diff options
Diffstat (limited to 'src/io.h')
| -rw-r--r-- | src/io.h | 36 |
1 files changed, 34 insertions, 2 deletions
@@ -16,7 +16,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef __IO_H__ +#ifndef __IO_H__ #define __IO_H__ @@ -26,6 +26,8 @@ #include "gsl/gsl_vector.h" #include "gsl/gsl_matrix.h" +#include "gzstream.h" + #ifdef FORCE_FLOAT #include "param_float.h" #else @@ -34,6 +36,9 @@ 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); @@ -51,17 +56,21 @@ bool ReadFile_column (const string &file_pheno, vector<int> &indicator_idv, vect 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); +bool Bimbam_ReadOneSNP (const size_t inc, const vector<int> &indicator_idv, igzstream &infile, gsl_vector *geno, double &geno_mean); +void Plink_ReadOneSNP (const int pos, const vector<int> &indicator_idv, ifstream &infile, gsl_vector *geno, double &geno_mean); 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); +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_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 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, const size_t ns_test); bool ReadFile_est (const string &file_est, const vector<size_t> &est_column, map<string, double> &mapRS2est); @@ -69,6 +78,29 @@ 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); +bool ReadHeader (const string &line, HEADER &header); +bool ReadFile_cat (const string &file_cat, 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 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); + + +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); + +// 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, const vector<size_t> &p_column, vector<int> &indicator_cvt, vector<vector<double> > &cvt, size_t &n_cvt); + + #endif |