feat(pipeline): port the UMI-correction step (R1c) - #821
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WalkthroughThe PR adds typed UMI correction steps for kept-only and rejects-enabled output. It exposes correction internals within the crate, processes batches, serializes rejected BAM records, and adds routing and accounting tests. ChangesUMI correction pipeline
Estimated code review effort: 4 (Complex) | ~45 minutes Merge Risk: 🔵 Low · up to The PR adds the UMI-correction pipeline step and shared metrics without changing the active command path. It is mergeable with owner awareness and follow-up for bounded test coverage around queue limits, original-UMI handling, clean-reject ordering, and distinguishing duplicated from missing batches. Sequence Diagram(s)sequenceDiagram
participant BamTemplateBatch
participant CorrectStep
participant CorrectWorkerState
participant CorrectUmis
participant OrderedOutputs
BamTemplateBatch->>CorrectStep: submit batch
CorrectStep->>CorrectWorkerState: access per-worker cache
CorrectWorkerState->>CorrectUmis: extract and correct UMIs
CorrectUmis-->>CorrectStep: return correction and metrics
CorrectStep->>OrderedOutputs: emit kept templates and framed rejects
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In `@src/lib/pipeline/steps/correct/tests.rs`:
- Around line 537-559: Update the test around sorted_kept_qnames and
reject_block_qnames to validate batch serials on both output branches, not just
QNAME counts. Extract and assert kept-batch serials and reject-block serials
equal 0..n_batches in output order, preserving the existing QNAME assertions as
appropriate.
- Around line 211-223: Replace the helper-only clean-batch test with an
end-to-end case invoking correct_step_with_rejects, using clean input and the
normal pipeline configuration. Assert completion, one kept output, and exactly
one empty rejects block for every input serial, preserving dense serial ordering
to exercise the factory and rejects reorder stage.
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Inline comments:
In `@src/lib/pipeline/steps/correct/tests.rs`:
- Around line 18-23: Update the Rust documentation comments near CorrectOptions
to wrap all referenced Rust identifiers, including Default, max_mismatches,
min_distance_diff, and cache_size, in backticks; apply the same formatting to
any other newly added documentation comments in this file.
- Around line 67-69: Update the queue assertions in the test around
CorrectStepConfig and profile.output_queues to destructure each
QueueSpec::ByteBounded and assert its limit_bytes equals the configured
output_byte_limit. Reject other queue variants so the test verifies every output
queue has the expected byte bound.
- Around line 155-200: Extend run_batch_with_rejects_splits_kept_and_rejected to
cover corrected-input records, asserting apply_correction_to_raw preserves the
pre-correction UMI under cfg.original_tag when dont_store_original_umis is false
and omits that tag when it is true. Keep the existing corrected RX, routing,
identity, and emission assertions intact.
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Adds `pipeline/steps/correct/`, the typed `Step` wrapping UMI correction, completing the mid-step group #743 left unfinished. `steps/mod.rs` recorded `correct/` as blocked on the command-layer options refactor; `CorrectOptions` arrived with #744, so the block is lifted. The step needs a little more of `commands::correct` than that type alone. `feat-runall` refactored that file and `main` has since developed it independently -- main's copy is the larger of the two -- so taking the upstream version wholesale would revert main's work. Widen only what the step names instead: - `pub(crate)` on `credit_umi_metrics`, so the step and the legacy `execute` path share ONE definition of fgbio's per-segment UMI accounting rather than each carrying its own. - `pub(crate)` on `RejectionReason`, `TemplateCorrection` (plus its `matched`, `matches` and `rejection_reason` fields), and the `CollectedCorrectMetrics` fields, plus the three associated functions the step calls. - `CollectedCorrectMetrics::merge_into`, to fold the per-thread accumulator slots once the pipeline has drained. This is genuinely new -- the legacy path aggregates its slots inline. The legacy path is unchanged. Metrics follow `execute` exactly, which follows fgbio: every template counts once in `templates_processed`; per-UMI crediting happens for every template that reached matching, *before* the keep/reject decision, so a template rejected on one segment still credits its matched segments and credits the all-`N` bucket only for the segments that actually failed; and missing-UMI and wrong-length templates credit no per-UMI bucket at all (`CorrectUmis.scala:199-202`). `per_umi_crediting_matches_fgbio` pins each of these; its `AAAA-TTTT` case is the discriminating one, since a template rejected on its second segment must still credit `AAAA` for its first. Both output shapes share one `run_batch`, which takes an optional rejects sink, so that accounting has a single definition and cannot drift between them. Forward-ports one behaviour the ported source predates: `apply_correction_to_raw` grew an `original_tag` parameter, so `CorrectStepConfig` carries `original_tag` beside `umi_tag`, both derived from `Target`. The module is `#![allow(dead_code)]` until the command rewiring gives it a caller: the surface cannot be `pub` without leaking `pub(crate)` command internals. The tests build `CorrectOptions` explicitly rather than via `Default`, which upstream got from the `multi_options` macro -- deriving it here would yield `cache_size: 0`, contradicting the flag's `default_value` and tripping a ported assertion that the default is non-zero. No command is rewired, so nothing executes on the ported path yet; that starts at R2.
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Adds `pipeline/steps/correct/`, the typed `Step` wrapping UMI correction, completing the mid-step group #743 left unfinished. `steps/mod.rs` recorded `correct/` as blocked on the command-layer options refactor; `CorrectOptions` arrived with #744, so the block is lifted. The step needs a little more of `commands::correct` than that type alone. `feat-runall` refactored that file and `main` has since developed it independently -- main's copy is the larger of the two -- so taking the upstream version wholesale would revert main's work. Widen only what the step names instead: - `pub(crate)` on `credit_umi_metrics`, so the step and the legacy `execute` path share ONE definition of fgbio's per-segment UMI accounting rather than each carrying its own. - `pub(crate)` on `RejectionReason`, `TemplateCorrection` (plus its `matched`, `matches` and `rejection_reason` fields), and the `CollectedCorrectMetrics` fields, plus the three associated functions the step calls. - `CollectedCorrectMetrics::merge_into`, to fold the per-thread accumulator slots once the pipeline has drained. This is genuinely new -- the legacy path aggregates its slots inline. The legacy path is unchanged. Metrics follow `execute` exactly, which follows fgbio: every template counts once in `templates_processed`; per-UMI crediting happens for every template that reached matching, *before* the keep/reject decision, so a template rejected on one segment still credits its matched segments and credits the all-`N` bucket only for the segments that actually failed; and missing-UMI and wrong-length templates credit no per-UMI bucket at all (`CorrectUmis.scala:199-202`). `per_umi_crediting_matches_fgbio` pins each of these; its `AAAA-TTTT` case is the discriminating one, since a template rejected on its second segment must still credit `AAAA` for its first. Both output shapes share one `run_batch`, which takes an optional rejects sink, so that accounting has a single definition and cannot drift between them. Forward-ports one behaviour the ported source predates: `apply_correction_to_raw` grew an `original_tag` parameter, so `CorrectStepConfig` carries `original_tag` beside `umi_tag`, both derived from `Target`. The module is `#![allow(dead_code)]` until the command rewiring gives it a caller: the surface cannot be `pub` without leaking `pub(crate)` command internals. The tests build `CorrectOptions` explicitly rather than via `Default`, which upstream got from the `multi_options` macro -- deriving it here would yield `cache_size: 0`, contradicting the flag's `default_value` and tripping a ported assertion that the default is non-zero. No command is rewired, so nothing executes on the ported path yet; that starts at R2.
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Ports
pipeline/steps/correct/— the typedStepwrapping UMI correction — completing the mid-step group that #743 left unfinished.Why now
steps/mod.rsrecordedcorrect/as blocked on the command-layer options refactor.CorrectOptionsarrived with #744, so the block is lifted — but the step needs more ofcommands::correctthan just that type, which is why this PR also touches the command layer.What it does to
commands/correct.rsfeat-runallrefactored this file;mainhas since developed it independently, andmain's copy is the larger of the two (4,212 vs 3,257 lines, a 726/1,681 diff). Takingfeat-runall's version wholesale would revert that work, so this widens only what the step actually names:pub(crate)oncredit_umi_metrics, so the step and the legacyexecutepath share one definition of fgbio's per-segment UMI accounting instead of each carrying its own.pub(crate)onRejectionReason,TemplateCorrection(and itsmatched,matches,rejection_reasonfields), and theCollectedCorrectMetricsfields.CollectedCorrectMetrics::merge_into, to fold the per-thread accumulator slots after the pipeline drains. Genuinely new — the legacy path aggregates its slots inline.No behaviour change on the legacy path.
Metrics parity
This is the part worth reviewing closely, because no CI job runs fgbio. Metrics follow
executeexactly, which follows fgbio:missing_umisonly — no per-UMI bucket (CorrectUmis.scala:199-202)wrong_lengthonly —matchesis empty, so no bucketNbuckettemplates_processedcounts every template exactly once.per_umi_crediting_matches_fgbiopins all four rows; each case fails if the corresponding credit is wrong.Both output shapes share one
run_batchtaking an optional rejects sink, so this accounting has a single definition and cannot drift between them.One forward-port
apply_correction_to_rawgrew anoriginal_tag: [u8; 2]parameter onmainthat the ported source predates.CorrectStepConfignow carriesoriginal_tagalongsideumi_tag, both derived fromTarget(sequence_tag()/original_tag()).Two deliberate deviations from the ported source
#![allow(dead_code)]on the module. Every item ispub(crate), because the config namesCollectedCorrectMetrics, which ispub(crate)— so the surface cannot bepubwithout leaking command internals. Until the command rewiring gives it a caller, nothing outside the module's own tests constructs it. Theallowis scoped to this module and should be deleted by the PR that adds the caller.CorrectOptions::default(). Upstream got one from themulti_optionsmacro;main's hand-writtenCorrectOptionshas none, and derivingDefaultwould yieldmax_mismatches: 0,min_distance_diff: 0,cache_size: 0— none of which match the flags'default_values. One ported test asserteddefault cache_size > 0, which such a derive would have made panic. The tests build the options explicitly instead, so no misleadingDefaultlands on a public type.The two copy-pasted
*_profiletests are folded into one#[rstest]case table.Sequencing
Additive: no command is rewired, so nothing executes on the ported path yet. This is within R1, the last additive-only phase; the "every PR leaves a command on the ported path" rule starts at R2.
Verification
Full local gate green —
ci-fmt,ci-lint,ci-tag-literals,ci-publish-order,ci-doc,ci-test.Risk: command output changes: none until the step is wired; tests pin corrected UMIs, reject routing, and fgbio-compatible metrics;
unsafe: none, so noCLAUDE.mdallowlist update applies; memory, queue, and backpressure policy: none.Add the typed
CorrectStepwrapper for UMI correction. Expose required correction internals withpub(crate)visibility. Forwardoriginal_tagand share batch processing across kept-only and reject outputs. Add coverage for correction, rejection, metrics, output framing, and worker state.