Merge branch 'master' of github.com:genetics-statistics/GEMMA

1 files changed, 159 insertions, 179 deletions

diff --git a/src/io.h b/src/io.h
index 9d6f8cc..27f145f 100644
--- a/src/io.h
+++ b/src/io.h
@@ -19,195 +19,175 @@
 #ifndef __IO_H__
 #define __IO_H__
 
-#include <vector>
-#include <map>
-#include <algorithm>
-#include "gsl/gsl_vector.h"
 #include "gsl/gsl_matrix.h"
+#include "gsl/gsl_vector.h"
+#include <algorithm>
+#include <map>
+#include <vector>
 
 #include "gzstream.h"
 #include "param.h"
 
 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);
-
-bool ReadFile_snps (const string &file_snps, set<string> &setSnps);
-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);
-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 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 ReadHeader_io (const string &line, HEADER &header);
-bool ReadFile_cat (const string &file_cat, map<string, size_t> &mapRS2cat,
-		   size_t &n_vc);
-bool ReadFile_mcat (const string &file_mcat, map<string, size_t> &mapRS2cat,
-		    size_t &n_vc);
-
-bool ReadFile_catc (const string &file_cat,
-		    map<string, vector<double> > &mapRS2catc,
-		    size_t &n_cat);
-bool ReadFile_mcatc (const string &file_mcat, map<string,
-		     vector<double> > &mapRS2catc, size_t &n_cat);
-
-bool BimbamKin (const string &file_geno, const int display_pace,
-		const vector<int> &indicator_idv,
-		const vector<int> &indicator_snp,
-		const map<string, double> &mapRS2weight,
-		const map<string, size_t> &mapRS2cat,
-		const vector<SNPINFO> &snpInfo, const gsl_matrix *W,
-		gsl_matrix *matrix_kin, gsl_vector *vector_ns);
-bool PlinkKin (const string &file_bed, const int display_pace,
-	       const vector<int> &indicator_idv,
-	       const vector<int> &indicator_snp,
-	       const map<string, double> &mapRS2weight,
-	       const map<string, size_t> &mapRS2cat,
-	       const vector<SNPINFO> &snpInfo,
-	       const gsl_matrix *W, gsl_matrix *matrix_kin,
-	       gsl_vector *vector_ns);
-bool MFILEKin (const size_t mfile_mode, const string &file_mfile,
-	       const int display_pace, const vector<int> &indicator_idv,
-	       const vector<vector<int> > &mindicator_snp,
-	       const map<string, double> &mapRS2weight,
-	       const map<string, size_t> &mapRS2cat,
-	       const vector<vector<SNPINFO> > &msnpInfo,
-	       const gsl_matrix *W, gsl_matrix *matrix_kin,
-	       gsl_vector *vector_ns);
-
-bool ReadFile_wsnp (const string &file_wsnp,
-		    map<string, double> &mapRS2double);
-bool ReadFile_wsnp (const string &file_wcat, const size_t n_vc,
-		    map<string, vector<double> > &mapRS2vector);
-
-void ReadFile_beta (const string &file_beta,
-		    const map<string, size_t> &mapRS2cat,
-		    const map<string, double> &mapRS2wA,
-		    vector<size_t> &vec_cat, vector<size_t> &vec_ni,
-		    vector<double> &vec_weight, vector<double> &vec_z2,
-		    size_t &ni_total, size_t &ns_total, size_t &ns_test);
-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);
+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);
+
+bool ReadFile_snps(const string file_snps, set<string> &setSnps);
+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);
+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, const set<string> ksnps,
+               vector<int> &indicator_snp, const int k_mode,
+               const int display_pace, gsl_matrix *matrix_kin,
+               const bool test_nind);
+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 ReadHeader_io(const string &line, HEADER &header);
+bool ReadFile_cat(const string &file_cat, map<string, size_t> &mapRS2cat,
+                  size_t &n_vc);
+bool ReadFile_mcat(const string &file_mcat, map<string, size_t> &mapRS2cat,
+                   size_t &n_vc);
+
+bool ReadFile_catc(const string &file_cat,
+                   map<string, vector<double>> &mapRS2catc, size_t &n_cat);
+bool ReadFile_mcatc(const string &file_mcat,
+                    map<string, vector<double>> &mapRS2catc, size_t &n_cat);
+
+bool BimbamKinUncentered(const string &file_geno, const set<string> ksnps,
+                         const int display_pace,
+                         const vector<int> &indicator_idv,
+                         const vector<int> &indicator_snp,
+                         const map<string, double> &mapRS2weight,
+                         const map<string, size_t> &mapRS2cat,
+                         const vector<SNPINFO> &snpInfo, const gsl_matrix *W,
+                         gsl_matrix *matrix_kin, gsl_vector *vector_ns);
+bool PlinkKin(const string &file_bed, const int display_pace,
+              const vector<int> &indicator_idv,
+              const vector<int> &indicator_snp,
+              const map<string, double> &mapRS2weight,
+              const map<string, size_t> &mapRS2cat,
+              const vector<SNPINFO> &snpInfo, const gsl_matrix *W,
+              gsl_matrix *matrix_kin, gsl_vector *vector_ns);
+bool MFILEKin(const size_t mfile_mode, const string &file_mfile,
+              const set<string> setKSnps, const int display_pace,
+              const vector<int> &indicator_idv,
+              const vector<vector<int>> &mindicator_snp,
+              const map<string, double> &mapRS2weight,
+              const map<string, size_t> &mapRS2cat,
+              const vector<vector<SNPINFO>> &msnpInfo, const gsl_matrix *W,
+              gsl_matrix *matrix_kin, gsl_vector *vector_ns);
+
+bool ReadFile_wsnp(const string &file_wsnp, map<string, double> &mapRS2double);
+bool ReadFile_wsnp(const string &file_wcat, const size_t n_vc,
+                   map<string, vector<double>> &mapRS2vector);
+
+void ReadFile_beta(const string &file_beta,
+                   const map<string, size_t> &mapRS2cat,
+                   const map<string, double> &mapRS2wA, vector<size_t> &vec_cat,
+                   vector<size_t> &vec_ni, vector<double> &vec_weight,
+                   vector<double> &vec_z2, size_t &ni_total, size_t &ns_total,
+                   size_t &ns_test);
+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 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);
+                   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);
+                     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
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