From 90451d426124362dfd8ada807b15c733c718eb21 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 5 Dec 2019 14:37:09 -0600
Subject: Fixed issue that caused Y chromosome and mitochondrial markers to
 cause an error

---
 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 5b34e837..3d3f26f3 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -214,7 +214,7 @@ def parse_loco_output(this_dataset, gwa_output_filename):
                 else:
                     marker = {}
                     marker['name'] = line.split("\t")[1]
-                    if line.split("\t")[0] != "X" and line.split("\t")[0] != "X/Y":
+                    if line.split("\t")[0] != "X" and line.split("\t")[0] != "X/Y" and line.split("\t")[0] != "Y" and line.split("\t")[0] != "M":
                         if "chr" in line.split("\t")[0]:
                             marker['chr'] = int(line.split("\t")[0][3:])
                         else:
-- 
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