diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/io.cpp | 94 | ||||
| -rw-r--r-- | src/io.h | 149 |
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 |