From e3207cbb0068e1f9580ae5c9c585bc3a2b2c6ca6 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 5 Dec 2025 11:23:47 +0100
Subject: Output is on par with earlier gemma - only allele values are missing

---
 src/lmm.cpp | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

(limited to 'src/lmm.cpp')

diff --git a/src/lmm.cpp b/src/lmm.cpp
index 08b4d41..10e3e53 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -153,7 +153,7 @@ void LMM::WriteFiles() {
     outfile << scientific << setprecision(6);
 
     if (a_mode != M_LMM2) {
-      outfile << st.beta << "\t";
+      outfile << scientific << st.beta << "\t";
       outfile << st.se << "\t";
     }
 
@@ -2103,14 +2103,13 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp,
     auto m = st.markerinfo;
     auto name = m.name;
     auto chr  = m.chr;
-    auto pos  = m.pos;
 
     outfile << chr << "\t";
     outfile << name << "\t";
-    outfile << pos << "\t";
-    auto n_miss = 0;
-    outfile << n_miss << "\t-\t-\t"; // n_miss column
-    // outfile << st.maf << "\t" ;
+    outfile << m.pos << "\t";
+    outfile << m.n_miss << "\t-\t-\t"; // n_miss column + allele1 + allele0
+    outfile << fixed << setprecision(3) << m.maf << "\t";
+    outfile << scientific << setprecision(6);
     if (a_mode != M_LMM2) {
       outfile << st.beta << "\t";
       outfile << st.se << "\t";
@@ -2253,9 +2252,9 @@ void LMM::mdb_calc_gwa(const gsl_matrix *U, const gsl_vector *eval,
 
       // compute maf and n_miss (NAs)
       size_t n_miss = 0; // count NAs: FIXME
-      double maf = compute_maf(ni_total, ni_test, n_miss, gs.data());
+      double maf = compute_maf(ni_total, ni_test, n_miss, gs.data(), indicator_idv);
 
-      markerinfo = MarkerInfo { .name=marker,.chr=chr,.pos=pos,.line_no=num };
+      markerinfo = MarkerInfo { .name=marker,.chr=chr,.pos=pos,.line_no=num,.n_miss=n_miss,.maf=maf };
 
       // cout << "!!!!" << size << marker << ": af" << maf << " " << gs[0] << "," << gs[1] << "," << gs[2] << "," << gs[3] << endl;
     }
-- 
cgit 1.4.1