diff options
Diffstat (limited to 'src/io.h')
| -rw-r--r-- | src/io.h | 24 |
1 files changed, 14 insertions, 10 deletions
@@ -44,6 +44,7 @@ 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); @@ -80,20 +81,23 @@ bool ReadFile_gene (const string &file_gene, vector<double> &vec_read, vector<SN bool ReadHeader (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 BimbamKin (const string &file_geno, vector<int> &indicator_idv, vector<int> &indicator_snp, const int k_mode, const int display_pace, const map<string, size_t> &mapRS2cat, map<string, double> &mapRS2var, vector<SNPINFO> &snpInfo, gsl_matrix *matrix_kin); -bool PlinkKin (const string &file_bed, vector<int> &indicator_idv, vector<int> &indicator_snp, const int k_mode, const int display_pace, const map<string, size_t> &mapRS2cat, map<string, double> &mapRS2var, vector<SNPINFO> &snpInfo, gsl_matrix *matrix_kin); +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_var (const string &file_var, map<string, double> &mapRS2var); -void ReadFile_beta (const string &file_beta, const int k_mode, const map<string, size_t> &mapRS2cat, const map<string, double> &mapRS2var, gsl_vector *q, gsl_vector *s, size_t &ni_total, size_t &ns_total, size_t &ns_test); +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_s (const string &file_s, gsl_matrix *S, gsl_matrix *Svar); -void ReadFile_ms (const string &file_ms, gsl_matrix *S, gsl_matrix *Svar); -void ReadFile_v (const string &file_v, gsl_matrix *V); -void ReadFile_mv (const string &file_mq, gsl_matrix *V); -void ReadFile_q (const string &file_s, gsl_vector *q_vec, gsl_vector *s_vec, double &df); -void ReadFile_mq (const string &file_mq, gsl_vector *q_vec, gsl_vector *s_vec, double &df); +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); |