diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/checkpoint.cpp | 4 | ||||
| -rw-r--r-- | src/checkpoint.h | 3 | ||||
| -rw-r--r-- | src/gemma.cpp | 2 | ||||
| -rw-r--r-- | src/gemma_io.cpp | 25 | ||||
| -rw-r--r-- | src/version.h | 8 |
5 files changed, 35 insertions, 7 deletions
diff --git a/src/checkpoint.cpp b/src/checkpoint.cpp index a37c1be..9bcf53b 100644 --- a/src/checkpoint.cpp +++ b/src/checkpoint.cpp @@ -27,9 +27,9 @@ using namespace std; void checkpoint_run(string msg, string filename, string srcfilename, int line, string funcname) { - is_debug_mode() && std::cerr << "**** DEBUG: checkpoint " << msg << " passed with " << filename << " in " << srcfilename << " at line " << line << " in " << funcname << endl; + is_debug_mode() && std::cerr << "**** DEBUG: checkpoint '" << msg << "' passed with file " << filename << " in " << srcfilename << " at line " << line << " in func " << funcname << endl; if (msg == checkpoint_name) { - cerr << "**** Checkpoint reached: " << msg << " (normal exit)" << endl; + cerr << "**** Checkpoint reached: " << msg << " with file " << filename << " (normal exit)" << endl; exit(0); } } diff --git a/src/checkpoint.h b/src/checkpoint.h index 2792fac..c2457d9 100644 --- a/src/checkpoint.h +++ b/src/checkpoint.h @@ -30,4 +30,7 @@ void checkpoint_run(string msg, string filename, string srcfilename, int line, s #define checkpoint(msg, fname) \ checkpoint_run(msg, fname, __FILE__, __LINE__, __SHOW_FUNC) +#define checkpoint_nofile(msg) \ + checkpoint_run(msg,"none", __FILE__, __LINE__, __SHOW_FUNC) + #endif diff --git a/src/gemma.cpp b/src/gemma.cpp index a50d8ab..6c2b3f4 100644 --- a/src/gemma.cpp +++ b/src/gemma.cpp @@ -84,7 +84,7 @@ void gemma_gsl_error_handler (const char * reason, void GEMMA::PrintHeader(void) { cout << - "GEMMA " << version << " (" << date << ") by Xiang Zhou, Pjotr Prins and team (C) 2012-" << year << endl; + "GEMMA forked executable --- part of PanGEMMA " << version << " (" << date << ") by Xiang Zhou, Pjotr Prins and team (C) 2012-" << year << endl; return; } diff --git a/src/gemma_io.cpp b/src/gemma_io.cpp index 698d3e2..f5a79a2 100644 --- a/src/gemma_io.cpp +++ b/src/gemma_io.cpp @@ -441,6 +441,7 @@ bool ReadFile_pheno(const string &file_pheno, infile.close(); infile.clear(); + checkpoint("read-pheno-file",file_pheno); return true; } @@ -507,6 +508,7 @@ bool ReadFile_cvt(const string &file_cvt, vector<int> &indicator_cvt, infile.close(); infile.clear(); + checkpoint("read-cvt-file",file_cvt); return true; } @@ -633,6 +635,7 @@ bool ReadFile_fam(const string &file_fam, vector<vector<int>> &indicator_pheno, infile.close(); infile.clear(); + checkpoint("read-fam-file",file_fam); return true; } @@ -1062,6 +1065,7 @@ bool ReadFile_bed(const string &file_bed, const set<string> &setSnps, infile.close(); infile.clear(); + checkpoint("read-bed-file",file_bed); return true; } @@ -1292,6 +1296,7 @@ void ReadFile_kin(const string &file_kin, vector<int> &indicator_idv, infile.close(); infile.clear(); + checkpoint("read-kinship-file",file_kin); return; } @@ -1595,6 +1600,7 @@ bool BimbamKin(const string file_geno, const set<string> ksnps, infile.close(); infile.clear(); + checkpoint_nofile("bimbam-kinship-matrix"); return true; } @@ -1736,6 +1742,7 @@ bool PlinkKin(const string &file_bed, vector<int> &indicator_snp, infile.close(); infile.clear(); + checkpoint_nofile("plink-kinship-matrix"); return true; } @@ -1840,6 +1847,7 @@ bool ReadFile_geno(const string file_geno, vector<int> &indicator_idv, infile.clear(); infile.close(); + checkpoint("read-genotypes",file_geno); return true; } @@ -2082,6 +2090,7 @@ bool ReadFile_bed(const string &file_bed, vector<int> &indicator_idv, gsl_vector_free(genotype); infile.clear(); infile.close(); + checkpoint("read-bed-file",file_bed); return true; } @@ -2220,6 +2229,7 @@ bool ReadFile_bed(const string &file_bed, vector<int> &indicator_idv, gsl_vector_free(genotype); infile.clear(); infile.close(); + checkpoint("read-bed2-file",file_bed); return true; } @@ -2288,6 +2298,7 @@ bool ReadFile_est(const string &file_est, const vector<size_t> &est_column, infile.clear(); infile.close(); + checkpoint("read-est-file",file_est); return true; } @@ -2362,6 +2373,7 @@ bool ReadFile_gene(const string &file_gene, vector<double> &vec_read, infile.close(); infile.clear(); + checkpoint("read-gene-exp-file",file_gene); return true; } @@ -2716,6 +2728,7 @@ bool ReadFile_cat(const string &file_cat, map<string, size_t> &mapRS2cat, infile.clear(); infile.close(); + checkpoint("read-category-file",file_cat); return true; } @@ -2746,6 +2759,7 @@ bool ReadFile_mcat(const string &file_mcat, map<string, size_t> &mapRS2cat, } t++; } + checkpoint("read-mcat-file",file_mcat); return true; } @@ -2943,6 +2957,7 @@ bool BimbamKinUncentered(const string &file_geno, const set<string> ksnps, infile.close(); infile.clear(); + checkpoint_nofile("read-uncenterer-kinship-file"); return true; } @@ -3168,6 +3183,7 @@ bool PlinkKin(const string &file_bed, const int display_pace, infile.close(); infile.clear(); + checkpoint("read-plink-kinship-file",file_bed); return true; } @@ -3549,6 +3565,7 @@ void ReadFile_beta(const string &file_beta, infile.clear(); infile.close(); + checkpoint("read-beta-file",file_beta); return; } @@ -3712,6 +3729,7 @@ void ReadFile_beta(const string &file_beta, const map<string, double> &mapRS2wA, infile.clear(); infile.close(); + checkpoint("read-beta2-file",file_beta); return; } @@ -3892,6 +3910,7 @@ void ReadFile_vector(const string &file_vec, gsl_vector *vec) { infile.clear(); infile.close(); + checkpoint("read-vec-file",file_vec); return; } @@ -3919,6 +3938,7 @@ void ReadFile_matrix(const string &file_mat, gsl_matrix *mat) { infile.clear(); infile.close(); + checkpoint("read-matrix-file",file_mat); return; } @@ -3957,6 +3977,7 @@ void ReadFile_matrix(const string &file_mat, gsl_matrix *mat1, infile.clear(); infile.close(); + checkpoint("read-matrix2-file",file_mat); return; } @@ -3983,6 +4004,7 @@ void ReadFile_study(const string &file_study, gsl_matrix *Vq_mat, ni = gsl_vector_get(s, s_vec->size); gsl_vector_free(s); + checkpoint("read-study-file",file_study); return; } @@ -4007,6 +4029,7 @@ void ReadFile_ref(const string &file_ref, gsl_matrix *S_mat, ni = gsl_vector_get(s, s_vec->size); gsl_vector_free(s); + checkpoint("read-ref-file",file_ref); return; } @@ -4098,6 +4121,7 @@ void ReadFile_mstudy(const string &file_mstudy, gsl_matrix *Vq_mat, gsl_matrix_free(Vq_sub); gsl_vector_free(q_sub); gsl_vector_free(s); + checkpoint("read-mstudy-file",file_mstudy); return; } @@ -4185,6 +4209,7 @@ void ReadFile_mref(const string &file_mref, gsl_matrix *S_mat, gsl_matrix_free(S_sub); gsl_matrix_free(Svar_sub); gsl_vector_free(s); + checkpoint("read-mref-file",file_mref); return; } diff --git a/src/version.h b/src/version.h index 25ccfcd..3382003 100644 --- a/src/version.h +++ b/src/version.h @@ -1,5 +1,5 @@ // version.h generated by GEMMA scripts/gen_version_info.sh -#define GEMMA_VERSION "0.98.6" -#define GEMMA_DATE "2022-08-05" -#define GEMMA_YEAR "2022" -#define GEMMA_PROFILE "/gnu/store/8rvid272yb53bgascf5c468z0jhsyflj-profile" +#define GEMMA_VERSION "0.0.1" +#define GEMMA_DATE "2025-01-04" +#define GEMMA_YEAR "2025" +#define GEMMA_PROFILE "/gnu/store/ln160n2kzn791jwgv36yrxlxygjwl9hh-profile" |