diff options
Diffstat (limited to 'src/gemma_io.h')
| -rw-r--r-- | src/gemma_io.h | 14 |
1 files changed, 8 insertions, 6 deletions
diff --git a/src/gemma_io.h b/src/gemma_io.h index 5c14227..06cd0ee 100644 --- a/src/gemma_io.h +++ b/src/gemma_io.h @@ -26,12 +26,17 @@ #include <algorithm> #include <map> #include <vector> +#include <cstdint> #include "gzstream.h" #include "param.h" #define tab(col) ( col ? "\t" : "") +constexpr uint8_t CHR_X = 'X'; +constexpr uint8_t CHR_Y = 'Y'; +constexpr uint8_t CHR_M = 'M'; + using namespace std; void ProgressBar(string str, double p, double total, double ratio = -1.0); @@ -59,7 +64,7 @@ bool ReadFile_pheno(const string &file_pheno, 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, +bool ReadFile_bimbam_geno(const string &file_geno, const set<string> &setSnps, const gsl_matrix *W, const vector<int> &indicator_idv, vector<int> &indicator_snp, const double &maf_level, const double &miss_level, const double &hwe_level, @@ -87,6 +92,8 @@ 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); +gsl_matrix *mdb_calc_kin(const string file_geno, const int k_mode, const string loco); + 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, @@ -100,11 +107,6 @@ bool ReadFile_geno(const string file_geno, vector<int> &indicator_idv, 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, |