From 8f303cfc8a7bfc3c2520f1706c249485c848ce98 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sat, 25 Nov 2023 20:19:25 +0000
Subject: Fix bug caused by NaN p-values in GEMMA mapping

---
 wqflask/wqflask/marker_regression/gemma_mapping.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 5d424c97..47ad5638 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -234,7 +234,7 @@ def parse_loco_output(this_dataset, gwa_output_filename, loco="True"):
                     marker['p_value'] = float(line.split("\t")[10])
                     marker['additive'] = -(float(line.split("\t")[7])/2)
                     if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
-                        marker['lod_score'] = 0
+                        marker['lod_score'] = marker['p_value'] = 0
                     else:
                         marker['lod_score'] = -math.log10(marker['p_value'])
                     marker_obs.append(marker)
-- 
cgit 1.4.1