Removed FORCE_FLOAT from a few more files.

1 files changed, 450 insertions, 389 deletions

diff --git a/src/bslmm.cpp b/src/bslmm.cpp
index d295fd8..92762e2 100644
--- a/src/bslmm.cpp
+++ b/src/bslmm.cpp
@@ -14,7 +14,7 @@
  
  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>
@@ -47,8 +47,7 @@
 
 using namespace std;
 
-void BSLMM::CopyFromParam (PARAM &cPar) 
-{
+void BSLMM::CopyFromParam (PARAM &cPar) {
 	a_mode=cPar.a_mode;
 	d_pace=cPar.d_pace;
 	
@@ -101,9 +100,7 @@ void BSLMM::CopyFromParam (PARAM &cPar)
 	return;
 }
 
-
-void BSLMM::CopyToParam (PARAM &cPar) 
-{
+void BSLMM::CopyToParam (PARAM &cPar) {
 	cPar.time_UtZ=time_UtZ;
 	cPar.time_Omega=time_Omega;
 	cPar.time_Proposal=time_Proposal;
@@ -115,16 +112,16 @@ void BSLMM::CopyToParam (PARAM &cPar)
 	return;
 }
 
-
-
-void BSLMM::WriteBV (const gsl_vector *bv) 
-{
+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;}
+	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) {
@@ -132,7 +129,8 @@ void BSLMM::WriteBV (const gsl_vector *bv)
 			outfile<<"NA"<<endl;
 		}		
 		else {
-			outfile<<scientific<<setprecision(6)<<gsl_vector_get(bv, t)<<endl;
+			outfile<<scientific<<setprecision(6)<<
+			  gsl_vector_get(bv, t)<<endl;
 			t++;
 		}
 	}		
@@ -142,17 +140,16 @@ void BSLMM::WriteBV (const gsl_vector *bv)
 	return;
 }
 
-
-
-
-void BSLMM::WriteParam (vector<pair<double, double> > &beta_g, const gsl_vector *alpha, const size_t w) 
-{
+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;}
+	if (!outfile) {
+	  cout<<"error writing file: "<<file_str.c_str()<<endl; 
+	  return;}
 	
 	outfile<<"chr"<<"\t"<<"rs"<<"\t"
 			<<"ps"<<"\t"<<"n_miss"<<"\t"<<"alpha"<<"\t"
@@ -163,11 +160,13 @@ void BSLMM::WriteParam (vector<pair<double, double> > &beta_g, const gsl_vector
 		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";	
+		<<snpInfo[i].base_position<<"\t"<<snpInfo[i].n_miss<<"\t";
 				
-		outfile<<scientific<<setprecision(6)<<gsl_vector_get(alpha, t)<<"\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;
+			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;
@@ -180,15 +179,16 @@ void BSLMM::WriteParam (vector<pair<double, double> > &beta_g, const gsl_vector
 	return;
 }
 
-
-void BSLMM::WriteParam (const gsl_vector *alpha) 
-{
+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;}
+	if (!outfile) {
+	  cout<<"error writing file: "<<file_str.c_str()<<endl; 
+	  return;
+	}
 	
 	outfile<<"chr"<<"\t"<<"rs"<<"\t"
 			<<"ps"<<"\t"<<"n_miss"<<"\t"<<"alpha"<<"\t"
@@ -198,9 +198,10 @@ void BSLMM::WriteParam (const gsl_vector *alpha)
 	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<<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++;
 	}		
@@ -210,9 +211,8 @@ void BSLMM::WriteParam (const gsl_vector *alpha)
 	return;
 }
 
-
-void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp, const gsl_matrix *Result_gamma, const size_t w_col) 
-{
+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";
@@ -224,8 +224,14 @@ void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp, const gsl
 	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;}
+		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;
 		
@@ -237,8 +243,14 @@ void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp, const gsl
 	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;}
+		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;}
@@ -247,16 +259,19 @@ void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp, const gsl
 		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)<<
+				  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<<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<<
+				  (int)gsl_matrix_get(Result_gamma,i,j)<<"\t";
 			}
 			outfile_gamma<<endl;
 		}
@@ -270,13 +285,11 @@ void BSLMM::WriteResult (const int flag, const gsl_matrix *Result_hyp, const gsl
 	return;
 }
 
-
-
-void BSLMM::CalcPgamma (double *p_gamma)
-{
+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=0.7*gsl_ran_geometric_pdf (i+1, 1.0/geo_mean)+0.3/
+		  (double)ns_test;
 		p_gamma[i]=p;
 		s+=p;
 	}
@@ -287,10 +300,8 @@ void BSLMM::CalcPgamma (double *p_gamma)
 	return;
 }
 
-
-
-void BSLMM::SetXgamma (gsl_matrix *Xgamma, const gsl_matrix *X, vector<size_t> &rank)
-{
+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]];
@@ -302,10 +313,8 @@ void BSLMM::SetXgamma (gsl_matrix *Xgamma, const gsl_matrix *X, vector<size_t> &
 	return;
 }
 
-
-
-double BSLMM::CalcPveLM (const gsl_matrix *UtXgamma, const gsl_vector *Uty, const double sigma_a2) 
-{
+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);
@@ -333,9 +342,9 @@ double BSLMM::CalcPveLM (const gsl_matrix *UtXgamma, const gsl_vector *Uty, cons
 	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)
-{
+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;
@@ -362,7 +371,8 @@ void BSLMM::InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty, vector<si
 	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);
+	  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);
 	}
@@ -379,18 +389,6 @@ void BSLMM::InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty, vector<si
 	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;
@@ -399,10 +397,9 @@ void BSLMM::InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty, vector<si
 	return;
 }
 
-
-
-double BSLMM::CalcPosterior (const gsl_vector *Uty, const gsl_vector *K_eval, gsl_vector *Utu, gsl_vector *alpha_prime, class HYPBSLMM &cHyp)
-{
+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);	
@@ -420,25 +417,28 @@ double BSLMM::CalcPosterior (const gsl_vector *Uty, const gsl_vector *K_eval, gs
 		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));
+		gsl_vector_set (Utu_rand, i, 
+				gsl_ran_gaussian(gsl_r, 1)*sqrt(ds));
 	}
 	
-	//sample tau
+	// 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); }
+	if (a_mode==11) {
+	  tau = gsl_ran_gamma (gsl_r, (double)ni_test/2.0,  2.0/Hi_yy); 
+	}
 	
-	//sample alpha
+	// Sample alpha.
 	gsl_vector_memcpy (alpha_prime, Uty);
 	gsl_vector_mul (alpha_prime, weight_Hi);
 	gsl_vector_scale (alpha_prime, sigma_b2);
 	
-	//sample u
+	// 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
+	// For quantitative traits, calculate pve and ppe.
 	if (a_mode==11) {
 		gsl_blas_ddot (Utu, Utu, &d);
 		cHyp.pve=d/(double)ni_test;	
@@ -446,12 +446,13 @@ double BSLMM::CalcPosterior (const gsl_vector *Uty, const gsl_vector *K_eval, gs
 		cHyp.pge=0.0;	
 	}
 
-	//calculate likelihood
+	// 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));
+	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);
@@ -459,18 +460,22 @@ double BSLMM::CalcPosterior (const gsl_vector *Uty, const gsl_vector *K_eval, gs
 	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)
-{
+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_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);
@@ -481,7 +486,8 @@ double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
 	
 	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);
+		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);
@@ -492,10 +498,10 @@ double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
 		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));
+		gsl_vector_set(Utu_rand,i,gsl_ran_gaussian(gsl_r,1)*sqrt(ds));
 	}
 	
-	//calculate Omega
+	// Calculate Omega.
 	gsl_matrix_set_identity (Omega);
 	
 	time_start=clock();
@@ -504,8 +510,8 @@ double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
 	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);	
+	// Calculate beta_hat.
+	gsl_blas_dgemv (CblasTrans, 1.0, UtXgamma_eval, Uty, 0.0, XtHiy);
 
 	logdet_O=CholeskySolve(Omega, XtHiy, beta_hat);
 	
@@ -514,11 +520,13 @@ double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
 	gsl_blas_ddot (XtHiy, beta_hat, &d);
 	P_yy-=d;
 	
-	//sample tau
+	// 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); }
+	if (a_mode==11) {
+	  tau =gsl_ran_gamma (gsl_r, (double)ni_test/2.0,  2.0/P_yy); 
+	}
 
-	//sample beta
+	// Sample beta.
 	for (size_t i=0; i<beta->size; i++)
 	{
 		d=gsl_ran_gaussian(gsl_r, 1); 
@@ -526,27 +534,25 @@ double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
 	}
 	gsl_blas_dtrsv(CblasUpper, CblasNoTrans, CblasNonUnit, Omega, beta); 
 	
-	
-	//it compuates inv(L^T(Omega)) %*% beta;  
+	// This computes 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
+	// 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
+	// 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
+	// For quantitative traits, calculate pve and pge.
 	if (a_mode==11) {
 		gsl_blas_ddot (UtXb, UtXb, &d);
 		cHyp.pge=d/(double)ni_test;
@@ -558,7 +564,6 @@ double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
 		else {cHyp.pge/=cHyp.pve;}
 		cHyp.pve/=cHyp.pve+1.0/tau;	
 	}	
-	
 
 	gsl_matrix_free (UtXgamma_eval);
 	gsl_matrix_free (Omega);
@@ -570,17 +575,15 @@ double BSLMM::CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
 	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));
+	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) 
-{
+// 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);
@@ -594,10 +597,10 @@ void BSLMM::CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *Utu, gsl_vector
 	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) 
-{
+// 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);
 	
@@ -620,18 +623,17 @@ void BSLMM::CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *UtXb, const gsl
 	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);
 		d2=gsl_vector_get (z_hat, i);
-		//y is centerred for case control studies
+
+		// y is centered for case control studies.
 		if (d1<=0.0) {
-			//control, right truncated
+
+		        // Control, right truncated.
 			do {				
 				z_rand=d2+gsl_ran_gaussian(gsl_r, 1.0);
 			} while (z_rand>0.0);
@@ -648,12 +650,8 @@ void BSLMM::SampleZ (const gsl_vector *y, const gsl_vector *z_hat, gsl_vector *z
 	return;
 }
 
-
-
-
-
-double BSLMM::ProposeHnRho (const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_new, const size_t &repeat)
-{
+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;
 	
@@ -668,30 +666,13 @@ double BSLMM::ProposeHnRho (const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp
 		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 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;
 	
@@ -700,36 +681,25 @@ double BSLMM::ProposePi (const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_ne
 	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;}		
-		
+		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)
-{
+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)
-{
+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;
@@ -752,11 +722,19 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old, vector<size_t> &rank
 		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 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; 
+		if(flag_gamma==1)  {
+
+		        // Add a SNP.
 			do {
 				r_add=gsl_ran_discrete (gsl_r, gsl_t);
 			} while (mapRank2in.count(r_add)!=0); 
@@ -770,10 +748,13 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old, vector<size_t> &rank
 			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);
+			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);		
+		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;
@@ -785,13 +766,17 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old, vector<size_t> &rank
 		
 			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);
+			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);		
+		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
+
+		        // Be careful with the proposal.
 			do {
 				r_add=gsl_ran_discrete (gsl_r, gsl_t);
 			} while (mapRank2in.count(r_add)!=0); 
@@ -802,7 +787,8 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old, vector<size_t> &rank
 				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_remove]/
+			  (prob_total+p_gamma[r_remove]-p_gamma[r_add]));
 			logp-=log(p_gamma[r_add]/prob_total);
 			
 			mapRank2in.erase(r_remove);
@@ -810,7 +796,7 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old, vector<size_t> &rank
 			rank_new.erase(rank_new.begin()+col_id);
 			rank_new.push_back(r_add);
 		}
-		else {logp+=0;}//do not change
+		else {logp+=0;} // Do not change.
 	}
 	
 	stable_sort (rank_new.begin(), rank_new.end(), comp_vec);
@@ -819,24 +805,14 @@ double BSLMM::ProposeGamma (const vector<size_t> &rank_old, vector<size_t> &rank
 	return logp;
 }
 
-
-
-
-
-
-bool comp_lr (pair<size_t, double> a, pair<size_t, double> b)
-{
+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) {
+// 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;
@@ -890,9 +866,10 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
 		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;                                               
+	// 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)
 	{
@@ -900,7 +877,8 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
 		time (&rawtime);
 		tm * ptm = gmtime (&rawtime);
 		
-		randseed = (unsigned) (ptm->tm_hour%24*3600+ptm->tm_min*60+ptm->tm_sec);
+		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);
@@ -910,17 +888,14 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
 	
 	gsl_t=gsl_ran_discrete_preproc (ns_test, p_gamma);
 	
-	//initial parameters
+	// 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);
+		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) {
@@ -928,10 +903,12 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
 		}	
 	}
 	else {
-		gsl_matrix *UtXgamma=gsl_matrix_alloc (ni_test, cHyp_old.n_gamma);
+		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);
+		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) {
@@ -941,7 +918,7 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
 		gsl_vector_free (beta);
 	}	
 	
-	//calculate centered z_hat, and pve
+	// Calculate centered z_hat, and pve.
 	if (a_mode==13) {
 		time_start=clock();
 		if (cHyp_old.n_gamma==0 || cHyp_old.rho==0) {
@@ -953,15 +930,17 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
 		time_UtZ+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
 	}
 	
-	//start MCMC
+	// 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 (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);		
@@ -969,60 +948,75 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
 			
 			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);
+			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);
+			// 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);
+				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);
+				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));
+				  beta_old.push_back(gsl_vector_get(beta, i));
 				}
 				gsl_matrix_free (UtXgamma);
 				gsl_vector_free (beta);
 			}
 		}
 		
-		//MH steps
+		// M-H 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;}
+			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+=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);
+				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);
+				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);
+				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));
+				  beta_new.push_back(gsl_vector_get(beta, i));
 				}
 				gsl_matrix_free (UtXgamma);
 				gsl_vector_free (beta);
@@ -1030,17 +1024,20 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
 			
 			logMHratio+=logPost_new-logPost_old;		
 		
-			if (logMHratio>0 || log(gsl_rng_uniform(gsl_r))<logMHratio) {accept=1; n_accept++;}
+			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]);
-					}
+				  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);
@@ -1050,51 +1047,58 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
 			else {cHyp_new=cHyp_old;}
 		}				
 		
-		//calculate z_hat, and pve
+		// 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);
+				CalcCC_PVEnZ (U, UtXb_old, Utu_old,
+					      z_hat, cHyp_old);
 			}
 			
-			//sample mu and update z hat
+			// 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) );			
-			
+			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);
+			time_UtZ+=(clock()-time_start)/
+			  (double(CLOCKS_PER_SEC)*60.0);
 		}
 		
-		//Save data
+		// 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);}					
+					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);
+					  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);
+				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);
+					gsl_matrix_set(Result_gamma,w_col,i,
+						       pos);
 					
 					beta_g[pos-1].first+=beta_old[i];
 					beta_g[pos-1].second+=1.0;	
@@ -1138,7 +1142,8 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
 	}
 	
 	gsl_vector *alpha=gsl_vector_alloc (ns_test);
-	gsl_blas_dgemv (CblasTrans, 1.0/(double)ns_test, UtX, alpha_prime, 0.0, alpha);	
+	gsl_blas_dgemv (CblasTrans, 1.0/(double)ns_test, UtX,
+			alpha_prime, 0.0, alpha);	
 	WriteParam (beta_g, alpha, w);
 	gsl_vector_free(alpha);
 	
@@ -1154,10 +1159,9 @@ void BSLMM::MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *
 	return;
 }
 
-
-
-void BSLMM::RidgeR(const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *eval, const double lambda)
-{
+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);
@@ -1169,7 +1173,8 @@ void BSLMM::RidgeR(const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector
 	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_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);
@@ -1183,28 +1188,13 @@ void BSLMM::RidgeR(const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector
 	
 	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)
-{
+// 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_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);
 
@@ -1217,29 +1207,34 @@ void BSLMM::CalcXtX (const gsl_matrix *X, const gsl_vector *y, const size_t s_si
   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)
-{
+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
+  // rank_old and rank_new are sorted already inside PorposeGamma
+  // calculate vectors rank_remove and rank_add.
+  // 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> 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());
+  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());
+  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());
+  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 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;
@@ -1248,16 +1243,23 @@ void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old, const gsl_m
     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
+  // 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);
@@ -1295,13 +1297,13 @@ void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old, const gsl_m
       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
+      // Get X_add.
       SetXgamma (X_add, X, rank_add);
 
-      //get t(X_add)X_add and t(X_add)X_temp	
+      // 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
+      // Somehow the lapack_dgemm does not work here.
       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,
@@ -1310,18 +1312,26 @@ void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old, const gsl_m
 
       time_Omega+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
 
-      //save to X_new, XtX_new and Xty_new
+      // 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;}
+	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_const_view Xcopy_col=
+	    gsl_matrix_const_column(X_old, i_old);	  
 	  gsl_vector_memcpy (&Xnew_col.vector, &Xcopy_col.vector);
 	}	
 
@@ -1334,8 +1344,15 @@ void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old, const gsl_m
 
 	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 (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);
@@ -1372,37 +1389,40 @@ void BSLMM::SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old, const gsl_m
   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
+	// 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
+	// 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));
+	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 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_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);
@@ -1411,38 +1431,42 @@ double BSLMM::CalcPosterior (const gsl_matrix *Xgamma, const gsl_matrix *XtX, co
 
 	gsl_vector_memcpy (Xty_temp, &Xty_sub.vector);
 
-	//calculate Omega
+	// 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
+	// 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
+	// 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); }
+	if (a_mode==11) {
+	  tau = gsl_ran_gamma (gsl_r, (double)ni_test/2.0,  2.0/P_yy);
+	}
 
-	//sample beta
+	// 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); 
+	gsl_blas_dtrsv(CblasUpper, CblasNoTrans, CblasNonUnit, Omega,
+		       &beta_sub.vector); 
 		
-	//it compuates inv(L^T(Omega)) %*% beta;  
+	// 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_blas_dgemv (CblasNoTrans, 1.0, &Xgamma_sub.matrix, &beta_sub.vector, 0.0, Xb);		
+	gsl_blas_dgemv (CblasNoTrans, 1.0, &Xgamma_sub.matrix,
+			&beta_sub.vector, 0.0, Xb);		
 	
-	//for quantitative traits, calculate pve and pge
+	// For quantitative traits, calculate pve and pge.
 	if (a_mode==11) {
 		gsl_blas_ddot (Xb, Xb, &d);
 		cHyp.pve=d/(double)ni_test;
@@ -1454,7 +1478,8 @@ double BSLMM::CalcPosterior (const gsl_matrix *Xgamma, const gsl_matrix *XtX, co
 	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));
+	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);
@@ -1464,9 +1489,7 @@ double BSLMM::CalcPosterior (const gsl_matrix *Xgamma, const gsl_matrix *XtX, co
 	return logpost;
 }
 
-
-
-//calculate pve and pge, and calculate z_hat for case-control data	
+// 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);
@@ -1475,10 +1498,9 @@ void BSLMM::CalcCC_PVEnZ (gsl_vector *z_hat, class HYPBSLMM &cHyp)
   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) 
-{
+// 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);
@@ -1491,9 +1513,7 @@ void BSLMM::CalcCC_PVEnZ (const gsl_vector *Xb, gsl_vector *z_hat, class HYPBSLM
 	return;
 }
 
-
-
-//if a_mode==13, then run probit model
+// 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;
@@ -1520,7 +1540,9 @@ 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
+	
+	// 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);
 
@@ -1549,9 +1571,10 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 		mapRank2pos[i]=pos_loglr[i].first;
 	}
 	
-	//calculate proposal distribution for gamma (unnormalized), and set up gsl_r and gsl_t		
+	// Calculate proposal distribution for gamma (unnormalized),
+	// and set up gsl_r and gsl_t.
 	gsl_rng_env_setup();                
-	const gsl_rng_type * gslType;                                               
+	const gsl_rng_type * gslType;
 	gslType = gsl_rng_default; 
 	if (randseed<0)
 	{
@@ -1559,7 +1582,8 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 		time (&rawtime);
 		tm * ptm = gmtime (&rawtime);
 		
-		randseed = (unsigned) (ptm->tm_hour%24*3600+ptm->tm_min*60+ptm->tm_sec);
+		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);
@@ -1569,7 +1593,7 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 	
 	gsl_t=gsl_ran_discrete_preproc (ns_test, p_gamma);
 	
-	//initial parameters
+	// Initial parameters.
 	InitialMCMC (X, z, rank_old, cHyp_old, pos_loglr);
 	
 	cHyp_initial=cHyp_old;
@@ -1580,10 +1604,12 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 	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);
+	  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
+	// Calculate centered z_hat, and pve.
 	if (a_mode==13) {
 		if (cHyp_old.n_gamma==0) {
 			CalcCC_PVEnZ (z_hat, cHyp_old);
@@ -1593,65 +1619,94 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 		}
 	}
 	
-	//start MCMC
+	// 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 (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);
 			gsl_blas_ddot(z,z,&ztz);
 					
-			//First proposal		
+			// 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);
+			  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
+		// M-H 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);}
+			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+=
+			  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
+			  
+			  // 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);	  
-			    CalcXtX (Xgamma_new, z, rank_new.size(), XtX_new, Xtz_new);	
-			    time_set+=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
+			    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);
+			    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);
+			  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++;}
+			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;
@@ -1659,8 +1714,10 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 
 				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]);
+					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());
@@ -1684,7 +1741,7 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 			
 		}				
 
-		//calculate z_hat, and pve
+		// Calculate z_hat, and pve.
 		if (a_mode==13) {
 			if (cHyp_old.n_gamma==0) {
 				CalcCC_PVEnZ (z_hat, cHyp_old);
@@ -1693,41 +1750,47 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 				CalcCC_PVEnZ (Xb_old, z_hat, cHyp_old);
 			}
 			
-			//sample mu and update z hat
+			// 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) );			
+			mean_z+=gsl_ran_gaussian(gsl_r,
+						 sqrt(1.0/(double) ni_test));
 			
 			gsl_vector_add_constant (z_hat, mean_z);
 		}
 		
-		//Save data
+		// 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);}					
+					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);
+					  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);
+				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);
+					gsl_matrix_set(Result_gamma,w_col,
+						       i,pos);
 					
-					beta_g[pos-1].first+=gsl_vector_get(beta_old, i);
+					beta_g[pos-1].first+=
+					  gsl_vector_get(beta_old, i);
 					beta_g[pos-1].second+=1.0;	
 				}
 				
@@ -1736,9 +1799,7 @@ void BSLMM::MCMC (const gsl_matrix *X, const gsl_vector *y) {
 				}
 				
 				w++;
-				
 			}
-			
 		}
 	}
 	cout<<endl;