From a59bc9ac72e3edd27ff1b36a70c001c8d1949c56 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 28 Sep 2020 13:47:21 +0100
Subject: Add note

---
 src/gemma.cpp    | 4 ++--
 src/gemma_io.cpp | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/gemma.cpp b/src/gemma.cpp
index 7b955cd..1938e56 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -1129,7 +1129,7 @@ void GEMMA::Assign(int argc, char **argv, PARAM &cPar) {
         break;
       }
       if (argv[i + 1] == NULL || argv[i + 1][0] == '-') {
-        cPar.a_mode = M_KIN;
+        cPar.a_mode = M_KIN; // default
         continue;
       }
       ++i;
@@ -1913,7 +1913,7 @@ void GEMMA::BatchRun(PARAM &cPar) {
 
     if (cPar.a_mode == M_KIN) {
       cPar.WriteMatrix(G, "cXX");
-    } else {
+    } else { // M_KIN2
       cPar.WriteMatrix(G, "sXX");
     }
 
diff --git a/src/gemma_io.cpp b/src/gemma_io.cpp
index 3302bad..b4f8d39 100644
--- a/src/gemma_io.cpp
+++ b/src/gemma_io.cpp
@@ -1671,7 +1671,7 @@ bool PlinkKin(const string &file_bed, vector<int> &indicator_snp,
 
     gsl_vector_add_constant(geno, -1.0 * geno_mean);
 
-    if (k_mode == 2 && geno_var != 0) {
+    if (k_mode == 2 && geno_var != 0) { // k_mode is a_mode-20
       gsl_vector_scale(geno, 1.0 / sqrt(geno_var));
     }
     gsl_vector_view Xlarge_col = gsl_matrix_column(Xlarge, ns_test % msize);
-- 
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