Code review

[vincent-octo]

Suggestions

1. Use pathlib instead of os.path.

   • Replacing os.path.join():

     os.path.join(dir_path, "test", "raw_data_test.txt")

     becomes

     dir_path / "test" / "raw_data_test.txt"

   • Using type=Path in argparse:

     parser.add_argument("--out", type=str)

     becomes

     from pathlib import Path
     parser.add_argument("--out", type=Path)

2. Be consistent about formatting code.

   In the current code there is sometimes 0, or 1, or 2 whitespaces in function calls:

   https://github.com/FINNGEN/kanta_lab_preprocessing/blob/6eef71523f9f9b424751cdce0a073a802b05d435/finngen_qc/main.py#L91

   Sometimes no new line: https://github.com/FINNGEN/kanta_lab_preprocessing/blob/6eef71523f9f9b424751cdce0a073a802b05d435/finngen_qc/main.py#L120 and sometimes yes new line: https://github.com/FINNGEN/kanta_lab_preprocessing/blob/6eef71523f9f9b424751cdce0a073a802b05d435/finngen_qc/main.py#L124-L125

   Could use a code formatter to automatically and consistently fix this (e.g. ruff)