Merge pull request #51 from genenetwork/spacing

Spacing fixes.

31 files changed, 834 insertions, 834 deletions

diff --git a/Makefile.linux b/Makefile.linux
index 0b2c0b9..b51bbfe 100644
--- a/Makefile.linux
+++ b/Makefile.linux
@@ -14,8 +14,8 @@ SYS = LNX
 # Disable WITH_LAPACK option can slow computation speed significantly and is not recommended
 # Disable WITH_ARPACK option only disable -apprx option in the software
 WITH_LAPACK = 1
-FORCE_32BIT = 
-FORCE_DYNAMIC = 
+FORCE_32BIT =
+FORCE_DYNAMIC =
 DIST_NAME = gemma-0.96alpha
 
 # --------------------------------------------------------------------
@@ -45,7 +45,7 @@ OUTPUT = $(BIN_DIR)/gemma
 
 SOURCES = $(SRC_DIR)/main.cpp
 
-HDR = 
+HDR =
 
 # Detailed libary paths, D for dynamic and S for static
 LIBS_LNX_D_LAPACK = -llapack
@@ -54,7 +54,7 @@ LIBS_LNX_S_LAPACK = /software/atlas-3.10.3-el7-x86_64/lib/liblapack.a \
    /software/atlas-3.10.3-el7-x86_64/lib/libcblas.a \
    /software/atlas-3.10.3-el7-x86_64/lib/libf77blas.a \
    /software/atlas-3.10.3-el7-x86_64/lib/libatlas.a -lgfortran \
-   -Wl,--allow-multiple-definition 
+   -Wl,--allow-multiple-definition
 
 SOURCES += $(SRC_DIR)/param.cpp $(SRC_DIR)/gemma.cpp $(SRC_DIR)/io.cpp $(SRC_DIR)/lm.cpp $(SRC_DIR)/lmm.cpp $(SRC_DIR)/vc.cpp $(SRC_DIR)/mvlmm.cpp $(SRC_DIR)/bslmm.cpp $(SRC_DIR)/prdt.cpp $(SRC_DIR)/mathfunc.cpp $(SRC_DIR)/gzstream.cpp $(SRC_DIR)/eigenlib.cpp $(SRC_DIR)/ldr.cpp $(SRC_DIR)/bslmmdap.cpp $(SRC_DIR)/logistic.cpp $(SRC_DIR)/varcov.cpp
 HDR += $(SRC_DIR)/param.h $(SRC_DIR)/gemma.h $(SRC_DIR)/io.h $(SRC_DIR)/lm.h $(SRC_DIR)/lmm.h $(SRC_DIR)/vc.h $(SRC_DIR)/mvlmm.h $(SRC_DIR)/bslmm.h $(SRC_DIR)/prdt.h $(SRC_DIR)/mathfunc.h $(SRC_DIR)/gzstream.h $(SRC_DIR)/eigenlib.h
@@ -91,7 +91,7 @@ $(OUTPUT): $(OBJS)
 
 $(OBJS) : $(HDR)
 
-.cpp.o: 
+.cpp.o:
 	$(CPP) $(CPPFLAGS) $(HEADERS) -c $*.cpp -o $*.o
 .SUFFIXES : .cpp .c .o $(SUFFIXES)
 
diff --git a/Makefile.macosx b/Makefile.macosx
index 992e442..00467d6 100644
--- a/Makefile.macosx
+++ b/Makefile.macosx
@@ -14,7 +14,7 @@ SYS = MAC
 # Disable WITH_LAPACK option can slow computation speed significantly and is not recommended
 # Disable WITH_ARPACK option only disable -apprx option in the software
 WITH_LAPACK = 1
-FORCE_32BIT = 
+FORCE_32BIT =
 FORCE_DYNAMIC = 1
 DIST_NAME = gemma-0.96
 
@@ -37,13 +37,13 @@ OUTPUT = $(BIN_DIR)/gemma
 
 SOURCES = $(SRC_DIR)/main.cpp
 
-HDR = 
+HDR =
 
 # Detailed libary paths, D for dynamic and S for static
 
 LIBS_LNX_D_LAPACK = -llapack
 LIBS_MAC_D_LAPACK = -framework Accelerate
-LIBS_LNX_S_LAPACK = /usr/lib/lapack/liblapack.a -lgfortran  /usr/lib/atlas-base/libatlas.a /usr/lib/libblas/libblas.a -Wl,--allow-multiple-definition 
+LIBS_LNX_S_LAPACK = /usr/lib/lapack/liblapack.a -lgfortran  /usr/lib/atlas-base/libatlas.a /usr/lib/libblas/libblas.a -Wl,--allow-multiple-definition
 
 # Options
 
@@ -82,7 +82,7 @@ $(OUTPUT): $(OBJS)
 
 $(OBJS) : $(HDR)
 
-.cpp.o: 
+.cpp.o:
 	$(CPP) $(CPPFLAGS) $(HEADERS) -c $*.cpp -o $*.o
 .SUFFIXES : .cpp .c .o $(SUFFIXES)
 
diff --git a/README.md b/README.md
index bb6cf1e..a539cc0 100644
--- a/README.md
+++ b/README.md
@@ -61,7 +61,7 @@ MQS algorithm to estimate variance components.
 If you use GEMMA for published work, please cite our paper:
 
 + Xiang Zhou and Matthew Stephens (2012). [Genome-wide efficient
-mixed-model analysis for association studies.](http://doi.org/10.1038/ng.2310) 
+mixed-model analysis for association studies.](http://doi.org/10.1038/ng.2310)
 *Nature Genetics* **44**, 821–824.
 
 If you use the multivariate linear mixed model (mvLMM) in your
@@ -77,7 +77,7 @@ If you use the Bayesian sparse linear mixed model (BSLMM), please cite:
 + Xiang Zhou, Peter Carbonetto and Matthew Stephens (2013). [Polygenic
 modeling with bayesian sparse linear mixed
 models.](http://doi.org/10.1371/journal.pgen.1003264) *PLoS Genetics*
-**9**, e1003264. 
+**9**, e1003264.
 
 And if you use of the variance component estimation using summary
 statistics, please cite:
@@ -118,7 +118,7 @@ This is the current structure of the GEMMA source repository:
 subfolders; see Wilson et al "Good Enough Practices" paper for example
 of this.*
 
-## Setup 
+## Setup
 
 There are two ways to install GEMMA:
 
diff --git a/doc/manual.tex b/doc/manual.tex
index d47aa22..c0119dc 100644
--- a/doc/manual.tex
+++ b/doc/manual.tex
@@ -100,11 +100,11 @@ available open-source numerical libraries.
   Stephens (2014). Efficient multivariate linear mixed model
   algorithms for genome-wide association studies. Nature Methods. 11:
   407-409.
-  
+
 \item Bayesian sparse linear mixed models \\ Xiang Zhou, Peter
   Carbonetto and Matthew Stephens (2013). Polygenic modeling with
   Bayesian sparse linear mixed models. PLoS Genetics. 9(2): e1003264.
-  
+
 \item Variance component estimation with individual-level or summary
   data\\ Xiang Zhou (2016). A unified framework for variance component
   estimation with summary statistics in genome-wide association
@@ -212,10 +212,10 @@ effects terms ($\mathbf X\boldsymbol\beta$). These two parameters are
 defined as follows:
 \begin{align*}
 \mbox{PVE}(\bbeta, \bu, \tau) &
-  :=\frac{\mbox{V}(\bX\bbeta+\bu)}{\mbox{V}(\bX\bbeta+\bu)+\tau^{-1}}, \\  
+  :=\frac{\mbox{V}(\bX\bbeta+\bu)}{\mbox{V}(\bX\bbeta+\bu)+\tau^{-1}}, \\
 \mbox{PGE}(\bbeta, \bu)
   & :=\frac{\mbox{V}(\bX\bbeta)}{\mbox{V}(\bX\bbeta+\bu)}, \\
-\intertext{where}  
+\intertext{where}
 \mbox{V}({\bf x}) &:=\frac{1}{n}\sum_{i=1}^n (x_i-\overline {x})^2.
 \end{align*}
 
@@ -429,7 +429,7 @@ BIMBAM mean genotype file from IMPUTE genotype files
 (\url{http://www.stats.ox.ac.uk/~marchini/software/gwas/file_format.html})\cite{Howie:2009}:
 %
 \begin{verbatim}
-cat [impute filename] | awk -v s=[number of samples/individuals] 
+cat [impute filename] | awk -v s=[number of samples/individuals]
 '{ printf $2 "," $4 "," $5; for(i=1; i<=s; i++) printf "," $(i*3+3)*2+$(i*3+4); printf "\n" }'
 > [bimbam filename]
 \end{verbatim}
@@ -815,7 +815,7 @@ chr     rs      ps      n_mis   n_obs   allele1 allele0 af      beta    se
 \end{verbatim}
 %
 
-The 11 columns are: chromosome numbers, snp ids, base pair positions on the chromosome, number of missing individuals for a given snp, number of non-missing individuals for a given snp, minor allele, major allele, allele frequency, beta estimates, standard errors for beta, and $p$ values from the Wald test. 
+The 11 columns are: chromosome numbers, snp ids, base pair positions on the chromosome, number of missing individuals for a given snp, number of non-missing individuals for a given snp, minor allele, major allele, allele frequency, beta estimates, standard errors for beta, and $p$ values from the Wald test.
 
 \subsection{Estimate Relatedness Matrix from Genotypes}
 
@@ -1009,7 +1009,7 @@ ped format or the BIMBAM format are:
 
 \begin{verbatim}
 ./gemma -bfile [prefix] -k [filename] -lmm [num] -n [num1] [num2] [num3] -o [prefix]
-./gemma -g [filename] -p [filename] -a [filename] -k [filename] -lmm [num] 
+./gemma -g [filename] -p [filename] -a [filename] -k [filename] -lmm [num]
 -n [num1] [num2] [num3] -o [prefix]
 \end{verbatim}
 
@@ -1041,7 +1041,7 @@ missing, one can impute these missing values before association tests:
 
 \begin{verbatim}
 ./gemma -bfile [prefix] -k [filename] -predict -n [num1] [num2] [num3] -o [prefix]
-./gemma -g [filename] -p [filename] -a [filename] -k [filename] -predict 
+./gemma -g [filename] -p [filename] -a [filename] -k [filename] -predict
 -n [num1] [num2] [num3] -o [prefix]
 \end{verbatim}
 
@@ -1154,10 +1154,10 @@ below:
 %
 \begin{verbatim}
 h 	 pve 	 rho 	 pge 	 pi 	 n_gamma
-4.777635e-01	5.829042e-01	4.181280e-01	4.327976e-01	2.106763e-03	25	
-5.278073e-01	5.667885e-01	3.339020e-01	4.411859e-01	2.084355e-03	26	
-5.278073e-01	5.667885e-01	3.339020e-01	4.411859e-01	2.084355e-03	26	
-6.361674e-01	6.461678e-01	3.130355e-01	3.659850e-01	2.188401e-03	25	
+4.777635e-01	5.829042e-01	4.181280e-01	4.327976e-01	2.106763e-03	25
+5.278073e-01	5.667885e-01	3.339020e-01	4.411859e-01	2.084355e-03	26
+5.278073e-01	5.667885e-01	3.339020e-01	4.411859e-01	2.084355e-03	26
+6.361674e-01	6.461678e-01	3.130355e-01	3.659850e-01	2.188401e-03	25
 5.479237e-01	6.228036e-01	3.231856e-01	4.326231e-01	2.164183e-03	27
 \end{verbatim}
 %
@@ -1196,9 +1196,9 @@ The basic usages for association analysis with either the PLINK binary
 ped format or the BIMBAM format are:
 
 \begin{verbatim}
-./gemma -bfile [prefix] -epm [filename] -emu [filename] -ebv [filename] -k [filename] 
+./gemma -bfile [prefix] -epm [filename] -emu [filename] -ebv [filename] -k [filename]
 -predict [num] -o [prefix]
-./gemma -g [filename] -p [filename] -epm [filename] -emu [filename] -ebv [filename] 
+./gemma -g [filename] -p [filename] -epm [filename] -emu [filename] -ebv [filename]
 -k [filename] -predict [num] -o [prefix]
 \end{verbatim}
 
@@ -1544,7 +1544,7 @@ source code for detailed examples.
 \item  \textcolor{red}{-ci       [num]}     \quad          specify fitting algorithm to compute the standard errors. (default 1; valid value 1-2; 1: MQS-HEW; 2: MQS-LDW.)
 \end{itemize}
 %
-	
+
 \clearpage
 
 \bibliographystyle{plain}
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;
 }
diff --git a/src/bslmm.h b/src/bslmm.h
index da185fa..c7768a2 100644
--- a/src/bslmm.h
+++ b/src/bslmm.h
@@ -1,22 +1,22 @@
 /*
  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/>.
 */
 
-#ifndef __BSLMM_H__                
+#ifndef __BSLMM_H__
 #define __BSLMM_H__
 
 #include <vector>
@@ -30,23 +30,23 @@ using namespace std;
 
 class BSLMM {
 
-public:	
+public:
 	// IO-related parameters.
-	int a_mode;	
+	int a_mode;
 	size_t d_pace;
-	
+
 	string file_bfile;
 	string file_geno;
 	string file_out;
 	string path_out;
-	
+
 	// LMM-related parameters.
 	double l_min;
 	double l_max;
 	size_t n_region;
 	double pve_null;
 	double pheno_mean;
-	
+
 	// BSLMM MCMC-related parameters
 	double h_min, h_max, h_scale;	       // Priors for h.
 	double rho_min, rho_max, rho_scale;    // Priors for rho.
@@ -61,8 +61,8 @@ public:
 	size_t n_mh;			       // Number of MH steps per iter.
 	double geo_mean;		       // Mean of geometric dist.
 	long int randseed;
-	double trace_G;	
-	
+	double trace_G;
+
 	HYPBSLMM cHyp_initial;
 
 	// Summary statistics.
@@ -74,32 +74,32 @@ public:
 
         // Time spent on constructing the proposal distribution for
         // gamma (i.e. lmm or lm analysis).
-	double time_Proposal;        
+	double time_Proposal;
 
         // Indicator for individuals (phenotypes): 0 missing, 1
         // available for analysis.
-	vector<int> indicator_idv;				
+	vector<int> indicator_idv;
 
 	// Sequence indicator for SNPs: 0 ignored because of (a) maf,
 	// (b) miss, (c) non-poly; 1 available for analysis.
-	vector<int> indicator_snp;	
+	vector<int> indicator_snp;
 
         // Record SNP information.
-	vector<SNPINFO> snpInfo;		
-	
+	vector<SNPINFO> snpInfo;
+
 	// Not included in PARAM.
-	gsl_rng *gsl_r; 
-	gsl_ran_discrete_t *gsl_t;	
-	map<size_t, size_t> mapRank2pos;	
-	
+	gsl_rng *gsl_r;
+	gsl_ran_discrete_t *gsl_t;
+	map<size_t, size_t> mapRank2pos;
+
 	// Main functions.
 	void CopyFromParam (PARAM &cPar);
 	void CopyToParam (PARAM &cPar);
-	
+
 	void RidgeR(const gsl_matrix *U, const gsl_matrix *UtX,
 		    const gsl_vector *Uty, const gsl_vector *eval,
 		    const double lambda);
-	
+
 	void MCMC (const gsl_matrix *U, const gsl_matrix *UtX,
 		   const gsl_vector *Uty, const gsl_vector *K_eval,
 		   const gsl_vector *y);
@@ -111,10 +111,10 @@ public:
 	void WriteParam (const gsl_vector *alpha);
 	void WriteResult (const int flag, const gsl_matrix *Result_hyp,
 			  const gsl_matrix *Result_gamma, const size_t w_col);
-	
+
 	// Subfunctions inside MCMC.
 	void CalcPgamma (double *p_gammar);
-	
+
 	double CalcPveLM (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
 			  const double sigma_a2);
 	void InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty,
diff --git a/src/bslmmdap.cpp b/src/bslmmdap.cpp
index ebbff70..e1a53a6 100644
--- a/src/bslmmdap.cpp
+++ b/src/bslmmdap.cpp
@@ -92,13 +92,13 @@ void BSLMMDAP::CopyToParam (PARAM &cPar) {
 
 
 // Read hyp file.
-void ReadFile_hyb (const string &file_hyp, vector<double> &vec_sa2, 
+void ReadFile_hyb (const string &file_hyp, vector<double> &vec_sa2,
 		   vector<double> &vec_sb2, vector<double> &vec_wab) {
   vec_sa2.clear(); vec_sb2.clear(); vec_wab.clear();
 
   igzstream infile (file_hyp.c_str(), igzstream::in);
   if (!infile) {
-    cout<<"error! fail to open hyp file: "<<file_hyp<<endl; 
+    cout<<"error! fail to open hyp file: "<<file_hyp<<endl;
     return;
   }
 
@@ -128,7 +128,7 @@ void ReadFile_hyb (const string &file_hyp, vector<double> &vec_sa2,
 }
 
 // Read bf file.
-void ReadFile_bf (const string &file_bf, vector<string> &vec_rs, 
+void ReadFile_bf (const string &file_bf, vector<string> &vec_rs,
 		  vector<vector<vector<double> > > &BF) {
   BF.clear(); vec_rs.clear();
 
@@ -196,12 +196,12 @@ void ReadFile_bf (const string &file_bf, vector<string> &vec_rs,
 
 // Read category files.
 // Read both continuous and discrete category file, record mapRS2catc.
-void ReadFile_cat (const string &file_cat, const vector<string> &vec_rs, 
+void ReadFile_cat (const string &file_cat, const vector<string> &vec_rs,
 		   gsl_matrix *Ac, gsl_matrix_int *Ad, gsl_vector_int *dlevel,
 		   size_t &kc, size_t &kd) {
   igzstream infile (file_cat.c_str(), igzstream::in);
   if (!infile) {
-    cout<<"error! fail to open category file: "<<file_cat<<endl; 
+    cout<<"error! fail to open category file: "<<file_cat<<endl;
     return;
   }
 
@@ -323,11 +323,11 @@ void BSLMMDAP::WriteResult (const gsl_matrix *Hyper, const gsl_matrix *BF) {
 	outfile_hyp.open (file_hyp.c_str(), ofstream::out);
 
 	if (!outfile_bf) {
-	  cout<<"error writing file: "<<file_bf<<endl; 
+	  cout<<"error writing file: "<<file_bf<<endl;
 	  return;
 	}
 	if (!outfile_hyp) {
-	  cout<<"error writing file: "<<file_hyp<<endl; 
+	  cout<<"error writing file: "<<file_hyp<<endl;
 	  return;
 	}
 
@@ -370,8 +370,8 @@ void BSLMMDAP::WriteResult (const gsl_matrix *Hyper, const gsl_matrix *BF) {
 	return;
 }
 
-void BSLMMDAP::WriteResult (const vector<string> &vec_rs, 
-			    const gsl_matrix *Hyper, const gsl_vector *pip, 
+void BSLMMDAP::WriteResult (const vector<string> &vec_rs,
+			    const gsl_matrix *Hyper, const gsl_vector *pip,
 			    const gsl_vector *coef) {
   string file_gamma, file_hyp, file_coef;
 	file_gamma=path_out+"/"+file_out;
@@ -388,15 +388,15 @@ void BSLMMDAP::WriteResult (const vector<string> &vec_rs,
 	outfile_coef.open (file_coef.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;
 	}
 	if (!outfile_coef) {
-	  cout<<"error writing file: "<<file_coef<<endl; 
+	  cout<<"error writing file: "<<file_coef<<endl;
 	  return;
 	}
 
@@ -432,8 +432,8 @@ void BSLMMDAP::WriteResult (const vector<string> &vec_rs,
 }
 
 
-double BSLMMDAP::CalcMarginal (const gsl_vector *Uty, 
-			       const gsl_vector *K_eval, 
+double BSLMMDAP::CalcMarginal (const gsl_vector *Uty,
+			       const gsl_vector *K_eval,
 			       const double sigma_b2, const double tau) {
 	gsl_vector *weight_Hi=gsl_vector_alloc (Uty->size);
 
@@ -457,16 +457,16 @@ double BSLMMDAP::CalcMarginal (const gsl_vector *Uty,
 	return logm;
 }
 
-double BSLMMDAP::CalcMarginal (const gsl_matrix *UtXgamma, 
-			       const gsl_vector *Uty, 
-			       const gsl_vector *K_eval, 
-			       const double sigma_a2, 
+double BSLMMDAP::CalcMarginal (const gsl_matrix *UtXgamma,
+			       const gsl_vector *Uty,
+			       const gsl_vector *K_eval,
+			       const double sigma_a2,
 			       const double sigma_b2, const double tau) {
   clock_t  time_start;
 	double logm=0.0;
 	double d, uy, P_yy=0, logdet_O=0.0, logdet_H=0.0;
 
-	gsl_matrix *UtXgamma_eval=gsl_matrix_alloc (UtXgamma->size1, 
+	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);
@@ -526,8 +526,8 @@ double BSLMMDAP::CalcPrior (class HYPBSLMM &cHyp) {
 }
 
 // Where A is the ni_test by n_cat matrix of annotations.
-void BSLMMDAP::DAP_CalcBF (const gsl_matrix *U, const gsl_matrix *UtX, 
-			   const gsl_vector *Uty, const gsl_vector *K_eval, 
+void BSLMMDAP::DAP_CalcBF (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;
 
@@ -601,9 +601,9 @@ void BSLMMDAP::DAP_CalcBF (const gsl_matrix *U, const gsl_matrix *UtX,
 	return;
 }
 
-void single_ct_regression(const gsl_matrix_int *Xd, 
+void single_ct_regression(const gsl_matrix_int *Xd,
 			  const gsl_vector_int *dlevel,
-			  const gsl_vector *pip_vec, 
+			  const gsl_vector *pip_vec,
 			  gsl_vector *coef, gsl_vector *prior_vec) {
 
   map<int,double> sum_pip;
@@ -635,13 +635,13 @@ void single_ct_regression(const gsl_matrix_int *Xd,
 }
 
 // Where A is the ni_test by n_cat matrix of annotations.
-void BSLMMDAP::DAP_EstimateHyper (const size_t kc, const size_t kd, 
-				  const vector<string> &vec_rs, 
-				  const vector<double> &vec_sa2, 
-				  const vector<double> &vec_sb2, 
-				  const vector<double> &wab, 
-				  const vector<vector<vector<double> > > &BF, 
-				  gsl_matrix *Ac, gsl_matrix_int *Ad, 
+void BSLMMDAP::DAP_EstimateHyper (const size_t kc, const size_t kd,
+				  const vector<string> &vec_rs,
+				  const vector<double> &vec_sa2,
+				  const vector<double> &vec_sb2,
+				  const vector<double> &wab,
+				  const vector<vector<vector<double> > > &BF,
+				  gsl_matrix *Ac, gsl_matrix_int *Ad,
 				  gsl_vector_int *dlevel) {
 	clock_t time_start;
 
diff --git a/src/bslmmdap.h b/src/bslmmdap.h
index 8445669..db5774b 100644
--- a/src/bslmmdap.h
+++ b/src/bslmmdap.h
@@ -78,35 +78,35 @@ public:
 	void CopyToParam (PARAM &cPar);
 
 	void WriteResult (const gsl_matrix *Hyper, const gsl_matrix *BF);
-	void WriteResult (const vector<string> &vec_rs, 
-			  const gsl_matrix *Hyper, const gsl_vector *pip, 
+	void WriteResult (const vector<string> &vec_rs,
+			  const gsl_matrix *Hyper, const gsl_vector *pip,
 			  const gsl_vector *coef);
-	double CalcMarginal (const gsl_vector *Uty, const gsl_vector *K_eval, 
+	double CalcMarginal (const gsl_vector *Uty, const gsl_vector *K_eval,
 			     const double sigma_b2, const double tau);
-	double CalcMarginal (const gsl_matrix *UtXgamma, 
-			     const gsl_vector *Uty, const gsl_vector *K_eval, 
-			     const double sigma_a2, const double sigma_b2, 
+	double CalcMarginal (const gsl_matrix *UtXgamma,
+			     const gsl_vector *Uty, const gsl_vector *K_eval,
+			     const double sigma_a2, const double sigma_b2,
 			     const double tau);
 	double CalcPrior (class HYPBSLMM &cHyp);
 
-	void DAP_CalcBF (const gsl_matrix *U, const gsl_matrix *UtX, 
-			 const gsl_vector *Uty, const gsl_vector *K_eval, 
+	void DAP_CalcBF (const gsl_matrix *U, const gsl_matrix *UtX,
+			 const gsl_vector *Uty, const gsl_vector *K_eval,
 			 const gsl_vector *y);
-	void DAP_EstimateHyper (const size_t kc, const size_t kd, 
-				const vector<string> &vec_rs, 
-				const vector<double> &vec_sa2, 
-				const vector<double> &vec_sb2, 
-				const vector<double> &wab, 
-				const vector<vector<vector<double> > > &BF, 
-				gsl_matrix *Ac, gsl_matrix_int *Ad, 
+	void DAP_EstimateHyper (const size_t kc, const size_t kd,
+				const vector<string> &vec_rs,
+				const vector<double> &vec_sa2,
+				const vector<double> &vec_sb2,
+				const vector<double> &wab,
+				const vector<vector<vector<double> > > &BF,
+				gsl_matrix *Ac, gsl_matrix_int *Ad,
 				gsl_vector_int *dlevel);
 };
 
-void ReadFile_hyb (const string &file_hyp, vector<double> &vec_sa2, 
+void ReadFile_hyb (const string &file_hyp, vector<double> &vec_sa2,
 		   vector<double> &vec_sb2, vector<double> &vec_wab);
-void ReadFile_bf (const string &file_bf, vector<string> &vec_rs, 
+void ReadFile_bf (const string &file_bf, vector<string> &vec_rs,
 		  vector<vector<vector<double> > > &BF);
-void ReadFile_cat (const string &file_cat, const vector<string> &vec_rs, 
+void ReadFile_cat (const string &file_cat, const vector<string> &vec_rs,
 		   gsl_matrix *Ac, gsl_matrix_int *Ad, gsl_vector_int *dlevel,
 		   size_t &kc, size_t &kd);
 
diff --git a/src/eigenlib.cpp b/src/eigenlib.cpp
index 7ad250f..733dae1 100644
--- a/src/eigenlib.cpp
+++ b/src/eigenlib.cpp
@@ -28,9 +28,9 @@ using namespace std;
 using namespace Eigen;
 
 // On two different clusters, compare eigen vs lapack/gsl:
-// 
+//
 // dgemm, 5x or 0.5x faster or slower than lapack, 5x or 4x faster than gsl
-// dgemv, 20x or 4x faster than gsl, 
+// dgemv, 20x or 4x faster than gsl,
 // eigen, 1x or 0.3x slower than lapack
 // invert, 20x or 10x faster than lapack
 //
diff --git a/src/eigenlib.h b/src/eigenlib.h
index 8cb8880..3659dc1 100644
--- a/src/eigenlib.h
+++ b/src/eigenlib.h
@@ -16,7 +16,7 @@
     along with this program. If not, see <http://www.gnu.org/licenses/>.
 */
 
-#ifndef __EIGENLIB_H__                
+#ifndef __EIGENLIB_H__
 #define __EIGENLIB_H__
 
 #include <vector>
diff --git a/src/gemma.cpp b/src/gemma.cpp
index 18179f3..f4902fe 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -31,7 +31,7 @@
 #include "gsl/gsl_eigen.h"
 #include "gsl/gsl_cdf.h"
 
-#include "lapack.h"  
+#include "lapack.h"
 #include "io.h"
 #include "gemma.h"
 #include "vc.h"
@@ -211,7 +211,7 @@ void GEMMA::PrintHelp(size_t option) {
     cout<<"         ./gemma -g [filename] -p [filename] -calccor -o [prefix]"<<endl;
     cout<<endl;
   }
-  
+
   if (option==2) {
     cout<<" FILE I/O RELATED OPTIONS" << endl;
     cout<<" -bfile    [prefix]       "<<" specify input PLINK binary ped file prefix."<<endl;
@@ -231,11 +231,11 @@ void GEMMA::PrintHelp(size_t option) {
     cout<<"          format: rs#1, base_position, chr_number"<<endl;
     cout<<"                  rs#2, base_position, chr_number"<<endl;
     cout<<"                  ..."<<endl;
-    
+
     // WJA added.
     cout<<" -oxford    [prefix]       "<<" specify input Oxford genotype bgen file prefix."<<endl;
     cout<<"          requires: *.bgen, *.sample files"<<endl;
-    
+
     cout<<" -gxe      [filename]     "<<" specify input file that contains a column of environmental factor for g by e tests"<<endl;
     cout<<"          format: variable for individual 1"<<endl;
     cout<<"                  variable for individual 2"<<endl;
@@ -308,7 +308,7 @@ void GEMMA::PrintHelp(size_t option) {
     cout<<" -notsnp                  "<<" minor allele frequency cutoff is not used" << endl;
     cout<<endl;
   }
-  
+
   if (option==4) {
     cout<<" RELATEDNESS MATRIX CALCULATION OPTIONS" << endl;
     cout<<" -gk       [num]          "<<" specify which type of kinship/relatedness matrix to generate (default 1)" << endl;
@@ -317,13 +317,13 @@ void GEMMA::PrintHelp(size_t option) {
     cout<<"          note: non-polymorphic SNPs are excluded "<<endl;
     cout<<endl;
   }
-  
+
   if (option==5) {
     cout<<" EIGEN-DECOMPOSITION OPTIONS" << endl;
     cout<<" -eigen                   "<<" specify to perform eigen decomposition of the loaded relatedness matrix" << endl;
     cout<<endl;
   }
-  
+
   if (option==6) {
     cout<<" VARIANCE COMPONENT ESTIMATION OPTIONS" << endl;
     cout<<" -vc                      "<<" specify to perform variance component estimation for the loaded relatedness matrix/matrices" << endl;
@@ -336,7 +336,7 @@ void GEMMA::PrintHelp(size_t option) {
     cout<<"                                         -crt -windowns [num]"<<" specify the window size based on number of snps (default 0)"<<endl;
     cout<<endl;
   }
-  
+
   if (option==7) {
     cout<<" LINEAR MODEL OPTIONS" << endl;
     cout<<" -lm       [num]         "<<" specify analysis options (default 1)."<<endl;
@@ -346,7 +346,7 @@ void GEMMA::PrintHelp(size_t option) {
     cout<<"                   4: 1-3"<<endl;
     cout<<endl;
   }
-  
+
   if (option==8) {
     cout<<" LINEAR MIXED MODEL OPTIONS" << endl;
     cout<<" -lmm      [num]         "<<" specify analysis options (default 1)."<<endl;
@@ -360,7 +360,7 @@ void GEMMA::PrintHelp(size_t option) {
     cout<<" -region   [num]          "<<" specify the number of regions used to evaluate lambda (default 10)" << endl;
     cout<<endl;
   }
-  
+
   if (option==9) {
     cout<<" MULTIVARIATE LINEAR MIXED MODEL OPTIONS" << endl;
     cout<<" -pnr				     "<<" specify the pvalue threshold to use the Newton-Raphson's method (default 0.001)"<<endl;
@@ -371,7 +371,7 @@ void GEMMA::PrintHelp(size_t option) {
     cout<<" -crt				     "<<" specify to output corrected pvalues for these pvalues that are below the -pnr threshold"<<endl;
     cout<<endl;
   }
-  
+
   if (option==10) {
     cout<<" MULTI-LOCUS ANALYSIS OPTIONS" << endl;
     cout<<" -bslmm	  [num]			 "<<" specify analysis options (default 1)."<<endl;
@@ -380,10 +380,10 @@ void GEMMA::PrintHelp(size_t option) {
     cout<<"                   3: probit BSLMM (requires 0/1 phenotypes)"<<endl;
     cout<<"                   4: BSLMM with DAP for Hyper Parameter Estimation"<<endl;
     cout<<"                   5: BSLMM with DAP for Fine Mapping"<<endl;
-    
+
     cout<<" -ldr	  [num]			 "<<" specify analysis options (default 1)."<<endl;
     cout<<"          options: 1: LDR"<<endl;
-    
+
     cout<<"   MCMC OPTIONS" << endl;
     cout<<"   Prior" << endl;
     cout<<" -hmin     [num]          "<<" specify minimum value for h (default 0)" << endl;
@@ -394,13 +394,13 @@ void GEMMA::PrintHelp(size_t option) {
     cout<<" -pmax     [num]          "<<" specify maximum value for log10(pi) (default log10(1) )" << endl;
     cout<<" -smin     [num]          "<<" specify minimum value for |gamma| (default 0)" << endl;
     cout<<" -smax     [num]          "<<" specify maximum value for |gamma| (default 300)" << endl;
-    
+
     cout<<"   Proposal" << endl;
     cout<<" -gmean    [num]          "<<" specify the mean for the geometric distribution (default: 2000)" << endl;
     cout<<" -hscale   [num]          "<<" specify the step size scale for the proposal distribution of h (value between 0 and 1, default min(10/sqrt(n),1) )" << endl;
     cout<<" -rscale   [num]          "<<" specify the step size scale for the proposal distribution of rho (value between 0 and 1, default min(10/sqrt(n),1) )" << endl;
     cout<<" -pscale   [num]          "<<" specify the step size scale for the proposal distribution of log10(pi) (value between 0 and 1, default min(5/sqrt(n),1) )" << endl;
-    
+
     cout<<"   Others" << endl;
     cout<<" -w        [num]          "<<" specify burn-in steps (default 100,000)" << endl;
     cout<<" -s        [num]          "<<" specify sampling steps (default 1,000,000)" << endl;
@@ -411,7 +411,7 @@ void GEMMA::PrintHelp(size_t option) {
     cout<<"          requires: 0/1 phenotypes and -bslmm 3 option"<<endl;
     cout<<endl;
   }
-  
+
   if (option==11) {
     cout<<" PREDICTION OPTIONS" << endl;
     cout<<" -predict  [num]			 "<<" specify prediction options (default 1)."<<endl;
@@ -419,7 +419,7 @@ void GEMMA::PrintHelp(size_t option) {
     cout<<"                   2: predict for individuals with missing phenotypes, and convert the predicted values to probability scale. Use only for files fitted with -bslmm 3 option"<<endl;
     cout<<endl;
   }
-  
+
   if (option==12) {
     cout<<" CALC CORRELATION OPTIONS" << endl;
     cout<<" -calccor       			 "<<endl;
@@ -428,7 +428,7 @@ void GEMMA::PrintHelp(size_t option) {
     cout<<" -windowns       [num]            "<<" specify the window size based on number of snps (default 0; not used)" << endl;
     cout<<endl;
   }
-  
+
   if (option==13) {
     cout<<" NOTE"<<endl;
     cout<<" 1. Only individuals with non-missing phenotoypes and covariates will be analyzed."<<endl;
@@ -438,7 +438,7 @@ void GEMMA::PrintHelp(size_t option) {
     cout<<" 5. For bslmm analysis, in addition to 3, memory should be large enough to hold the whole genotype matrix."<<endl;
     cout<<endl;
   }
-  
+
   return;
 }
 
@@ -522,7 +522,7 @@ void GEMMA::Assign(int argc, char ** argv, PARAM &cPar) {
 			str.assign(argv[i]);
 			cPar.file_anno=str;
 		}
-		
+
 		// WJA added.
 		else if (strcmp(argv[i], "-oxford")==0 ||
 			 strcmp(argv[i], "--oxford")==0 ||
@@ -1262,7 +1262,7 @@ void GEMMA::BatchRun (PARAM &cPar) {
 
 		gsl_matrix *Y_full=gsl_matrix_alloc (cPar.ni_cvt, cPar.n_ph);
 		gsl_matrix *W_full=gsl_matrix_alloc (Y_full->size1, cPar.n_cvt);
-		
+
 		//set covariates matrix W and phenotype matrix Y
 		//an intercept should be included in W,
 		cPar.CopyCvtPhen (W, Y, 0);
@@ -1545,7 +1545,7 @@ void GEMMA::BatchRun (PARAM &cPar) {
 
 	  cVarcov.CopyToParam(cPar);
 	}
-	
+
 	// LM.
 	if (cPar.a_mode==51 || cPar.a_mode==52 || cPar.a_mode==53 || cPar.a_mode==54) {  //Fit LM
 		gsl_matrix *Y=gsl_matrix_alloc (cPar.ni_test, cPar.n_ph);
@@ -2581,7 +2581,7 @@ void GEMMA::BatchRun (PARAM &cPar) {
 	    } else {
 	      kc=0; kd=0;
 	    }
-	    
+
 	    cout<<"## number of blocks = "<<BF.size()<<endl;
 	    cout<<"## number of analyzed SNPs = "<<vec_rs.size()<<endl;
 	    cout<<"## grid size for hyperparameters = "<<wab.size()<<endl;
diff --git a/src/gemma.h b/src/gemma.h
index 8393470..78828ef 100644
--- a/src/gemma.h
+++ b/src/gemma.h
@@ -16,7 +16,7 @@
     along with this program. If not, see <http://www.gnu.org/licenses/>.
 */
 
-#ifndef __GEMMA_H__                
+#ifndef __GEMMA_H__
 #define __GEMMA_H__
 
 #include "param.h"
@@ -25,15 +25,15 @@ using namespace std;
 
 class GEMMA {
 
-public:			
+public:
 	// Parameters.
 	string version;
 	string date;
 	string year;
-	
+
 	// Constructor.
 	GEMMA(void);
-	
+
 	// Functions.
 	void PrintHeader (void);
 	void PrintHelp (size_t option);
diff --git a/src/gzstream.cpp b/src/gzstream.cpp
index bbb4ba8..688b625 100644
--- a/src/gzstream.cpp
+++ b/src/gzstream.cpp
@@ -21,8 +21,8 @@
 // Revision      : $Revision: 1.7 $
 // Revision_date : $Date: 2003/01/08 14:41:27 $
 // Author(s)     : Deepak Bandyopadhyay, Lutz Kettner
-// 
-// Standard streambuf implementation following Nicolai Josuttis, "The 
+//
+// Standard streambuf implementation following Nicolai Josuttis, "The
 // Standard C++ Library".
 // ============================================================================
 
@@ -97,7 +97,7 @@ int gzstreambuf::underflow() { // used for input buffer only
           buffer + 4 + num);          // end of buffer
 
     // return next character
-    return * reinterpret_cast<unsigned char *>( gptr());    
+    return * reinterpret_cast<unsigned char *>( gptr());
 }
 
 int gzstreambuf::flush_buffer() {
diff --git a/src/gzstream.h b/src/gzstream.h
index 4e86ad9..241ff76 100644
--- a/src/gzstream.h
+++ b/src/gzstream.h
@@ -21,8 +21,8 @@
 // Revision      : $Revision: 1.5 $
 // Revision_date : $Date: 2002/04/26 23:30:15 $
 // Author(s)     : Deepak Bandyopadhyay, Lutz Kettner
-// 
-// Standard streambuf implementation following Nicolai Josuttis, "The 
+//
+// Standard streambuf implementation following Nicolai Josuttis, "The
 // Standard C++ Library".
 // ============================================================================
 
@@ -58,14 +58,14 @@ public:
         setp( buffer, buffer + (bufferSize-1));
         setg( buffer + 4,     // beginning of putback area
               buffer + 4,     // read position
-              buffer + 4);    // end position      
+              buffer + 4);    // end position
         // ASSERT: both input & output capabilities will not be used together
     }
     int is_open() { return opened; }
     gzstreambuf* open( const char* name, int open_mode);
     gzstreambuf* close();
     ~gzstreambuf() { close(); }
-    
+
     virtual int     overflow( int c = EOF);
     virtual int     underflow();
     virtual int     sync();
@@ -85,15 +85,15 @@ public:
 
 // ----------------------------------------------------------------------------
 // User classes. Use igzstream and ogzstream analogously to ifstream and
-// ofstream respectively. They read and write files based on the gz* 
+// ofstream respectively. They read and write files based on the gz*
 // function interface of the zlib. Files are compatible with gzip compression.
 // ----------------------------------------------------------------------------
 
 class igzstream : public gzstreambase, public std::istream {
 public:
-    igzstream() : std::istream( &buf) {} 
+    igzstream() : std::istream( &buf) {}
     igzstream( const char* name, int open_mode = std::ios::in)
-        : gzstreambase( name, open_mode), std::istream( &buf) {}  
+        : gzstreambase( name, open_mode), std::istream( &buf) {}
     gzstreambuf* rdbuf() { return gzstreambase::rdbuf(); }
     void open( const char* name, int open_mode = std::ios::in) {
         gzstreambase::open( name, open_mode);
@@ -104,7 +104,7 @@ class ogzstream : public gzstreambase, public std::ostream {
 public:
     ogzstream() : std::ostream( &buf) {}
     ogzstream( const char* name, int mode = std::ios::out)
-        : gzstreambase( name, mode), std::ostream( &buf) {}  
+        : gzstreambase( name, mode), std::ostream( &buf) {}
     gzstreambuf* rdbuf() { return gzstreambase::rdbuf(); }
     void open( const char* name, int open_mode = std::ios::out) {
         gzstreambase::open( name, open_mode);
diff --git a/src/lapack.h b/src/lapack.h
index 88fc509..5e1db35 100644
--- a/src/lapack.h
+++ b/src/lapack.h
@@ -16,7 +16,7 @@
     along with this program. If not, see <http://www.gnu.org/licenses/>.
 */
 
-#ifndef __LAPACK_H__                
+#ifndef __LAPACK_H__
 #define __LAPACK_H__
 
 #include <vector>
diff --git a/src/ldr.cpp b/src/ldr.cpp
index a1e5791..f0a1b37 100644
--- a/src/ldr.cpp
+++ b/src/ldr.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>
@@ -51,7 +51,7 @@ using namespace Eigen;
 void LDR::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;
@@ -62,11 +62,11 @@ void LDR::CopyFromParam (PARAM &cPar) {
 	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;
 }
 
@@ -77,7 +77,7 @@ void LDR::CopyToParam (PARAM &cPar) {
 //X is a p by n matrix.
 void LDR::VB (const vector<vector<unsigned char> > &Xt,
 	      const gsl_matrix *W_gsl, const gsl_vector *y_gsl) {
-  
+
   // Save gsl_vector and gsl_matrix into Eigen library formats.
   MatrixXd W(W_gsl->size1, W_gsl->size2);
   VectorXd y(y_gsl->size);
@@ -105,6 +105,6 @@ void LDR::VB (const vector<vector<unsigned char> > &Xt,
 
   // Save results.
   // TO DO.
-  
+
   return;
 }
diff --git a/src/ldr.h b/src/ldr.h
index ceb08cf..ab55fe2 100644
--- a/src/ldr.h
+++ b/src/ldr.h
@@ -1,22 +1,22 @@
 /*
  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/>.
 */
 
-#ifndef __LDR_H__                
+#ifndef __LDR_H__
 #define __LDR_H__
 
 #include <vector>
@@ -29,16 +29,16 @@ using namespace std;
 
 class LDR {
 
-public:	
+public:
 	// IO-related parameters.
-	int a_mode;	
+	int a_mode;
 	size_t d_pace;
-	
+
 	string file_bfile;
 	string file_geno;
 	string file_out;
 	string path_out;
-		
+
 	// Summary statistics.
 	size_t ni_total, ns_total; // Total number of individuals & SNPs.
 	size_t ni_test, ns_test;   // Number of individuals & SNPs used
@@ -52,16 +52,16 @@ public:
        	// Sequence indicator for SNPs: 0 ignored because of (a) maf,
        	// (b) miss, (c) non-poly; 1 available for analysis.
 	vector<int> indicator_snp;
-	
+
 	vector<SNPINFO> snpInfo; // Record SNP information.
-	
+
 	// Not included in PARAM.
-	gsl_rng *gsl_r; 	
-	
+	gsl_rng *gsl_r;
+
 	// Main functions.
 	void CopyFromParam (PARAM &cPar);
 	void CopyToParam (PARAM &cPar);
-	
+
 	void VB(const vector<vector<unsigned char> > &Xt,
 		const gsl_matrix *W_gsl, const gsl_vector *y_gsl);
 };
diff --git a/src/lm.cpp b/src/lm.cpp
index d3ad7f3..94729db 100644
--- a/src/lm.cpp
+++ b/src/lm.cpp
@@ -412,13 +412,13 @@ void LM::Analyzebgen (const gsl_matrix *W, const gsl_vector *y) {
 	string chr;
 	std::cout << "Warning: WJA hard coded SNP missingness " <<
 	  "threshold of 10%" << std::endl;
-	
+
 	// Start reading genotypes and analyze.
 	for (size_t t=0; t<indicator_snp.size(); ++t) {
 		if (t%d_pace==0 || t==(ns_total-1)) {
 		  ProgressBar ("Reading SNPs  ", t, ns_total-1);
 		}
-		
+
 		// Read SNP header.
 		id.clear();
 		rs.clear();
@@ -500,7 +500,7 @@ void LM::Analyzebgen (const gsl_matrix *W, const gsl_vector *y) {
 			    static_cast<double>(unzipped_data[i*3+1])/32768.0;
 			  bgen_geno_prob_BB=
 			    static_cast<double>(unzipped_data[i*3+2])/32768.0;
-			  
+
 				// WJA
 			  bgen_geno_prob_non_miss=
 			    bgen_geno_prob_AA +
diff --git a/src/lm.h b/src/lm.h
index fac84e1..cf428f0 100644
--- a/src/lm.h
+++ b/src/lm.h
@@ -54,7 +54,7 @@ public:
 
         // Sequence indicator for SNPs: 0 ignored because of (a) maf,
         // (b) miss, (c) non-poly; 1 available for analysis.
-	vector<int> indicator_snp;				
+	vector<int> indicator_snp;
 
 	vector<SNPINFO> snpInfo;  // Record SNP information.
 
diff --git a/src/lmm.cpp b/src/lmm.cpp
index 73a9232..2b5ca84 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -55,7 +55,7 @@ void LMM::CopyFromParam (PARAM &cPar) {
 	file_out=cPar.file_out;
 	path_out=cPar.path_out;
 	file_gene=cPar.file_gene;
-	
+
 	// WJA added.
 	file_oxford=cPar.file_oxford;
 
@@ -228,12 +228,12 @@ void CalcPab (const size_t n_cvt, const size_t e_mode,
 				  index_aw=GetabIndex (a, p, n_cvt);
 				  index_bw=GetabIndex (b, p, n_cvt);
 				  index_ww=GetabIndex (p, p, n_cvt);
-				  
+
 				  ps_ab=gsl_matrix_get (Pab, p-1, index_ab);
 				  ps_aw=gsl_matrix_get (Pab, p-1, index_aw);
 				  ps_bw=gsl_matrix_get (Pab, p-1, index_bw);
 				  ps_ww=gsl_matrix_get (Pab, p-1, index_ww);
-				  
+
 				  p_ab=ps_ab-ps_aw*ps_bw/ps_ww;
 				  gsl_matrix_set (Pab, p, index_ab, p_ab);
 				}
@@ -269,7 +269,7 @@ void CalcPPab (const size_t n_cvt, const size_t e_mode,
 				  index_aw=GetabIndex (a, p, n_cvt);
 				  index_bw=GetabIndex (b, p, n_cvt);
 				  index_ww=GetabIndex (p, p, n_cvt);
-				  
+
 				  ps2_ab=gsl_matrix_get (PPab, p-1, index_ab);
 				  ps_aw=gsl_matrix_get (Pab, p-1, index_aw);
 				  ps_bw=gsl_matrix_get (Pab, p-1, index_bw);
@@ -277,7 +277,7 @@ void CalcPPab (const size_t n_cvt, const size_t e_mode,
 				  ps2_aw=gsl_matrix_get (PPab, p-1, index_aw);
 				  ps2_bw=gsl_matrix_get (PPab, p-1, index_bw);
 				  ps2_ww=gsl_matrix_get (PPab, p-1, index_ww);
-				  
+
 				  p2_ab=ps2_ab+ps_aw*ps_bw*
 				    ps2_ww/(ps_ww*ps_ww);
 				  p2_ab-=(ps_aw*ps2_bw+ps_bw*ps2_aw)/ps_ww;
@@ -318,7 +318,7 @@ void CalcPPPab (const size_t n_cvt, const size_t e_mode,
 				  index_aw=GetabIndex (a, p, n_cvt);
 				  index_bw=GetabIndex (b, p, n_cvt);
 				  index_ww=GetabIndex (p, p, n_cvt);
-				  
+
 				  ps3_ab=gsl_matrix_get (PPPab, p-1, index_ab);
 				  ps_aw=gsl_matrix_get (Pab, p-1, index_aw);
 				  ps_bw=gsl_matrix_get (Pab, p-1, index_bw);
@@ -337,7 +337,7 @@ void CalcPPPab (const size_t n_cvt, const size_t e_mode,
 				  p3_ab+=(ps_aw*ps2_bw*ps2_ww+ps_bw*
 					  ps2_aw*ps2_ww+ps_aw*ps_bw*ps3_ww)/
 				    (ps_ww*ps_ww);
-				  
+
 				  gsl_matrix_set (PPPab, p, index_ab, p3_ab);
 				}
 			}
@@ -1479,7 +1479,7 @@ void LMM::AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval,
 			b=ch[0];
 
 			// Minor allele homozygous: 2.0; major: 0.0.
-			for (size_t j=0; j<4; ++j) {                
+			for (size_t j=0; j<4; ++j) {
 			  if ((i==(n_bit-1)) && ci_total==(int)ni_total) {
 			    break;
 			  }
@@ -1487,7 +1487,7 @@ void LMM::AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval,
 			    ci_total++;
 			    continue;
 			  }
-			  
+
 			  if (b[2*j]==0) {
 			    if (b[2*j+1]==0) {
 			      gsl_vector_set(x, ci_test, 2);
@@ -1499,7 +1499,7 @@ void LMM::AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval,
 			    if (b[2*j+1]==1) {gsl_vector_set(x, ci_test, 0); }
 			    else {gsl_vector_set(x, ci_test, -9); n_miss++; }
 			  }
-			  
+
 			  ci_total++;
 			  ci_test++;
 			}
@@ -1678,7 +1678,7 @@ void LMM::Analyzebgen (const gsl_matrix *U, const gsl_vector *eval,
 		  ProgressBar ("Reading SNPs  ", t, ns_total-1);
 		}
 		if (indicator_snp[t]==0) {continue;}
-		
+
 		// Read SNP header.
 		id.clear();
 		rs.clear();
@@ -1752,14 +1752,14 @@ void LMM::Analyzebgen (const gsl_matrix *U, const gsl_vector *eval,
 		gsl_vector_set_zero(x_miss);
 		for (size_t i=0; i<bgen_N; ++i) {
 		  if (indicator_idv[i]==0) {continue;}
-		  
+
 		  bgen_geno_prob_AA=
 		    static_cast<double>(unzipped_data[i*3])/32768.0;
 		  bgen_geno_prob_AB=
 		    static_cast<double>(unzipped_data[i*3+1])/32768.0;
 		  bgen_geno_prob_BB=
 		    static_cast<double>(unzipped_data[i*3+2])/32768.0;
-		  
+
 		  // WJA.
 		  bgen_geno_prob_non_miss = bgen_geno_prob_AA +
 		    bgen_geno_prob_AB+bgen_geno_prob_BB;
@@ -1768,13 +1768,13 @@ void LMM::Analyzebgen (const gsl_matrix *U, const gsl_vector *eval,
 		    n_miss++;
 		  }
 		  else {
-		    
+
 		    bgen_geno_prob_AA/=bgen_geno_prob_non_miss;
 		    bgen_geno_prob_AB/=bgen_geno_prob_non_miss;
 		    bgen_geno_prob_BB/=bgen_geno_prob_non_miss;
-		    
+
 		    geno=2.0*bgen_geno_prob_BB+bgen_geno_prob_AB;
-		    
+
 		    gsl_vector_set(x, c_phen, geno);
 		    gsl_vector_set(x_miss, c_phen, 1.0);
 		    x_mean+=geno;
@@ -1962,7 +1962,7 @@ void CalcLambda (const char func_name, FUNC_PARAM &params,
 		}
 	}
 	else {
-	  
+
 		// If derivates change signs.
 		int status;
 		int iter=0, max_iter=100;
@@ -2010,11 +2010,11 @@ void CalcLambda (const char func_name, FUNC_PARAM &params,
 		    status=gsl_root_test_interval(lambda_l,lambda_h,0,1e-1);
 		  }
 		  while (status==GSL_CONTINUE && iter<max_iter);
-		  
+
 		  iter=0;
-		  
+
 		  gsl_root_fdfsolver_set (s_fdf, &FDF, l);
-		  
+
 		  do {
 		    iter++;
 		    status=gsl_root_fdfsolver_iterate (s_fdf);
@@ -2034,7 +2034,7 @@ void CalcLambda (const char func_name, FUNC_PARAM &params,
 		  } else {
 		    logf_l=LogL_f (l, &params);
 		  }
-		  
+
 		  if (i==0) {logf=logf_l; lambda=l;}
 		  else if (logf<logf_l) {logf=logf_l; lambda=l;}
 		  else {}
@@ -2228,7 +2228,7 @@ void LMM::AnalyzeBimbamGXE (const gsl_matrix *U, const gsl_vector *eval,
 	gsl_blas_dgemv (CblasTrans, 1.0, U, env, 0.0, &UtW_expand_env.vector);
 	gsl_vector_view UtW_expand_x=
 	  gsl_matrix_column(UtW_expand, UtW->size2+1);
-	
+
 	// Start reading genotypes and analyze.
 	for (size_t t=0; t<indicator_snp.size(); ++t) {
 		!safeGetline(infile, line).eof();
@@ -2400,7 +2400,7 @@ void LMM::AnalyzePlinkGXE (const gsl_matrix *U, const gsl_vector *eval,
 			b=ch[0];
 
 			// Minor allele homozygous: 2.0; major: 0.0.
-			for (size_t j=0; j<4; ++j) {                
+			for (size_t j=0; j<4; ++j) {
 			  if ((i==(n_bit-1)) && ci_total==(int)ni_total) {
 			    break;
 			  }
@@ -2408,7 +2408,7 @@ void LMM::AnalyzePlinkGXE (const gsl_matrix *U, const gsl_vector *eval,
 			    ci_total++;
 			    continue;
 			  }
-			  
+
 			  if (b[2*j]==0) {
 			    if (b[2*j+1]==0) {
 			      gsl_vector_set(x, ci_test, 2);
@@ -2420,7 +2420,7 @@ void LMM::AnalyzePlinkGXE (const gsl_matrix *U, const gsl_vector *eval,
 			    if (b[2*j+1]==1) {gsl_vector_set(x, ci_test, 0); }
 			    else {gsl_vector_set(x, ci_test, -9); n_miss++; }
 			  }
-			  
+
 			  ci_total++;
 			  ci_test++;
 			}
diff --git a/src/lmm.h b/src/lmm.h
index 1e88cec..9c3de9d 100644
--- a/src/lmm.h
+++ b/src/lmm.h
@@ -1,4 +1,4 @@
-/* 
+/*
     Genome-wide Efficient Mixed Model Association (GEMMA)
     Copyright (C) 2011-2017, Xiang Zhou
 
@@ -71,7 +71,7 @@ public:
 
         // Indicator for individuals (phenotypes): 0 missing, 1
         // available for analysis.
-	vector<int> indicator_idv;				
+	vector<int> indicator_idv;
 
         // Sequence indicator for SNPs: 0 ignored because of (a) maf,
         // (b) miss, (c) non-poly; 1 available for analysis.
diff --git a/src/logistic.h b/src/logistic.h
index 7f9e133..b61ab14 100644
--- a/src/logistic.h
+++ b/src/logistic.h
@@ -1,75 +1,75 @@
-#ifndef LOGISTIC_H_

-#define LOGISTIC_H_

-

-// Mixed interface.

-void logistic_mixed_pred(gsl_vector *beta,     // Vector of parameters

-					       // length = 1+Sum_k(C_k-1)+Kc.

-			 gsl_matrix_int *X,    // Matrix Nobs x K.

-			 gsl_vector_int *nlev, // Vector with num. categories.

-			 gsl_matrix *Xc,       // Continuous covariates matrix

-					       // Nobs x Kc

-			 gsl_vector *yhat);    // Vector of prob. predicted by

-					       // the logistic.

- 

-int logistic_mixed_fit(gsl_vector *beta,     // Vector of parameters

-					     // length = 1+Sum_k(C_k-1)+Kc

-		       gsl_matrix_int *X,    // Matrix Nobs x K.

-		       gsl_vector_int *nlev, // Vector with number categories.

-		       gsl_matrix *Xc,       // Continuous covariates

-					     // matrix Nobs x Kc

-		       gsl_vector *y,        // Vector of prob. to predict.

-		       double lambdaL1,      // Reg. L1 0.0 if not used.

-		       double lambdaL2);     // Reg. L2 0.0 if not used.

-

-double fLogit_mixed(gsl_vector *beta,

-		    gsl_matrix_int *X,

-		    gsl_vector_int *nlev,

-		    gsl_matrix *Xc, // continuous covariates matrix Nobs x Kc 

-		    gsl_vector *y,

-		    double lambdaL1,

-		    double lambdaL2);

-

-// Categorical-only interface.

-void logistic_cat_pred(gsl_vector *beta,     // Vector of parameters

-					     // length = 1+Sum_k(C_k-1)+Kc.

-		       gsl_matrix_int *X,    // Matrix Nobs x K.

-		       gsl_vector_int *nlev, // Vector with number categories.

-		       gsl_vector *yhat);    // Vector of prob. predicted by 

-					     // the logistic.

- 

-int logistic_cat_fit(gsl_vector *beta,     // Vector of parameters

-					   // length = 1+Sum_k(C_k-1)+Kc.

-		     gsl_matrix_int *X,    // Matrix Nobs x K .

-		     gsl_vector_int *nlev, // Vector with number categories.

-		     gsl_vector *y,        // Vector of prob. to predict.

-		     double lambdaL1,      // Regularization L1, 0 if not used

-		     double lambdaL2);     // Regularization L2, 0 if not used

-

-double fLogit_cat(gsl_vector *beta,

-		  gsl_matrix_int *X,

-		  gsl_vector_int *nlev,

-		  gsl_vector *y,

-		  double lambdaL1,

-		  double lambdaL2);

-

-// Continuous-only interface.

-void logistic_cont_pred(gsl_vector *beta, // Vector of parameters

-					  // length = 1 + Sum_k(C_k-1) + Kc.

-			gsl_matrix *Xc,   // Continuous cov's matrix Nobs x Kc.

-			gsl_vector *yhat);// Vector of prob. predicted

-					  // by the logistic.

- 

-int logistic_cont_fit(gsl_vector *beta, // Vector of parameters

-					// length = 1+Sum_k(C_k-1)+Kc.

-		      gsl_matrix *Xc,   // Continuous cov's matrix Nobs x Kc.

-		      gsl_vector *y,    // Vector of prob. to predict.

-		      double lambdaL1,  // Regularization L1, 0 if not used.

-		      double lambdaL2); // Regularization L2, 0 if not used.

-

-double fLogit_cont(gsl_vector *beta,

-		   gsl_matrix *Xc, // Continuous covariates matrix Nobs x Kc.

-		   gsl_vector *y,

-		   double lambdaL1,

-		   double lambdaL2);

-

-#endif

+#ifndef LOGISTIC_H_
+#define LOGISTIC_H_
+
+// Mixed interface.
+void logistic_mixed_pred(gsl_vector *beta,     // Vector of parameters
+					       // length = 1+Sum_k(C_k-1)+Kc.
+			 gsl_matrix_int *X,    // Matrix Nobs x K.
+			 gsl_vector_int *nlev, // Vector with num. categories.
+			 gsl_matrix *Xc,       // Continuous covariates matrix
+					       // Nobs x Kc
+			 gsl_vector *yhat);    // Vector of prob. predicted by
+					       // the logistic.
+
+int logistic_mixed_fit(gsl_vector *beta,     // Vector of parameters
+					     // length = 1+Sum_k(C_k-1)+Kc
+		       gsl_matrix_int *X,    // Matrix Nobs x K.
+		       gsl_vector_int *nlev, // Vector with number categories.
+		       gsl_matrix *Xc,       // Continuous covariates
+					     // matrix Nobs x Kc
+		       gsl_vector *y,        // Vector of prob. to predict.
+		       double lambdaL1,      // Reg. L1 0.0 if not used.
+		       double lambdaL2);     // Reg. L2 0.0 if not used.
+
+double fLogit_mixed(gsl_vector *beta,
+		    gsl_matrix_int *X,
+		    gsl_vector_int *nlev,
+		    gsl_matrix *Xc, // continuous covariates matrix Nobs x Kc
+		    gsl_vector *y,
+		    double lambdaL1,
+		    double lambdaL2);
+
+// Categorical-only interface.
+void logistic_cat_pred(gsl_vector *beta,     // Vector of parameters
+					     // length = 1+Sum_k(C_k-1)+Kc.
+		       gsl_matrix_int *X,    // Matrix Nobs x K.
+		       gsl_vector_int *nlev, // Vector with number categories.
+		       gsl_vector *yhat);    // Vector of prob. predicted by
+					     // the logistic.
+
+int logistic_cat_fit(gsl_vector *beta,     // Vector of parameters
+					   // length = 1+Sum_k(C_k-1)+Kc.
+		     gsl_matrix_int *X,    // Matrix Nobs x K .
+		     gsl_vector_int *nlev, // Vector with number categories.
+		     gsl_vector *y,        // Vector of prob. to predict.
+		     double lambdaL1,      // Regularization L1, 0 if not used
+		     double lambdaL2);     // Regularization L2, 0 if not used
+
+double fLogit_cat(gsl_vector *beta,
+		  gsl_matrix_int *X,
+		  gsl_vector_int *nlev,
+		  gsl_vector *y,
+		  double lambdaL1,
+		  double lambdaL2);
+
+// Continuous-only interface.
+void logistic_cont_pred(gsl_vector *beta, // Vector of parameters
+					  // length = 1 + Sum_k(C_k-1) + Kc.
+			gsl_matrix *Xc,   // Continuous cov's matrix Nobs x Kc.
+			gsl_vector *yhat);// Vector of prob. predicted
+					  // by the logistic.
+
+int logistic_cont_fit(gsl_vector *beta, // Vector of parameters
+					// length = 1+Sum_k(C_k-1)+Kc.
+		      gsl_matrix *Xc,   // Continuous cov's matrix Nobs x Kc.
+		      gsl_vector *y,    // Vector of prob. to predict.
+		      double lambdaL1,  // Regularization L1, 0 if not used.
+		      double lambdaL2); // Regularization L2, 0 if not used.
+
+double fLogit_cont(gsl_vector *beta,
+		   gsl_matrix *Xc, // Continuous covariates matrix Nobs x Kc.
+		   gsl_vector *y,
+		   double lambdaL1,
+		   double lambdaL2);
+
+#endif
diff --git a/src/main.cpp b/src/main.cpp
index b7ac884..c7f0573 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -25,12 +25,12 @@
 
 using namespace std;
 
-int main(int argc, char * argv[]) { 	
-	GEMMA cGemma;	
+int main(int argc, char * argv[]) {
+	GEMMA cGemma;
 	PARAM cPar;
 
 	if (argc <= 1) {
-		cGemma.PrintHeader(); 
+		cGemma.PrintHeader();
 		return EXIT_SUCCESS;
 	}
 	if (argc==2 && argv[1][0] == '-' && argv[1][1] == 'h') {
@@ -46,27 +46,27 @@ int main(int argc, char * argv[]) {
 	if (argc==2 && argv[1][0] == '-' && argv[1][1] == 'l') {
 		cGemma.PrintLicense();
 		return EXIT_SUCCESS;
-	}	
-	
-	cGemma.Assign(argc, argv, cPar); 
+	}
+
+	cGemma.Assign(argc, argv, cPar);
 
 	ifstream check_dir((cPar.path_out).c_str());
 	if (!check_dir) {
 	  mkdir((cPar.path_out).c_str(), S_IRWXU|S_IRGRP|S_IROTH);
-	}	
-		
+	}
+
 	if (cPar.error==true) {return EXIT_FAILURE;}
-	     
+
 	if (cPar.mode_silence) {stringstream ss; cout.rdbuf (ss.rdbuf());}
-	
+
 	cPar.CheckParam();
-	
+
 	if (cPar.error==true) {return EXIT_FAILURE;}
-	
+
 	cGemma.BatchRun(cPar);
-	
+
 	if (cPar.error==true) {return EXIT_FAILURE;}
-	
+
 	cGemma.WriteLog(argc, argv, cPar);
-	
+
     return EXIT_SUCCESS;                                                       }
diff --git a/src/mathfunc.cpp b/src/mathfunc.cpp
index c09b587..709bdde 100644
--- a/src/mathfunc.cpp
+++ b/src/mathfunc.cpp
@@ -375,7 +375,7 @@ double CalcHWE (const size_t n_hom1, const size_t n_hom2, const size_t n_ab) {
 		het_probs[i] /= sum;
 
 		double p_hwe = 0.0;
-		
+
 	        // p-value calculation for p_hwe.
 		for (i = 0; i <= rare_copies; i++)
 		{
diff --git a/src/param.cpp b/src/param.cpp
index a56f5eb..413d517 100644
--- a/src/param.cpp
+++ b/src/param.cpp
@@ -66,7 +66,7 @@ time_UtZ(0.0), time_opt(0.0), time_Omega(0.0)
 // Read files: obtain ns_total, ng_total, ns_test, ni_test.
 void PARAM::ReadFiles (void) {
 	string file_str;
-	
+
 	// Read cat file.
 	if (!file_mcat.empty()) {
 	  if (ReadFile_mcat (file_mcat, mapRS2cat, n_vc)==false) {error=true;}
@@ -216,7 +216,7 @@ void PARAM::ReadFiles (void) {
 		// If both fam file and pheno files are used, use
 		// phenotypes inside the pheno file.
 		if (!file_pheno.empty()) {
-		  
+
 		  // Phenotype file before genotype file.
 		  if (ReadFile_pheno (file_pheno, indicator_pheno, pheno,
 				      p_column)==false) {error=true;}
@@ -247,7 +247,7 @@ void PARAM::ReadFiles (void) {
 
 	// Read genotype and phenotype file for BIMBAM format.
 	if (!file_geno.empty()) {
-	  
+
 	        // Annotation file before genotype file.
 		if (!file_anno.empty() ) {
 			if (ReadFile_anno (file_anno, mapRS2chr, mapRS2bp,
@@ -297,11 +297,11 @@ void PARAM::ReadFiles (void) {
 		if (ReadFile_bim (file_str, snpInfo)==false) {error=true;}
 
 		if (t==0) {
-		  
+
 		  // If both fam file and pheno files are used, use
 		  // phenotypes inside the pheno file.
 		  if (!file_pheno.empty()) {
-		    
+
 		    // Phenotype file before genotype file.
 		    if (ReadFile_pheno (file_pheno, indicator_pheno, pheno,
 					p_column)==false) {
@@ -347,7 +347,7 @@ void PARAM::ReadFiles (void) {
 
 	// Read genotype and phenotype file for multiple BIMBAM files.
 	if (!file_mgeno.empty()) {
-	  
+
 	  // Annotation file before genotype file.
 	  if (!file_anno.empty() ) {
 	    if (ReadFile_anno (file_anno, mapRS2chr, mapRS2bp,
@@ -788,7 +788,7 @@ void PARAM::CheckParam (void) {
 	if (!file_bfile.empty()) {flag++;}
 	if (!file_geno.empty()) {flag++;}
 	if (!file_gene.empty()) {flag++;}
-	
+
 	// WJA added.
 	if (!file_oxford.empty()) {flag++;}
 
@@ -982,7 +982,7 @@ void PARAM::CheckData (void) {
 
   // WJA NOTE: I added this condition so that covariates can be added
   // through sample, probably not exactly what is wanted.
-  if(file_oxford.empty())	
+  if(file_oxford.empty())
 	{
 	  if ((file_cvt).empty() || (indicator_cvt).size()==0) {
 	    n_cvt=1;
@@ -1017,7 +1017,7 @@ void PARAM::CheckData (void) {
       "the number of individuals. "<<endl;
     return;
   }
-  
+
   if ( (indicator_read).size()!=0 &&
        (indicator_read).size()!=(indicator_idv).size()) {
     error=true;
@@ -1025,7 +1025,7 @@ void PARAM::CheckData (void) {
       "match the number of individuals. "<<endl;
     return;
   }
-  
+
 	// Calculate ni_total and ni_test, and set indicator_idv to 0
 	// whenever indicator_cvt=0, and calculate np_obs and np_miss.
 	ni_total=(indicator_idv).size();
@@ -1896,7 +1896,7 @@ void PARAM::CheckCvt () {
 
 // Post-process phentoypes and covariates.
 void PARAM::ProcessCvtPhen () {
-  
+
  	// Convert indicator_pheno to indicator_idv.
 	int k=1;
 	indicator_idv.clear();
@@ -1949,7 +1949,7 @@ void PARAM::ProcessCvtPhen () {
 	    cout<<"error! number of subsamples is less than number of"<<
 	      "analyzed individuals. "<<endl;
 	  } else {
-	    
+
 	    // Set up random environment.
 	    gsl_rng_env_setup();
 	    gsl_rng *gsl_r;
diff --git a/src/param.h b/src/param.h
index 9707790..f58da53 100644
--- a/src/param.h
+++ b/src/param.h
@@ -141,7 +141,7 @@ public:
 	string file_read; // File containing total number of reads.
 	string file_gene; // Gene expression file.
 	string file_snps; // File containing analyzed SNPs or genes.
-  
+
         // WJA added.
 	string file_oxford;
 
@@ -212,7 +212,7 @@ public:
 
 	// Summary statistics.
 	bool error;
-  
+
         // Number of individuals.
 	size_t ni_total, ni_test, ni_cvt, ni_study, ni_ref;
 
@@ -221,7 +221,7 @@ public:
 
         // Number of SNPs.
 	size_t ns_total, ns_test, ns_study, ns_ref;
-  
+
 	size_t ng_total, ng_test;   // Number of genes.
 	size_t ni_control, ni_case; // Number of controls and number of cases.
 	size_t ni_subsample;        // Number of subsampled individuals.
diff --git a/src/prdt.cpp b/src/prdt.cpp
index db0fa14..b29d150 100644
--- a/src/prdt.cpp
+++ b/src/prdt.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 <bitset>
 #include <vector>
 #include <stdio.h>
-#include <stdlib.h> 
+#include <stdlib.h>
 #include <cmath>
 #include "gsl/gsl_vector.h"
 #include "gsl/gsl_matrix.h"
@@ -43,36 +43,36 @@ using namespace std;
 void PRDT::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;
-	
-	indicator_pheno=cPar.indicator_pheno;	
+
+	indicator_pheno=cPar.indicator_pheno;
 	indicator_cvt=cPar.indicator_cvt;
 	indicator_idv=cPar.indicator_idv;
-	
+
 	snpInfo=cPar.snpInfo;
 	mapRS2est=cPar.mapRS2est;
-	
+
 	time_eigen=0;
-	
+
 	n_ph=cPar.n_ph;
 	np_obs=cPar.np_obs;
 	np_miss=cPar.np_miss;
 	ns_total=cPar.ns_total;
-	ns_test=0;	
-	
+	ns_test=0;
+
 	return;
 }
 
 void PRDT::CopyToParam (PARAM &cPar) {
 	cPar.ns_test=ns_test;
 	cPar.time_eigen=time_eigen;
-	
+
 	return;
-}               
+}
 
 void PRDT::WriteFiles (gsl_vector *y_prdt) {
 	string file_str;
@@ -80,13 +80,13 @@ void PRDT::WriteFiles (gsl_vector *y_prdt) {
 	file_str+=".";
 	file_str+="prdt";
 	file_str+=".txt";
-	
+
 	ofstream outfile (file_str.c_str(), ofstream::out);
 	if (!outfile) {
 	  cout<<"error writing file: "<<file_str.c_str()<<endl;
 	  return;
 	}
-	
+
 	size_t ci_test=0;
 	for (size_t i=0; i<indicator_idv.size(); i++) {
 		if (indicator_idv[i]==1) {
@@ -96,7 +96,7 @@ void PRDT::WriteFiles (gsl_vector *y_prdt) {
 			ci_test++;
 		}
 	}
-	
+
 	outfile.close();
 	outfile.clear();
 	return;
@@ -106,13 +106,13 @@ void PRDT::WriteFiles (gsl_matrix *Y_full)  {
 	string file_str;
 	file_str=path_out+"/"+file_out;
 	file_str+=".prdt.txt";
-	
+
 	ofstream outfile (file_str.c_str(), ofstream::out);
 	if (!outfile) {
 	  cout<<"error writing file: "<<file_str.c_str()<<endl;
 	  return;
 	}
-	
+
 	size_t ci_test=0;
 	for (size_t i=0; i<indicator_cvt.size(); i++) {
 		if (indicator_cvt[i]==0) {
@@ -126,7 +126,7 @@ void PRDT::WriteFiles (gsl_matrix *Y_full)  {
 			ci_test++;
 		}
 	}
-	
+
 	outfile.close();
 	outfile.clear();
 	return;
@@ -134,21 +134,21 @@ void PRDT::WriteFiles (gsl_matrix *Y_full)  {
 
 void PRDT::AddBV (gsl_matrix *G, const gsl_vector *u_hat, gsl_vector *y_prdt) {
 	size_t ni_test=u_hat->size, ni_total=G->size1;
-	
+
 	gsl_matrix *Goo=gsl_matrix_alloc (ni_test, ni_test);
 	gsl_matrix *Gfo=gsl_matrix_alloc (ni_total-ni_test, ni_test);
-	gsl_matrix *U=gsl_matrix_alloc (ni_test, ni_test); 
+	gsl_matrix *U=gsl_matrix_alloc (ni_test, ni_test);
 	gsl_vector *eval=gsl_vector_alloc (ni_test);
 	gsl_vector *Utu=gsl_vector_alloc (ni_test);
 	gsl_vector *w=gsl_vector_alloc (ni_total);
 	gsl_permutation *pmt=gsl_permutation_alloc (ni_test);
-	
+
 	//center matrix G based on indicator_idv
 	for (size_t i=0; i<ni_total; i++) {
 		gsl_vector_set(w, i, indicator_idv[i]);
 	}
 	CenterMatrix(G, w);
-		
+
 	//obtain Koo and Kfo
 	size_t o_i=0, o_j=0;
 	double d;
@@ -166,7 +166,7 @@ void PRDT::AddBV (gsl_matrix *G, const gsl_vector *u_hat, gsl_vector *y_prdt) {
 		}
 		if (indicator_idv[i]==1) {o_i++;}
 	}
-		
+
 	//matrix operations to get u_prdt
 	cout<<"Start Eigen-Decomposition..."<<endl;
 	clock_t time_start=clock();
@@ -177,8 +177,8 @@ void PRDT::AddBV (gsl_matrix *G, const gsl_vector *u_hat, gsl_vector *y_prdt) {
 		}
 	}
 
-	time_eigen=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);	
-	
+	time_eigen=(clock()-time_start)/(double(CLOCKS_PER_SEC)*60.0);
+
 	gsl_blas_dgemv (CblasTrans, 1.0, U, u_hat, 0.0, Utu);
 	for (size_t i=0; i<eval->size; i++) {
 		d=gsl_vector_get(eval, i);
@@ -189,7 +189,7 @@ void PRDT::AddBV (gsl_matrix *G, const gsl_vector *u_hat, gsl_vector *y_prdt) {
 	}
 	gsl_blas_dgemv (CblasNoTrans, 1.0, U, Utu, 0.0, eval);
 	gsl_blas_dgemv (CblasNoTrans, 1.0, Gfo, eval, 1.0, y_prdt);
-	
+
 	// Free matrices.
 	gsl_matrix_free(Goo);
 	gsl_matrix_free(Gfo);
@@ -199,7 +199,7 @@ void PRDT::AddBV (gsl_matrix *G, const gsl_vector *u_hat, gsl_vector *y_prdt) {
 	gsl_vector_free(w);
 	gsl_permutation_free(pmt);
 
-	return;	
+	return;
 }
 
 void PRDT::AnalyzeBimbam (gsl_vector *y_prdt) {
@@ -208,17 +208,17 @@ void PRDT::AnalyzeBimbam (gsl_vector *y_prdt) {
 	  cout<<"error reading genotype file:"<<file_geno<<endl;
 	  return;
 	}
-	
+
 	string line;
 	char *ch_ptr;
 	string rs;
-	
+
 	size_t n_miss, n_train_nomiss, c_phen;
 	double geno, x_mean, x_train_mean, effect_size;
-	
+
 	gsl_vector *x=gsl_vector_alloc (y_prdt->size);
 	gsl_vector *x_miss=gsl_vector_alloc (y_prdt->size);
-	
+
 	ns_test=0;
 
 	// Start reading genotypes and analyze.
@@ -227,24 +227,24 @@ void PRDT::AnalyzeBimbam (gsl_vector *y_prdt) {
 		if (t%d_pace==0 || t==(ns_total-1)) {
 		  ProgressBar ("Reading SNPs  ", t, ns_total-1);
 		}
-		
+
 		ch_ptr=strtok ((char *)line.c_str(), " , \t");
 		rs=ch_ptr;
 		ch_ptr=strtok (NULL, " , \t");
-		ch_ptr=strtok (NULL, " , \t");		
-		
+		ch_ptr=strtok (NULL, " , \t");
+
 		if (mapRS2est.count(rs)==0) {
 		  continue;
 		} else {
 		  effect_size=mapRS2est[rs];
 		}
-		
+
 		x_mean=0.0;
 		c_phen=0;
 		n_miss=0;
 		x_train_mean=0;
 		n_train_nomiss=0;
-		
+
 		gsl_vector_set_zero(x_miss);
 
 		for (size_t i=0; i<indicator_idv.size(); ++i) {
@@ -260,10 +260,10 @@ void PRDT::AnalyzeBimbam (gsl_vector *y_prdt) {
 					gsl_vector_set(x_miss, c_phen, 0.0);
 					n_miss++;
 				} else {
-					geno=atof(ch_ptr); 	
-					
-					gsl_vector_set(x, c_phen, geno); 
-					gsl_vector_set(x_miss, c_phen, 1.0); 
+					geno=atof(ch_ptr);
+
+					gsl_vector_set(x, c_phen, geno);
+					gsl_vector_set(x_miss, c_phen, 1.0);
 					x_mean+=geno;
 				}
 				c_phen++;
@@ -274,12 +274,12 @@ void PRDT::AnalyzeBimbam (gsl_vector *y_prdt) {
 		  cout << "snp " << rs << " has missing genotype for all " <<
 		    "individuals and will be ignored." << endl;
 		  continue;}
-		
+
 
 		x_mean/=(double)(x->size-n_miss);
 		x_train_mean/=(double)(n_train_nomiss);
-		
-		
+
+
 		for (size_t i=0; i<x->size; ++i) {
 			geno=gsl_vector_get(x, i);
 			if (gsl_vector_get (x_miss, i)==0) {
@@ -291,17 +291,17 @@ void PRDT::AnalyzeBimbam (gsl_vector *y_prdt) {
 
 		gsl_vector_scale (x, effect_size);
 		gsl_vector_add (y_prdt, x);
-		
+
 		ns_test++;
-	}	
+	}
 	cout<<endl;
-	
+
 	gsl_vector_free (x);
 	gsl_vector_free (x_miss);
-	
+
 	infile.close();
 	infile.clear();
-	
+
 	return;
 }
 
@@ -312,35 +312,35 @@ void PRDT::AnalyzePlink (gsl_vector *y_prdt) {
 	  cout<<"error reading bed file:"<<file_bed<<endl;
 	  return;
 	}
-	
+
 	char ch[1];
-	bitset<8> b;	
+	bitset<8> b;
 	string rs;
-	
+
 	size_t n_bit, n_miss, ci_total, ci_test, n_train_nomiss;
 	double geno, x_mean, x_train_mean, effect_size;
-	
+
 	gsl_vector *x=gsl_vector_alloc (y_prdt->size);
-	
+
 	// Calculate n_bit and c, the number of bit for each SNP.
 	if (indicator_idv.size()%4==0) {n_bit=indicator_idv.size()/4;}
 	else {n_bit=indicator_idv.size()/4+1; }
-	
+
 	// Print the first 3 magic numbers.
 	for (size_t i=0; i<3; ++i) {
 		infile.read(ch,1);
 		b=ch[0];
-	}	
-	
+	}
+
 	ns_test=0;
-	
+
 	for (vector<SNPINFO>::size_type t=0; t<snpInfo.size(); ++t) {
 		if (t%d_pace==0 || t==snpInfo.size()-1) {
 		  ProgressBar ("Reading SNPs  ", t, snpInfo.size()-1);
 		}
-		
+
 		rs=snpInfo[t].rs_number;
-		
+
 		if (mapRS2est.count(rs)==0) {
 		  continue;
 		} else {
@@ -349,7 +349,7 @@ void PRDT::AnalyzePlink (gsl_vector *y_prdt) {
 
 		// n_bit, and 3 is the number of magic numbers.
 		infile.seekg(t*n_bit+3);
-		
+
 		// Read genotypes.
 		x_mean=0.0;
 		n_miss=0;
@@ -359,7 +359,7 @@ void PRDT::AnalyzePlink (gsl_vector *y_prdt) {
 			b=ch[0];
 
 			// Minor allele homozygous: 2.0; major: 0.0.
-			for (size_t j=0; j<4; ++j) {                
+			for (size_t j=0; j<4; ++j) {
 				if ((i==(n_bit-1)) &&
 				    ci_total==indicator_idv.size()) {
 				  break;
@@ -404,19 +404,19 @@ void PRDT::AnalyzePlink (gsl_vector *y_prdt) {
 					ci_test++;
 				}
 				ci_total++;
-				
+
 			}
 		}
-		
+
 		if (x->size==n_miss) {
 		  cout << "snp " << rs << " has missing genotype for all " <<
 		    "individuals and will be ignored."<<endl;
 		  continue;
 		}
-		
+
 		x_mean/=(double)(x->size-n_miss);
 		x_train_mean/=(double)(n_train_nomiss);
-		
+
 		for (size_t i=0; i<x->size; ++i) {
 			geno=gsl_vector_get(x, i);
 			if (geno==-9) {
@@ -425,47 +425,47 @@ void PRDT::AnalyzePlink (gsl_vector *y_prdt) {
 				gsl_vector_set(x, i, geno-x_train_mean);
 			}
 		}
-		
+
 		gsl_vector_scale (x, effect_size);
 		gsl_vector_add (y_prdt, x);
-		
+
 		ns_test++;
-	}	
+	}
 	cout<<endl;
-	
+
 	gsl_vector_free (x);
-	
+
 	infile.close();
-	infile.clear();	
-	
+	infile.clear();
+
 	return;
 }
 
 // Predict missing phenotypes using ridge regression.
 // Y_hat contains fixed effects
 void PRDT::MvnormPrdt (const gsl_matrix *Y_hat, const gsl_matrix *H,
-		       gsl_matrix *Y_full) {	
+		       gsl_matrix *Y_full) {
 	gsl_vector *y_obs=gsl_vector_alloc (np_obs);
 	gsl_vector *y_miss=gsl_vector_alloc (np_miss);
 	gsl_matrix *H_oo=gsl_matrix_alloc (np_obs, np_obs);
 	gsl_matrix *H_mo=gsl_matrix_alloc (np_miss, np_obs);
 	gsl_vector *Hiy=gsl_vector_alloc (np_obs);
-	
+
 	size_t c_obs1=0, c_obs2=0, c_miss1=0, c_miss2=0;
-	
+
 	// Obtain H_oo, H_mo.
-	c_obs1=0; c_miss1=0; 
+	c_obs1=0; c_miss1=0;
 	for (vector<int>::size_type i1=0; i1<indicator_pheno.size(); ++i1) {
 		if (indicator_cvt[i1]==0) {continue;}
 		for (vector<int>::size_type j1=0; j1<n_ph; ++j1) {
-			
+
 			c_obs2=0; c_miss2=0;
 			for (vector<int>::size_type i2=0;
 			     i2<indicator_pheno.size(); ++i2) {
 				if (indicator_cvt[i2]==0) {continue;}
 				for (vector<int>::size_type j2=0;
 				     j2<n_ph; j2++) {
-					
+
 					if (indicator_pheno[i2][j2]==1) {
 					      if (indicator_pheno[i1][j1]==1) {
 						gsl_matrix_set(H_oo,c_obs1, c_obs2, gsl_matrix_get (H, c_obs1+c_miss1, c_obs2+c_miss2) );
@@ -476,30 +476,30 @@ void PRDT::MvnormPrdt (const gsl_matrix *Y_hat, const gsl_matrix *H,
 					} else {
 						c_miss2++;
 					}
-				}				
+				}
 			}
-			
+
 			if (indicator_pheno[i1][j1]==1) {
 				c_obs1++;
 			} else {
 				c_miss1++;
 			}
 		}
-		
-	}	
-	
+
+	}
+
 	// Do LU decomposition of H_oo.
 	int sig;
 	gsl_permutation * pmt=gsl_permutation_alloc (np_obs);
 	LUDecomp (H_oo, pmt, &sig);
-	
+
 		// Obtain y_obs=y_full-y_hat.
 		// Add the fixed effects part to y_miss: y_miss=y_hat.
 		c_obs1=0; c_miss1=0;
 		for (vector<int>::size_type i=0;
 		     i<indicator_pheno.size(); ++i) {
 			if (indicator_cvt[i]==0) {continue;}
-			
+
 			for (vector<int>::size_type j=0; j<n_ph; ++j) {
 				if (indicator_pheno[i][j]==1) {
 					gsl_vector_set (y_obs, c_obs1, gsl_matrix_get (Y_full, i, j)-gsl_matrix_get (Y_hat, i, j) );
@@ -509,18 +509,18 @@ void PRDT::MvnormPrdt (const gsl_matrix *Y_hat, const gsl_matrix *H,
 					c_miss1++;
 				}
 			}
-		}	
-		
+		}
+
 		LUSolve (H_oo, pmt, y_obs, Hiy);
-		
+
 		gsl_blas_dgemv (CblasNoTrans, 1.0, H_mo, Hiy, 1.0, y_miss);
-		
+
 		// Put back predicted y_miss to Y_full.
 		c_miss1=0;
 		for (vector<int>::size_type i=0;
 		     i<indicator_pheno.size(); ++i) {
 			if (indicator_cvt[i]==0) {continue;}
-			
+
 			for (vector<int>::size_type j=0; j<n_ph; ++j) {
 				if (indicator_pheno[i][j]==0) {
 					gsl_matrix_set (Y_full, i, j, gsl_vector_get (y_miss, c_miss1) );
@@ -528,14 +528,14 @@ void PRDT::MvnormPrdt (const gsl_matrix *Y_hat, const gsl_matrix *H,
 				}
 			}
 		}
-		
+
 	// Free matrices.
 	gsl_vector_free(y_obs);
 	gsl_vector_free(y_miss);
 	gsl_matrix_free(H_oo);
 	gsl_matrix_free(H_mo);
 	gsl_vector_free(Hiy);
-	
+
 	return;
 }
 
diff --git a/src/prdt.h b/src/prdt.h
index 2da9fd0..0939b36 100644
--- a/src/prdt.h
+++ b/src/prdt.h
@@ -16,7 +16,7 @@
     along with this program. If not, see <http://www.gnu.org/licenses/>.
 */
 
-#ifndef __PRDT_H__                
+#ifndef __PRDT_H__
 #define __PRDT_H__
 
 #include <vector>
@@ -29,30 +29,30 @@
 using namespace std;
 
 class PRDT {
-	
+
 public:
 	// IO-related parameters.
 	size_t a_mode;
 	size_t d_pace;
-	
+
 	string file_bfile;
 	string file_geno;
 	string file_out;
 	string path_out;
-	
+
 	vector<vector<int> > indicator_pheno;
 	vector<int> indicator_cvt;
 	vector<int> indicator_idv;
 	vector<SNPINFO> snpInfo;
 	map<string, double> mapRS2est;
-	
+
 	size_t n_ph;
 	size_t np_obs, np_miss;
 	size_t ns_total;
 	size_t ns_test;
-	
+
 	double time_eigen;
-	
+
 	// Main functions.
 	void CopyFromParam (PARAM &cPar);
 	void CopyToParam (PARAM &cPar);
diff --git a/src/varcov.cpp b/src/varcov.cpp
index 48a4fc5..46b5bf8 100644
--- a/src/varcov.cpp
+++ b/src/varcov.cpp
@@ -28,7 +28,7 @@
 #include <cstring>
 #include <cmath>
 #include <stdio.h>
-#include <stdlib.h> 
+#include <stdlib.h>
 
 #include "gsl/gsl_vector.h"
 #include "gsl/gsl_matrix.h"
@@ -47,22 +47,22 @@ using namespace std;
 
 void VARCOV::CopyFromParam (PARAM &cPar) {
 	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;
-	
+
 	time_opt=0.0;
 
 	window_cm=cPar.window_cm;
 	window_bp=cPar.window_bp;
 	window_ns=cPar.window_ns;
-	
+
 	indicator_idv=cPar.indicator_idv;
 	indicator_snp=cPar.indicator_snp;
 	snpInfo=cPar.snpInfo;
-	
+
 	return;
 }
 
@@ -82,7 +82,7 @@ void VARCOV::WriteCov (const int flag, const vector<SNPINFO> &snpInfo_sub,
   if (flag==0) {
     outfile.open (file_cov.c_str(), ofstream::out);
     if (!outfile) {cout<<"error writing file: "<<file_cov<<endl; return;}
-		
+
     outfile<<"chr"<<"\t"<<"rs"<<"\t"<<"ps"<<"\t"<<"n_mis"
 	   <<"\t"<<"n_obs"<<"\t"<<"allele1"<<"\t"<<"allele0"
 	   <<"\t"<<"af"<<"\t"<<"window_size"
@@ -111,11 +111,11 @@ void VARCOV::WriteCov (const int flag, const vector<SNPINFO> &snpInfo_sub,
 	  }
 	}
       }
-      
+
       outfile<<endl;
     }
   }
-	
+
   outfile.close();
   outfile.clear();
   return;
@@ -147,7 +147,7 @@ void VARCOV::CalcNB (vector<SNPINFO> &snpInfo_sort) {
   size_t t2=0, n_nb=0;
   for (size_t t=0; t<indicator_snp.size(); ++t) {
     if (indicator_snp[t]==0) {continue;}
-    
+
     if (snpInfo_sort[t].chr=="-9" ||
 	(snpInfo_sort[t].cM==-9 && window_cm!=0) ||
 	(snpInfo_sort[t].base_position==-9 && window_bp!=0) ) {
@@ -203,7 +203,7 @@ void Calc_Cor(vector<vector<double> > &X_mat, vector<double> &cov_vec) {
   }
 
   return;
-} 
+}
 
 // Read the genotype file again, calculate r2 between pairs of SNPs
 // within a window, output the file every 10K SNPs the output results
@@ -229,7 +229,7 @@ void VARCOV::AnalyzeBimbam () {
   for (size_t i=0; i<indicator_idv.size(); i++) {
     ni_test+=indicator_idv[i];
   }
-  
+
   gsl_vector *geno=gsl_vector_alloc (ni_test);
   double geno_mean;
 
@@ -253,29 +253,29 @@ void VARCOV::AnalyzeBimbam () {
     if (X_mat.size()==0) {
       n_nb=snpInfo[t].n_nb+1;
     } else {
-      n_nb=snpInfo[t].n_nb-n_nb+1;       
+      n_nb=snpInfo[t].n_nb-n_nb+1;
     }
 
     for (int i=0; i<n_nb; i++) {
-      if (X_mat.size()==0) {t2=t;} 
+      if (X_mat.size()==0) {t2=t;}
 
       // Read a line of the snp is filtered out.
       inc=0;
       while (t2<indicator_snp.size() && indicator_snp[t2]==0) {
-	t2++; inc++; 
+	t2++; inc++;
       }
 
       Bimbam_ReadOneSNP (inc, indicator_idv, infile, geno, geno_mean);
       gsl_vector_add_constant (geno, -1.0*geno_mean);
-            
+
       for (size_t j=0; j<geno->size; j++) {
 	x_vec[j]=gsl_vector_get(geno, j);
       }
       X_mat.push_back(x_vec);
 
       t2++;
-    }     
-    
+    }
+
     n_nb=snpInfo[t].n_nb;
 
     Calc_Cor(X_mat, cov_vec);
@@ -301,8 +301,8 @@ void VARCOV::AnalyzeBimbam () {
   gsl_vector_free(geno);
 
   infile.close();
-  infile.clear();	
-	
+  infile.clear();
+
   return;
 }
 
@@ -314,7 +314,7 @@ void VARCOV::AnalyzePlink () {
   // Calculate the number of right-hand-side neighbours for each SNP.
   vector<SNPINFO> snpInfo_sub;
   CalcNB(snpInfo);
-  
+
   size_t ni_test=0;
   for (size_t i=0; i<indicator_idv.size(); i++) {
     ni_test+=indicator_idv[i];
@@ -343,30 +343,30 @@ void VARCOV::AnalyzePlink () {
     if (X_mat.size()==0) {
       n_nb=snpInfo[t].n_nb+1;
     } else {
-      n_nb=snpInfo[t].n_nb-n_nb+1;       
+      n_nb=snpInfo[t].n_nb-n_nb+1;
     }
 
     for (int i=0; i<n_nb; i++) {
-      if (X_mat.size()==0) {t2=t;} 
+      if (X_mat.size()==0) {t2=t;}
 
       // Read a line if the SNP is filtered out.
       inc=0;
       while (t2<indicator_snp.size() && indicator_snp[t2]==0) {
 	t2++;
-	inc++; 
+	inc++;
       }
 
       Plink_ReadOneSNP (t2, indicator_idv, infile, geno, geno_mean);
       gsl_vector_add_constant (geno, -1.0*geno_mean);
-            
+
       for (size_t j=0; j<geno->size; j++) {
 	x_vec[j]=gsl_vector_get(geno, j);
       }
       X_mat.push_back(x_vec);
 
       t2++;
-    }     
-    
+    }
+
     n_nb=snpInfo[t].n_nb;
 
     Calc_Cor(X_mat, cov_vec);
@@ -392,7 +392,7 @@ void VARCOV::AnalyzePlink () {
   gsl_vector_free(geno);
 
   infile.close();
-  infile.clear();	
-	
+  infile.clear();
+
   return;
 }
diff --git a/src/varcov.h b/src/varcov.h
index 3b45123..4a1eb3a 100644
--- a/src/varcov.h
+++ b/src/varcov.h
@@ -16,7 +16,7 @@
     along with this program. If not, see <http://www.gnu.org/licenses/>.
 */
 
-#ifndef __VARCOV_H__                
+#ifndef __VARCOV_H__
 #define __VARCOV_H__
 
 #include "gsl/gsl_vector.h"
@@ -47,7 +47,7 @@ public:
 	double window_cm;
 	size_t window_bp;
 	size_t window_ns;
-	
+
 	// Main functions.
 	void CopyFromParam (PARAM &cPar);
 	void CopyToParam (PARAM &cPar);
diff --git a/src/vc.cpp b/src/vc.cpp
index 9fe1894..e8ccece 100644
--- a/src/vc.cpp
+++ b/src/vc.cpp
@@ -175,7 +175,7 @@ void UpdateParam (const gsl_vector *log_sigma2, VC_PARAM *p) {
   gsl_matrix *WtHiWiWtHi=gsl_matrix_alloc(n_cvt, n1);
 
   double sigma2;
-  
+
   // Calculate H = \sum_i^{k+1} \sigma_i^2 K_i.
   gsl_matrix_set_zero (p->P);
   for (size_t i=0; i<n_vc+1; i++) {
@@ -196,7 +196,7 @@ void UpdateParam (const gsl_vector *log_sigma2, VC_PARAM *p) {
     gsl_matrix_scale(K_temp, sigma2);
     gsl_matrix_add (p->P, K_temp);
   }
-  
+
   // Calculate H^{-1}.
   eigenlib_invert(p->P);
 
@@ -211,7 +211,7 @@ void UpdateParam (const gsl_vector *log_sigma2, VC_PARAM *p) {
 
   // Calculate Py, KPy, PKPy.
   gsl_blas_dgemv(CblasNoTrans, 1.0, p->P, p->y, 0.0, p->Py);
-  
+
   double d;
   for (size_t i=0; i<n_vc+1; i++) {
     gsl_vector_view KPy=gsl_matrix_column (p->KPy_mat, i);
@@ -221,7 +221,7 @@ void UpdateParam (const gsl_vector *log_sigma2, VC_PARAM *p) {
       gsl_vector_memcpy (&KPy.vector, p->Py);
     } else {
       gsl_matrix_const_view K_sub=gsl_matrix_const_submatrix (p->K, 0, n1*i, n1, n1);
-      
+
       // Seems to be important to use gsl dgemv here instead of
       // eigenlib_dgemv; otherwise.
       gsl_blas_dgemv(CblasNoTrans, 1.0, &K_sub.matrix, p->Py, 0.0,
@@ -643,7 +643,7 @@ void ReadFile_cor (const string &file_cor, const set<string> &setSnps,
   }
 
   while (!safeGetline(infile, line).eof()) {
-    
+
     //do not read cor values this time; upto col_n-1.
     ch_ptr=strtok ((char *)line.c_str(), " , \t");
 
@@ -942,7 +942,7 @@ void ReadFile_cor (const string &file_cor, const vector<string> &vec_rs,
   ReadHeader_vc (line, header);
 
   while (!safeGetline(infile, line).eof()) {
-    
+
     // Do not read cor values this time; upto col_n-1.
     d_pos1=0; d_cm1=0;
     ch_ptr=strtok ((char *)line.c_str(), " , \t");
@@ -1115,7 +1115,7 @@ void ReadFile_cor (const string &file_cor, const vector<string> &vec_rs,
 	    mat_S[i][j]*=crt_factor; mat_S[j][i]*=crt_factor;
 	  }
 	  cout<<crt_factor<<endl;
-	  
+
 	  // Correct qvar.
 	  if (i==j) {
 	    vec_qvar[i]*=crt_factor;
@@ -1198,7 +1198,7 @@ void CalcVCss(const gsl_matrix *Vq, const gsl_matrix *S_mat,
   // Get qvar_mat.
   gsl_matrix_memcpy (qvar_mat, Vq);
   gsl_matrix_scale (qvar_mat, 1.0/(df*df));
-  
+
   // Calculate variance for these estimates.
   for (size_t i=0; i<n_vc; i++) {
     for (size_t j=i; j<n_vc; j++) {
@@ -1873,7 +1873,7 @@ void VC::CalcVCacl (const gsl_matrix *K, const gsl_matrix *W,
   size_t it=0;
   double s=1;
   while (abs(s)>1e-3 && it<100) {
-    
+
     // Update tau_inv.
     gsl_blas_ddot (q_vec, pve, &d);
     if (it>0) {s=y2_sum/(double)n1-d/((double)n1*((double)n1-1))-tau_inv;}
@@ -2143,7 +2143,7 @@ bool PlinkXwz (const string &file_bed, const int display_pace,
 	gsl_vector_mul(wz, w);
 
 	int n_bit;
-	
+
 	// Calculate n_bit and c, the number of bit for each snp.
 	if (ni_total%4==0) {n_bit=ni_total/4;}
 	else {n_bit=ni_total/4+1; }
@@ -2170,7 +2170,7 @@ bool PlinkXwz (const string &file_bed, const int display_pace,
 			b=ch[0];
 
 			// Minor allele homozygous: 2.0; major: 0.0.
-			for (size_t j=0; j<4; ++j) {                
+			for (size_t j=0; j<4; ++j) {
 				if ((i==(n_bit-1)) && ci_total==ni_total) {
 				  break;
 				}
@@ -2393,7 +2393,7 @@ bool PlinkXtXwz (const string &file_bed, const int display_pace,
 		if (indicator_snp[t]==0) {continue;}
 
 		// n_bit, and 3 is the number of magic numbers.
-		infile.seekg(t*n_bit+3); 
+		infile.seekg(t*n_bit+3);
 
 		// Read genotypes.
 		geno_mean=0.0;	n_miss=0; ci_total=0; geno_var=0.0; ci_test=0;
@@ -2402,7 +2402,7 @@ bool PlinkXtXwz (const string &file_bed, const int display_pace,
 			b=ch[0];
 
 			// Minor allele homozygous: 2.0; major: 0.0;
-			for (size_t j=0; j<4; ++j) {                
+			for (size_t j=0; j<4; ++j) {
 				if ((i==(n_bit-1)) && ci_total==ni_total) {
 				  break;
 				}