Update to minimap2 2.29 - support for scoring junctions #124
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okay sorry for the delay - I realized to score junctions you need to have CIGAR set as an option.
That should be set by the user though, so for tools that use
minimap2-rswho want to support a--write-junclike flag they'll need to make sure they build the indexwith_cigar()I wrote up a little test to go with the junction scoring which is passing now.
Let me know if you see any problems and feel free to edit as you see fit.
Apologies for all the line edits, I made some extraneous style changes outside of adding this functionality to silence clippy.
Cheers!