maf not af for prune

Zilong-Li · Dec 22, 2023 · f68eb57 · f68eb57
1 parent a99399c
commit f68eb57
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/src/Utils.cpp b/src/Utils.cpp
@@ -374,7 +374,7 @@ void calc_ld_metrics(std::string fileout,
             double r = (G.col(i).array() * G.col(k).array() * (sds(i) * sds(k))).sum() * df;
             if(r * r > r2_tol)
             {
-                int o = F(k) > F(i) ? i : k;
+                int o = MAF(F(k)) > MAF(F(i)) ? i : k;
                 keep(o) = false;
             }
         }

diff --git a/src/Utils.hpp b/src/Utils.hpp
@@ -40,6 +40,8 @@ typedef unsigned long long uint64;
 using Int1D = std::vector<int>;
 using Int2D = std::vector<Int1D>;
 
+#define MAF(a) ((a)>0.5?(1-a):(a))
+
 struct Line
 {
     std::string data;