bumped version

.vscode/settings.json

@@ -13,7 +13,6 @@
         "bioconda",
         "CHROM",
         "modvcfsamples",
-        "ploidy",
         "pytest",
         "pyvcf",
         "vcfpy",

src/modvcfsamples/cli.py

@@ -8,7 +8,6 @@ def run(
     vcfs: list[str],
     only: list[str],
     gt: Union[int, None],
-    rename_samples: Union[list[str], None],
     filename_replace: Union[str, None],
     output_dir: str,
 ):
@@ -23,14 +22,6 @@ def run(
         if gt is not None:
             modified_vcfs = sample.normalize_gt_to_length(modified_vcfs, gt)
 
-        if rename_samples is not None:
-            modified_vcfs, modified_header = sample.replace_sample_names(
-                modified_vcfs,
-                modified_header,
-                rename_samples[0],
-                rename_samples[1],
-            )
-
         if filename_replace is not None:
             modified_vcfs, modified_header = sample.replace_sample_names(
                 modified_vcfs,
@@ -57,7 +48,7 @@ def main():
     parser.add_argument(
         "--gt-norm",
         "-g",
-        help="Resizes haploid genotypes to n-ploidy by repeating it.",
+        help="Resizes haploid genotypes to n-ploid by repeating it.",
         type=int,
         required=False,
     )
@@ -69,17 +60,6 @@ def main():
         type=str,
         required=False,
     )
-
-    parser.add_argument(
-        "--replace-name",
-        "p",
-        help="Similar to '--filename-replace', you may choose what to replace with what. "
-        "Ex. '-p a b' will replace all 'a' characters in a sample name with 'b'.",
-        nargs=2,
-        type=str,
-        required=False,
-    )
-
     parser.add_argument(
         "--filename-replace",
         "-e",
@@ -91,14 +71,7 @@ def main():
     )
 
     args = parser.parse_args()
-    run(
-        args.vcfs,
-        args.only,
-        args.gt_norm,
-        args.replace_name,
-        args.filename_replace,
-        args.output_dir,
-    )
+    run(args.vcfs, args.only, args.gt_norm, args.filename_replace, args.output_dir)
 
 
 if __name__ == "__main__":