Fixed never-ending run when analyzing only a single SNP, ref

  https://groups.google.com/forum/#!topic/gemma-discussion/a-ommTiucC8

2 files changed, 14 insertions, 2 deletions

diff --git a/src/io.cpp b/src/io.cpp
index fb0f0e7..7e682b3 100644
--- a/src/io.cpp
+++ b/src/io.cpp
@@ -52,10 +52,17 @@ using namespace std;
 // Print progress bar.
 void ProgressBar(string str, double p, double total, double ratio) {
   assert(p<=total);
+  assert(p>=0);
+  if (total <= 0.0) return;
   const double progress = (100.0 * p / total);
   const uint barsize = (int)(progress / 2.0); // characters
-  cout << str << " ";
-  cout << std::string(barsize,'=');
+  // cout << barsize << endl;
+  // cout << str << " ";
+  // cout << p << "/" << total << endl;
+  assert(barsize < 101); // corrupted data somehow
+  if (barsize > 0) {
+    cout << std::string(barsize,'=');
+  }
   cout << std::string(50-barsize,' ');
   cout << setprecision(0) << fixed << " " << progress << "%";
   if (ratio != -1.0)
diff --git a/src/lmm.cpp b/src/lmm.cpp
index 99a8436..0102ac0 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -1365,6 +1365,11 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp,
   };
 
   const auto num_snps = indicator_snp.size();
+  enforce_msg(num_snps > 0,"Zero SNPs to process - data corrupt?");
+  if (num_snps < 50) {
+    cerr << num_snps << " SNPs" << endl;
+    warning_msg("very few SNPs processed");
+  }
   const size_t progress_step = (num_snps/50>d_pace ? num_snps/50 : d_pace);
 
   for (size_t t = 0; t < num_snps; ++t) {