From 2701a364228d91ba2c52f511ad6619d070e2235b Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 4 Jan 2025 01:59:26 -0600
Subject: Show checkpoints passed with -debug switch

---
 VERSION              |  2 +-
 doc/code/pangemma.md | 14 ++++++++++++++
 src/checkpoint.cpp   |  3 ++-
 src/checkpoint.h     |  6 ++++--
 4 files changed, 21 insertions(+), 4 deletions(-)

diff --git a/VERSION b/VERSION
index 57c861a..8acdd82 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.98.5
+0.0.1
diff --git a/doc/code/pangemma.md b/doc/code/pangemma.md
index d65245e..223e2ae 100644
--- a/doc/code/pangemma.md
+++ b/doc/code/pangemma.md
@@ -204,6 +204,20 @@ multiple outputs - in that case we may add filenames. And exits with:
 **** Checkpoint reached: read-geno-file (normal exit)
 ```
 
+# List check points
+
+When you compile PanGEMMA with debug information
+
+```
+make debug
+```
+
+and run a computation with the '-debug' switch it should output the check-points it passes. You should see something like
+
+```
+**** DEBUG: checkpoint read-geno-file passed with ./example/mouse_hs1940.geno.txt.gz in src/gemma_io.cpp at line 874 in ReadFile_geno
+```
+
 # Other
 
 ## Example
diff --git a/src/checkpoint.cpp b/src/checkpoint.cpp
index 6fcc1a2..a37c1be 100644
--- a/src/checkpoint.cpp
+++ b/src/checkpoint.cpp
@@ -26,7 +26,8 @@
 
 using namespace std;
 
-void checkpoint(string msg, string filename) {
+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;
     if (msg == checkpoint_name) {
 	cerr << "**** Checkpoint reached: " << msg << " (normal exit)" << endl;
 	exit(0);
diff --git a/src/checkpoint.h b/src/checkpoint.h
index 7a70855..2792fac 100644
--- a/src/checkpoint.h
+++ b/src/checkpoint.h
@@ -20,12 +20,14 @@
 #ifndef __CHECKPOINT_H__
 #define __CHECKPOINT_H__
 
-#include <string>
+#include <debug.h>
 
 using namespace std;
 
 extern string checkpoint_name;
 
-void checkpoint(string msg, string filename);
+void checkpoint_run(string msg, string filename, string srcfilename, int line, string funcname);
 
+#define checkpoint(msg, fname)						\
+    checkpoint_run(msg, fname, __FILE__, __LINE__, __SHOW_FUNC)
 #endif
-- 
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