dorado aligner

[iiSeymour]

Hey @lh3

We are starting to add alignment support to dorado and I would like to get some patches upstreamed if possible.

The following pull requests #1028 #1029 fix the Windows compatibility in minimap2 v2.24 (and closes #818 for v2.22).

I've put together the follwing repo that applies these patches and builds minimap2 on Linux, Windows and Mac.

See https://github.com/nanoporetech/ont-minimap2.

As part of this work, I'd also like to get map-ont updated as per #1004. I can send another pull request for this if it's something you're interested in?

[tijyojwad]

Hi @lh3 - we have another patch to get access to the rep_len attributes in the thread buffer structure. Would you be open to accepting that as well?

[lh3]

I am happy to accept a patch for that.

[iiSeymour]

Added #1048