fix: add processed sample paths to mapping

balajtimate commented 1 year ago

Description

Add the paths to the processed subset of samples to the mapping function in get_library_type.py, so that STAR makes use of them instead of the original (unprocessed) samples, when aligning to determinate the mate relationship.

Fixes #149

Type of change

[X] 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.

[X] I have performed a self-review of my own code
[X] My code follows the existing coding style, lints and generates no new warnings
[X] 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.
[X] I have commented my code in hard-to-understand areas
[X] I have added ["Google-style docstrings"] to all new modules, classes, methods/functions or updated previously existing ones
[X] I have added tests that prove my fix is effective or that my feature works
[X] New and existing unit tests pass locally with my changes and I have not reduced the code coverage relative to the previous state
[X] 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.

codecov[bot] commented 1 year ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (8443c05) 100.00% compared to head (4c33968) 100.00%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #150 +/- ## ========================================= Coverage 100.00% 100.00% ========================================= Files 13 13 Lines 1108 1109 +1 ========================================= + Hits 1108 1109 +1 ```

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uniqueg commented 1 year ago

Hmm, coverage test is failing. Maybe you need to update the unit tests (or add one)?

balajtimate commented 1 year ago

I'm not sure why, the detailed coverage run says 100% (also for the PR). Can it be rerun?

uniqueg commented 1 year ago

Really weird. And no, I don't know how to rerun it without rerunning all the tests. Well, I think I'll just merge it then. If it persists, we can still investigate

zavolanlab / htsinfer