diff options
Diffstat (limited to 'src/io.cpp')
| -rw-r--r-- | src/io.cpp | 27 |
1 files changed, 14 insertions, 13 deletions
@@ -41,6 +41,7 @@ #include "debug.h" #include "eigenlib.h" +#include "fastblas.h" #include "gzstream.h" #include "io.h" #include "lapack.h" @@ -594,7 +595,7 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps, 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 debug) { + size_t &ns_test) { debug_msg("entered"); indicator_snp.clear(); snpInfo.clear(); @@ -667,7 +668,7 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps, } if (mapRS2bp.count(rs) == 0) { - if (debug && count_warnings++ < 10) { + if (is_debug_mode() && count_warnings++ < 10) { std::string msg = "Can't figure out position for "; msg += rs; debug_msg(msg); @@ -1454,12 +1455,12 @@ bool BimbamKin(const string file_geno, const set<string> ksnps, // compute kinship matrix and return in matrix_kin a SNP at a time if (ns_test % msize == 0) { - eigenlib_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); + fast_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); gsl_matrix_set_zero(Xlarge); } } if (ns_test % msize != 0) { - eigenlib_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); + fast_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); } cout << endl; @@ -1600,13 +1601,13 @@ bool PlinkKin(const string &file_bed, vector<int> &indicator_snp, ns_test++; if (ns_test % msize == 0) { - eigenlib_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); + fast_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); gsl_matrix_set_zero(Xlarge); } } if (ns_test % msize != 0) { - eigenlib_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); + fast_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); } cout << endl; @@ -1633,7 +1634,7 @@ bool PlinkKin(const string &file_bed, vector<int> &indicator_snp, // genotype and calculate K. 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 debug) { + const bool calc_K) { debug_msg("entered"); igzstream infile(file_geno.c_str(), igzstream::in); if (!infile) { @@ -1738,7 +1739,7 @@ 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 debug) { + const size_t ns_test) { debug_msg("entered"); igzstream infile(file_geno.c_str(), igzstream::in); if (!infile) { @@ -2757,7 +2758,7 @@ bool BimbamKinUncentered(const string &file_geno, const set<string> ksnps, ns_vec[0]++; if (ns_vec[0] % msize == 0) { - eigenlib_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); + fast_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); gsl_matrix_set_zero(Xlarge); } } else if (mapRS2cat.count(rs) != 0) { @@ -2774,7 +2775,7 @@ bool BimbamKinUncentered(const string &file_geno, const set<string> ksnps, gsl_matrix_submatrix(Xlarge, 0, msize * i_vc, ni_test, msize); gsl_matrix_view kin_sub = gsl_matrix_submatrix( matrix_kin, 0, ni_test * i_vc, ni_test, ni_test); - eigenlib_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0, + fast_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0, &kin_sub.matrix); gsl_matrix_set_zero(&X_sub.matrix); @@ -2790,7 +2791,7 @@ bool BimbamKinUncentered(const string &file_geno, const set<string> ksnps, gsl_matrix_submatrix(Xlarge, 0, msize * i_vc, ni_test, msize); gsl_matrix_view kin_sub = gsl_matrix_submatrix(matrix_kin, 0, ni_test * i_vc, ni_test, ni_test); - eigenlib_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0, + fast_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0, &kin_sub.matrix); } } @@ -2983,7 +2984,7 @@ bool PlinkKin(const string &file_bed, const int display_pace, ns_vec[0]++; if (ns_vec[0] % msize == 0) { - eigenlib_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); + fast_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); gsl_matrix_set_zero(Xlarge); } } else if (mapRS2cat.count(rs) != 0) { @@ -3000,7 +3001,7 @@ bool PlinkKin(const string &file_bed, const int display_pace, gsl_matrix_submatrix(Xlarge, 0, msize * i_vc, ni_test, msize); gsl_matrix_view kin_sub = gsl_matrix_submatrix( matrix_kin, 0, ni_test * i_vc, ni_test, ni_test); - eigenlib_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0, + fast_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0, &kin_sub.matrix); gsl_matrix_set_zero(&X_sub.matrix); |