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refactor(extract): retire the legacy single-threaded path; the chain is the only path - #922
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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. WalkthroughExtract now uses the declarative chain for all executions, including runs without ChangesExtract chain execution cutover
Estimated code review effort: 4 (Complex) | ~45 minutes Merge Risk: ⚪ Minimal · up to Extract now consistently uses the declarative chain, with added parity coverage for supported input forms. No concrete merge-blocking risk remains. Sequence Diagram(s)sequenceDiagram
participant Extract
participant ChainBuilder
participant FASTQSource
participant PipelineWorkers
participant BAMWriter
Extract->>ChainBuilder: dispatch execute_chain
ChainBuilder->>FASTQSource: open and decode FASTQ
FASTQSource->>PipelineWorkers: provide detected quality and records
PipelineWorkers->>BAMWriter: construct and write BAM records
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #922 +/- ##
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+ Coverage 93.55% 94.02% +0.46%
==========================================
Files 301 302 +1
Lines 150626 152566 +1940
==========================================
+ Hits 140923 143452 +2529
+ Misses 9703 9114 -589 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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In `@tests/integration/test_extract_cutover_parity.rs`:
- Around line 314-320: The default-CI fallback oracle in assert_self_consistent
must validate every output record’s QNAME, paired/first/last flags, and numeric
quality values in addition to sequence, RX, and RG. Use unambiguous Phred+33
input qualities and compare each record against the expected identity and flags
while preserving the existing per-record checks.
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src/lib/commands/extract.rssrc/lib/pipeline/chains/commands/extract.rstests/integration/main.rstests/integration/test_extract_command.rstests/integration/test_extract_cutover_parity.rs
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…is the only path `Extract::execute` no longer branches on `--threads`: it runs its pre-flight validation (`self.validate()`) and then always dispatches to the declarative chain builder via `execute_chain`. The serial in-process oracle is removed — `process_singlethreaded` (the read->extract->write loop), `make_raw_records` (its RawBamWriter record builder), `build_template_record`, the serial `create_header`/`add_to_read_group`, and `validate_read_names_match` — along with the imports only they used (OperationTimer, ProgressTracker, RawBamWriter/ create_raw_bam_writer, ReadSetIterator, fastq_out_of_sync_error, and the header-builder noodles imports). Absent `--threads`, the chain runs at a single worker. Every user-observable behavior the serial tail produced is already produced by the chain: - Diagnostics: the chain emits the `Extracting UMIs` OperationTimer + the `Processed records` progress the serial path had, PLUS the `Starting Extract` banner, Input/Output lines, and `Extract: completed (N records emitted)` summary (a strict superset — nothing is lost). - Features confirmed on the chain before removal: interleaved input (SourceSpec::InterleavedFastq), two-file input (SourceSpec::Fastqs), read structures, `--check-crc`/`--no-check-crc`, UMI-from-read-names, and the QX/CY/QT quality-storage flags — all carried in ExtractOptions and consumed by the shared reader-open/record-build helpers. - Read-name-mismatch and out-of-sync rejection: the serial `validate_read_names_match`/`fastq_out_of_sync_error` messages are replaced by the chain FASTQ source's own checks (same rejection, the wording a `--threads` run already produced). Two unit tests' expected messages are updated accordingly. The record-building free function `make_raw_records_from_fastq_set` is now the single per-read builder (the serial and static copies are both gone), so there is no second copy to keep in sync. Adds tests/integration/test_extract_cutover_parity.rs: a no-`--threads` run now emits the chain's `Starting Extract` banner (the RED->GREEN cutover discriminator), and its output records (byte-identical modulo @pg) match the frozen pre-removal serial baseline binary via FGUMI_BASELINE_BIN across two-file, interleaved, and BGZF `--check-crc` inputs, degrading to a self-consistency oracle when unset. The chain-vs-oracle determinism tests in test_extract_command.rs are reframed as no-`--threads`-vs-`--threads` cross-worker-count parity.
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What
Retire the legacy single-threaded
fgumi extractpath so the declarative chain builder is the only execution path (extractcarried the largest serial oracle of the per-command cutovers).execute()keeps all its pre-flight validation and then always dispatches to the chain; the serial engine and its now-dead helpers are deleted.Output is unchanged: the chain is a strict superset of the serial path.
Parity analysis (done before deleting)
Confirmed the chain already supports every extract feature before removing the serial path: interleaved (
SourceSpec::InterleavedFastq) and two-file (SourceSpec::Fastqs) input, read structures,--check-crc/--no-check-crc, UMI-from-read-names, and the QX/CY/QT quality-storage flags. Diagnostics: theExtracting UMIstimer andProcessed recordsprogress line were already on the chain; the chain additionally emitsStarting Extract+ Input/Output banners and anExtract: completedsummary (additive). The read-name-mismatch / out-of-sync rejection is now produced by the chain FASTQ source — the exact wording a--threadsrun already emitted (two#[should_panic]unit tests updated from "Read names do not match" to "FASTQ read name mismatch"). Nothing user-observable is lost.Deleted (serial-only):
process_singlethreaded,make_raw_records,build_template_record, serialcreate_header/add_to_read_group,validate_read_names_match, and their now-dead imports.Tests
tests/integration/test_extract_cutover_parity.rs— pins chain output == the pre-removal serial baseline viaFGUMI_BASELINE_BIN(records byte-identical modulo@PG) across two-file, interleaved, and--check-crc. When the env var is unset, the self-consistency oracle validates every produced record (sequence +RX+RG) against the input read structure — not just the first pair — so default CI genuinely pins the full output.no_threads_matches_threaded_barcode_and_annotate_tagsnow feeds per-position-distinct qualities and asserts exactCY/QT/QXbyte values (not just presence).Full gate green (
cargo ci-test9957 passed / 31 skipped withFGUMI_BASELINE_BINset proving cutover byte-parity, plus fmt/lint/doc and--no-default-features/--all-features). Part of the per-command R6-0 legacy-path retirements; no user-facing behavior change. (No---threadsnow runs the chain at a single worker — the intended chain-only architecture.)Risk: extract data output changes: none; parity tests pin output.
unsafechanges: none; CLAUDE.md needs no update. Thread policy changes: no---threadsuses one chain worker; queue capacity and backpressure remain unchanged.extractexecutions through the declarative chain.PLbehavior.