Added checkpoints for file readers

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"