Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

fix: correctly infer read stats from second mate #152

Merged
merged 2 commits into from
Dec 4, 2023
Merged

Conversation

balajtimate
Copy link
Collaborator

Description

  • Update get_library_stats.py so that the read statistics from the second mate would correctly get inferred
  • Report median as int instead of float (this fixes the issue with the zarp-cli integration htsinfer pipeline, as the results json md5sums wouldn't match unless the median was int)

Fixes #151

Type of change

  • Bug fix (non-breaking change which fixes an issue)

Checklist

Please carefully read these items and tick them off if the statements are true
or do not apply.

  • I have performed a self-review of my own code
  • My code follows the existing coding style, lints and generates no new
    warnings
  • I have added type annotations to all function/method signatures, and I
    have added type annotations for any local variables that are non-trivial,
    potentially ambiguous or might otherwise benefit from explicit typing.
  • I have commented my code in hard-to-understand areas
  • I have added ["Google-style docstrings"] to all new modules, classes,
    methods/functions or updated previously existing ones
  • I have added tests that prove my fix is effective or that my feature
    works
  • New and existing unit tests pass locally with my changes and I have not
    reduced the code coverage relative to the previous state
  • I have updated any sections of the app's documentation that are affected
    by the proposed changes

If for some reason you are unable to tick off all boxes, please leave a
comment explaining the issue you are facing so that we can work on it
together.

Copy link

codecov bot commented Dec 3, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (62fbf72) 100.00% compared to head (fccce2b) 100.00%.

Additional details and impacted files
@@            Coverage Diff            @@
##               dev      #152   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           13        13           
  Lines         1109      1109           
=========================================
  Hits          1109      1109           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@balajtimate balajtimate requested a review from uniqueg December 3, 2023 15:13
@balajtimate balajtimate merged commit 930b741 into dev Dec 4, 2023
21 checks passed
@balajtimate balajtimate deleted the fix_read_stats branch December 4, 2023 09:54
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.

Compare inferred read length statistics to SRA metadata
2 participants