v0.5.0

0.5.0 (2026-07-04)

Features

• add opt-in --seed-order seed reordering (default off, byte-identical) (#186) (04749a1)
• add opt-in --smem-dedup (dedup identical SMEMs before chaining) (#187) (1384972)
• mem: add --adaptive-band (chain-geometry adaptive banding) for long reads (#194) (4fe92a6)
• mem: add --extend-mate-concordant; fix --fast --meth placement regression (#195) (c9ffef1)
• mem: add --fast speed preset (#189) (a946af8)
• mem: add --max-extend-chains and bundle it into --fast (#193) (e39b3d4)
• mem: add --skip-contained-ext and enable it under --fast (#192) (2d2b2b4)

Bug Fixes

• bandedSWA: 8-bit SW drops query-end gscore/gtle on zero-score-row exit (#198) (611e21b)
• bandedSWA: getScores{8,16} must not scribble padding past numPairs (#199) (9aae808)

Performance

• bandedSWA: gate the getScores overshoot guard to sub-slice callers (#201) (162e909)

Refactoring

• kswv: drop duplicate F warm-up prefetch in kswv512_16 (#191) (6e4cf2b)

Documentation

• changelog: backfill the 0.4.0 breaking-change notice (#183) (e1c381a)
• changelog: render the live changelog, not the frozen NEWS.md (#184) (12a46d8)
• contributing: document breaking-change commit footers (#181) (4ebd122)
• release: describe the release-please flow, not manual tagging (#182) (fc0c4b6)

For packagers

A vendored source tarball (all submodules bundled, no .git/ directories) is available as a release asset:

• File: Source_code_including_submodules.tar.gz
• sha256: 5e8bf61d13976a24508201374694f07efec789b6f3154ba8945ec8258bff07b1
• URL: https://github.com/fg-labs/bwa-mem3/releases/download/v0.5.0/Source_code_including_submodules.tar.gz

Downstream package recipes (e.g. bioconda) should pin against this asset rather than GitHub's auto-generated source tarball, which omits submodule contents.