khmer
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dib-lab
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Hi! I have an issue/question about the trim-low-abund.py script. An example: I have two diffent files -> file_1.fq.gz and file_2.fq.gz The resulting output for file_1.fq.gz is not the same between...
Had to temporarily revert part of commit e94c0d9a65c7f34e44ee205fb1b52997de30b971 to be able to rebuild the `khmer/_oxli/*.cpp` files ``` diff --git a/setup.py b/setup.py index 86291415..eecc8ff0 100755 --- a/setup.py +++ b/setup.py @@ -64,9...
Enable running tests with Pytest 8 https://docs.pytest.org/en/stable/deprecations.html#support-for-tests-written-for-nose Fixes Debian bug https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1063977 ---------------------------------------- > Message from the khmer maintainers: > > *Please provide a description of the pull request above, including...
Ever since Python 3.2, `configparser.SafeConfigParser` has been deprecated in favor of `configparser.ConfigParser`. An alias existed for backward compatibility but the alias was dropped from Python 3.12. The `imp` module was...
Dear khmer team, Amazed at how many efforts have been devoted to such a widely used project/software. As mentioned in the first version of the paper and also many places,...
The error appears to be the same as discussed at https://github.com/pydata/pandas-datareader/issues/969. When I try installing with Python 3.12, I get ``` ~ ❯ python3 -m venv khmerEnv source khmerEnv/bin/activate (khmerEnv)...
ref discussion in: https://github.com/dib-lab/khmer/issues/1927 hi folks, I'm afraid we aren't able to maintain khmer at all moving forward - it's basically been in unmaintained mode since 2018 at the latest....
