diff options
Diffstat (limited to 'src/io.cpp')
| -rw-r--r-- | src/io.cpp | 94 |
1 files changed, 35 insertions, 59 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; } - - - - - - |