Skip to content

Conversation

@TomCharlesRousseau
Copy link
Member

@TomCharlesRousseau TomCharlesRousseau commented Nov 24, 2025

This PR fixes issue #7 by adding a fallback mechanism for invalid BAM locations.

  • Logs warnings when a location is not recognized
  • Ensures processing continues without crashing

Closes #7

@JosePizarro3
Copy link
Member

There is an extension in VSCode you can use to automatically apply ruff when CTRL+S files: https://marketplace.visualstudio.com/items?itemName=charliermarsh.ruff

This one + the .vscode/settings.json file you have in your repo, should be enough to work, but let me know if for some reason it does not

@coveralls
Copy link

Pull Request Test Coverage Report for Build 19632004616

Details

  • 0 of 7 (0.0%) changed or added relevant lines in 1 file are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage decreased (-0.9%) to 17.886%

Changes Missing Coverage Covered Lines Changed/Added Lines %
src/sigmabam2openbis/parser.py 0 7 0.0%
Totals Coverage Status
Change from base Build 19435655091: -0.9%
Covered Lines: 22
Relevant Lines: 123

💛 - Coveralls

@TomCharlesRousseau TomCharlesRousseau merged commit fdcb594 into main Nov 24, 2025
7 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

Handle invalid BAM locations by applying fallback and logging warnings

4 participants