fix(runall): honor --extract::no-check-crc on BGZF FASTQ input

[nh13]

Summary

fgumi runall --start-from extract --extract::no-check-crc aborted with a BGZF CRC32 mismatch on all-BGZF FASTQ file input — while logging CRC verify: off — where standalone fgumi extract --no-check-crc succeeds.

The all-file BGZF FASTQ parallel-decode split (build_bgzf_fastq_split) took its CRC policy from ChainSpec::verify_crc, while the fused FASTQ readers resolved theirs from the extract options' check_crc/no_check_crc. runall set verify_crc to a hardcoded true for a FASTQ source (commented as inert); standalone extract only worked because it resolved the field a second time itself.

The split's policy is now resolved once in open_fastq_source from the same extract options the fused readers use (via the shared resolve_check_crc) and carried in PendingSource::Fastq, so no FASTQ command can leave the two decode fronts out of sync. ChainSpec::verify_crc is now genuinely inert for FASTQ sources (doc corrected), extract's redundant resolution is removed, and open_fastq_reader uses the shared resolve_check_crc/check_crc_reason instead of inline copies. The settled default policy (verify a file, skip trusted stdin; #786/#798) is unchanged.

Found by a sweep for siblings of #991. Blocks v0.8.0.

Test plan

• runall integration test: a 350k-record BGZF FASTQ with a corrupted CRC in its last data block (past quality-detection's window) is accepted under --extract::no-check-crc with every record present in order and identical to standalone extract, and rejected by default with the mismatch raised by FastqDecompress. Fails without the builder change, as does the existing standalone split test.
• A BAM start without -i still reports --input is required.
• cargo ci-fmt, ci-lint, ci-doc, ci-test (10474 passed), ci-doctest.

Risk: Command output data: none; CRC rejection behavior changes for BGZF FASTQ, and integration tests pin record names, order, and parity with standalone extract. unsafe: none added or modified; CLAUDE.md’s allowlist does not need an update. Memory bounds, queue capacity, and thread/backpressure policy: none.

Fix: BGZF FASTQ split decoding now uses the CRC policy resolved from extract options. This aligns runall with fused FASTQ readers. The default CRC policy remains unchanged.

Coverage: Added integration tests for corrupted BGZF FASTQ with CRC checks disabled and enabled, and for missing input when starting from sort. Test execution results were not provided.

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• src/lib/pipeline/chains/builder.rs

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Walkthrough

FASTQ BGZF split decoding now uses CRC policy resolved from extract options rather than ChainSpec.verify_crc. Integration tests cover corrupted CRC handling and a missing-input error from runall.

Changes

FASTQ CRC policy

Layer / File(s)	Summary
Resolve and document FASTQ CRC policy src/lib/commands/extract.rs, src/lib/commands/runall.rs, src/lib/pipeline/chains/spec.rs	Shared helpers resolve CRC policy. ChainSpec.verify_crc is set to true, and documentation states that FASTQ CRC policy comes from extract options. The test for deriving ChainSpec.verify_crc from CRC flags was removed.
Pass policy to BGZF split decoding src/lib/pipeline/chains/builder.rs	open_fastq_source stores the resolved policy in PendingSource::Fastq. The BGZF split decoder uses that policy instead of ChainSpec.verify_crc.
Exercise CRC and runall error paths tests/integration/helpers/fastq.rs, tests/integration/test_runall_command.rs	A new fixture corrupts the final BGZF CRC. Integration tests check that --extract::no-check-crc accepts the input and preserves record order, that default CRC checking rejects it, and that runall reports the missing --input option.

Priority: ⬇️ Low

Estimated code review effort: 3 (Moderate) | ~20 minutes

Change: Bug fix

Merge Risk: ⚪ Minimal · up to fd744

The runall FASTQ path follows the requested CRC policy, and the added tests cover both disabled-check acceptance and default rejection. No actionable merge-readiness risk remains.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title follows Conventional Commit format, uses the valid fix type and runall scope, clearly describes the CRC-policy fix, uses a lowercase imperative description, and has no trailing period.
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 96.66667% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 96.27%. Comparing base (27c3a4f) to head (fd74432).

Files with missing lines	Patch %	Lines
src/lib/pipeline/chains/builder.rs	96.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #996      +/-   ##
==========================================
- Coverage   96.29%   96.27%   -0.02%     
==========================================
  Files         296      296              
  Lines      149023   149032       +9     
==========================================
- Hits       143496   143475      -21     
- Misses       5527     5557      +30     

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