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Diffstat (limited to 'src/io.h')
| -rw-r--r-- | src/io.h | 79 |
1 files changed, 79 insertions, 0 deletions
diff --git a/src/io.h b/src/io.h new file mode 100644 index 0000000..13e3e47 --- /dev/null +++ b/src/io.h @@ -0,0 +1,79 @@ +/* + Genome-wide Efficient Mixed Model Association (GEMMA) + Copyright (C) 2011 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 + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + 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/>. +*/ + +#ifndef __IO_H__ +#define __IO_H__ + + +#include <vector> +#include <map> +#include <algorithm> +#include "gsl/gsl_vector.h" +#include "gsl/gsl_matrix.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); + +bool ReadFile_snps (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); + +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_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); + +#endif + + + + + + + |