Adding support for checkpoints and relevant documentation

5 files changed, 82 insertions, 2 deletions

diff --git a/src/checkpoint.cpp b/src/checkpoint.cpp
new file mode 100644
index 0000000..6fcc1a2
--- /dev/null
+++ b/src/checkpoint.cpp
@@ -0,0 +1,34 @@
+/*
+    Copyright © 2025, Pjotr Prins
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program. If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <checkpoint.h>
+
+#include <assert.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <iostream>
+
+#include <param.h>
+
+using namespace std;
+
+void checkpoint(string msg, string filename) {
+    if (msg == checkpoint_name) {
+	cerr << "**** Checkpoint reached: " << msg << " (normal exit)" << endl;
+	exit(0);
+    }
+}
diff --git a/src/checkpoint.h b/src/checkpoint.h
new file mode 100644
index 0000000..7a70855
--- /dev/null
+++ b/src/checkpoint.h
@@ -0,0 +1,31 @@
+/*
+    Checkpoints for pangemma propagators
+
+    Copyright © 2015, Pjotr Prins
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program. If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef __CHECKPOINT_H__
+#define __CHECKPOINT_H__
+
+#include <string>
+
+using namespace std;
+
+extern string checkpoint_name;
+
+void checkpoint(string msg, string filename);
+
+#endif
diff --git a/src/gemma.cpp b/src/gemma.cpp
index c73c174..a50d8ab 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -2,7 +2,7 @@
     Genome-wide Efficient Mixed Model Association (GEMMA)
     Copyright © 2011-2017, Xiang Zhou
     Copyright © 2017, Peter Carbonetto
-    Copyright © 2017-2021, Pjotr Prins
+    Copyright © 2017-2025, Pjotr Prins
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -65,6 +65,8 @@ extern "C" {
 
 using namespace std;
 
+string checkpoint_name;   // -checkpoint switch is global
+
 GEMMA::GEMMA(void) : version(GEMMA_VERSION), date(GEMMA_DATE), year(GEMMA_YEAR) {}
 
 void gemma_gsl_error_handler (const char * reason,
@@ -726,6 +728,7 @@ void GEMMA::PrintHelp(size_t option) {
     cout << " -nind       [num]        read up to num individuals" << endl;
     cout << " -issue      [num]        enable tests relevant to issue tracker" << endl;
     cout << " -legacy                  run gemma in legacy mode" << endl;
+    cout << " -checkpoint [name]       set checkpoint (see pangemma docs)" << endl;
     cout << endl;
   }
 
@@ -1623,6 +1626,14 @@ void GEMMA::Assign(int argc, char **argv, PARAM &cPar) {
     } else if (strcmp(argv[i], "-legacy") == 0) {
       debug_set_legacy_mode(true);
       warning_msg("you are running in legacy mode - support may drop in future versions of gemma");
+    } else if (strcmp(argv[i], "-checkpoint") == 0) {
+      if (argv[i + 1] == NULL || argv[i + 1][0] == '-') {
+        continue;
+      }
+      ++i;
+      str.clear();
+      str.assign(argv[i]);
+      checkpoint_name = str;
     } else {
       cout << "error! unrecognized option: " << argv[i] << endl;
       cPar.error = true;
diff --git a/src/gemma_io.cpp b/src/gemma_io.cpp
index b11bf88..698d3e2 100644
--- a/src/gemma_io.cpp
+++ b/src/gemma_io.cpp
@@ -42,6 +42,7 @@
 #include "gsl/gsl_matrix.h"
 #include "gsl/gsl_vector.h"
 
+#include "checkpoint.h"
 #include "debug.h"
 // #include "eigenlib.h"
 #include "fastblas.h"
@@ -552,6 +553,7 @@ bool ReadFile_bim(const string &file_bim, vector<SNPINFO> &snpInfo) {
 
   infile.close();
   infile.clear();
+  checkpoint("read-bimbam-file",file_bim);
   return true;
 }
 
@@ -869,6 +871,7 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps,
   infile.close();
   infile.clear();
 
+  checkpoint("read-geno-file",file_geno);
   return true;
 }
 
diff --git a/src/param.h b/src/param.h
index e747182..d3ce686 100644
--- a/src/param.h
+++ b/src/param.h
@@ -148,7 +148,8 @@ public:
   string file_weight, file_wsnp, file_wcat;
   string file_out;
   string file_bf, file_hyp;
-  string path_out;
+  string path_out;     // -outdir switch
+    // string checkpoint;   // -checkpoint switch is global
 
   string file_epm;     // Estimated parameter file.
   string file_ebv;     // Estimated breeding value file.