From 2ee943581dc1e0d508a919eab8f8bdf3d73b2b5e Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi <fredmanglis@gmail.com>
Date: Mon, 28 Sep 2026 12:29:24 -0500
Subject: Add format-specific CLI options for CSV files.

---
 scripts/genotypes/preprocess_csv_collect_info.py | 25 +++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/scripts/genotypes/preprocess_csv_collect_info.py b/scripts/genotypes/preprocess_csv_collect_info.py
index eaad1d7..b4b627c 100644
--- a/scripts/genotypes/preprocess_csv_collect_info.py
+++ b/scripts/genotypes/preprocess_csv_collect_info.py
@@ -159,17 +159,40 @@ if __name__ == "__main__":
                     "basic file information and statistics.")))
 
         parser.add_argument(
-            "csv-file",
+            "csv_file",
             metavar="CSV-FILE",
             type=Path, #file_exists,
             help="The CSV file to process.")
 
+        ## format-specific arguments
         parser.add_argument(
             "--is-transposed",
             action="store_true",
             default=False,
             help="Are the rows and columns in the CSV file flipped?")
 
+        parser.add_argument(
+            "--separator",
+            metavar="FIELDS-SEPARATOR",
+            type=str,
+            default=",",
+            help=(
+                "The character acting as the fields' separator in the CSV file."))
+
+        parser.add_argument(
+            "--comment_char",
+            metavar="COMMENTS-CHARACTER",
+            type=str,
+            default="#",
+            help="The character indicating a comment line.")
+
+        parser.add_argument(
+            "--na_strings",
+            metavar="MISSING-VALUES-STRING",
+            action="append",
+            type=str,
+            default=["-", "NA", "N/A"],
+            help="The character indicating a comment line.")
         return parser.parse_args()
 
 
-- 
cgit 1.4.1