From 93dee1a1c1c0399c4e8deaa03c35d60bc293bd1e Mon Sep 17 00:00:00 2001
From: Neil Shephard <n.shephard@sheffield.ac.uk>
Date: Wed, 27 Nov 2024 14:29:49 +0000
Subject: [PATCH] feature: Adds subparser for creating configuration file

In anticipation of #72 a subparser is added to the `processing.create_parser()` function so that we can write
configuration files with `isoslam create_config`. Still needs a `create_config()` function to load the
`isoslam/default_config.yaml` and then write to disk.
---
 isoslam/processing.py | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/isoslam/processing.py b/isoslam/processing.py
index 0e63be7..8226676 100644
--- a/isoslam/processing.py
+++ b/isoslam/processing.py
@@ -55,6 +55,8 @@ def create_parser() -> arg.ArgumentParser:
     subparsers = parser.add_subparsers(title="program", description="Available programs listed below:", dest="program")
 
     # Create sub-parsers for different stages
+
+    # Process processes all files
     process_parser = subparsers.add_parser(
         "process",
         description="Process all files and run all summary plotting and statistics.",
@@ -83,6 +85,33 @@ def create_parser() -> arg.ArgumentParser:
         "-v", "--vcf-file", dest="vcf_file", type=Path, required=False, help="Path to '.vcf.gz' file."
     )
     process_parser.set_defaults(func=process)
+
+    # Create configuration sub-parser
+    create_config_parser = subparsers.add_parser(
+        "create-config",
+        description="Create a configuration file using the defaults.",
+        help="Create a configuration file using the defaults.",
+    )
+    create_config_parser.add_argument(
+        "-f",
+        "--filename",
+        dest="filename",
+        type=Path,
+        required=False,
+        default="config.yaml",
+        help="Name of YAML file to save configuration to (default 'config.yaml').",
+    )
+    create_config_parser.add_argument(
+        "-o",
+        "--output-dir",
+        dest="output_dir",
+        type=Path,
+        required=False,
+        default="./",
+        help="Path to where the YAML file should be saved (default './' the current directory).",
+    )
+    # create_config_parser.set_defaults(func=create_config)
+
     # Additional parsers for future functionality
     # summarize_counts_parser = subparsers.add_parser(
     #     "summarize",