diff options
Diffstat (limited to 'src/io.h')
| -rw-r--r-- | src/io.h | 24 |
1 files changed, 8 insertions, 16 deletions
@@ -1,6 +1,8 @@ /* Genome-wide Efficient Mixed Model Association (GEMMA) - Copyright (C) 2011-2017, Xiang Zhou + Copyright © 2011-2017, Xiang Zhou + Copyright © 2017, Peter Carbonetto + Copyright © 2017, Pjotr Prins 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 @@ -32,8 +34,8 @@ using namespace std; -void ProgressBar(string str, double p, double total); -void ProgressBar(string str, double p, double total, double ratio); +void ProgressBar(string str, double p, double total, double ratio = -1.0); + std::istream &safeGetline(std::istream &is, std::string &t); bool ReadFile_snps(const string file_snps, set<string> &setSnps); @@ -64,7 +66,7 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps, 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 debug); + 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, @@ -94,7 +96,7 @@ bool PlinkKin(const string &file_bed, vector<int> &indicator_snp, 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 debug); + 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); @@ -102,7 +104,7 @@ 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 debug); + 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, @@ -176,16 +178,6 @@ 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, |