feat: output read orientation fractions to json

balajtimate commented 1 month ago

Description

Add json output of the fractions of read orientation (number of mapped reads, fraction of SF, SR and final orientation) per input sample
Clean up debug logging

Type of change

[X] New feature (non-breaking change which adds functionality)

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 month ago

Codecov Report

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

Project coverage is 100.00%. Comparing base (d3cbe0e) to head (6828a24). Report is 1 commits behind head on dev.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #169 +/- ## ========================================= Coverage 100.00% 100.00% ========================================= Files 13 13 Lines 1142 1164 +22 ========================================= + Hits 1142 1164 +22 ```

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balajtimate commented 1 month ago

No docs update needed right now. I'll rewrite the full documentation on RtD, there it will be included.

uniqueg commented 1 month ago

No docs update needed right now. I'll rewrite the full documentation on RtD, there it will be included.

Oh, never mind. Had only a brief look and thought that you'd ended up including the stats in the main output after all. But seeing now that you're just writing it into a separate file, as discussed 👍

zavolanlab / htsinfer