Almost ready to run GWA

1 files changed, 8 insertions, 3 deletions

diff --git a/src/param.cpp b/src/param.cpp
index a81d18f..45904cd 100644
--- a/src/param.cpp
+++ b/src/param.cpp
@@ -227,8 +227,6 @@ void PARAM::ReadFiles(void) {
       indicator_idv.push_back(k);
     }
 
-    ns_test = 0; // number of snps to test
-
     return;
   }
 
@@ -339,7 +337,14 @@ void PARAM::ReadFiles(void) {
   }
   // lmdb-type genotype file:
   if (is_mdb && !file_geno.empty()) {
-    ns_total = indicator_snp.size();
+    if (!file_kin.empty()) { // GWA
+      // Phenotype file before genotype file. Already done this(?!)
+      if (ReadFile_pheno(file_pheno, indicator_pheno, pheno, p_column) == false) {
+        error = true;
+      }
+      ProcessInclusionIndicators();
+      ns_total = indicator_snp.size();
+    }
   }
 
   // Read genotype file for multiple PLINK files.