From 98545d91072ab6e6809fb7b45d565daec5e4f753 Mon Sep 17 00:00:00 2001
From: Haibao Tang <tanghaibao@gmail.com>
Date: Fri, 12 Apr 2024 10:47:02 -0700
Subject: [PATCH] update inbreeding formula

---
 jcvi/apps/pedigree.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/jcvi/apps/pedigree.py b/jcvi/apps/pedigree.py
index d91f9f85..57ceaceb 100644
--- a/jcvi/apps/pedigree.py
+++ b/jcvi/apps/pedigree.py
@@ -84,12 +84,8 @@ def inbreeding_coef(self, s: str) -> float:
         """
         genotype = self[s]
         ploidy = len(genotype)
-        pairs = ploidy * (ploidy - 1) // 2
-        counter = Counter(genotype)
-        collisions = 0
-        for count in counter.values():
-            collisions += count * (count - 1) // 2
-        return collisions / pairs
+        unique = len(set(genotype))
+        return 1 - unique / ploidy
 
 
 def simulate_one_iteration(ped: Pedigree, ploidy: int) -> GenotypeCollection: