Slow odgi depth no paths

slow_odgi/slow_odgi/__main__.py

@@ -1,7 +1,7 @@
 import argparse
 import sys
 import io
-from typing import Dict, Tuple, List
+from typing import Dict, Tuple, List, Optional
 from collections.abc import Callable
 from mygfa import mygfa
 
@@ -58,9 +58,8 @@ def parse_args() -> Tuple[argparse.ArgumentParser, argparse.Namespace]:
     )
     depth_parser.add_argument(
         "--paths",
-        nargs="?",
         help="A file describing the paths you wish to query.",
-        required=True,
+        required=False,
     )
 
     subparsers.add_parser(
@@ -167,7 +166,9 @@ def dispatch(args: argparse.Namespace) -> None:
     # Other functions, which typically print their own output.
     other_funcs: Dict[str, Callable[[mygfa.Graph], object]] = {
         "degree": degree.degree,
-        "depth": lambda g: depth.depth(g, parse_paths(args.paths)),
+        "depth": lambda g: depth.depth(
+            g, parse_paths(args.paths) if args.paths else None
+        ),
         "flatten": lambda g: flatten.flatten(g, f"{args.graph[:-4]}.og"),
         "matrix": matrix.matrix,
         "overlap": lambda g: overlap.overlap(g, parse_paths(args.paths)),

slow_odgi/slow_odgi/depth.py

@@ -1,14 +1,14 @@
-from typing import List
+from typing import List, Optional
 from mygfa import mygfa, preprocess
 
 
-def depth(graph: mygfa.Graph, inputpaths: List[str]) -> mygfa.Graph:
+def depth(graph: mygfa.Graph, inputpaths: Optional[List[str]]) -> mygfa.Graph:
     """The depth of a node is the cardinality of node_step for that node."""
     print("\t".join(["#node.id", "depth", "depth.uniq"]))
     for seg, crossings in preprocess.node_steps(graph).items():
         # Each crossing is a (path name, index on path, direction) tuple.
         # We only want to count crossings that are on input paths.
-        crossings = [c for c in crossings if c[0] in inputpaths]
+        crossings = [c for c in crossings if inputpaths is None or c[0] in inputpaths]
         # For depth.uniq, we need to know how many unique path-names there are.
         uniq_path_names = set(c[0] for c in crossings)
         print("\t".join([seg, str(len(crossings)), str(len(uniq_path_names))]))

slow_odgi/slow_odgi/overlap.py

@@ -1,4 +1,4 @@
-from typing import List
+from typing import List, Optional
 from mygfa import mygfa, preprocess