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refactor(copy-umi): retire the legacy single-threaded path; the chain is the only path - #927
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WalkthroughCopy-UMI now uses the chain pipeline for every thread configuration. Finalize hooks preserve summary and metrics behavior. Error conversion retains full causes. Integration tests add shared fixtures and baseline parity coverage. ChangesCopy-UMI chain execution cutover
Estimated code review effort: 4 (Complex) | ~45 minutes Change: Refactor Merge Risk: 🔵 Low · up to Copy-UMI now always uses the chain pipeline. Failure-path coverage can still pass when no output file is created, leaving a bounded regression in failed-output behavior undetected until the test requires the output path to exist. 🚥 Pre-merge checks | ✅ 3✅ Passed checks (3 passed)
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #927 +/- ##
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- Coverage 94.45% 94.44% -0.01%
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Files 302 302
Lines 150873 150830 -43
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- Hits 142511 142456 -55
- Misses 8362 8374 +12 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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In `@tests/integration/test_copy_umi_cutover_parity.rs`:
- Around line 203-220: Extend the fallback assertions in the integration test
around read_name_and_rx and RECORD_SPECS to compare complete BAM record identity
and relevant header fields with the expected transformed input for all three
fallback cases, not only QNAME, RX, and metrics. Preserve the existing
FGUMI_BASELINE_BIN comparison when available and keep the current per-record
name and RX checks.
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Inline comments:
In `@tests/integration/test_copy_umi_cutover_parity.rs`:
- Line 129: The assert_alignment_fields_preserved oracle must enforce full
record identity without a baseline: populate fixture records with mate fields,
template length, non-RX auxiliary tags, and non-@PG header values, then compare
those values while excluding only the expected read-name, RX, and `@PG`
differences. Strengthen the assertions in assert_alignment_fields_preserved so
regressions dropping any preserved identity fields fail.
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Inline comments:
In `@tests/integration/test_copy_umi_cutover_parity.rs`:
- Around line 138-142: Strengthen the baseline-free oracle in the copy-UMI
parity test beyond reference_sequences() by comparing normalized input and
output headers while excluding only the expected `@PG` differences. Ensure records
such as `@HD` remain covered by the record-identity assertion, preserving the
existing behavior for expected program-record changes.
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Inline comments:
In `@tests/integration/test_copy_umi_cutover_parity.rs`:
- Around line 461-462: Extend the failure case around run_copy_umi and the
--fail-if-tag-present argument to assert the state of current_out after the
expected error. Compare it with the baseline output state when available,
accounting for the documented possibility of a partial BAM, so output-state
regressions are detected in addition to stderr validation.
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Inline comments:
In `@tests/integration/test_copy_umi_cutover_parity.rs`:
- Around line 233-234: Update recover_records_lenient so read_header failures
return the header-less empty-record state instead of panicking. Preserve the
existing lenient record-recovery behavior and ensure failed_output_state can
still produce a comparable FailedOutputState for zero-byte or truncated-header
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Inline comments:
In `@tests/integration/test_copy_umi_cutover_parity.rs`:
- Line 538: In the failed-output validation around failed_output_state, assert
current_state.exists before checking finalized and recovered-record values.
Preserve the existing partial-output assertions after confirming the output path
exists.
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… is the only path CopyUmi::execute() gated on --threads: unset ran a serial read->copy-umi->write loop (run_single_threaded), set routed through the declarative chain builder. Delete the serial loop and CollectedCopyUmiMetrics's serial-path use so execute() always runs through execute_chain, matching the C4 cutover already applied to other per-record-transform commands. The chain (add_copy_umi) already reproduced every diagnostic the serial path emitted (start/input/output banner, OperationTimer, progress heartbeat, overwrite warning + summary block, --metrics TSV), so no chain behavior changes here beyond the deletion. Add tests/integration/test_copy_umi_cutover_parity.rs: pins the chain-only output (BAM bytes modulo @pg, and the --metrics TSV) against the frozen pre-cutover baseline binary via FGUMI_BASELINE_BIN, and degrades to a non-vacuous self-consistency oracle (fixed expected RX values, independently pinned in umi::read_name's own unit tests) when the baseline is unavailable. Update test_copy_umi_command.rs's serial-vs-chain comments and three errors_on_malformed_name cases: those errors already flattened to Display-only once routed through the chain's step-failure reconstruction (an existing, documented framework property), and now every invocation takes that path, so the assertions are updated to the outer context message that survives the flattening rather than the inner cause that no longer does.
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What
Retire the legacy single-threaded
fgumi copy-umipath so the declarative chain builder is the only execution path.execute()keeps its reader-free pre-flight validation and then always dispatches to the chain (Stage::CopyUmi), with or without--threads. DeletedCopyUmi::run_single_threadedand its now-dead serial-only imports. Output is byte-identical (modulo@PG).Parity analysis (done before deleting)
Every diagnostic the serial path emitted is already produced by the chain (
ChainBuilder::add_copy_umi+ its finalize hooks): theStarting copy-umi/Input/Output banner,OperationTimer, the periodic progress heartbeat, the=== Summary ===block + overwrite warning (sharedwarn_and_log_copy_umi_summary), the--metricsTSV (sharedwrite_copy_umi_metrics), and@HD/@PGhandling.CollectedCopyUmiMetricsis retained — the chain finalize hooks use it. Nothing needed adding.Error-diagnostic parity restored
Deleting the serial path made the chain the only path, and the chain step converted the UMI-normalization
anyhow::Errorwithio::Error::other, whoseDisplayrenders only anyhow's top context — so a malformed-name failure lost its inner cause (e.g.illegal character 'K') on the default no---threadsinvocation, which previously showed it. Fixed by flattening the full cause chain before it crosses theio::Errorboundary (io::Error::other(format!("{e:#}"))). Verified against the frozen baseline binary: the no---threadschain error now carries the sameextracting UMI from read name '…'context and the innerInvalid UMI '…' (illegal character '…')cause. Theerrors_on_malformed_nameand two-level fail-fast tests assert both levels again.Tests
tests/integration/test_copy_umi_cutover_parity.rs— pins the no---threadschain output against the frozen pre-removal serial baseline viaFGUMI_BASELINE_BIN(records byte-identical modulo@PG, plus the--metricsTSV) across default /--remove-umi/--reverse-complement-r-umis/ combined, RX-overwrite +--fail-if-tag-presentrejection, and a custom--field-delimiter. WhenFGUMI_BASELINE_BINis unset (default CI), the self-consistency oracle asserts the exact copiedRXvalues (e.g.rAAAA+CCCC→TTTT-CCCC, fromread_name's own unit tests) — a passthrough or a dropped reverse-complement/strip step fails it.serial/oracletwo-path framing intest_copy_umi_command.rs(case labels, function names, locals) is renamed to thread-count-consistency wording, since there is now one path exercised at different worker counts.tests/integration/helpers/copy_umi_fixtures.rs; the--metricsTSV is now read via the typedfgumi_metricsreader againstCopyUmiMetricrather than hand-parsed.Full gate green:
cargo checkin all three feature configs (default,--all-features,--no-default-features),ci-fmt/ci-lint/ci-doc, andci-test(9994 passed / 31 skipped) both with and withoutFGUMI_BASELINE_BINset proving byte-parity. Part of the per-command R6-0 legacy-path retirements; no user-facing behavior change (no---threadsnow runs the chain at a single worker).Risk: output changes only in
copy-umi, pinned by frozen-baseline and parity tests; grouping, consensus, sort order, and corrected UMIs: none;unsafe: none, andCLAUDE.mdneeds no update; memory bounds, queue capacity, and backpressure: none; thread policy changes because all runs use the chain configuration.copy-umipath.Stage::CopyUmi.@HD/@PGhandling.io::Errorboundary.