Massive patch using LLVM coding style. It was generated with:

  clang-format -style=LLVM -i *.cpp *.h

Please set your editor to replace tabs with spaces and use indentation of 2 spaces.

1 files changed, 136 insertions, 146 deletions

diff --git a/src/bslmm.h b/src/bslmm.h
index c7768a2..d2dadbf 100644
--- a/src/bslmm.h
+++ b/src/bslmm.h
@@ -19,10 +19,10 @@
 #ifndef __BSLMM_H__
 #define __BSLMM_H__
 
-#include <vector>
-#include <map>
-#include <gsl/gsl_rng.h>
 #include <gsl/gsl_randist.h>
+#include <gsl/gsl_rng.h>
+#include <map>
+#include <vector>
 
 #include "param.h"
 
@@ -31,149 +31,139 @@ using namespace std;
 class BSLMM {
 
 public:
-	// IO-related parameters.
-	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.
-	double logp_min, logp_max, logp_scale; // Priors for log(pi).
-	size_t s_min, s_max;		       // Min. & max. number of gammas.
-	size_t w_step;			       // Number of warm up/burn in
-                                               // iterations.
-	size_t s_step;			       // Num. sampling iterations.
-	size_t r_pace;			       // Record pace.
-	size_t w_pace;			       // Write pace.
-	size_t n_accept;		       // Number of acceptances.
-	size_t n_mh;			       // Number of MH steps per iter.
-	double geo_mean;		       // Mean of geometric dist.
-	long int randseed;
-	double trace_G;
-
-	HYPBSLMM cHyp_initial;
-
-	// Summary statistics.
-	size_t ni_total, ns_total; // Number of total individuals and SNPs
-	size_t ni_test, ns_test;   // Num. individuals & SNPs used in analysis.
-	size_t n_cvt;		   // Number of covariates.
-	double time_UtZ;
-	double time_Omega;	   // Time spent on optimization iterations.
-
-        // Time spent on constructing the proposal distribution for
-        // gamma (i.e. lmm or lm analysis).
-	double time_Proposal;
-
-        // Indicator for individuals (phenotypes): 0 missing, 1
-        // available for analysis.
-	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;
-
-        // Record SNP information.
-	vector<SNPINFO> snpInfo;
-
-	// Not included in PARAM.
-	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);
-	void WriteLog ();
-	void WriteLR ();
-	void WriteBV (const gsl_vector *bv);
-	void WriteParam (vector<pair<double, double> > &beta_g,
-			 const gsl_vector *alpha, const size_t w);
-	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,
-			  vector<size_t> &rank_old, class HYPBSLMM &cHyp,
-			  vector<pair<size_t, double> > &pos_loglr);
-	double CalcPosterior (const gsl_vector *Uty, const gsl_vector *K_eval,
-			      gsl_vector *Utu, gsl_vector *alpha_prime,
-			      class HYPBSLMM &cHyp);
-	double 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);
-	void CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *Utu,
-			   gsl_vector *z_hat, class HYPBSLMM &cHyp);
-	void CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *UtXb,
-			   const gsl_vector *Utu, gsl_vector *z_hat,
-			   class HYPBSLMM &cHyp);
-	double CalcREMLE (const gsl_matrix *Utw, const gsl_vector *Uty,
-			  const gsl_vector *K_eval);
-
-        // Calculate the maximum marginal likelihood ratio for each
-        // analyzed SNPs with gemma, use it to rank SNPs.
-	double CalcLR (const gsl_matrix *U, const gsl_matrix *UtX,
-		       const gsl_vector *Uty, const gsl_vector *K_eval,
-		       vector<pair<size_t, double> > &loglr_sort);
-	void SampleZ (const gsl_vector *y, const gsl_vector *z_hat,
-		      gsl_vector *z);
-	double ProposeHnRho (const class HYPBSLMM &cHyp_old,
-			     class HYPBSLMM &cHyp_new, const size_t &repeat);
-	double ProposePi (const class HYPBSLMM &cHyp_old,
-			  class HYPBSLMM &cHyp_new,
-			  const size_t &repeat);
-	double 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);
-	void SetXgamma (gsl_matrix *Xgamma, const gsl_matrix *X,
-			vector<size_t> &rank);
-
-	void CalcXtX (const gsl_matrix *X_new, const gsl_vector *y,
-		      const size_t s_size, gsl_matrix *XtX_new,
-		      gsl_vector *Xty_new);
-	void SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old,
-			const gsl_matrix *XtX_old, const gsl_vector *Xty_old,
-			const gsl_vector *y, const vector<size_t> &rank_old,
-			const vector<size_t> &rank_new, gsl_matrix *X_new,
-			gsl_matrix *XtX_new, gsl_vector *Xty_new);
-	double CalcPosterior (const double yty, class HYPBSLMM &cHyp);
-	double 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);
-	void CalcCC_PVEnZ (gsl_vector *z_hat, class HYPBSLMM &cHyp);
-	void CalcCC_PVEnZ (const gsl_vector *Xb, gsl_vector *z_hat,
-			   class HYPBSLMM &cHyp);
-	void MCMC (const gsl_matrix *X, const gsl_vector *y);
+  // IO-related parameters.
+  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.
+  double logp_min, logp_max, logp_scale; // Priors for log(pi).
+  size_t s_min, s_max;                   // Min. & max. number of gammas.
+  size_t w_step;                         // Number of warm up/burn in
+                                         // iterations.
+  size_t s_step;                         // Num. sampling iterations.
+  size_t r_pace;                         // Record pace.
+  size_t w_pace;                         // Write pace.
+  size_t n_accept;                       // Number of acceptances.
+  size_t n_mh;                           // Number of MH steps per iter.
+  double geo_mean;                       // Mean of geometric dist.
+  long int randseed;
+  double trace_G;
+
+  HYPBSLMM cHyp_initial;
+
+  // Summary statistics.
+  size_t ni_total, ns_total; // Number of total individuals and SNPs
+  size_t ni_test, ns_test;   // Num. individuals & SNPs used in analysis.
+  size_t n_cvt;              // Number of covariates.
+  double time_UtZ;
+  double time_Omega; // Time spent on optimization iterations.
+
+  // Time spent on constructing the proposal distribution for
+  // gamma (i.e. lmm or lm analysis).
+  double time_Proposal;
+
+  // Indicator for individuals (phenotypes): 0 missing, 1
+  // available for analysis.
+  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;
+
+  // Record SNP information.
+  vector<SNPINFO> snpInfo;
+
+  // Not included in PARAM.
+  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);
+  void WriteLog();
+  void WriteLR();
+  void WriteBV(const gsl_vector *bv);
+  void WriteParam(vector<pair<double, double>> &beta_g, const gsl_vector *alpha,
+                  const size_t w);
+  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,
+                   vector<size_t> &rank_old, class HYPBSLMM &cHyp,
+                   vector<pair<size_t, double>> &pos_loglr);
+  double CalcPosterior(const gsl_vector *Uty, const gsl_vector *K_eval,
+                       gsl_vector *Utu, gsl_vector *alpha_prime,
+                       class HYPBSLMM &cHyp);
+  double 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);
+  void CalcCC_PVEnZ(const gsl_matrix *U, const gsl_vector *Utu,
+                    gsl_vector *z_hat, class HYPBSLMM &cHyp);
+  void CalcCC_PVEnZ(const gsl_matrix *U, const gsl_vector *UtXb,
+                    const gsl_vector *Utu, gsl_vector *z_hat,
+                    class HYPBSLMM &cHyp);
+  double CalcREMLE(const gsl_matrix *Utw, const gsl_vector *Uty,
+                   const gsl_vector *K_eval);
+
+  // Calculate the maximum marginal likelihood ratio for each
+  // analyzed SNPs with gemma, use it to rank SNPs.
+  double CalcLR(const gsl_matrix *U, const gsl_matrix *UtX,
+                const gsl_vector *Uty, const gsl_vector *K_eval,
+                vector<pair<size_t, double>> &loglr_sort);
+  void SampleZ(const gsl_vector *y, const gsl_vector *z_hat, gsl_vector *z);
+  double ProposeHnRho(const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_new,
+                      const size_t &repeat);
+  double ProposePi(const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_new,
+                   const size_t &repeat);
+  double 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);
+  void SetXgamma(gsl_matrix *Xgamma, const gsl_matrix *X, vector<size_t> &rank);
+
+  void CalcXtX(const gsl_matrix *X_new, const gsl_vector *y,
+               const size_t s_size, gsl_matrix *XtX_new, gsl_vector *Xty_new);
+  void SetXgamma(const gsl_matrix *X, const gsl_matrix *X_old,
+                 const gsl_matrix *XtX_old, const gsl_vector *Xty_old,
+                 const gsl_vector *y, const vector<size_t> &rank_old,
+                 const vector<size_t> &rank_new, gsl_matrix *X_new,
+                 gsl_matrix *XtX_new, gsl_vector *Xty_new);
+  double CalcPosterior(const double yty, class HYPBSLMM &cHyp);
+  double 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);
+  void CalcCC_PVEnZ(gsl_vector *z_hat, class HYPBSLMM &cHyp);
+  void CalcCC_PVEnZ(const gsl_vector *Xb, gsl_vector *z_hat,
+                    class HYPBSLMM &cHyp);
+  void MCMC(const gsl_matrix *X, const gsl_vector *y);
 };
 
 #endif
-
-