Removing FORCE_FLOAT from some more C++ source files.

2 files changed, 138 insertions, 105 deletions

diff --git a/src/io.cpp b/src/io.cpp
index ccaec30..1a4d466 100644
--- a/src/io.cpp
+++ b/src/io.cpp
@@ -1,6 +1,6 @@
 /*
-	Genome-wide Efficient Mixed Model Association (GEMMA)
-    Copyright (C) 2011  Xiang Zhou
+    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
@@ -13,7 +13,7 @@
     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/>.
+    along with this program. If not, see <http://www.gnu.org/licenses/>.
 */
 
 #include <iostream>
@@ -40,19 +40,12 @@
 #include "gzstream.h"
 #include "mathfunc.h"
 #include "eigenlib.h"
-
-#ifdef FORCE_FLOAT
-#include "io_float.h"
-#else
 #include "io.h"
-#endif
-
 
 using namespace std;
 
-//Print process bar
-void ProgressBar (string str, double p, double total)
-{
+// Print progress bar.
+void ProgressBar (string str, double p, double total) {
 	double progress = (100.0 * p / total);
 	int barsize = (int) (progress / 2.0);
 	char bar[51];
@@ -68,10 +61,8 @@ void ProgressBar (string str, double p, double total)
 	return;
 }
 
-
-//Print process bar (with acceptance ratio)
-void ProgressBar (string str, double p, double total, double ratio)
-{
+// Print progress bar with acceptance ratio.
+void ProgressBar (string str, double p, double total, double ratio) {
 	double progress = (100.0 * p / total);
 	int barsize = (int) (progress / 2.0);
 	char bar[51];
@@ -83,37 +74,31 @@ void ProgressBar (string str, double p, double total, double ratio)
 		cout<<bar[i];
 	}
 	cout<<setprecision(2)<<fixed<<progress<<"%    "<<ratio<<"\r"<<flush;
-
-
 	return;
 }
 
-
-bool isBlankLine(char const* line)
-{
-    for ( char const* cp = line; *cp; ++cp )
-    {
-        if ( !isspace(*cp) ) return false;
+bool isBlankLine(char const* line) {
+    for ( char const* cp = line; *cp; ++cp ) {
+        if ( !isspace(*cp) )
+	  return false;
     }
     return true;
 }
 
-bool isBlankLine(std::string const& line)
-{
+bool isBlankLine(std::string const& line) {
    return isBlankLine(line.c_str());
 }
 
-// in case files are ended with "\r" or "\r\n"
-std::istream& safeGetline(std::istream& is, std::string& t)
-{
+// In case files are ended with "\r" or "\r\n".
+std::istream& safeGetline(std::istream& is, std::string& t) {
     t.clear();
 
-    // The characters in the stream are read one-by-one using a std::streambuf.
-    // That is faster than reading them one-by-one using the std::istream.
-    // Code that uses streambuf this way must be guarded by a sentry object.
-    // The sentry object performs various tasks,
-    // such as thread synchronization and updating the stream state.
-
+    // The characters in the stream are read one-by-one using a
+    // std::streambuf. That is faster than reading them one-by-one
+    // using the std::istream. Code that uses streambuf this way must
+    // be guarded by a sentry object. The sentry object performs
+    // various tasks, such as thread synchronization and updating the
+    // stream state.
     std::istream::sentry se(is, true);
     std::streambuf* sb = is.rdbuf();
 
@@ -127,7 +112,9 @@ std::istream& safeGetline(std::istream& is, std::string& t)
                 sb->sbumpc();
             return is;
         case EOF:
-            // Also handle the case when the last line has no line ending
+	  
+            // Also handle the case when the last line has no line
+            // ending.
             if(t.empty())
                 is.setstate(std::ios::eofbit);
             return is;
@@ -137,16 +124,15 @@ std::istream& safeGetline(std::istream& is, std::string& t)
     }
 }
 
-//Read snp file
-bool ReadFile_snps (const string &file_snps, set<string> &setSnps)
-{
+// Read SNP file.
+bool ReadFile_snps (const string &file_snps, set<string> &setSnps) {
 	setSnps.clear();
 
-	//ifstream infile (file_snps.c_str(), ifstream::in);
-	//if (!infile) {cout<<"error! fail to open snps file: "<<file_snps<<endl; return false;}
-
 	igzstream infile (file_snps.c_str(), igzstream::in);
-	if (!infile) {cout<<"error! fail to open snps file: "<<file_snps<<endl; return false;}
+	if (!infile) {
+	  cout << "error! fail to open snps file: " << file_snps << endl;
+	  return false;
+	}
 
 	string line;
 	char *ch_ptr;
@@ -162,21 +148,19 @@ bool ReadFile_snps (const string &file_snps, set<string> &setSnps)
 	return true;
 }
 
-
-bool ReadFile_snps_header (const string &file_snps, set<string> &setSnps)
-{
+bool ReadFile_snps_header (const string &file_snps, set<string> &setSnps) {
 	setSnps.clear();
 
-	//ifstream infile (file_snps.c_str(), ifstream::in);
-	//if (!infile) {cout<<"error! fail to open snps file: "<<file_snps<<endl; return false;}
-
 	igzstream infile (file_snps.c_str(), igzstream::in);
-	if (!infile) {cout<<"error! fail to open snps file: "<<file_snps<<endl; return false;}
+	if (!infile) {
+	  cout << "error! fail to open snps file: " << file_snps << endl;
+	  return false;
+	}
 
 	string line, rs, chr, pos;
 	char *ch_ptr;
 
-	//read header
+	// Read header.
 	HEADER header;
 	!safeGetline(infile, line).eof();
 	ReadHeader_io (line, header);
@@ -210,7 +194,6 @@ bool ReadFile_snps_header (const string &file_snps, set<string> &setSnps)
 	return true;
 }
 
-
 //Read log file
 bool ReadFile_log (const string &file_log, double &pheno_mean)
 {
@@ -4085,14 +4068,7 @@ void ReadFile_mref (const string &file_mref, gsl_matrix *S_mat, gsl_matrix *Svar
   //free matrices
   gsl_matrix_free(S_sub);
   gsl_matrix_free(Svar_sub);
-  //gsl_matrix_free(V_sub);
   gsl_vector_free(s);
 
   return;
 }
-
-
-
-
-
-
diff --git a/src/io.h b/src/io.h
index 073812c..365127a 100644
--- a/src/io.h
+++ b/src/io.h
@@ -1,6 +1,6 @@
 /*
-	Genome-wide Efficient Mixed Model Association (GEMMA)
-    Copyright (C) 2011  Xiang Zhou
+    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
@@ -13,13 +13,12 @@
     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/>.
+    along with this program. If not, see <http://www.gnu.org/licenses/>.
 */
 
 #ifndef __IO_H__
 #define __IO_H__
 
-
 #include <vector>
 #include <map>
 #include <algorithm>
@@ -27,18 +26,10 @@
 #include "gsl/gsl_matrix.h"
 
 #include "gzstream.h"
-
-#ifdef FORCE_FLOAT
-#include "param_float.h"
-#else
 #include "param.h"
-#endif
 
 using namespace std;
 
-
-
-
 void ProgressBar (string str, double p, double total);
 void ProgressBar (string str, double p, double total, double ratio);
 std::istream& safeGetline(std::istream& is, std::string& t);
@@ -48,36 +39,86 @@ bool ReadFile_snps_header (const string &file_snps, set<string> &setSnps);
 bool ReadFile_log (const string &file_log, double &pheno_mean);
 
 bool ReadFile_bim (const string &file_bim, vector<SNPINFO> &snpInfo);
-bool ReadFile_fam (const string &file_fam, vector<vector<int> > &indicator_pheno, vector<vector<double> > &pheno, map<string, int> &mapID2num, const vector<size_t> &p_column);
-
-bool ReadFile_cvt (const string &file_cvt, vector<int> &indicator_cvt, vector<vector<double> > &cvt, size_t &n_cvt);
-bool ReadFile_anno (const string &file_bim, map<string, string> &mapRS2chr, map<string, long int> &mapRS2bp, map<string, double> &mapRS2cM);
-bool ReadFile_pheno (const string &file_pheno, vector<vector<int> > &indicator_pheno, vector<vector<double> > &pheno, const vector<size_t> &p_column);
-bool ReadFile_column (const string &file_pheno, vector<int> &indicator_idv, vector<double> &pheno, const int &p_column);
-
-bool ReadFile_geno (const string &file_geno, const set<string> &setSnps, const gsl_matrix *W, vector<int> &indicator_idv, vector<int> &indicator_snp, const double &maf_level, const double &miss_level, const double &hwe_level, const double &r2_level, map<string, string> &mapRS2chr, map<string, long int> &mapRS2bp, map<string, double> &mapRS2cM, vector<SNPINFO> &snpInfo, size_t &ns_test);
-bool ReadFile_bed (const string &file_bed, const set<string> &setSnps, const gsl_matrix *W, vector<int> &indicator_idv, vector<int> &indicator_snp, vector<SNPINFO> &snpInfo, const double &maf_level, const double &miss_level, const double &hwe_level, const double &r2_level, size_t &ns_test);
-bool Bimbam_ReadOneSNP (const size_t inc, const vector<int> &indicator_idv, igzstream &infile, gsl_vector *geno, double &geno_mean);
-void Plink_ReadOneSNP (const int pos, const vector<int> &indicator_idv, ifstream &infile, gsl_vector *geno, double &geno_mean);
-
-void ReadFile_kin (const string &file_kin, vector<int> &indicator_idv, map<string, int> &mapID2num, const size_t k_mode, bool &error, gsl_matrix *G);
-void ReadFile_mk (const string &file_mk, vector<int> &indicator_idv, map<string, int> &mapID2num, const size_t k_mode, bool &error, gsl_matrix *G);
+bool ReadFile_fam (const string &file_fam,
+		   vector<vector<int> > &indicator_pheno,
+		   vector<vector<double> > &pheno,
+		   map<string, int> &mapID2num,
+		   const vector<size_t> &p_column);
+
+bool ReadFile_cvt (const string &file_cvt,
+		   vector<int> &indicator_cvt,
+		   vector<vector<double> > &cvt,
+		   size_t &n_cvt);
+bool ReadFile_anno (const string &file_bim, map<string, string> &mapRS2chr,
+		    map<string, long int> &mapRS2bp,
+		    map<string, double> &mapRS2cM);
+bool ReadFile_pheno (const string &file_pheno,
+		     vector<vector<int> > &indicator_pheno,
+		     vector<vector<double> > &pheno,
+		     const vector<size_t> &p_column);
+bool ReadFile_column (const string &file_pheno, vector<int> &indicator_idv,
+		      vector<double> &pheno, const int &p_column);
+
+bool ReadFile_geno (const string &file_geno, const set<string> &setSnps,
+		    const gsl_matrix *W, vector<int> &indicator_idv,
+		    vector<int> &indicator_snp, const double &maf_level,
+		    const double &miss_level, const double &hwe_level,
+		    const double &r2_level, map<string, string> &mapRS2chr,
+		    map<string, long int> &mapRS2bp,
+		    map<string, double> &mapRS2cM, vector<SNPINFO> &snpInfo,
+		    size_t &ns_test);
+bool ReadFile_bed (const string &file_bed, const set<string> &setSnps,
+		   const gsl_matrix *W, vector<int> &indicator_idv,
+		   vector<int> &indicator_snp, vector<SNPINFO> &snpInfo,
+		   const double &maf_level, const double &miss_level,
+		   const double &hwe_level, const double &r2_level,
+		   size_t &ns_test);
+bool Bimbam_ReadOneSNP (const size_t inc, const vector<int> &indicator_idv,
+			igzstream &infile, gsl_vector *geno,
+			double &geno_mean);
+void Plink_ReadOneSNP (const int pos, const vector<int> &indicator_idv,
+		       ifstream &infile, gsl_vector *geno, double &geno_mean);
+
+void ReadFile_kin (const string &file_kin, vector<int> &indicator_idv,
+		   map<string, int> &mapID2num, const size_t k_mode,
+		   bool &error, gsl_matrix *G);
+void ReadFile_mk (const string &file_mk, vector<int> &indicator_idv,
+		  map<string, int> &mapID2num, const size_t k_mode,
+		  bool &error, gsl_matrix *G);
 void ReadFile_eigenU (const string &file_u, bool &error, gsl_matrix *U);
 void ReadFile_eigenD (const string &file_d, bool &error, gsl_vector *eval);
 
-bool BimbamKin (const string &file_geno, vector<int> &indicator_snp, const int k_mode, const int display_pace, gsl_matrix *matrix_kin);
-bool PlinkKin (const string &file_bed, vector<int> &indicator_snp, const int k_mode, const int display_pace, gsl_matrix *matrix_kin);
-
-bool ReadFile_geno (const string &file_geno, vector<int> &indicator_idv, vector<int> &indicator_snp, gsl_matrix *UtX, gsl_matrix *K, const bool calc_K);
-bool ReadFile_bed (const string &file_bed, vector<int> &indicator_idv, vector<int> &indicator_snp, gsl_matrix *UtX, gsl_matrix *K, const bool calc_K);
-bool ReadFile_geno (const string &file_geno, vector<int> &indicator_idv, vector<int> &indicator_snp, vector<vector<unsigned char> > &Xt, gsl_matrix *K, const bool calc_K, const size_t ni_test, const size_t ns_test);
-bool ReadFile_bed (const string &file_bed, vector<int> &indicator_idv, vector<int> &indicator_snp, vector<vector<unsigned char> > &Xt, gsl_matrix *K, const bool calc_K, const size_t ni_test, const size_t ns_test);
-
-bool ReadFile_est (const string &file_est, const vector<size_t> &est_column, map<string, double> &mapRS2est);
+bool BimbamKin (const string &file_geno, vector<int> &indicator_snp,
+		const int k_mode, const int display_pace,
+		gsl_matrix *matrix_kin);
+bool PlinkKin (const string &file_bed, vector<int> &indicator_snp,
+	       const int k_mode, const int display_pace,
+	       gsl_matrix *matrix_kin);
+
+bool ReadFile_geno (const string &file_geno, vector<int> &indicator_idv,
+		    vector<int> &indicator_snp, gsl_matrix *UtX,
+		    gsl_matrix *K, const bool calc_K);
+bool ReadFile_bed (const string &file_bed, vector<int> &indicator_idv,
+		   vector<int> &indicator_snp, gsl_matrix *UtX,
+		   gsl_matrix *K, const bool calc_K);
+bool ReadFile_geno (const string &file_geno, vector<int> &indicator_idv,
+		    vector<int> &indicator_snp,
+		    vector<vector<unsigned char> > &Xt, gsl_matrix *K,
+		    const bool calc_K, const size_t ni_test,
+		    const size_t ns_test);
+bool ReadFile_bed (const string &file_bed, vector<int> &indicator_idv,
+		   vector<int> &indicator_snp,
+		   vector<vector<unsigned char> > &Xt, gsl_matrix *K,
+		   const bool calc_K, const size_t ni_test,
+		   const size_t ns_test);
+
+bool ReadFile_est (const string &file_est, const vector<size_t> &est_column,
+		   map<string, double> &mapRS2est);
 
 bool CountFileLines (const string &file_input, size_t &n_lines);
 
-bool ReadFile_gene (const string &file_gene, vector<double> &vec_read, vector<SNPINFO> &snpInfo, size_t &ng_total);
+bool ReadFile_gene (const string &file_gene, vector<double> &vec_read,
+		    vector<SNPINFO> &snpInfo, size_t &ng_total);
 
 bool ReadHeader_io (const string &line, HEADER &header);
 bool ReadFile_cat (const string &file_cat, map<string, size_t> &mapRS2cat, size_t &n_vc);
@@ -97,16 +138,32 @@ void ReadFile_beta (const string &file_beta, const map<string, size_t> &mapRS2ca
 void ReadFile_beta (const string &file_beta, const map<string, double> &mapRS2wA, map<string, string> &mapRS2A1, map<string, double> &mapRS2z);
 void Calcq (const size_t n_block, const vector<size_t> &vec_cat, const vector<size_t> &vec_ni, const vector<double> &vec_weight, const vector<double> &vec_z2, gsl_matrix *Vq, gsl_vector *q, gsl_vector *s);
 
-void ReadFile_study (const string &file_study, gsl_matrix *Vq, gsl_vector *q_vec, gsl_vector *s_vec, size_t &ni);
-void ReadFile_ref (const string &file_ref, gsl_matrix *S_mat, gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni);
-void ReadFile_mstudy (const string &file_mstudy, gsl_matrix *Vq, gsl_vector *q_vec, gsl_vector *s_vec, size_t &ni);
-void ReadFile_mref (const string &file_mref, gsl_matrix *S_mat, gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni);
-
-// WJA added
-bool bgenKin (const string &file_geno, vector<int> &indicator_snp, const int k_mode, const int display_pace, gsl_matrix *matrix_kin);
-bool ReadFile_bgen(const string &file_bgen, const set<string> &setSnps, const gsl_matrix *W, vector<int> &indicator_idv, vector<int> &indicator_snp, vector<SNPINFO> &snpInfo, const double &maf_level, const double &miss_level, const double &hwe_level, const double &r2_level, size_t &ns_test);
-bool ReadFile_sample(const string &file_sample, vector<vector<int> > &indicator_pheno, vector<vector<double> > &pheno, const vector<size_t> &p_column, vector<int> &indicator_cvt, vector<vector<double> > &cvt, size_t &n_cvt);
-
+void ReadFile_study (const string &file_study, gsl_matrix *Vq,
+		     gsl_vector *q_vec, gsl_vector *s_vec, size_t &ni);
+void ReadFile_ref (const string &file_ref, gsl_matrix *S_mat,
+		   gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni);
+void ReadFile_mstudy (const string &file_mstudy, gsl_matrix *Vq,
+		      gsl_vector *q_vec, gsl_vector *s_vec, size_t &ni);
+void ReadFile_mref (const string &file_mref, gsl_matrix *S_mat,
+		    gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni);
+
+// WJA added.
+bool bgenKin (const string &file_geno, vector<int> &indicator_snp,
+	      const int k_mode, const int display_pace,
+	      gsl_matrix *matrix_kin);
+bool ReadFile_bgen(const string &file_bgen, const set<string> &setSnps,
+		   const gsl_matrix *W, vector<int> &indicator_idv,
+		   vector<int> &indicator_snp, vector<SNPINFO> &snpInfo,
+		   const double &maf_level, const double &miss_level,
+		   const double &hwe_level, const double &r2_level,
+		   size_t &ns_test);
+bool ReadFile_sample(const string &file_sample,
+		     vector<vector<int> > &indicator_pheno,
+		     vector<vector<double> > &pheno,
+		     const vector<size_t> &p_column,
+		     vector<int> &indicator_cvt,
+		     vector<vector<double> > &cvt,
+		     size_t &n_cvt);
 
 #endif