diff options
Diffstat (limited to 'src/io.cpp')
| -rw-r--r-- | src/io.cpp | 24 |
1 files changed, 12 insertions, 12 deletions
@@ -1396,12 +1396,12 @@ bool BimbamKin(const string file_geno, const set<string> ksnps, uint token_num = 0; for (auto x = tokens; x != rend; x++) token_num++; - if (token_num != ni_total) { + if (token_num != ni_total+3) { cerr << line << endl; cerr << token_num << " != " << ni_total << endl; warning_msg("Columns in geno file do not match # individuals"); } - enforce_msg(token_num < ni_total + 3,"not enough genotype fields"); + enforce_msg(token_num <= ni_total + 3,"not enough genotype fields"); } auto snp = *tokens; // first field @@ -1460,12 +1460,12 @@ 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) { - fast_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); + fast_eigen_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); gsl_matrix_set_zero(Xlarge); } } if (ns_test % msize != 0) { - fast_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); + fast_eigen_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); } cout << endl; @@ -1606,13 +1606,13 @@ bool PlinkKin(const string &file_bed, vector<int> &indicator_snp, ns_test++; if (ns_test % msize == 0) { - fast_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); + fast_eigen_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); gsl_matrix_set_zero(Xlarge); } } if (ns_test % msize != 0) { - fast_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); + fast_eigen_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); } cout << endl; @@ -2768,7 +2768,7 @@ bool BimbamKinUncentered(const string &file_geno, const set<string> ksnps, ns_vec[0]++; if (ns_vec[0] % msize == 0) { - fast_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); + fast_eigen_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); gsl_matrix_set_zero(Xlarge); } } else if (mapRS2cat.count(rs) != 0) { @@ -2785,7 +2785,7 @@ 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); - fast_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0, + fast_eigen_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0, &kin_sub.matrix); gsl_matrix_set_zero(&X_sub.matrix); @@ -2801,7 +2801,7 @@ 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); - fast_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0, + fast_eigen_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0, &kin_sub.matrix); } } @@ -2994,7 +2994,7 @@ bool PlinkKin(const string &file_bed, const int display_pace, ns_vec[0]++; if (ns_vec[0] % msize == 0) { - fast_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); + fast_eigen_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); gsl_matrix_set_zero(Xlarge); } } else if (mapRS2cat.count(rs) != 0) { @@ -3011,7 +3011,7 @@ 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); - fast_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0, + fast_eigen_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0, &kin_sub.matrix); gsl_matrix_set_zero(&X_sub.matrix); @@ -3027,7 +3027,7 @@ 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); - fast_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0, + fast_eigen_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0, &kin_sub.matrix); } } |