Ecosyste.ms: Issues

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GitHub / rki-mf1/breakfast issues and pull requests

#24 - Bump all deps, including python (>=3.11,<3.13)

Pull Request - State: closed - Opened by matthuska 16 days ago

#23 - Bump dependabot mentioned deps, bump version

Pull Request - State: closed - Opened by matthuska 16 days ago

#22 - Update dependencies, resolve dependabot alerts

Issue - State: closed - Opened by matthuska 16 days ago

#21 - Ultrafast and accurate sequence alignment and clustering of viral genomes

Issue - State: open - Opened by hoelzer 5 months ago
Labels: documentation

#19 - Update dependencies to deal with joblib security advisory

Pull Request - State: closed - Opened by matthuska about 2 years ago

#18 - Visalize or summarize the results

Issue - State: open - Opened by matthuska about 2 years ago

#17 - Feature/py39

Pull Request - State: closed - Opened by matthuska over 2 years ago

#16 - Require Python 3.10+ only instead of 3.9 and 3.10

Pull Request - State: closed - Opened by matthuska over 2 years ago

#15 - Create output cache dir if it doesn't exist. Depends on PR #14.

Pull Request - State: closed - Opened by matthuska over 2 years ago

#13 - Check for duplicates of sequence IDs

Issue - State: closed - Opened by denisbeslic over 2 years ago
Labels: enhancement

#12 - Add option to show only sequences where the pairwise distance is below max-dist

Issue - State: open - Opened by denisbeslic over 2 years ago
Labels: enhancement

#11 - Exporting the pickle file to a non-existing directory

Issue - State: closed - Opened by denisbeslic over 2 years ago
Labels: bug

#10 - Submat-batches can lead to non-stable cluster IDs

Issue - State: open - Opened by denisbeslic over 2 years ago
Labels: bug

#9 - Feature/speedup submat batches tweaked

Pull Request - State: closed - Opened by matthuska over 2 years ago

#8 - Speedup by splitting up sparse matrix into batches

Pull Request - State: closed - Opened by denisbeslic over 2 years ago - 4 comments

#7 - Add contributing docs and update the README

Pull Request - State: closed - Opened by matthuska over 2 years ago

#6 - Feature/caching

Pull Request - State: closed - Opened by denisbeslic over 2 years ago

#5 - Rewrite caching to handle deletions, modifications, reordering, etc

Pull Request - State: closed - Opened by matthuska over 2 years ago

#4 - Fix/caching delete

Pull Request - State: closed - Opened by matthuska over 2 years ago

#3 - Additional stats about intra- and inter-cluster distance in the result file

Issue - State: open - Opened by denisbeslic almost 3 years ago
Labels: enhancement

#2 - Automated Testing and stable Cluster IDs

Pull Request - State: closed - Opened by denisbeslic about 3 years ago

#1 - Implement function to deal with overlapping Indels

Issue - State: open - Opened by denisbeslic about 3 years ago
Labels: enhancement