feat: add tax_id parameter

Description

To have better control over the read orientation inference process, allow users to define the organism of the given sample, instead of inferring it. When the organism ID is given, the transcripts file is filtered based on that organism, and the filtered file is used for to infer the orientation.

Add parameter --org-id (int) to specify the taxonomy ID of the organism to map the reads against
Add function to find the short name belonging to the given org-id, to be reported in the results; if org-id is not found in transcript list, infer it
Add tests
Update README.md and .gitignore
Fix typo in get_read_layout.py and pylint config, remove unused option value 'C0330'
Replace .json method with .model_dump_json for Pydantic version >2 in htsinfer.py (in connection to #146)

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.

zavolanlab / htsinfer