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feat(commands): give stage option structs a clap::Args surface for runall (PR A) - #907
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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. WalkthroughChangesCommand option types now support prefixed multi-stage CLI parsing through Multi-stage option integration
Estimated code review effort: 4 (Complex) | ~45 minutes Merge Risk: ⚪ Minimal · up to Sort option parsing now shares spill-setting validation while preserving existing standalone behavior; no current merge-blocking production risk is identified. Sequence Diagram(s)sequenceDiagram
participant MultiExtractRunallOptions
participant ExtractRunallOptions
participant ExtractOptions
MultiExtractRunallOptions->>ExtractRunallOptions: parse prefixed extract flags
ExtractRunallOptions->>ExtractRunallOptions: validate conflicting flags
ExtractRunallOptions->>ExtractOptions: project runtime settings
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+ Coverage 93.64% 93.67% +0.02%
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Inline comments:
In `@src/lib/commands/sort.rs`:
- Line 575: Move the zstd level-zero combination validation from
Sort::execute_sort into shared validation used by ChainBuilder::add_sort,
ensuring temp_codec and temp_compression are checked before constructing spill
stages. Reject zstd with compression level 0 while preserving valid codec and
level combinations.
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src/lib/commands/codec.rssrc/lib/commands/correct.rssrc/lib/commands/duplex.rssrc/lib/commands/extract.rssrc/lib/commands/filter.rssrc/lib/commands/group.rssrc/lib/commands/simplex.rssrc/lib/commands/sort.rssrc/lib/commands/zipper.rssrc/lib/pipeline/steps/correct/tests.rs
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Inline comments:
In `@src/lib/commands/group.rs`:
- Around line 765-766: Update both resolver documentation comments around the
effective grouping strategy logic to wrap Rust identifiers in backticks, using
`Strategy::Identity` for the enum variant and `edits` for the field or concept.
- Line 1723: Extend the staged-option default and round-trip tests around
MultiGroupOptions to assert verify matches the base default, and include verify
in GroupOptions::default() parity checks. In the prefixed-flag round-trip test,
parse the enabled --group::verify=true option through validate() and assert the
resulting verify value.
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src/lib/commands/group.rs
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Inline comments:
In `@src/lib/commands/group.rs`:
- Line 678: Update the Rust documentation comments near the references to
execute so both occurrences are formatted as the identifier `execute` using
backticks, without changing the surrounding wording.
- Around line 1791-1799: Extend the parity assertions in the GroupOptions
default/parsed test to cover min_umi_length, parallel_group_min_templates,
family_size_histogram, grouping_metrics, and metrics_prefix, comparing each
parsed field with the default instance d.
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Copy each 1:1 CLI field's #[arg] verbatim from Sort onto SortOptions,
skip the 2 chain-engine knobs (block_batch, file_granularity) that have
no CLI flag, and add an impl Default matching Sort::to_sort_options's
projection. Annotate with #[multi_options("sort", "Sort Options")] so a
future fused runall command can re-expose these as prefixed
--sort::<flag> options via the generated MultiSortOptions companion.
SortOptions is not parsed by clap anywhere today (it's built only via
Sort::to_sort_options), so this is purely additive: the standalone sort
command's CLI, to_sort_options, and every consumer are unchanged.
Adds clap::Args, an impl Default, and #[fgumi_cli_macros::multi_options] to CorrectOptions, generating MultiCorrectOptions for a future runall command. rejects_path is re-exposed directly as --correct::rejects rather than nesting RejectsOptions, which the macro rejects outright. min_distance_diff has no CLI default, so the macro lifts it to a staged-required field enforced by MultiCorrectOptions::validate(). CorrectUmis::to_correct_options and all consumers are unchanged; the standalone correct command's CLI behavior is unaffected.
Adds clap::Args, an impl Default, and #[fgumi_cli_macros::multi_options] to FilterOptions, generating MultiFilterOptions for a future runall command. rejects/stats are re-exposed directly as --filter::rejects and --filter::stats rather than nesting sub-structs, matching how Filter itself exposes them. methylation_mode is #[arg(skip)] since --methylation-mode is a cross-stage top-level runall flag, not a --filter:: flag; it falls back to MethylationMode::Disabled via FilterOptions::default(). min_reads has no CLI default, so the macro lifts it to a staged-required field enforced by MultiFilterOptions::validate(). Filter::to_filter_options and all consumers are unchanged; the standalone filter command's CLI behavior is unaffected.
Adds per-field #[arg] attributes (copied verbatim from
ConsensusCallingOptions / OverlappingConsensusOptions) and
#[fgumi_cli_macros::multi_options("duplex", "Duplex Options")] to
DuplexOptions, generating a MultiDuplexOptions companion for a future
fused runall command. tie_rule, allow_unmapped, io, rejects_opts,
stats_opts, read_group, methylation_mode, and reference are #[arg(skip)]
(the latter two are cross-stage runall flags landing in a later PR;
the rest are hidden or data-carrier fields).
DuplexOptions is not flattened anywhere by this change; Duplex,
to_duplex_options, and DuplexOptions::consensus()/overlapping() are
untouched.
Adds per-field #[arg] attributes (copied verbatim from
ConsensusCallingOptions / OverlappingConsensusOptions) and
#[fgumi_cli_macros::multi_options("simplex", "Simplex Options")] to
SimplexOptions, generating a MultiSimplexOptions companion for a future
fused runall command. tie_rule, allow_unmapped, io, rejects_opts,
stats_opts, read_group, methylation_mode, and reference are #[arg(skip)]
(the latter two are cross-stage runall flags landing in a later PR; the
rest are hidden or data-carrier fields). min_reads has no default_value
on the standalone command, so the macro lifts it to a staged-required
field on MultiSimplexOptions.
SimplexOptions previously had no Default impl; this adds one (min_reads
defaults to 1, matching the smallest valid family size, since it is
never read back through the staged-required validate() path).
SimplexOptions is not flattened anywhere by this change; Simplex,
to_simplex_options, and SimplexOptions::consensus()/overlapping()/
validate_read_bounds() are untouched.
Adds per-field #[arg] annotations matching GroupReadsByUmi's flags and
the #[fgumi_cli_macros::multi_options("group", "Group Options")] macro
to GroupOptions, so it can be re-exposed as a prefixed --group::* flag
set for a future runall stage. strategy has no default, so the macro
lifts it to a staged-required field enforced by validate() rather than
clap. effective_strategy/effective_edits stay at their #[arg(skip)]
placeholders in this change; resolving them via
resolve_strategy_and_edits is deferred to a later change.
to_group_options, resolve_strategy_and_edits (both copies),
resolved_min_map_q, and the existing Default impl are untouched.
Adds per-field #[arg] attrs and #[fgumi_cli_macros::multi_options("codec",
"Codec Options")] to CodecOptions, mirroring the pattern already landed for
DuplexOptions/SimplexOptions. Codec has no overlapping/methylation/reference
fields, so its field set is a strict subset of duplex/simplex's. Also adds
the (previously missing) Default impl, matching the standalone codec
command's defaults.
to_codec_options() and CodecOptions::validate() are untouched -- both keep
reading the same flat fields.
Add a runall-only clap::Args variant of extract's options. The standalone Extract CLI struct owns --output and the flattened engine sub-structs (threading/compression/scheduler/queue-memory), so it cannot be flattened into a fused runall command directly. ExtractRunallOptions mirrors the current Extract CLI-struct field shapes minus those, carries the multi_options macro so runall can re-expose each field as --extract::<flag>, and provides a verbatim-logic to_extract_options projection plus a validate() that re-enforces the three cross-field conflicts the macro requires be dropped from #[arg].
GroupOptions::resolve_strategy_and_edits and GroupReadsByUmi::resolve_strategy_and_edits carried identical logic for applying the --no-umi and identity-implies-zero-edits rules. Extract a single private free function and have both methods delegate to it, so the standalone command and the chain builder cannot drift apart by editing one copy and not the other.
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only still-valid issues, skip the rest with a brief reason, keep changes
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Inline comments:
In `@src/lib/commands/sort.rs`:
- Around line 685-687: Rename SortOptions::validate() to a name that clearly
identifies its zstd/level-0 validation purpose, avoiding confusion with
MultiSortOptions::validate(). Update any references to the renamed method while
preserving the existing reject_zstd_uncompressed behavior.
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src/lib/commands/group.rssrc/lib/commands/sort.rs
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…enforcement SortOptions::temp_compression and SortOptions::max_temp_files stated zstd-level-0 rejection and the fd-budget-overrun warning as unconditional properties, but both checks live only in Sort::execute_sort, not on SortOptions/MultiSortOptions itself; reword both field docs to attribute the check to the standalone command. CodecOptions' doc comment claimed duplex's --min-reads has no default_value, contradicting duplex.rs (it does, default_value = "1"); correct the comparison to name simplex, whose --min-reads is the one that's actually required. ExtractRunallOptions::validate doc now states explicitly that it re-enforces only the two macro-dropped conflicts_with checks (store-umi-quals/extract-umis-from-read-names and check-crc/no-check-crc), leaving the remaining Extract::validate checks (template-count, single_tag collision, read-structure non-emptiness) to the future runall command once it builds the FASTQ source.
…CLI defaults Each of the 9 pipeline stage option structs (SortOptions, CorrectOptions, FilterOptions, DuplexOptions, SimplexOptions, CodecOptions, ZipperOptions, GroupOptions, ExtractRunallOptions) carries a hand-written impl Default required by the multi_options macro (its generated Multi<X> code references X::default() for bare #[arg(skip)] fields). The existing parity tests only compare Multi<X>::validate() against the standalone command's projection, so a drift between impl Default and a #[arg(default_value...)] literal was never caught. Add one guard test per struct that parses the standalone command with only its required flags and asserts every default-bearing field equals X::default()'s value, so such a drift now fails CI. Required-no-default fields (min_reads for filter/simplex, strategy for group, min_distance for correct) are supplied but not asserted, since they have no CLI default to compare against. Carrier skip fields (io, rejects_opts, stats_opts, read_group, allow_unmapped) are excluded as tautological by construction and PartialEq-less; group's effective_strategy/effective_edits are checked directly against the deliberate PR-A skip default (Identity/0) rather than against the parsed projection.
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Gives each pipeline stage's projection option struct a
clap::Argssurface and a generated--<stage>::<flag>companion (Multi<X>via the in-repo#[fgumi_cli_macros::multi_options]proc-macro), so the upcomingfgumi runallcommand (PR B) can flatten them into one multi-stage chain. This PR is purely additive and behavior-preserving — no standalone command's CLI, projection (to_<stage>_options), or existing test changes. It is the mechanical, self-contained groundwork; PR B (therunallcommand itself) stacks on top.What changes
The nine plain
#[derive(Debug, Clone)]stage option structs —ZipperOptions,SortOptions,CorrectOptions,FilterOptions,DuplexOptions,SimplexOptions,GroupOptions,CodecOptions— each gain#[derive(clap::Args)], per-field#[arg(...)]copied 1:1 from the standalone command's own clap struct,#[arg(skip)]/#[arg(skip = <expr>)]for the non-CLI/derived fields, a hand-writtenDefault, and#[fgumi_cli_macros::multi_options("<prefix>", "<Heading>")]. A newExtractRunallOptionsclap::Args variant covers extract (the standaloneExtractowns--outputand the engine sub-structs, so it can't be reused directly).These structs are parsed by clap nowhere today — they are pure projection targets built via each command's
to_<stage>_options(&self). Addingclap::Argsis therefore additive: theMulti<X>companions and their generatedvalidate()are flattened into no command in this PR; nothing consumes them until PR B.Correctness
Every converted struct gets a default-parity test (
Multi<X>parsed with only required flags →.validate()compared field-by-field against the standalone command's projection), proving no#[arg]default drifted during the copy; plus a round-trip test and, where a field is staged-required, a validation-error test. Each hand-writtenDefaultalso gets aDefault-vs-CLI-parse guard test so theimpl Defaultliterals can't silently drift from the#[arg(default_value)]attributes.Full local gate green:
cargo ci-fmt,cargo ci-lint(clippy-D warnings -W clippy::pedantic),RUSTDOCFLAGS="-D warnings" cargo ci-doc, andcargo ci-test(9920 passed, 31 skipped), pluscargo checkwith--no-default-featuresand--all-features.Deliberate decisions (intentional, called out for review)
effective_strategy/effective_editsare left at their skip defaults (Identity/0) in this PR and resolved in PR B; the Group default-parity test excludes them and asserts(Identity, 0)with a comment. A shared free function now backsGroupOptions::resolve_strategy_and_editsandGroupReadsByUmi::resolve_strategy_and_editsso the rule has a single home.ExtractRunallOptionshas noquality_encodingfield (mirrors the standaloneExtractCLI struct;to_extract_optionshardcodesQualityEncoding::Standard, the placeholder the chain FASTQ source overrides at run time). It drops the threeconflicts_withattributes the macro rejects and re-enforces them inExtractRunallOptions::validate().--extract::read-structuresis required (diverges from the standalone's+Tdefault — runall always demands it).ExtractRunallOptions::validate()re-enforces only those two conflicts. The remainingExtract::validatechecks (template-count 1–2,single_tagreserved-tag collision, non-empty read structures) are PR B's responsibility when it builds the FASTQ source — documented on the method.--<consensus>::allow-unmappedand--<consensus>::tie-ruleare not exposed (both are#[arg(skip)]on the consensus structs) — deferred follow-ups.ExtractRunallOptionsremains a hand-maintained field set rather than sharing a#[command(flatten)]sub-struct withExtract: themulti_optionsmacro deliberately rejects field-level#[command(flatten)](it needs each field's#[arg]to re-prefix it), so a shared flattened sub-struct cannot compile. The duplication is the accepted cost of extract's runall variant needing CLI-only fields the projection doesn't.Reading order
crates/fgumi-cli-macros/tests/real_world.rsfor theMulti<X>flatten-wrapper test pattern (context, unchanged here).src/lib/commands/zipper.rs— the cleanest conversion (all fields 1:1).src/lib/commands/sort.rs/group.rs— conversions with skip fields, a type change (min_map_q), and staged-required lifting.src/lib/commands/extract.rs— the net-newExtractRunallOptions.Risk: command output changes—none;
unsafechanges—none, with noCLAUDE.mdallowlist update needed; memory bounds, queue capacity, and thread/backpressure policy changes—none. No output fix is required.Adds
clap::Argssupport and prefixedMulti<X>variants for pipeline stage options. AddsExtractRunallOptionswith projection and validation. Aligns defaults with standalone CLI defaults. Adds parsing, validation, round-trip, projection, and default-parity tests. Shares Group strategy and edit resolution.