Improves documentation of input and output for sgkit.genee
The Example for the sgkit.genee doc string is not a final version. It would need a better treatment of the LD matrix situation to be useful. The major point of this suggestion is to start a discussion about how to make the method more usable and also have an example that explains a user how to provide windows for regions of interest.
Changing the example code to have more contigs and overlapping windows in different contigs produces some edge cases that are not handled by the method.
How can the test_genee.py file be made active during unit tests? I was only able to run it specifically using pytest -v path/to/file. I added the path to the data default because I don't know how to properly configure that as part of the testing framework.
sgkit.geneesgkit.geneedoc string is not a final version. It would need a better treatment of the LD matrix situation to be useful. The major point of this suggestion is to start a discussion about how to make the method more usable and also have an example that explains a user how to provide windows for regions of interest.test_genee.pyfile be made active during unit tests? I was only able to run it specifically usingpytest -v path/to/file. I added the path to the data default because I don't know how to properly configure that as part of the testing framework.