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feat(runall/inproc): add the aligner-bwa-mem3 feature, cohort math and the AlignEngine abstraction - #989
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Included review availability: This review used your included allowance. 0 included reviews remain after this review. Your included PR review attempts over the past 7 days set your current allowance at 1 review per hour. WalkthroughAdds an opt-in ChangesIn-process aligner backend
Priority: ⬇️ Low Estimated code review effort: 4 (Complex) | ~60 minutes Change: Feature Suggested labels: Merge Risk: ⚪ Minimal · up to The feature remains unwired to the pipeline, and unsupported architectures now receive a clear build error. No actionable merge-blocking risk is established. 🚥 Pre-merge checks | ✅ 3✅ Passed checks (3 passed)
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## main #989 +/- ##
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- Coverage 96.29% 96.27% -0.02%
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Inline comments:
Review comments at @.github/workflows/check.yml:
- Around line 114-115: Update the “Unit tests (aligner-bwa-mem3)” step in the
aligner-ffi job to create a small valid bwa-mem3 index, then run the cargo
nextest command with FGUMI_BWA_MEM3_TEST_REF pointing to that index and
FGUMI_BWA_MEM3_REQUIRE_TOOLS set to 1 so BwaMem3Engine is exercised rather than
skipped.
Review comments at @Cargo.toml:
- Around line 184-189: Add a target-architecture guard next to the `inproc`
module declaration in the align module so enabling `aligner-bwa-mem3` on
architectures other than x86_64 or aarch64 produces a clear compile-time error.
Correct the `Cargo.toml` dependency comment to clarify that the dependency is
target-gated and unsupported feature use is rejected by that guard.
Review comments at @src/lib/pipeline/steps/align/inproc/cohort.rs:
- Around line 223-227: Update `cohort.rs` to use the `IdBases` re-export from
`super::engine` instead of naming `bwa_mem3_rs` directly. Change the `id_bases`
return type and constructor, plus the `PairWork` field and any corresponding
test references, while keeping `engine.rs` as the sole module that names the
binding crate.
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.github/workflows/check.ymlCLAUDE.mdCargo.tomlsrc/lib/pipeline/steps/align/inproc/cohort.rssrc/lib/pipeline/steps/align/inproc/engine.rssrc/lib/pipeline/steps/align/inproc/gate.rssrc/lib/pipeline/steps/align/inproc/mod.rssrc/lib/pipeline/steps/align/inproc/scratch.rssrc/lib/pipeline/steps/align/mod.rs
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…s' tags With mixed single-end/paired input, bwa's even-read-count -K chunk cut can land between a pair's two reads; with -p smart pairing bwa then aligns them as two unpaired reads and emits them back to back under the pair's name. The subprocess reader failed on that output. It now recognizes the shape (no record paired, exactly two primaries) and splits the pair's unmapped template to match, clearing each half's pairing bits so the zipper merge copies each read's own tags and QC-fail flag. The split is accepted only from the bwa and bwa-mem3 presets, which run `mem -p -K`; a free-form --aligner::command keeps the loud "multiple primaries" error, since the same shape from an aligner that never pairs would otherwise split every pair silently. Also cap a preset's --aligner::chunk-size at i32::MAX: bwa parses -K with atoi into an int. And add a subprocess align/merge guard (tests/align_subprocess_split_parity.rs) that runs the preset over a fixture of substitutions, indels, unmappable, chimeric, discordant, repeat and zero-length reads with RX tags, checks every read keeps its tags (including across a forced mid-pair split), and that the output is identical across --threads values; it runs where a bwa-mem3 binary is available and skips otherwise.
…eep mimalloc from purging - The bwa-mem3 preset now runs `bwa-mem3 mem --bam=0`, so fgumi's single reader thread takes records zero-copy instead of parsing SAM text, which at 32 threads kept bwa-mem3 blocked on its output (a fused extract -> correct -> align ran 36% faster). The merged records are identical. - With an align stage, runall sets mimalloc's purge delay to -1 (never return freed pages to the OS) unless MIMALLOC_PURGE_DELAY or its legacy name is set (any case, as mimalloc matches them), and passes the same setting to the aligner child through its environment. The per-batch buffer churn otherwise costs hundreds of thousands of page faults. The setting is process-wide, so later stages keep freed pages too; measured end to end (extract through simplex consensus, 1M pairs, 32 threads, with and without a spilling sort) it is ~4% faster for ~0.4 GB more peak RSS. The setter lives next to the existing mimalloc FFI in fgumi-sort's memory_probe (CLAUDE.md allowlist updated); the option index is pinned by a test against mimalloc v3's 1000 ms default.
…d the AlignEngine abstraction The foundation of an in-process bwa-mem3 aligner backend, behind a new off-by-default `aligner-bwa-mem3` cargo feature that pulls bwa-mem3-rs 0.3.0 (the vendored bwa-mem3 C++, C++17 toolchain required; target-gated to x86_64/aarch64) and makes mimalloc interpose the C allocator for it. - inproc::cohort: the parity-critical pure logic the steps will need to reproduce `bwa-mem3 mem -p -K` exactly: the -K even-read-count cohort cut, the per-cohort SE/PE layout that -p smart pairing produces, and the per-sub-batch read-id bases, each pinned by a proptest against a literal Rust port of the upstream rule. - inproc::engine: the AlignEngine trait over bwa-mem3-rs's three-phase API (seed/extend, per-cohort pestat, pair/emit), the BwaMem3Engine implementation, and a test fake; plus an env-gated smoke test against a real index. - inproc::gate: the cohort-granularity in-flight gate and its lease, with the refill signal the refill-drain scheduler reads. - inproc::scratch: the per-pool-thread aligner scratch pool. Nothing is wired into runall yet (the steps and the backend follow), so the module carries a scoped dead_code allow. A new `aligner-ffi` CI job builds the feature on x86_64 and arm64 and runs its tests, pedantic clippy and rustdoc.
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Part 4 of 5 of the in-process bwa-mem3 aligner stack (#986 → #987 → #988 → #989 (this PR) → #990).
Summary
Adds the opt-in
aligner-bwa-mem3cargo feature (off by default; it needs a C++17 toolchain), which pulls inbwa-mem3-rs0.3.0 from crates.io (vendoring bwa-mem351ceed7), and the pure, engine-agnostic pieces of the in-process backend. Nothing is wired into a pipeline until part 5.inproc/cohort.rs: the three bwa rules the in-process backend must reproduce exactly for byte parity withbwa-mem3 mem -p -K: the-Kcohort cut (including the even-read-count rule), the per-cohort SE/PE layout that-psmart pairing produces, and the per-sub-batch read-id bases. Each is pinned by a proptest against a literal Rust port of the upstream C rule.inproc/engine.rs: theAlignEnginetrait over bwa-mem3-rs's three-phase API (seed_extend→infer_cohort→pair_emit), aBwaMem3Engineimplementation, and a recording fake for unit tests.inproc/gate.rs: the cohort-granularity in-flight gate and lease (two cohorts resident at a time) and its refill signal.inproc/scratch.rs: the per-pool-thread aligner scratch.aligner-ffijob builds the feature and runs its tests, pedantic clippy and rustdoc with-D warnings.inproc/mod.rscarries a temporaryallow(dead_code)because nothing calls these yet; part 5 removes it.Risk: no output change (feature off by default, and nothing is wired even with it on); no new
unsafein fgumi's crates, which stay#; no memory or threading change.A detailed high-level summary could not be generated for this review. Here is an overview derived from the analyzed file changes: