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chore(main): release 0.17.0 - #730

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release-please--branches--main--components--bwa-mem3
Nov 9, 2026
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chore(main): release 0.17.0#730
nh13 merged 1 commit into
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release-please--branches--main--components--bwa-mem3

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@fg-labs-bot fg-labs-bot Bot commented Nov 2, 2026 •
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🤖 I have created a release beep boop

0.17.0 (2026-11-07)

⚠ BREAKING CHANGES

  • meth: bare --meth output changes (scores, MAPQ, NM, some placements and clipping). Pass --meth-scoring collapsed to keep the previous behaviour.
  • mem: under -u, the alternative-hit list is now written as XB:Z instead of XA:Z (SAM text, --bam and --meth). Output without -u is unchanged. A pipeline that ran -u and read XA:Z must read XB:Z instead.

Features

  • mem: add --md full|short|none to choose the MD tag (#754) (01f5f39)
  • meth: default EM-seq/bisulfite --meth-scoring to genomic (#756) (bb56c84)

Bug Fixes

  • bound finite pair scores before integer conversion (#743) (9f09cec)
  • build: keep LTO when lld needs ld.bfd's library search directories (#713) (14272d8)
  • build: match LLVM archive tools to clang-19 (#738) (a32a987)
  • build: probe the AVX2 floor from a plain x86-64 baseline (#753) (279fdc6)
  • build: validate LTO archives with native and LTO consumers (#736) (ef0216a)
  • defer inconclusive input metadata errors to open (#744) (6c43e96)
  • io: give SAM text and --bam one header, and map --bam contigs by name (#692) (175984e)
  • mem: name the -u hit list XB:Z, as bwa does (#690) (19a0574)
  • meth: warn when em-seq is combined with --meth-scoring neutral (#734) (cc888bb)
  • shm: hold the stager lock only for the registry update (#760) (99ac733)
  • shm: reject unregistered shared-memory segments (#745) (057b9d0)
  • track test archives and match reader compile flags (#746) (07b5d7d)

Performance

  • bam: sync the single-threaded BGZF writer every 32 MiB, not only at close (#727) (3ac3df8)
  • bsw: capture the 16-bit query end in-cell and fold it once per row (#708) (62123fc)
  • bsw: compact finished lanes in 16-bit NEON and x86 extension kernels (#720) (a96a22b)
  • bsw: lean per-row bookkeeping in the AVX-512BW 8-bit kernel (#710) (731e31a)
  • bsw: run the 128-bit 16-bit band trim as a counted loop (#711) (005dc99)
  • bwamem: pick the 16-bit pair order per call from the len1 < len2 majority (#715) (6a641a5)
  • chain: filter each read's chains at the end of chaining, while they are cached (#719) (c5b8653)
  • cigar: vectorize five-symbol CIGAR annotation walks on NEON (#739) (67dca71)
  • ext: probe non-HIT extensions up to 512 bases in the certified rung (#698) (ffcc9a9)
  • ext: scan the ungapped analyzer's tail in one 16-byte step on AVX2 (#696) (3773dec)
  • ext: use probe-rung buckets 8 apart and fill their lane groups (#695) (bec55f4)
  • kstring: format unsigned longs two digits at a time (#741) (18a4df5)
  • kswv: all-pad columns and backward query-end rescan in the AVX-512BW u8 kernel (#717) (43082bb)
  • mem: cut per-read memory under --meth with byte-identical output (#763) (597687c)
  • mem: put the occurrence table on 1 GB pages under --huge-pages (#716) (2cc0550)
  • rescue: return FULL from the prune filter once the hit gate is provably exceeded (#718) (d7b745b)
  • thp: skip the smaps walk when no THP warning is possible (#709) (a283e56)
  • xa: generate XA slots only for single-end alignments that will be emitted (#740) (6211043)

Documentation

  • HN:i is on supplementary records too, and counts shadowed hits (#691) (e3d7ad1)
  • mem,shm,ungapped_ext: correct proof and validation-scope statements (#759) (3b6abc6)
  • readme: update performance tables for v0.16.0 (#729) (7185269)
  • test: list the ext-tier-partition unit module in TESTING.md (#702) (1e39292)

This PR was generated with Release Please. See documentation.

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@fg-labs-bot
fg-labs-bot Bot force-pushed the release-please--branches--main--components--bwa-mem3 branch 2 times, most recently from c4a250f to 1d40616 Compare November 3, 2026 01:29
@fg-labs-bot fg-labs-bot Bot changed the title chore(main): release 0.16.1 chore(main): release 0.17.0 Nov 3, 2026
@fg-labs-bot
fg-labs-bot Bot force-pushed the release-please--branches--main--components--bwa-mem3 branch 23 times, most recently from 28ce552 to dd35c5b Compare November 5, 2026 18:29
@fg-labs-bot
fg-labs-bot Bot force-pushed the release-please--branches--main--components--bwa-mem3 branch 8 times, most recently from 53badde to b7509bd Compare November 7, 2026 08:46
@fg-labs-bot
fg-labs-bot Bot force-pushed the release-please--branches--main--components--bwa-mem3 branch from b7509bd to 22c1eaf Compare November 7, 2026 14:59
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nh13 added this pull request to the merge queue Nov 9, 2026
Merged via the queue into main with commit 58d55c1 Nov 9, 2026
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nh13 deleted the release-please--branches--main--components--bwa-mem3 branch November 9, 2026 02:49
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🤖 Created releases:

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@nh13 nh13 mentioned this pull request Nov 9, 2026
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nh13 added a commit to fg-labs/bwa-mem3-bench that referenced this pull request Nov 9, 2026
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chore(release): bless bwa-mem3 v0.17.0 as golden and bump the arena l…
e33c342 
…adder

Adds the v0.17.0 (1eaeb8ee, fg-labs/bwa-mem3#730) release-allowance entry,
aliases the shipped v0.17.0 tag (58d55c18; 1 commit ahead touching only
CHANGELOG, version.txt and the release-please manifest, so src/ is identical)
to it, bumps the arena ladder (arena.smk + Dockerfile.base) so the next bless
benches it as a historical arm, and publishes the v0.17.0 results pages.

The only alignment change on this corpus is fg-labs/bwa-mem3#756 (genomic
--meth scoring by default). This is also the first bless on the UMI-trimmed
meth inputs (#137), so Gate #2 has no meth cell to compare this once: it is
100.0000% on all 36 golden-backed DNA cells (180 compares, 5 reps).

Gate #1 passes on all 70 gating DNA cells (100.0000%); meth relocation vs
bwameth (0.82% / 0.87%) is report-only. Gate #1b passes on all 6 sim-truth
cells, with genomic scoring cutting mismapped-at-MAPQ>=20 on the bare --meth
arms (sim-meth-place 203 -> 84 ppm). Gate #3 passes on efficiency. This is
the first bless on LTO-built images (#136): 1.060x (m8a) / 1.015x (m8g) vs
v0.16.0 on the default preset (paired estimate), 1.016x / 1.009x on --fast.
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