Update sort.py

hyphaltip · web-flow · commit cfee87b358c2 · 2025-07-06T14:10:39.000-07:00
set a default minimum length for contigs in the argument part as well as the function defaults to minlen=0
diff --git a/funannotate/sort.py b/funannotate/sort.py
@@ -69,7 +69,7 @@ def __init__(self, prog):
         help="Try to simplify headers, split at first space",
     )
     parser.add_argument(
-        "-m", "--minlen", type=int, help="Contigs shorter than threshold are discarded"
+        "-m", "--minlen", type=int, default=0, help="Contigs shorter than threshold are discarded"
     )
     args = parser.parse_args(args)
 

Original file line number	Diff line number	Diff line change
`@@ -69,7 +69,7 @@ def __init__(self, prog):`
`69`	`69`	`help="Try to simplify headers, split at first space",`
`70`	`70`	`)`
`71`	`71`	`parser.add_argument(`
`72`		`- "-m", "--minlen", type=int, help="Contigs shorter than threshold are discarded"`
	`72`	`+ "-m", "--minlen", type=int, default=0, help="Contigs shorter than threshold are discarded"`
`73`	`73`	`)`
`74`	`74`	`args = parser.parse_args(args)`
`75`	`75`