z_hat,
 		if (d1<=0.0) {
 
 		        // Control, right truncated.
-			do {				
+			do {
 				z_rand=d2+gsl_ran_gaussian(gsl_r, 1.0);
 			} while (z_rand>0.0);
 		}
@@ -643,25 +643,25 @@ void BSLMM::SampleZ (const gsl_vector *y, const gsl_vector *z_hat,
 				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, 
+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;}
@@ -671,13 +671,13 @@ double BSLMM::ProposeHnRho (const class HYPBSLMM &cHyp_old,
 	return 0.0;
 }
 
-double BSLMM::ProposePi (const class HYPBSLMM &cHyp_old, 
+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;}
@@ -686,29 +686,29 @@ double BSLMM::ProposePi (const class HYPBSLMM &cHyp_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); 
+	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, 
+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];
@@ -716,29 +716,29 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old,
 			mapRank2in[r]=1;
 		}
 	}
-	cHyp_new.n_gamma=cHyp_old.n_gamma;	
-	
+	cHyp_new.n_gamma=cHyp_old.n_gamma;
+
 	for (size_t i=0; i<repeat; ++i) {
-		unif=gsl_rng_uniform(gsl_r); 
-	
+		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 && 
+		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 && 
+		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); 
-		
+			} 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];
@@ -756,14 +756,14 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old,
 		        // 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)+
@@ -779,18 +779,18 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old,
 		        // Be careful with the proposal.
 			do {
 				r_add=gsl_ran_discrete (gsl_r, gsl_t);
-			} while (mapRank2in.count(r_add)!=0); 
-			
+			} 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);
@@ -798,7 +798,7 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old,
 		}
 		else {logp+=0;} // Do not change.
 	}
-	
+
 	stable_sort (rank_new.begin(), rank_new.end(), comp_vec);
 
 	mapRank2in.clear();
@@ -806,54 +806,54 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old,
 }
 
 bool comp_lr (pair<size_t, double> a, pair<size_t, double> b) {
-	return (a.second > b.second); 
+	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, 
+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;	
+	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_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 *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 *Utz=gsl_vector_alloc (ni_test);
+
+	gsl_vector_memcpy (Utz, Uty);
 
-	gsl_vector_memcpy (Utz, Uty);			
-	
 	double logPost_new, logPost_old;
 	double logMHratio;
-	double mean_z=0.0;	
-	
+	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<double> beta_new, beta_old;
 
 	vector<pair<size_t, double> > pos_loglr;
 
@@ -865,59 +865,59 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX,
 	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; 
+	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_r = gsl_rng_alloc(gslType);
 	gsl_rng_set(gsl_r, randseed);
-	
-	double *p_gamma = new double[ns_test]; 
+
+	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);
-	
+
 	cHyp_initial=cHyp_old;
-	
+
 	if (cHyp_old.n_gamma==0 || cHyp_old.rho==0) {
-		logPost_old=CalcPosterior(Utz, K_eval, Utu_old, alpha_old, 
+		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, 
+		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, 
+		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();
@@ -929,28 +929,28 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX,
 		}
 		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 (a_mode==13) {			
-			SampleZ (y, z_hat, z);		
-			mean_z=CenterVector (z);	
-			
+		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=
@@ -959,7 +959,7 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX,
 				beta_old.clear();
 				for (size_t i=0; i<cHyp_old.n_gamma; ++i) {
 				  beta_old.push_back(0);
-				}	
+				}
 			}
 			else {
 				gsl_matrix *UtXgamma=
@@ -971,7 +971,7 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX,
 				  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));
@@ -980,7 +980,7 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX,
 				gsl_vector_free (beta);
 			}
 		}
-		
+
 		// M-H steps.
 		for (size_t i=0; i<n_mh; ++i) {
 			if (gsl_rng_uniform(gsl_r)<0.33) {
@@ -989,20 +989,20 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX,
 			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 || 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=
@@ -1020,17 +1020,17 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX,
 				}
 				gsl_matrix_free (UtXgamma);
 				gsl_vector_free (beta);
-			}	
-			
-			logMHratio+=logPost_new-logPost_old;		
-		
+			}
+
+			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) {			
+			if (accept==1) {
 				logPost_old=logPost_new;
 				rank_old.clear(); beta_old.clear();
 				if (rank_new.size()!=0) {
@@ -1045,8 +1045,8 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX,
 				gsl_vector_memcpy (Utu_old, Utu_new);
 			}
 			else {cHyp_new=cHyp_old;}
-		}				
-		
+		}
+
 		// Calculate z_hat, and pve.
 		if (a_mode==13) {
 			time_start=clock();
@@ -1057,21 +1057,21 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX,
 				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_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 {		
+		else {
 			if (t%r_pace==0) {
 				w_col=w%w_pace;
 				if (w_col==0) {
@@ -1086,76 +1086,76 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX,
 					  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;	
+					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);	
-	
+	WriteResult (1, Result_hyp, Result_gamma, w_col);
+
 	gsl_matrix_free(Result_hyp);
-	gsl_matrix_free(Result_gamma);	
-	
+	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(Utz);
+	gsl_vector_free(UtXb_new);
 	gsl_vector_free(UtXb_old);
-	gsl_vector_free(alpha_new);	
+	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);	
+	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);	
+			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);	
-		
+	WriteBV(alpha_prime);
+
+	gsl_vector_free(alpha_prime);
+	gsl_vector_free(Utu);
+
 	delete [] p_gamma;
 	beta_g.clear();
-	
+
 	return;
 }
 
@@ -1169,9 +1169,9 @@ void BSLMM::RidgeR(const gsl_matrix *U, const gsl_matrix *UtX,
 	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_vector_div (bv, H_eval);
 
 	gsl_blas_dgemv (CblasTrans, lambda/(double)UtX->size2,
 			UtX, bv, 0.0, beta);
@@ -1181,18 +1181,18 @@ void BSLMM::RidgeR(const gsl_matrix *U, const gsl_matrix *UtX,
 
 	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();	
+  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);
@@ -1271,7 +1271,7 @@ void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old,
       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_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);
 
@@ -1290,7 +1290,7 @@ void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old,
 	  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);
@@ -1302,7 +1302,7 @@ void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old,
 
       // 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.
       gsl_blas_dgemm (CblasTrans, CblasNoTrans, 1.0, X_add, X_add,
 		      0.0, XtX_aa);
@@ -1325,15 +1325,15 @@ void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old,
 	  i_flag=0;
 	}
 
-	gsl_vector_view Xnew_col=gsl_matrix_column(X_new, i_new); 
+	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_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);
@@ -1385,34 +1385,34 @@ void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old,
   rank_union.clear();
   mapRank2in_remove.clear();
   mapRank2in_add.clear();
-	
+
   return;
 }
 
-double BSLMM::CalcPosterior (const double yty, class HYPBSLMM &cHyp) {	
+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;	
+		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) {	
+			     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;
@@ -1423,10 +1423,10 @@ double BSLMM::CalcPosterior (const gsl_matrix *Xgamma, const gsl_matrix *XtX,
 	  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 *beta_hat=gsl_vector_alloc (s_size);
 	gsl_vector *Xty_temp=gsl_vector_alloc (s_size);
 
 	gsl_vector_memcpy (Xty_temp, &Xty_sub.vector);
@@ -1436,9 +1436,9 @@ double BSLMM::CalcPosterior (const gsl_matrix *Xgamma, const gsl_matrix *XtX,
 	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);	
+	logdet_O=CholeskySolve(Omega, Xty_temp, beta_hat);
 	gsl_vector_scale (beta_hat, sigma_a2);
 
 	gsl_blas_ddot (Xty_temp, beta_hat, &d);
@@ -1453,27 +1453,27 @@ double BSLMM::CalcPosterior (const gsl_matrix *Xgamma, const gsl_matrix *XtX,
 	// Sample beta.
 	for (size_t i=0; i<s_size; i++)
 	{
-		d=gsl_ran_gaussian(gsl_r, 1); 
-		gsl_vector_set(beta, i, d); 
+		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); 
-		
+		       &beta_sub.vector);
+
 	// This computes inv(L^T(Omega)) %*% beta.
 	gsl_vector_scale(&beta_sub.vector, sqrt(sigma_a2/tau));
-	gsl_vector_add(&beta_sub.vector, beta_hat); 
+	gsl_vector_add(&beta_sub.vector, beta_hat);
 	gsl_blas_dgemv (CblasNoTrans, 1.0, &Xgamma_sub.matrix,
-			&beta_sub.vector, 0.0, Xb);		
-	
+			&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;	
-	}	
-	
+		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;}
@@ -1490,11 +1490,11 @@ double BSLMM::CalcPosterior (const gsl_matrix *Xgamma, const gsl_matrix *XtX,
 }
 
 // Calculate pve and pge, and calculate z_hat for case-control data.
-void BSLMM::CalcCC_PVEnZ (gsl_vector *z_hat, class HYPBSLMM &cHyp) 
+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;		
+  cHyp.pge=1.0;
   return;
 }
 
@@ -1502,12 +1502,12 @@ void BSLMM::CalcCC_PVEnZ (gsl_vector *z_hat, class HYPBSLMM &cHyp)
 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;
@@ -1515,16 +1515,16 @@ void BSLMM::CalcCC_PVEnZ (const gsl_vector *Xb, gsl_vector *z_hat,
 
 // If a_mode==13, then run probit model.
 void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
-	clock_t time_start;	
+	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_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 *Xb_old=gsl_vector_alloc (ni_test);
 	gsl_vector *z_hat=gsl_vector_alloc (ni_test);
 	gsl_vector *z=gsl_vector_alloc (ni_test);
 
@@ -1540,28 +1540,28 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 
 	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);				
+	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);
@@ -1570,44 +1570,44 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 	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();                
+	gsl_rng_env_setup();
 	const gsl_rng_type * gslType;
-	gslType = gsl_rng_default; 
+	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_r = gsl_rng_alloc(gslType);
 	gsl_rng_set(gsl_r, randseed);
-	
-	double *p_gamma = new double[ns_test]; 
+
+	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) {	  
+	if (cHyp_old.n_gamma==0) {
 	    logPost_old=CalcPosterior (ztz, cHyp_old);
 	}
-	else {	  
-	  SetXgamma (Xgamma_old, X, rank_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) {
@@ -1618,28 +1618,28 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 			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 (a_mode==13) {			
-			SampleZ (y, z_hat, z);		
+		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) {	  
+			if (cHyp_old.n_gamma==0) {
 			  logPost_old=CalcPosterior (ztz, cHyp_old);
-			} else {	  
+			} else {
 			  gsl_matrix_view Xold_sub=
 			    gsl_matrix_submatrix(Xgamma_old, 0, 0, ni_test,
 						 rank_old.size());
@@ -1651,7 +1651,7 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 			    CalcPosterior (Xgamma_old, XtX_old, Xtz_old, ztz,
 					   rank_old.size(), Xb_old, beta_old,
 					   cHyp_old);
-			}	
+			}
 		}
 
 		// M-H steps.
@@ -1663,23 +1663,23 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 
 			logMHratio=0.0;
 			logMHratio+=
-			  ProposeHnRho(cHyp_old, cHyp_new, repeat);	
+			  ProposeHnRho(cHyp_old, cHyp_new, repeat);
 			logMHratio+=
 			  ProposeGamma (rank_old, rank_new, p_gamma,
-					cHyp_old, cHyp_new, repeat);	
+					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 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);	  
+			    SetXgamma (Xgamma_new, X, rank_new);
 			    CalcXtX (Xgamma_new, z, rank_new.size(),
-				     XtX_new, Xtz_new);	
+				     XtX_new, Xtz_new);
 			    time_set+=(clock()-time_start)/
 			      (double(CLOCKS_PER_SEC)*60.0);
 			  } else {
@@ -1697,17 +1697,17 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 					   cHyp_new);
 			  time_post+=(clock()-time_start)/
 			    (double(CLOCKS_PER_SEC)*60.0);
-			}	
-			logMHratio+=logPost_new-logPost_old;	
-		
+			}
+			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) {			
+
+			if (accept==1) {
 				logPost_old=logPost_new;
 				cHyp_old=cHyp_new;
 				gsl_vector_memcpy (Xb_old, Xb_new);
@@ -1719,7 +1719,7 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 					     ++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());
@@ -1742,8 +1742,8 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 			} else {
 			  cHyp_new=cHyp_old;
 			}
-			
-		}				
+
+		}
 
 		// Calculate z_hat, and pve.
 		if (a_mode==13) {
@@ -1753,19 +1753,19 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 			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 {		
+		else {
 			if (t%r_pace==0) {
 				w_col=w%w_pace;
 				if (w_col==0) {
@@ -1793,21 +1793,21 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 					       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;	
+					beta_g[pos-1].second+=1.0;
 				}
-				
+
 				if (a_mode==13) {
 					pheno_mean+=mean_z;
 				}
-				
+
 				w++;
 			}
 		}
@@ -1818,19 +1818,19 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 	cout<<"time on calculating posterior: "<<time_post<<endl;
 
 	w_col=w%w_pace;
-	WriteResult (1, Result_hyp, Result_gamma, w_col);	
-	
+	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_matrix_free(Result_gamma);
+
 	gsl_vector_free(z_hat);
 	gsl_vector_free(z);
-	gsl_vector_free(Xb_new);	
+	gsl_vector_free(Xb_new);
 	gsl_vector_free(Xb_old);
 
 	gsl_matrix_free(Xgamma_old);
@@ -1842,9 +1842,9 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 	gsl_matrix_free(XtX_new);
 	gsl_vector_free(Xtz_new);
 	gsl_vector_free(beta_new);
-	
+
 	delete [] p_gamma;
 	beta_g.clear();
-	
+
 	return;
 }