[med-svn] [Git][med-team/umis][upstream] New upstream version 1.0.9

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / umis


Commits:
89807230 by Étienne Mollier at 2023-06-16T22:04:51+02:00
New upstream version 1.0.9
- - - - -


3 changed files:

- HISTORY.md
- setup.py
- umis/umis.py


Changes:

=====================================
HISTORY.md
=====================================
@@ -1,3 +1,8 @@
+## 1.10.0 (in progress)
+
+## 1.0.9 
+- Support dual UMI indexes with bamtag.
+
 ## 1.0.8
 - Add support for dual UMI indexes. Thanks @lbeltrame!
 


=====================================
setup.py
=====================================
@@ -8,7 +8,7 @@ def read(fname):
 
 setup(
         name='umis',
-        version='1.0.8',
+        version='1.0.9',
         description='Package for estimating UMI counts in Transcript Tag Counting data.',
         packages=find_packages(),
         install_requires=['click', 'pysam>=0.8.3', 'pandas', 'regex', 'scipy', 'toolz'],


=====================================
umis/umis.py
=====================================
@@ -24,7 +24,7 @@ import numpy as np
 import scipy.io, scipy.sparse
 import click
 
-VERSION = "1.0.7"
+VERSION = "1.0.9"
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
@@ -157,7 +157,8 @@ def construct_transformed_regex(annotations):
     if "cellular" in annotations:
         re_string += ":CELL_(?P<CB>.*)"
     if "molecular" in annotations:
-        re_string += ":UMI_(?P<MB>\w*)"
+        # Detect dual UMIs spaced with either _ or - if present
+        re_string += ':UMI_(?P<MB>\w[-_\w]*)'
     if "sample" in annotations:
         re_string += ":SAMPLE_(?P<SB>\w*)"
     if re_string == ".*":



View it on GitLab: https://salsa.debian.org/med-team/umis/-/commit/898072302f723cdaca499a1c4bd92771952ec094

-- 
View it on GitLab: https://salsa.debian.org/med-team/umis/-/commit/898072302f723cdaca499a1c4bd92771952ec094
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