bwa-mem2 2.2.1

[gl-eb]

Created with brew bump-formula-pr.

[heuermh]

@gl-eb Might you be able to rebase this pull request?

[gl-eb]

Done!

[heuermh]

Sorry, will have to ask you to do it again, to pick up fixes to CI. 😬

Alternatively, I see some force pushed commits above, but I'm not certain how those were done?

$ git remote add gl-eb https://github.com/gl-eb/homebrew-bio.git
$ git fetch gl-eb
$ git checkout gl-eb/bump-bwa-mem2-2.2.1

# rebase, would require force push
$ git rebase -i upstream/develop

# or create merge commit, would also require a push to your branch?
$ git pull upstream/develop --no-rebase

[gl-eb]

No worries, my part is easy to do. Thanks for trying to get this to work!

[gl-eb]

I think the issue is an incompatibility between bwa-mem2 v2.2.1 with GCC 11 and higher. There's a fix for this already, but it has not been tagged as a release.

Does Homebrew allow formulas where tag and revision do not match? Otherwise the only other option would be to ask the bwa-mem2 maintainers to tag a new release. Or am I wrong here?

I am happy to do either, though the latter option could take longer. Do you have a preference @heuermh ?

[heuermh]

Yes, the CI issues have been resolved and now we're left with the actual issue with bwa-mem2!

Cleanest option is to wait until a new release happens upstream, otherwise we could patch and/or create a homebrew-specific revision with that commit included. Perhaps also this patch? I am not sure what the appetite for such here is though.

[YoshitakaMo]

@gl-eb I've created bwa-mem2 binaries for Apple Silicon (658fb60), though I don't guarantee whether it works as expected. If you are interested, please test it.