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update to latest minimap2 (Minimap2-2.31 (r1302))#163

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update to latest minimap2 (Minimap2-2.31 (r1302))#163
rob-p wants to merge 2 commits into
jguhlin:mainfrom
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@rob-p

@rob-p rob-p commented Jun 3, 2026

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Update the associated minimap2 version to Minimap2-2.31 (r1302), which includes the bug fixes upstreamed during rammap development.

rob-p added 2 commits June 2, 2026 22:01
… 2.31)

minimap2 2.31 dropped the bundled `lib/simde` submodule (it now ships only a
standalone Makefile.simde and expects the consumer to provide simde), so the
`simde` feature's `cc.include("minimap2/lib/simde")` pointed at a path that no
longer exists, failing with:

    minimap2/ksw2_ll_sse.c:7:10: fatal error: simde/x86/sse2.h: No such file or directory

Add simde as a minimap2-sys submodule (simd-everywhere/simde, pinned to v0.8.2)
and include it from build.rs instead. Exclude its test/ dir from the published
package (mirrors the old /minimap2/lib/simde/test exclude); packaged size stays
~1 MiB compressed. Verified `cargo test --features simde` passes for both
minimap2-sys and the top-level minimap2 crate.
@jguhlin

jguhlin commented Jun 7, 2026

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Will get onto this this week. Also thanks for publishing the https://github.com/COMBINE-lab/OUP-Bioinformatics-Typst repo

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2 participants