1 files changed, 8 insertions, 7 deletions

diff --git a/src/gemma_io.cpp b/src/gemma_io.cpp
index ef02429..cfa92d1 100644
--- a/src/gemma_io.cpp
+++ b/src/gemma_io.cpp
@@ -413,28 +413,28 @@ bool ReadFile_pheno(const string &file_pheno,
   double p;
 
   vector<double> pheno_row;
-  vector<int> ind_pheno_row;
+  vector<int> indicator_pheno_row;
 
   size_t p_max = *max_element(p_column.begin(), p_column.end());
   map<size_t, size_t> mapP2c;
   for (size_t i = 0; i < p_column.size(); i++) {
     mapP2c[p_column[i]] = i;
     pheno_row.push_back(-9);
-    ind_pheno_row.push_back(0);
+    indicator_pheno_row.push_back(0);
   }
 
   while (!safeGetline(infile, line).eof()) {
     ch_ptr = strtok((char *)line.c_str(), " ,\t");
     size_t i = 0;
     while (i < p_max) {
-      enforce_msg(ch_ptr,"Number of phenotypes in pheno file do not match phenotypes in geno file");
+      enforce_msg(ch_ptr,"Number of phenotypes in pheno file do not match selected columns");
       if (mapP2c.count(i + 1) != 0) {
         if (strcmp(ch_ptr, "NA") == 0) {
-          ind_pheno_row[mapP2c[i + 1]] = 0;
+          indicator_pheno_row[mapP2c[i + 1]] = 0; // skip this trait row
           pheno_row[mapP2c[i + 1]] = -9;
         } else {
           p = atof(ch_ptr);
-          ind_pheno_row[mapP2c[i + 1]] = 1;
+          indicator_pheno_row[mapP2c[i + 1]] = 1; // use this trait row
           pheno_row[mapP2c[i + 1]] = p;
         }
       }
@@ -442,7 +442,7 @@ bool ReadFile_pheno(const string &file_pheno,
       ch_ptr = strtok(NULL, " ,\t");
     }
 
-    indicator_pheno.push_back(ind_pheno_row);
+    indicator_pheno.push_back(indicator_pheno_row);
     pheno.push_back(pheno_row);
   }
 
@@ -2422,7 +2422,8 @@ bool ReadFile_est(const string &file_est, const vector<size_t> &est_column,
 }
 
 bool CountFileLines(const string &file_input, size_t &n_lines) {
-  debug_msg("entered");
+  checkpoint("count-lines",file_input);
+
   igzstream infile(file_input.c_str(), igzstream::in);
   if (!infile) {
     cout << "error! fail to open file: " << file_input << endl;