From f4ec4a98a52ef6880edbc1191565dcb2263aceb1 Mon Sep 17 00:00:00 2001
From: Sebastian Dall <semoda@bio.aau.dk>
Date: Mon, 11 Sep 2023 13:19:23 +0200
Subject: [PATCH] added optional arguments to run_pycoverm which failed in the
 avamb workflow rule bam_abundance

---
 vamb/parsebam.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/vamb/parsebam.py b/vamb/parsebam.py
index b2f73812..cfd2b132 100644
--- a/vamb/parsebam.py
+++ b/vamb/parsebam.py
@@ -194,9 +194,9 @@ def chunkwise_loading(
     def run_pycoverm(
         paths: list[Path],
         minid: float,
-        target_refhash: Optional[bytes],
-        target_identifiers: Optional[Iterable[str]],
         mask: _np.ndarray,
+        target_refhash: Optional[bytes] = None,
+        target_identifiers: Optional[Iterable[str]] = None,
     ) -> tuple[_np.ndarray, bytes]:
         (headers, coverage) = pycoverm.get_coverages_from_bam(
             [str(p) for p in paths],