sgkit
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`sgkit.genee` improvements
- 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 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. - Accompanies #1180