Étienne Mollier pushed to branch master at Debian Med / umis
Commits:
89807230 by Étienne Mollier at 2023-06-16T22:04:51+02:00
New upstream version 1.0.9
- - - - -
b07bf979 by Étienne Mollier at 2023-06-16T22:04:51+02:00
routine-update: New upstream version
- - - - -
873ac5d7 by Étienne Mollier at 2023-06-16T22:04:52+02:00
Update upstream source from tag 'upstream/1.0.9'
Update to upstream version '1.0.9'
with Debian dir 4d18b79d1dd75bda2594d576809411dc7e225ece
- - - - -
4b29afe4 by Étienne Mollier at 2023-06-16T22:04:53+02:00
routine-update: Standards-Version: 4.6.2
- - - - -
36a31cfb by Étienne Mollier at 2023-06-16T22:09:06+02:00
d/control: add myself to uploaders.
- - - - -
1ad71c1a by Étienne Mollier at 2023-06-16T22:10:26+02:00
d/*.lintian-overrides: update mismatched overrides.
- - - - -
d6d2b8ca by Étienne Mollier at 2023-06-16T22:11:23+02:00
ready to upload to unstable.
- - - - -
6 changed files:
- HISTORY.md
- debian/changelog
- debian/control
- debian/umis-examples.lintian-overrides
- 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!
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+umis (1.0.9-1) unstable; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.6.2 (routine-update)
+ * d/control: add myself to uploaders.
+ * d/*.lintian-overrides: update mismatched overrides.
+
+ -- Étienne Mollier <emollier at debian.org> Fri, 16 Jun 2023 22:10:53 +0200
+
umis (1.0.8-3) unstable; urgency=medium
* Fix watch file
=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
Source: umis
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -9,7 +10,7 @@ Build-Depends: debhelper-compat (= 13),
python3-dev,
python3-setuptools
Build-Depends-Arch: python3-pysam
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/umis
Vcs-Git: https://salsa.debian.org/med-team/umis.git
Homepage: https://github.com/vals/umis
=====================================
debian/umis-examples.lintian-overrides
=====================================
@@ -1,5 +1,4 @@
# These files are needed in compressed and uncompressed form
-umis-examples: compressed-duplicate usr/share/doc/umis/examples/CEL-Seq/SRP036633_1.fastq.gz
-umis-examples: compressed-duplicate usr/share/doc/umis/examples/CEL-Seq/SRP036633_2.fastq.gz
-umis-examples: compressed-duplicate usr/share/doc/umis/examples/tagcount/cb-histogram.txt.gz
-
+umis-examples: compressed-duplicate [usr/share/doc/umis/examples/CEL-Seq/SRP036633_1.fastq.gz]
+umis-examples: compressed-duplicate [usr/share/doc/umis/examples/CEL-Seq/SRP036633_2.fastq.gz]
+umis-examples: compressed-duplicate [usr/share/doc/umis/examples/tagcount/cb-histogram.txt.gz]
=====================================
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/-/compare/bef0f380bf6c4c35dcd9288e12f4d9ea6b7b5265...d6d2b8ca4c55bb149656d6e6bdc9c1b68730789a
--
View it on GitLab: https://salsa.debian.org/med-team/umis/-/compare/bef0f380bf6c4c35dcd9288e12f4d9ea6b7b5265...d6d2b8ca4c55bb149656d6e6bdc9c1b68730789a
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