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lh3 / minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences
https://lh3.github.io/minimap2
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dorado aligner #1030

Open iiSeymour opened 1 year ago

iiSeymour commented 1 year ago

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 https://github.com/lh3/minimap2/pull/1028 https://github.com/lh3/minimap2/pull/1029 fix the Windows compatibility in minimap2 v2.24 (and closes https://github.com/lh3/minimap2/pull/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 https://github.com/lh3/minimap2/issues/1004. I can send another pull request for this if it's something you're interested in?

tijyojwad commented 1 year ago

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 commented 1 year ago

I am happy to accept a patch for that.

iiSeymour commented 1 year ago

Added https://github.com/lh3/minimap2/pull/1048