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feat(commands): project per-stage options out of the CLI structs (R1e-a) - #744
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Included review availability: 0 reviews are currently available. Based on recent review activity, included reviews refill at 1 per hour. WalkthroughThe change adds public stage option structs and CLI-to-configuration projection methods. It also centralizes group option resolution and adds tests for defaults, overrides, and projected values. ChangesStage option projections
Group configuration resolution
Estimated code review effort: 3 (Moderate) | ~25 minutes Merge Risk: 🟡 Moderate · up to The new stage configuration projections do not yet preserve all CLI behavior and still expose CLI-specific types, so future chain construction could silently omit options or remain coupled to the command layer. Merge should wait for these bounded API and behavior gaps to be fixed or explicitly accepted. Possibly related PRs
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main-runall #744 +/- ##
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Inline comments:
In `@src/lib/commands/codec.rs`:
- Around line 284-356: Propagate the consensus tie rule into all stage option
structs: in src/lib/commands/codec.rs lines 284-356, add the matching tie_rule
field to CodecOptions and copy self.consensus.tie_rule in to_codec_options; make
the equivalent changes in src/lib/commands/duplex.rs lines 230-298 for
DuplexOptions/to_duplex_options and src/lib/commands/simplex.rs lines 243-311
for SimplexOptions/to_simplex_options.
In `@src/lib/commands/correct.rs`:
- Around line 333-386: Preserve the CorrectUmis target selection in the
projection by adding the target field to CorrectOptions and populating it from
CorrectUmis::to_correct_options, so --target barcode and other target values
reach chain builders. Update the nearby documentation to describe UMI-correction
options rather than consensus-calling knobs.
- Around line 1748-1788: Update the to_correct_options_carries_every_tuning_flag
test to pass a non-default value such as 5 for --max-mismatches and assert that
opts.max_mismatches equals 5, ensuring CorrectUmis::to_correct_options projects
the CLI value rather than relying on the default.
Apply the same fix in `@src/lib/commands/filter.rs` around lines 1230 - 1292: The
same test weakness affects two unset filter flags.
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crates/fgumi-umi/src/assigner.rssrc/lib/commands/codec.rssrc/lib/commands/correct.rssrc/lib/commands/duplex.rssrc/lib/commands/filter.rssrc/lib/commands/group.rssrc/lib/commands/simplex.rssrc/lib/commands/zipper.rs
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Inline comments:
In `@src/lib/commands/codec.rs`:
- Around line 293-357: Thread the parsed allow_unmapped setting through the
public options projections for Codec::to_codec_options,
Duplex::to_duplex_options, and Simplex::to_simplex_options, adding the field to
each corresponding options struct. Add projection assertions for both enabled
and default-disabled values in src/lib/commands/codec.rs lines 293-357,
src/lib/commands/duplex.rs lines 242-298, and src/lib/commands/simplex.rs lines
255-311; all three sites require the same direct change.
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src/lib/commands/codec.rssrc/lib/commands/correct.rssrc/lib/commands/duplex.rssrc/lib/commands/filter.rssrc/lib/commands/group.rssrc/lib/commands/simplex.rs
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Inline comments:
In `@src/lib/commands/codec.rs`:
- Around line 307-350: Remove CLI-domain types from the public stage option
structs: in src/lib/commands/codec.rs lines 307-350, store the domain tie-rule
type and convert self.consensus.tie_rule in Codec::to_codec_options(); in
src/lib/commands/duplex.rs lines 256-303 and src/lib/commands/simplex.rs lines
269-316, store domain tie-rule and methylation-mode types and convert both
parsed values in each to_*_options() method using the existing From conversions.
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src/lib/commands/codec.rssrc/lib/commands/duplex.rssrc/lib/commands/simplex.rs
The chain builder needs each stage's tuning knobs without depending on how they were supplied, so it can construct a chain with no CLI struct behind it. This adds one plain `<Command>Options` struct per stage, plus a `to_<command>_options()` method that projects the parsed flags into it, for correct, group, simplex, duplex, codec, filter, and zipper. The structs deliberately do not derive `clap::Args`. Flattening them into the command structs would move the fields off those structs and rewrite every `self.<field>` reference and its tests, which buys the chain builder nothing — it only ever reads the values. That refactor belongs with the fused command that actually needs prefixed `--<stage>::<flag>` flags. As a result this change is additive: no CLI surface moves, and the existing suite covers the commands unchanged. Two option structs hold resolved rather than raw values, because grouping cannot be configured from the raw flags alone: - `GroupOptions::min_map_q` applies the default `execute` would apply. - `GroupOptions::effective_strategy` / `effective_edits` carry the `--no-umi` and identity-implies-zero-edits rules. Both now come from `GroupReadsByUmi::resolved_min_map_q` and `resolve_strategy_and_edits`, extracted from `execute` so the command and the chain builder read them from one place instead of duplicating the rules. `execute` keeps its own validation and override logging; the new methods only compute. A case table pins both sets of rules. `GroupOptions::index_threshold` keeps the richer `IndexThreshold` type rather than a bare count: the flag also accepts `always` / `never`, which a number cannot express. Each projection is covered by a test that drives the command through `try_parse_from` rather than a struct literal, so a renamed or unwired flag fails the test instead of silently compiling. `Strategy` gains `PartialEq`/`Eq` so the resolution table can assert on it.
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The chain builder needs each stage's tuning knobs without depending on how they were supplied, so it can construct a chain with no CLI struct behind it. This adds one plain `<Command>Options` struct per stage, plus a `to_<command>_options()` method that projects the parsed flags into it, for correct, group, simplex, duplex, codec, filter, and zipper. The structs deliberately do not derive `clap::Args`. Flattening them into the command structs would move the fields off those structs and rewrite every `self.<field>` reference and its tests, which buys the chain builder nothing — it only ever reads the values. That refactor belongs with the fused command that actually needs prefixed `--<stage>::<flag>` flags. As a result this change is additive: no CLI surface moves, and the existing suite covers the commands unchanged. Two option structs hold resolved rather than raw values, because grouping cannot be configured from the raw flags alone: - `GroupOptions::min_map_q` applies the default `execute` would apply. - `GroupOptions::effective_strategy` / `effective_edits` carry the `--no-umi` and identity-implies-zero-edits rules. Both now come from `GroupReadsByUmi::resolved_min_map_q` and `resolve_strategy_and_edits`, extracted from `execute` so the command and the chain builder read them from one place instead of duplicating the rules. `execute` keeps its own validation and override logging; the new methods only compute. A case table pins both sets of rules. `GroupOptions::index_threshold` keeps the richer `IndexThreshold` type rather than a bare count: the flag also accepts `always` / `never`, which a number cannot express. Each projection is covered by a test that drives the command through `try_parse_from` rather than a struct literal, so a renamed or unwired flag fails the test instead of silently compiling. `Strategy` gains `PartialEq`/`Eq` so the resolution table can assert on it.
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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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The chain builder needs each stage's tuning knobs without depending on how they were supplied, so it can construct a chain with no CLI struct behind it. This adds one plain `<Command>Options` struct per stage, plus a `to_<command>_options()` method that projects the parsed flags into it, for correct, group, simplex, duplex, codec, filter, and zipper. The structs deliberately do not derive `clap::Args`. Flattening them into the command structs would move the fields off those structs and rewrite every `self.<field>` reference and its tests, which buys the chain builder nothing — it only ever reads the values. That refactor belongs with the fused command that actually needs prefixed `--<stage>::<flag>` flags. As a result this change is additive: no CLI surface moves, and the existing suite covers the commands unchanged. Two option structs hold resolved rather than raw values, because grouping cannot be configured from the raw flags alone: - `GroupOptions::min_map_q` applies the default `execute` would apply. - `GroupOptions::effective_strategy` / `effective_edits` carry the `--no-umi` and identity-implies-zero-edits rules. Both now come from `GroupReadsByUmi::resolved_min_map_q` and `resolve_strategy_and_edits`, extracted from `execute` so the command and the chain builder read them from one place instead of duplicating the rules. `execute` keeps its own validation and override logging; the new methods only compute. A case table pins both sets of rules. `GroupOptions::index_threshold` keeps the richer `IndexThreshold` type rather than a bare count: the flag also accepts `always` / `never`, which a number cannot express. Each projection is covered by a test that drives the command through `try_parse_from` rather than a struct literal, so a renamed or unwired flag fails the test instead of silently compiling. `Strategy` gains `PartialEq`/`Eq` so the resolution table can assert on it.
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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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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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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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Aug 22, 2026
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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Aug 23, 2026
The chain builder needs each stage's tuning knobs without depending on how they were supplied, so it can construct a chain with no CLI struct behind it. This adds one plain `<Command>Options` struct per stage, plus a `to_<command>_options()` method that projects the parsed flags into it, for correct, group, simplex, duplex, codec, filter, and zipper. The structs deliberately do not derive `clap::Args`. Flattening them into the command structs would move the fields off those structs and rewrite every `self.<field>` reference and its tests, which buys the chain builder nothing — it only ever reads the values. That refactor belongs with the fused command that actually needs prefixed `--<stage>::<flag>` flags. As a result this change is additive: no CLI surface moves, and the existing suite covers the commands unchanged. Two option structs hold resolved rather than raw values, because grouping cannot be configured from the raw flags alone: - `GroupOptions::min_map_q` applies the default `execute` would apply. - `GroupOptions::effective_strategy` / `effective_edits` carry the `--no-umi` and identity-implies-zero-edits rules. Both now come from `GroupReadsByUmi::resolved_min_map_q` and `resolve_strategy_and_edits`, extracted from `execute` so the command and the chain builder read them from one place instead of duplicating the rules. `execute` keeps its own validation and override logging; the new methods only compute. A case table pins both sets of rules. `GroupOptions::index_threshold` keeps the richer `IndexThreshold` type rather than a bare count: the flag also accepts `always` / `never`, which a number cannot express. Each projection is covered by a test that drives the command through `try_parse_from` rather than a struct literal, so a renamed or unwired flag fails the test instead of silently compiling. `Strategy` gains `PartialEq`/`Eq` so the resolution table can assert on it.
nh13
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that referenced
this pull request
Aug 23, 2026
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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Prerequisite for porting the chain builder. Based on
main-runallrather than stacked on #736/#741/#743 — it touches onlysrc/lib/commands/, disjoint from those, so it can merge in parallel.Why
The chain builder needs each stage's tuning knobs without depending on how they were supplied, so a chain can be constructed with no CLI struct behind it. Today those knobs are reachable only as fields on the clap command structs.
This adds one plain
<Command>Optionsstruct per stage plus ato_<command>_options()projection, for correct, group, simplex, duplex, codec, filter, zipper.Why these are not
clap::ArgsFlattening them into the command structs — the shape the fused command will eventually want, so it can expose
--<stage>::<flag>— would move the fields off those structs and rewrite everyself.<field>reference and its tests. That buys the chain builder nothing: it only ever reads the values, and never touches clap. So that refactor is deferred to the change that actually needs prefixed flags.The consequence is that this PR is additive: no CLI surface moves, no existing field is relocated, and the existing suite covers the seven commands unchanged. The trade is that those fields get touched twice — once here, once when they become flattened
Args. The field names do not change, so nothing downstream churns.Resolved vs. raw values
Two
GroupOptionsfields hold resolved values, because grouping cannot be configured from the raw flags alone:min_map_qapplies the defaultexecutewould otherwise apply at run time.effective_strategy/effective_editscarry the--no-umiand identity-implies-zero-edits rules.Both now come from
GroupReadsByUmi::resolved_min_map_qandresolve_strategy_and_edits, extracted fromexecuteso the command and the chain builder read them from one place rather than duplicating the rules.executekeeps its own validation and its override log line; the new methods only compute. This is the only behavior-adjacent change in the PR, and a case table pins both sets of rules as a regression test for the extraction.GroupOptions::index_thresholdkeeps the richerIndexThresholdtype rather than a bare count, since the flag also acceptsalways/never.Testing
Each projection has a test that drives the command through
try_parse_fromrather than a struct literal, with non-default values throughout — so a renamed or unwired flag fails the test instead of silently compiling, and a field read from the wrong source fails rather than coincidentally matching its default. Zipper additionally has a defaults test, since an all-non-default assertion cannot catch a field hard-coded to a non-default constant.StrategygainsPartialEq/Eq(additive, fieldless enum) so the resolution table can assert on it.8322 → 8339 tests, all passing.
ci-fmt,ci-lint,ci-tag-literals,ci-doc(withRUSTDOCFLAGS="-D warnings"), andpublish-crates.sh --checkall pass.Deliberately not included
warn_unwired_pipeline_flagsis part of the same upstream surface, but it warns that--scheduleris a deprecated no-op. On this branch the pluggable scheduler is still live —SchedulerOptions::scheduleris aSchedulerStrategywith a default, not anOption, andunified_pipelinestill consumes it. Porting the warning now would announce a removal that has not happened, so it travels with the change that actually removes it.Risk: command output changes: none;
unsafe: none, andCLAUDE.mdallowlist: unchanged; memory bounds, queue capacity, and thread/backpressure policy: none. Fix: add stage option projections without changing CLI interfaces.CorrectOptions,GroupOptions,SimplexOptions,DuplexOptions,CodecOptions,FilterOptions, andZipperOptions.to_*_options()methods for each stage.PartialEqandEqtoStrategy.