feat(runall/inproc): align in process with bwa-mem3 (--aligner::preset bwa-mem3-inproc)

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Part 5 of 5 of the in-process bwa-mem3 aligner stack (#986 → #987 → #988 → #989 → #990 (this PR)).

Summary

Adds the in-process bwa-mem3 backend to fgumi runall: --aligner::preset bwa-mem3-inproc aligns inside fgumi through bwa-mem3-rs instead of piping FASTQ to a bwa-mem3 subprocess, and its merged output is byte-identical to the bwa-mem3 subprocess preset. Requires the aligner-bwa-mem3 feature (part 4); default builds are unchanged.

Risk verdict

1. Output: unchanged for existing commands and presets. The new preset's output is pinned to the subprocess preset by the parity suite below, run in CI.
2. unsafe: none added in fgumi's crates.
3. Memory / threading: the in-process backend keeps two -K cohorts resident (cohort gate, byte-bounded queues). --pool-scheduler auto uses the refill-aware drain-first scheduler (part 1) for this backend, capped at one cohort in the aligner's input queue. The process-wide mimalloc purge setting (part 3) costs up to ~2 GB more peak RSS with this backend.

How the in-process backend matches the subprocess preset

The subprocess preset runs bwa-mem3 mem -p -K 150000000. The in-process backend reproduces what that command does to a stream of reads, then calls bwa-mem3's own kernels through the bindings' three-phase API (seed_extend → infer_cohort → pair_emit):

• the -K cohort cut, including bwa's even-read-count rule (so a pair can be split across cohorts exactly as the CLI splits it);
• the per-cohort SE/PE layout that -p smart pairing produces, and the per-sub-batch read-id bases;
• a per-cohort mem_pestat barrier, so every sub-batch is paired with the insert-size model the CLI would have computed for that cohort;
• bwa-mem3's index header sidecar (<prefix>.hdr or <baseprefix>.dict), merged into the output header the way the subprocess path merges the aligner's header.

Pipeline shape: AlignPrepare (Serial: cohort cut, sub-batch slicing, gate admission) → AlignSeedExtend (Parallel) → CohortPeStat (Serial barrier, releases cohorts in cohort order) → AlignPairEmit (Parallel, ordered by item ordinal, merges each sub-batch in place). Read names the CLI would alter before aligning (whitespace, a trailing /1-style suffix) are rejected up front with an error naming the template, rather than silently diverging.

Performance

c8g.8xlarge (32 vCPU Graviton4), hg38, bwa-mem3 51ceed7, 2 reps per cell (rep-to-rep spread ≤0.4%). Every run exits 0 with the expected record count and one samtools-view md5 per workload across all threads, pinning and backends; subprocess vs in-process outputs are identical (fgumi compare bams).

The subprocess preset is not a T-core configuration: bwa-mem3 runs -t T compute threads plus its own I/O threads beside fgumi's T workers and reader/writer threads, so below the core count it uses more than T cores. The fair comparison confines each run's whole process tree (fgumi and the bwa-mem3 child) to T cores with taskset -c 0-(T-1). The in-process backend's wall time is unchanged by pinning (within 0.2%); the subprocess's rises 3–4% (align only) and 10–13% (extract chain). At T=32 pinned and unpinned are the same thing.

Wall time, subprocess → in-process (Δ is in-process vs subprocess):

workload	threads	pinned to T cores (fair)	unpinned
align only, 5M WGS pairs (10,134,004 records)	4	225.8 → 221.3 s (−2.0%)	216.5 → 221.1 s (+2.1%)
	8	113.6 → 110.8 s (−2.5%)	109.3 → 110.7 s (+1.3%)
	16	58.3 → 56.1 s (−3.9%)	56.4 → 56.0 s (−0.8%)
	32	—	31.3 → 29.1 s (−7.1%)
extract → correct → align → zipper, 3M simulated UMI pairs (5,532,046 records)	4	55.2 → 56.7 s (+2.8%)	49.7 → 56.7 s (+14.2%)
	8	28.5 → 28.6 s (+0.1%)	25.4 → 28.6 s (+12.5%)
	16	15.1 → 14.5 s (−3.8%)	13.7 → 14.5 s (+6.1%)
	32	—	8.7 → 7.6 s (−12.0%)

CPU-seconds (user+sys) and peak RSS barely depend on pinning:

workload	threads	CPU-s sub → in-proc	peak RSS sub → in-proc
align only	4 / 8 / 16 / 32	−1.6% / −1.7% / −1.8% / −1.7% (899 → 885 at T=4)	14.1–16.1 → 15.3–18.2 GB
extract chain	4 / 8 / 16 / 32	+3.3% / +1.6% / +0.4% / −0.4% (219 → 226 at T=4)	13.4–15.0 → 15.5–16.9 GB

Pinned, in-process is faster everywhere except the extract chain at T≤8: there the subprocess is 2.8% faster at T=4 and tied at T=8, and it uses 1.6–3.3% less CPU. Unpinned, the subprocess also wins align-only at T≤8 (+1–2%) and the extract chain at T≤16, because it spills onto spare cores. In-process wins from T=16 (align only) or T=32 (extract chain) even unpinned, and costs 1–2 GB more peak RSS throughout.

Duplicate-rich input and #1002. The one fair case where the subprocess wins (the extract chain at T≤8) comes from bwa-mem3's --dedup-reads read-pair memo, which this PR's in-process backend doesn't have. #1002, stacked on this PR, adds it as --aligner::dedup-reads, on by default. On a UMI set with 39% duplicate pairs (align only), in-process CPU drops from 225.7 to 199.0 CPU-s at T=4 pinned (subprocess: 213.5) and from 235.1 to 208.3 at T=32 (subprocess: 224.0), which puts in-process ahead of the subprocess. On WGS it costs +0.09% CPU, within noise. Output is byte-identical.

On a duplicate-rich panel (agilent-qxt, 5M pairs, T=32), measured during development: in-process 18.3 s vs subprocess 23.3 s wall, 3% less CPU, 1 GB lower peak RSS, identical records.

mimalloc purge delay. With an align stage in the chain, runall sets mimalloc's purge delay to -1 (never return freed pages to the OS) unless MIMALLOC_PURGE_DELAY is set, and passes the same setting to the bwa-mem3 child. The setting is process-wide, so later stages keep freed pages too (fgumi-sort's force_mi_collect() no longer releases memory). Measured end to end (extract through simplex consensus, 1M pairs, 32 threads, with and without a spilling sort): 3–4% faster wall and 2–3% less CPU on both backends, page faults ~700k → under 40k, for up to ~2 GB (~12%) more peak RSS in-process and ~0.4 GB on the subprocess route.

Tests and CI

• tests/align_inproc_parity.rs: in-process vs subprocess byte parity (decoded BAM records, including aux type widths; only @PG CL, the VN git suffix and tag order are normalized) and determinism/thread invariance, across threads, sub-batch sizes, -K sizes that force mid-pair splits, and all three pool schedulers. The fixture exercises substitutions, indels, unmappable, chimeric (supplementary), discordant, repeat (XA/MAPQ 0) and zero-length reads, with RX on every record and some QC-fail, and asserts the output really contains each of those shapes and that every primary keeps its read's RX/QC-fail state.
• Unit tests for each step against the recording fake engine: cohort-order release and mis-delivery errors in the pestat barrier, per-template primary-count and layout guards in pair/emit, name rejection and gate stalls in prepare, the index-sidecar lookup, and the shared SEQ/QUAL decode.
• CI: an e2e-parity job builds the reference bwa-mem3 CLI at the vendored commit, checks it matches bwa-mem3-sys's vendor/COMMIT, and runs both parity suites plus a real-index engine smoke test with missing tools treated as failures.

Risk verdict: Alignment output changes for the new in-process backend; parity, determinism, and thread-invariance tests pin it against the subprocess preset. No new unsafe is reported in fgumi’s crates; CLAUDE.md says the existing allowlist needs no update. Memory and backpressure policy changes: cohort gating, byte-bounded queues, and refill-aware scheduling are added, and up to two cohorts may remain resident.

Summary

Adds the optional aligner-bwa-mem3 in-process backend for fgumi runall, selected with bwa-mem3-inproc. The backend prepares reads, runs seed/extend in parallel, applies a cohort-level insert-size-statistics barrier, then pairs and emits records. It supports deduplication within a -K cohort. Deduplication defaults on, is disabled for --meth, and is valid only with the in-process preset.

The backend synthesizes the alignment header from the index and an optional sidecar. It rejects read names that the CLI would alter. The default build remains unchanged.

Validation and performance

The integration suite compares output with the subprocess preset and checks repeatability and thread invariance across inputs, batching, and schedulers. The PR objectives report a CI job that builds the reference CLI and runs parity suites and a real-index smoke test. Test execution results are not supplied.

The PR objectives report that pinned-thread benchmarks were faster in most tested cases; the subprocess was faster for the extract chain at 4 threads and tied at 8. Unpinned results varied. The reported memory impact can increase peak RSS by up to about 2 GB.

Review findings

No review findings were supplied. Severity counts are unavailable.

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Walkthrough

Adds an opt-in in-process bwa-mem3 alignment preset. The change implements its cohort-based pipeline, header synthesis, deduplication, and scheduler integration. It adds parity, repeatability, thread-invariance, and real-tool CI checks.

Changes

In-process bwa-mem3 backend

Layer / File(s)	Summary
Resolve and wire the in-process preset src/lib/aligner.rs, src/lib/pipeline/steps/align/inproc/mod.rs, src/lib/pipeline/steps/align/inproc/header.rs, src/lib/pipeline/steps/align/mod.rs, src/lib/pipeline/chains/builder.rs, Cargo.toml	Adds the bwa-mem3-inproc preset and its options and validation. The backend loads the index, synthesizes and validates the output header, and wires the in-process pipeline with thread and refill hints.
Prepare cohorts and infer pair statistics src/lib/pipeline/steps/align/inproc/prepare.rs, src/lib/pipeline/steps/align/inproc/pestat.rs, src/lib/pipeline/steps/align/inproc/cohort.rs	Prepares primary reads as cohort-bounded sub-batches, splits pairs at cohort boundaries, and releases completed cohorts in order after pair-statistic inference.
Decode reads, seed, and extend src/lib/commands/fastq.rs, src/lib/pipeline/steps/align/inproc/seed_extend.rs, src/lib/pipeline/steps/align/inproc/engine.rs, crates/fgumi-sort/src/lib.rs	Shares FASTQ sequence and quality decoding with the in-process stage. Seed-and-extend uses reusable read arenas and shared engine and scratch state. The engine can memoize duplicate pairs when enabled.
Reassemble batches and select scheduler src/lib/pipeline/steps/align/inproc/pair_emit.rs, src/lib/pipeline/steps/align/mod.rs, src/lib/pipeline/steps/align/subprocess.rs, src/lib/pipeline/steps/align/merge.rs, src/lib/pipeline/chains/builder.rs	Reassembles emitted records in input-template order, merges batches in the in-process pair/emit step, and adds refill-aware scheduler selection for automatic drain-first policy.
Validate parity and configure CI tests/align_inproc_parity.rs, tests/align_common/mod.rs, .github/workflows/check.yml, CLAUDE.md	Adds parity, repeat-run determinism, and thread-invariance checks. CI builds the reference tools and requires parity and smoke tests to run. Documentation updates the feature description and allocator measurements.

Priority: ➖ Normal

Estimated code review effort: 4 (Complex) | ~60 minutes

Change: Feature

Sequence Diagram(s)

sequenceDiagram
  participant Runall
  participant AlignerResolution
  participant InProcessBwaMem3Backend
  participant AlignPrepareStep
  participant AlignSeedExtendStep
  participant CohortPeStatStep
  participant AlignPairEmitStep
  participant BAMOutput
  Runall->>AlignerResolution: Resolve bwa-mem3-inproc options
  AlignerResolution->>InProcessBwaMem3Backend: Create resolved backend
  InProcessBwaMem3Backend->>AlignPrepareStep: Wire cohort-bounded work
  AlignPrepareStep->>AlignSeedExtendStep: Send prepared sub-batches
  AlignSeedExtendStep->>CohortPeStatStep: Send extended work
  CohortPeStatStep->>AlignPairEmitStep: Send cohort-ordered pair work
  AlignPairEmitStep->>BAMOutput: Emit merged BAM batches

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Suggested labels: fgumi sort, continuous-integration

Merge Risk: ⚪ Minimal · up to 16f62

No actionable merge-blocking issue is identified in the scheduler wiring or allocator documentation changes. Merge readiness remains subject to normal build and parity checks.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title uses the required Conventional Commit format with type feat, scope runall/inproc, a lowercase imperative description, and no trailing period. It accurately describes the new in-process b…
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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Codecov Report

❌ Patch coverage is 92.95154% with 16 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.31%. Comparing base (bc7f67e) to head (16f62fb).

Files with missing lines	Patch %	Lines
src/lib/pipeline/chains/builder.rs	76.47%	8 Missing ⚠️
src/lib/aligner.rs	95.95%	7 Missing ⚠️
src/lib/pipeline/steps/align/mod.rs	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #990      +/-   ##
==========================================
- Coverage   96.33%   96.31%   -0.02%     
==========================================
  Files         298      298              
  Lines      149522   149706     +184     
==========================================
+ Hits       144040   144191     +151     
- Misses       5482     5515      +33     

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Inline comments:
Review comments at @src/lib/aligner.rs:
- Around line 1107-1109: Add an upper bound for `sub_batch_templates` in
`resolve_inproc` so oversized CLI values are rejected before they can drive
large allocations or overflow counters. Keep the existing zero-value validation,
and choose a safe maximum compatible with the `u32` counters and sub-batch
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presets accept valid paths without shell-safety restrictions.
- Around line 1589-1603: Add a command-mode case to the chunk-size validation
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• src/lib/pipeline/chains/builder.rs
• src/lib/pipeline/chains/commands/align.rs
• src/lib/pipeline/steps/align/inproc/cohort.rs
• src/lib/pipeline/steps/align/inproc/engine.rs
• src/lib/pipeline/steps/align/inproc/header.rs
• src/lib/pipeline/steps/align/inproc/mod.rs
• src/lib/pipeline/steps/align/inproc/pair_emit.rs
• src/lib/pipeline/steps/align/inproc/pestat.rs
• src/lib/pipeline/steps/align/inproc/prepare.rs
• src/lib/pipeline/steps/align/inproc/seed_extend.rs
• src/lib/pipeline/steps/align/merge.rs
• src/lib/pipeline/steps/align/mod.rs
• src/lib/pipeline/steps/align/subprocess.rs
• tests/align_common/mod.rs
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