Bugfix: Create out_dir/tmp in parsebam if needed

Temp files from PyCoverM are stored in out_dir/tmp/pycoverm, but the tmp directory was not created by the parsebam module. This led to a failure to make the pycoverm dir, crashing Vamb. Fix issue #167
RasmussenLab · Apr 28, 2023 · b486b6f · b486b6f
1 parent efa3e5a
commit b486b6f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,8 @@
 # Changelog
 
+## v4.1.1
+* Create tmp directory in parsebam if needed for pycoverm (issue # 167)
+
 ## v4.1.0
 * Fix typo in output AAE_Z cluster names. They are now called e.g. "aae_z_1"
   instead of "aae_z1"

diff --git a/vamb/__init__.py b/vamb/__init__.py
@@ -19,7 +19,7 @@
 7) Split bins using vamb.vambtools
 """
 
-__version__ = (4, 1, 0)
+__version__ = (4, 1, 1)
 
 from . import vambtools
 from . import parsebam

diff --git a/vamb/parsebam.py b/vamb/parsebam.py
@@ -164,7 +164,7 @@ def chunkwise_loading(
         target_refhash: Optional[bytes],
         mask: _np.ndarray,
     ) -> A:
-        _os.mkdir(cache_directory)
+        _os.makedirs(cache_directory)
 
         chunks = [
             (i, min(len(paths), i + nthreads)) for i in range(0, len(paths), nthreads)