Consider using `pybwa` package as a BWA provider

[althonos]

Hi Christian,

Just an issue here to list that there's a new Python package wrapping bwa: https://pypi.org/project/pybwa that came out in early 2025. The previous one I was aware of was bwapy, but it didn't implement the bwa mem command, only bwa index, so it was of limited value for this library. The new one apparently does everything, so I was thinking you may be interested in switching to that for easier setup of gqlib and dependent packages.

There's also mappy: https://pypi.org/project/mappy/ which is made by Heng Li directly and that binds to minimap2, maybe also helpful for Minimap2Runner.

Cheers!

[cschu]

Thanks Martin! I'll have a look at those when it's "refactoring season" (i.e., when I got downtime to work on this.)