From cb3851a91d63a29b808f44eb91c00df91641e380 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 2 Feb 2024 14:22:06 +0300
Subject: Ensure control file defaults are set up in code.

---
 r_qtl/r_qtl2.py | 5 +++++
 1 file changed, 5 insertions(+)

(limited to 'r_qtl')

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index 1755a05..9127dce 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -28,6 +28,11 @@ def control_data(zfile: ZipFile) -> dict:
         "na.strings": ["NA"],
         "comment.char": "#",
         "sep": ",",
+        **{
+            f"{key}_transposed": False for key in (
+                "geno", "founder_geno", "pheno", "covar", "phenocovar", "gmap",
+                "pmap", "phenose")
+        },
         **(json.loads(zfile.read(files[0]))
             if files[0].endswith(".json")
             else yaml.safe_load(zfile.read(files[0])))
-- 
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