Output is on par with earlier gemma - only allele values are missing

1 files changed, 5 insertions, 3 deletions

diff --git a/src/mathfunc.cpp b/src/mathfunc.cpp
index f132e6e..c82872e 100644
--- a/src/mathfunc.cpp
+++ b/src/mathfunc.cpp
@@ -666,12 +666,14 @@ std::tuple<size_t, size_t, size_t> compute_ratio(size_t ni_total, const gsl_vect
   return {n_0,n_1,n_2};
 }
 
-double compute_maf(size_t ni_total, size_t ni_test, size_t n_miss, const double *gs) {
+double compute_maf(size_t ni_total, size_t ni_test, size_t n_miss, const double *gs, const vector<int> &indicator) {
   double maf = 0.0;
 
   for (size_t i = 0; i < ni_total; ++i) { // read genotypes
-    double geno = gs[i];
-    maf += geno; // 0..2 range
+    if (indicator[i]) {
+      double geno = gs[i];
+      maf += geno; // 0..2 range
+    }
   }
   maf /= 2.0 * (double)(ni_test - n_miss); // Assumption is that geno value is between 0 and 2. FIXME
   return maf;