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jguhlin / minimap2-rs

Rust bindings to minimap2 library
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Question: Minimap2 Alignment options #70

Open Sam-Sims opened 4 weeks ago

Sam-Sims commented 4 weeks ago

Hello! Nice crate,

It would be nice to have the ability to build the minimap2 alignment options (i.e --score-N) in the same way the MapOpts or IdxOpts are currently implemented. I can see some of the alignment options in MapOpts - I think matching score, -A, and Gap open penalty, -O, Is --score-N supported?

Likewise for Input/Output options - for example id like to be able to exclude secondary alignments (in minimap2 thats --secondary=yes|no)

Might be missing something obvious.

Thanks!

jguhlin commented 3 weeks ago

Not missing anything obvious, everything is added on an as-needed basis! I'll look at adding more options to the Aligner builder-style, in line with how map opts and idx opts are handled now. If you've got important ones you need now, let me know, and I can prioritize, or feel free to open a PR.