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feat(retag): route the retag command onto the declarative chain builder - #898
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Included review availability: 0 reviews are currently available. Your included PR review attempts over the past 7 days set your current allowance at 1 review per hour. WalkthroughChangesThe PR adds Retag chain execution
Estimated code review effort: 4 (Complex) | ~45 minutes Merge Risk: ⚪ Minimal · up to The threaded retag path now uses the declarative chain builder while preserving the single-threaded parity path; supplied verification is green, so no actionable merge-blocking risk remains beyond normal checks. Sequence Diagram(s)sequenceDiagram
participant RetagCommand
participant ChainBuilder
participant RetagProcessStep
participant RetagFinalizeHook
RetagCommand->>ChainBuilder: build Stage::Retag chain
ChainBuilder->>RetagProcessStep: process decoded batches
RetagProcessStep-->>ChainBuilder: return preserved decompressed blocks
ChainBuilder->>RetagFinalizeHook: finalize accumulated counts
RetagFinalizeHook-->>RetagCommand: write summary and optional metrics
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #898 +/- ##
==========================================
+ Coverage 93.16% 93.54% +0.37%
==========================================
Files 299 300 +1
Lines 150391 150487 +96
==========================================
+ Hits 140119 140768 +649
+ Misses 10272 9719 -553 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Inline comments:
In `@src/lib/pipeline/chains/stage.rs`:
- Around line 29-30: Update the Rust documentation comment describing the
standalone stages to wrap the identifiers Clip, Dedup, and Downsample in
backticks, preserving the rest of the comment unchanged.
In `@src/lib/pipeline/chains/validate.rs`:
- Line 181: Update the Stage::Retag validation in the chain-spec construction or
validation flow to require RetagOptions::operations to be non-empty when retag
options are present, while preserving acceptance of populated options. Add unit
coverage for both empty and populated RetagOptions before chain construction.
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src/lib/commands/retag.rssrc/lib/pipeline/chains/builder.rssrc/lib/pipeline/chains/commands/mod.rssrc/lib/pipeline/chains/commands/retag.rssrc/lib/pipeline/chains/options_bag.rssrc/lib/pipeline/chains/stage.rssrc/lib/pipeline/chains/validate.rstests/integration/main.rstests/integration/test_retag_command.rs
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🤖 Prompt for all review comments with AI agents
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Inline comments:
In `@src/lib/pipeline/chains/validate.rs`:
- Line 45: Update validate_stage_progression to reject any multi-stage chain
containing Stage::Retag, including Stage::Sort followed by Stage::Retag, before
progression validation succeeds. Preserve valid single-stage Retag behavior if
supported, and add regression coverage for the rejected chain.
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src/lib/pipeline/chains/stage.rssrc/lib/pipeline/chains/validate.rs
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Route `fgumi retag --threads N` through the declarative chain builder (`ChainSpec::single_stage(Stage::Retag, …)` -> `build_for(spec)?.run()`), keeping the no-`--threads` `run_single_threaded` serial loop as the in-process parity oracle. retag is a pure per-record tag rewriter (no grouping, no rejects, un-feature-gated), so it mirrors filter's `build_filter_step_single_no_rejects` shape. Two-part change. Chains-core: add the `Stage::Retag` variant, the `StageOptionsBag::retag` slot + `RetagOptions` projector, `ChainBuilder::add_retag`, the step module `pipeline/chains/commands/retag.rs` (process step + finalize hooks), and the `stage_ord`/`validate_stage_opts_present` seams. Cutover: flip `Retag::execute`'s `--threads` arm to `execute_chain`; the warn/metrics/summary tail becomes the serial-oracle-only path. Dispatch sits after the reader-free pre-flight (output-collision + input-aliasing checks) but before the CRC log / banner / timer, so the chain path does not double-log or pre-consume stdin. The banner + `OperationTimer` are built inside `add_retag` (matching add_filter/add_dedup), and the timer is moved into the always-run `RetagFinalizeHook`; `record_count` for the summary comes from a shared progress counter (not from summing `records_applied`, which would undercount when a source tag is absent). The `--metrics` TSV + the warn-on-zero-match loop run in a success-only `RetagMetricsFinalizeHook`, so a failed run publishes neither — matching the oracle. `sum_slot_counts` and `RetagMetric::from_counts` are shared (`pub(crate)`) so the two paths cannot drift. The legacy `run_threaded` engine (the old `run_bam_pipeline_from_reader` path) is removed — it is dead once `--threads` routes to the chain, and it was never the parity oracle. Parity is asserted on decoded records + normalized header (`read_bam_output`) and the `--metrics` TSV, never raw BGZF bytes (parallel vs serial framing differs). New tests cover chain-vs-oracle parity across `--threads` 1/2/4 (including `--threads 1`, a distinct single-worker chain path), metrics byte-parity, a zero-match op, and a multi-batch run, plus the `to_retag_options` projector.
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What
Route
fgumi retagonto the declarative chain builder — R3 follow-on.retag --threads Nnow runs throughexecute_chain→ChainSpec::single_stage(Stage::Retag, …)→build_for(spec)?.run(). The no---threadsrun_single_threadedserial loop is kept unchanged as the in-process parity oracle; the oldrun_threaded/run_bam_pipeline_from_readerengine is removed in this PR.Because retag had no dormant chain stage, this is a 2-part change: (A) chains-core adds
Stage::Retag, theStageOptionsBagslot,ChainBuilder::add_retag, the step module (pipeline/chains/commands/retag.rs), the finalize hooks, and every stage-enumerating-pass edit; (B) the cutover flips the--threadsdispatch and makes the metrics/summary/warn tail oracle-only. retag is a pure per-record tag rewriter (SingleRawRecordGrouper, no rejects, no query-grouping guard, un-feature-gated), so it mirrors filter's single-no-rejects step shape.Design notes
RetagFinalizeHook(always-run) logs the=== Summary ===+timer.log_completion(record_count), readingrecord_countfrom a shared progressAtomicU64incremented once per record by the step (OpCountshas no total field);RetagMetricsFinalizeHook(success-only) does the warn-on-zero-match loop + writes the--metricsTSV. Reusesapply_op/sum_slot_counts/RetagMetric::from_counts(latter two madepub(crate)) so the oracle and chain metrics cannot drift.read_bam_output) + the--metricsTSV — never raw BAM bytes (parallel vs serial BGZF framing differs at the same compression level).OperationTimer+Starting Retagbanner + threading logs are built insideadd_retag(matchingadd_filter/add_dedup);execute_chainislog_effective_check_crc+ build/run only, so the--threadspath doesn't double-log.name_hash_onlygroup key with a defaultLibraryIndex(retag never reads the group key; a default index skips the per-record aux-tag scan + CIGAR walk and avoids the>65,535-libraryLibraryIndex::from_headerpanic the serial path doesn't have).Tests
Chain-vs-oracle parity across
--threads1/2/4 (records + normalized header),--metricsTSV byte-parity, zero-match op (assertsrecords_applied == 0), multi-op fan-out + chain-through, interleaved missing/empty-tag records, multi-batch cross-slot summation, empty (0-record) input, and the twoto_retag_optionsprojector tests.Review
/code-review(2 efficiency fixes folded in: cheap group-key routing; batch-local count merge with a single per-batch lock) and a deep multi-agent/gauntlet(8 raised → 1 refuted → 7 fixed: thefrom_headerpanic, doc-drift onsum_slot_counts/thethreadingfield, empty-input coverage, and the zero-match assertion strength) both ran; every surviving finding is addressed.Verification
cargo ci-fmt && cargo ci-lint && RUSTDOCFLAGS="-D warnings" cargo ci-doc && cargo ci-test— all green (9791 tests). All three feature legs compile (--no-default-features, default,--all-features, all--all-targets). No newunsafe.Risk:
retagoutput changes in threaded mode, pinned by serial parity tests for records, normalized headers, and metrics;unsafechanges: none, andCLAUDE.mdallowlist changes: none; memory bounds, queue capacity, and thread/backpressure policy changes: none.Fix: Route threaded
retagexecution through the declarative chain builder while retaining the serial loop as the parity oracle.Stage::Retag, option projection, validation, and terminal chain-builder support.