diff options
Diffstat (limited to 'src/io.h')
| -rw-r--r-- | src/io.h | 29 |
1 files changed, 16 insertions, 13 deletions
@@ -34,7 +34,7 @@ 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_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); @@ -83,13 +83,14 @@ void ReadFile_mk(const string &file_mk, vector<int> &indicator_idv, 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 BimbamKin(const string file_geno, const set<string> ksnps, + vector<int> &indicator_snp, const int k_mode, + const int display_pace, gsl_matrix *matrix_kin, + const bool test_nind); 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, +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, @@ -124,13 +125,14 @@ bool ReadFile_catc(const string &file_cat, bool ReadFile_mcatc(const string &file_mcat, map<string, vector<double>> &mapRS2catc, size_t &n_cat); -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 BimbamKinUncentered(const string &file_geno, const set<string> ksnps, + 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, @@ -139,7 +141,8 @@ bool PlinkKin(const string &file_bed, const int display_pace, 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 set<string> setKSnps, 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, |