change the --keep-nans argument to --remove-nans to change defaults behaviour

jass/__main__.py

@@ -79,7 +79,7 @@ def compute_worktable(args):
     init_table_path = absolute_path_of_the_file(args.init_table_path)
     worktable_path = absolute_path_of_the_file(args.worktable_path, True)
     selected_phenotypes = args.phenotypes
-    remove_nan = not (args.keep_nans)
+    remove_nan = (args.remove_nans)
     significance_treshold = float(args.significance_treshold)
     post_filtering = bool(args.post_filtering)
     custom_loadings = args.custom_loadings
@@ -197,7 +197,7 @@ def get_parser():
     parser_create_pd.add_argument(
         "--worktable-path", required=True, help="path to the worktable file to generate"
     )
-    parser_create_pd.add_argument("--keep-nans", action="store_true", default=True)
+    parser_create_pd.add_argument("--remove-nans", action="store_true", default=False)
     parser_create_pd.add_argument(
         "--manhattan-plot-path",
         required=True,
@@ -344,7 +344,7 @@ def get_parser():
         help="Number of region to load in memory at once",
     )
 
-    parser_create_wt.add_argument("--keep-nans", action="store_true", default=True)
+    parser_create_wt.add_argument("--remove-nans", action="store_true", default=False)
 
     parser_create_wt.add_argument(
         "--chromosome-number",