change default handling of missing value : the server and the command line...

change default handling of missing value : the server and the command line will keep SNPs with missing phenotypes

jass/__main__.py

@@ -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=False)
+    parser_create_pd.add_argument("--keep-nans", action="store_true", default=True)
     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=False)
+    parser_create_wt.add_argument("--keep-nans", action="store_true", default=True)
 
     parser_create_wt.add_argument(
         "--chromosome-number",