From cf4f018bd350c8202aef2ee085a2c536097895b4 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 26 Nov 2025 13:26:54 +0100
Subject: Fix progress bar and test larger file

---
 src/gemma_io.cpp | 4 ++--
 src/lmm.cpp      | 3 ++-
 2 files changed, 4 insertions(+), 3 deletions(-)

(limited to 'src')

diff --git a/src/gemma_io.cpp b/src/gemma_io.cpp
index 3bec483..3826cea 100644
--- a/src/gemma_io.cpp
+++ b/src/gemma_io.cpp
@@ -61,7 +61,7 @@ void ProgressBar(string str, double p, double total, double ratio) {
   const double progress = (100.0 * p / total);
   const uint barsize = (int)(progress / 2.0); // characters
   // cout << barsize << endl;
-  // cout << str << " ";
+  cout << str << " ";
   // cout << p << "/" << total << endl;
   assert(barsize < 101); // corrupted data somehow
   if (barsize > 0) {
@@ -1348,7 +1348,7 @@ void ReadFile_kin(const string &file_kin, vector<int> &indicator_idv,
 
   infile.close();
   infile.clear();
-  checkpoint("read-kinship-file",file_kin);
+  checkpoint("end-read-file-kin",file_kin);
 
   return;
 }
diff --git a/src/lmm.cpp b/src/lmm.cpp
index fb3a255..1ef3990 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -1723,6 +1723,7 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp,
 
     gsl_matrix_set_zero(Xlarge);
     for (size_t i = 0; i < l; i++) {
+      ProgressBar("GWA compute   ", i, l - 1);
       // for each snp batch item extract transformed genotype:
       gsl_vector_view UtXlarge_col = gsl_matrix_column(UtXlarge, i);
       gsl_vector_safe_memcpy(Utx, &UtXlarge_col.vector);
@@ -1850,7 +1851,7 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp,
   }
 
   batch_compute(c % msize);
-  ProgressBar("Reading SNPs", num_snps - 1, num_snps - 1);
+  ProgressBar("Computed      ", num_snps - 1, num_snps - 1);
   // cout << "Counted SNPs " << c << " sumStat " << sumStat.size() << endl;
   cout << endl;
   checkpoint_nofile("end-lmm-analyze");
-- 
cgit 1.4.1