diff options
Diffstat (limited to 'src/gemma_io.cpp')
| -rw-r--r-- | src/gemma_io.cpp | 8 |
1 files changed, 4 insertions, 4 deletions
diff --git a/src/gemma_io.cpp b/src/gemma_io.cpp index d92dc44..3c71ea6 100644 --- a/src/gemma_io.cpp +++ b/src/gemma_io.cpp @@ -1421,7 +1421,8 @@ bool BimbamKin(const string file_geno, const set<string> ksnps, for (size_t t = 0; t < indicator_snp.size(); ++t) { string line; safeGetline(infile, line).eof(); - if (t % display_pace == 0 || t == (indicator_snp.size() - 1)) { + // if (t % display_pace == 0 || t == (indicator_snp.size() - 1)) { + if (t % display_pace == 0) { ProgressBar("Reading SNPs", t, indicator_snp.size() - 1); } if (indicator_snp[t] == 0) @@ -1511,22 +1512,21 @@ bool BimbamKin(const string file_geno, const set<string> ksnps, if (ns_test % msize != 0) { fast_eigen_dgemm("N", "T", 1.0, Xlarge, Xlarge, 1.0, matrix_kin); } + ProgressBar("Reading SNPs", 100, 100); cout << endl; // scale the kinship matrix enforce_gsl(gsl_matrix_scale(matrix_kin, 1.0 / (double)ns_test)); // and transpose - // FIXME: the following is very slow + // FIXME: the following is not so slow - debug_msg("begin transpose"); for (size_t i = 0; i < ni_total; ++i) { for (size_t j = 0; j < i; ++j) { double d = gsl_matrix_get(matrix_kin, j, i); gsl_matrix_set(matrix_kin, i, j, d); } } - debug_msg("end transpose"); // GSL is faster - and there are even faster methods // enforce_gsl(gsl_matrix_transpose(matrix_kin)); |