From 32a5367f0a0a00bec7e610b74abc899521a75fa5 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 1 Dec 2025 11:23:04 +0100
Subject: Almost ready to run GWA

---
 src/param.cpp | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

(limited to 'src/param.cpp')

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.
-- 
cgit 1.4.1