From 507246a7a1695cd86202aaead960ea36e26bae60 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Thu, 9 Mar 2023 15:05:10 +0100
Subject: [PATCH] [fix] nucleotide diversity - account also for reference base

---
 workflow/scripts/compute_diversity_measures.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/workflow/scripts/compute_diversity_measures.py b/workflow/scripts/compute_diversity_measures.py
index ad7ae01e..d0939906 100644
--- a/workflow/scripts/compute_diversity_measures.py
+++ b/workflow/scripts/compute_diversity_measures.py
@@ -51,8 +51,11 @@ def population_nucleotide_diversity(df_mutations, length):
         if N == 0:
             continue
         freq = df_temp["frequency"].to_numpy()
+        ref_freq = 1 - freq.sum()
+
         position_pnd = freq**2
-        postion_pi = ( 1 - position_pnd.sum() )
+        postion_pi = ( 1 - (position_pnd.sum() + ref_freq**2))* N / (N-1 )
+
         pi += postion_pi
 
     return float(pi / length)