1 files changed, 7 insertions, 5 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index 13ac355..1755a05 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -24,16 +24,18 @@ def control_data(zfile: ZipFile) -> dict:
     if num_files > 1:
         raise InvalidFormat("Found more than one possible control file.")
 
-    return (json.loads(zfile.read(files[0]))
+    return {
+        "na.strings": ["NA"],
+        "comment.char": "#",
+        "sep": ",",
+        **(json.loads(zfile.read(files[0]))
             if files[0].endswith(".json")
             else yaml.safe_load(zfile.read(files[0])))
+    }
 
 def replace_na_strings(cdata, val):
     """Replace values indicated in `na.strings` with `None`."""
-    nastrings = cdata.get("na.strings")
-    if bool(nastrings):
-        return (None if val in nastrings else val)
-    return val
+    return (None if val in cdata.get("na.strings", ["NA"]) else val)
 
 def with_non_transposed(zfile: ZipFile,
                         member_key: str,