fix!: Edit logic in genomic breakpoint validator in exon_genomic_coords.py

[jarbesfeld]

closes #404

• Introduces a 150bp extension between the genomic coordinates for the start and end exons in a transcript. Breakpoints that occur beyond this boundary are likely erroneous.

[korikuzma]

Are there existing tests for this?

[jarbesfeld]

@korikuzma There had been an existing test for this but it looks like it was accidentally removed when I merged in main. I will add this test back.

[jarbesfeld]

Not sure if I need to add the test back considering we now have a warning statement as opposed to an error statement.

[korikuzma]

Not sure if I need to add the test back considering we now have a warning statement as opposed to an error statement.

You can check the caplog: https://docs.pytest.org/en/stable/how-to/logging.html#caplog-fixture

[jarbesfeld]

@ahwagner I modified the warning statement string a bit based on your feedback (see last commit). Please let me know if you would like to add the base pair distance computation part back.

[korikuzma]

Code looks fine to me, let's wait for @ahwagner 's confirmation on the change.

[jarbesfeld]

@korikuzma Discussed with Alex and he approves