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, 77 insertions, 83 deletions

diff --git a/src/bslmmdap.h b/src/bslmmdap.h
index db5774b..dc05e34 100644
--- a/src/bslmmdap.h
+++ b/src/bslmmdap.h
@@ -19,97 +19,91 @@
 #ifndef __BSLMMDAP_H__
 #define __BSLMMDAP_H__
 
-#include <vector>
-#include <map>
-#include <gsl/gsl_rng.h>
-#include <gsl/gsl_randist.h>
 #include "param.h"
+#include <gsl/gsl_randist.h>
+#include <gsl/gsl_rng.h>
+#include <map>
+#include <vector>
 
 using namespace std;
 
 class BSLMMDAP {
 
 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 pve_null;
-	double pheno_mean;
-
-	// BSLMM MCMC related parameters
-	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;   // Number of individuals and SNPs
-				   // used for analysis.
-
-	double h_min, h_max, rho_min, rho_max;
-	size_t h_ngrid, rho_ngrid;
-
-	double time_UtZ;
-	double time_Omega;	// Time spent on optimization iterations.
-	double time_Proposal;   // Time spent on constructing the
-				// proposal distribution for gamma
-				// (i.e., lmm or lm analysis).
-
-        // 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;
-
-	vector<SNPINFO> snpInfo;  // Record SNP information.
-
-	// Main functions.
-	void CopyFromParam (PARAM &cPar);
-	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,
-			  const gsl_vector *coef);
-	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,
-			     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,
-			 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,
-				gsl_vector_int *dlevel);
+  // 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 pve_null;
+  double pheno_mean;
+
+  // BSLMM MCMC related parameters
+  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;   // Number of individuals and SNPs
+                             // used for analysis.
+
+  double h_min, h_max, rho_min, rho_max;
+  size_t h_ngrid, rho_ngrid;
+
+  double time_UtZ;
+  double time_Omega;    // Time spent on optimization iterations.
+  double time_Proposal; // Time spent on constructing the
+                        // proposal distribution for gamma
+                        // (i.e., lmm or lm analysis).
+
+  // 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;
+
+  vector<SNPINFO> snpInfo; // Record SNP information.
+
+  // Main functions.
+  void CopyFromParam(PARAM &cPar);
+  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, const gsl_vector *coef);
+  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, 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,
+                  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, gsl_vector_int *dlevel);
 };
 
-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,
-		  vector<vector<vector<double> > > &BF);
-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);
+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,
+                 vector<vector<vector<double>>> &BF);
+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);
 
 #endif
-
-