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refactor(filter): retire the legacy single-threaded path; the chain is the only path - #924
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ChangesDeclarative filter execution
Estimated code review effort: 4 (Complex) | ~45 minutes Merge Risk: 🔵 Low · up to The filter cutover retains a minor documentation-formatting issue in a test helper, with no indicated effect on filter behavior or output. Sequence Diagram(s)sequenceDiagram
participant FilterExecute
participant ExecuteChain
participant DeclarativeChain
participant FilterOutputs
FilterExecute->>ExecuteChain: dispatch every run
ExecuteChain->>DeclarativeChain: build and execute filter chain
DeclarativeChain->>FilterOutputs: write BAM, rejects, and statistics
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #924 +/- ##
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- Coverage 94.04% 94.04% -0.01%
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Files 302 302
Lines 152831 152281 -550
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- Hits 143732 143207 -525
+ Misses 9099 9074 -25 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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In `@tests/integration/test_filter_cutover_parity.rs`:
- Around line 403-408: Strengthen the assertions around the pair_kept checks to
compare exact (read name, flags) multisets for both accepted and rejected
outputs in each filter_by_template mode. Verify single-read mode retains pair R1
with FIRST_SEGMENT and rejects only pair R2, while also ensuring low_depth
records are neither duplicated nor substituted; preserve the existing
template-mode expectation that the entire pair template is rejected.
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src/lib/commands/filter.rssrc/lib/pipeline/chains/builder.rssrc/lib/pipeline/chains/commands/filter.rssrc/lib/pipeline/steps/group/queryname.rssrc/lib/pipeline/steps/parse/decode.rstests/integration/main.rstests/integration/test_filter_command.rstests/integration/test_filter_cutover_parity.rs
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In `@tests/integration/test_filter_cutover_parity.rs`:
- Line 448: Replace the substring assertions around the total_reads,
passed_reads, and failed_reads checks with TSV row parsing that extracts each
named field and compares its value exactly to the expected total, passed, and
failed values. Preserve the existing test diagnostics for malformed or missing
statistics rows.
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tests/integration/test_filter_cutover_parity.rs
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In `@tests/integration/test_filter_cutover_parity.rs`:
- Line 135: Update the documentation comment describing the mapped consensus
read to wrap the parameter identifier name in backticks, while leaving the
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tests/integration/test_filter_cutover_parity.rs
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…s the only path `Filter::execute` no longer branches on `--threads`: it runs its pre-flight validation (io.validate, reject_output_collisions, reference existence, validate_parameters) and then always dispatches to the declarative chain builder via execute_chain. The serial no-`--threads` unified-pipeline path is removed: the two mode entry points (execute_threads_mode_template / _single_read), the run_filter_pipeline executor, build_filter_pipeline_config, the FilterProcessedBatchRaw batch type and its MemoryEstimate impl, the Filter setup_pipeline/process_captures delegating wrappers, the Filter::write_filter_stats writer, and the advance_progress / progress_heartbeat_total helpers (with their unit tests) all go, along with the imports they alone used (unified_pipeline::*, grouper::*, template::TemplateBatch, LibraryIndex, create_bam_reader_for_pipeline_with_opts, OperationTimer, build_pipeline_config, serialize_raw_bam_records, AHashMap, Ordering). Absent `--threads`, the chain runs at a single worker. Every user-observable diagnostic the serial path emitted is already produced by the chain path in ChainBuilder::add_filter and its finalize hooks: the CRC log (from execute_chain), the Starting Filter banner + Input/Output/Reference/parameter lines, the OperationTimer, the query-grouped input check, `@PG` injection, the Processed/kept/rejected summary, the Total bases masked line, the rejects BAM, and the --stats TSV (success-only). Nothing user-observable is lost. The shared record engine (process_record_raw and its check_filters_raw/check_duplex_filters_raw/ check_no_call_and_quality helpers, FilterOptions::setup_pipeline/process_captures/ validate_parameters) is unchanged and still drives the chain. Adds tests/integration/test_filter_cutover_parity.rs: a no-`--threads` run now emits the chain-only pipeline banner (the RED->GREEN cutover discriminator), and its kept records + rejects BAM (byte-identical modulo @pg) and --stats TSV match the frozen pre-removal serial baseline binary via FGUMI_BASELINE_BIN, degrading to a self-consistency oracle when unset. The corpus mixes single-end reads with a genuine paired template (R1 passes, R2 fails) so the filter-by-template cases exercise template-drop, distinct from single-read mode; cases cover --min-reads filtering, --ref NM/UQ/MD regeneration, base masking (position + regenerated NM), both filter-by-template modes, --rejects, and --stats. Because the post-cutover chain filter always takes the name_hash_only decode key (source_group_key_config), the reframed worker-count-independence tests in test_filter_command.rs can no longer guard that skip. That invariant is pinned directly at the decode consumer by a new unit test (decode::tests::name_hash_only_matches_full_key_grouping_when_rg_and_position_vary): name_hash_only reproduces the full key's name_hash and leaves all other fields at default even when RG/position vary, so filter's queryname grouping is unaffected — without needing FGUMI_BASELINE_BIN.
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What
Retire the legacy single-threaded
fgumi filterpath so the declarative chain builder is the only execution path.filterwas aunified_pipelinedefault consumer;execute()keeps its pre-flight validation and then always dispatches to the chain. Deleted: the--threadsbranch,execute_threads_mode_{template,single_read},run_filter_pipeline,build_filter_pipeline_config,FilterProcessedBatchRaw,Filter::write_filter_stats,advance_progress/progress_heartbeat_total, and now-dead imports (the shared engineprocess_record_raw+check_*+FilterOptions::*is kept). Stacked on #916. Output is byte-identical (modulo@PG).Parity analysis (done before deleting)
Every diagnostic the legacy path emitted is already produced by the chain (
ChainBuilder::add_filter+FilterFinalizeHook/FilterStatsFinalizeHook): the CRC line,Starting Filterbanner + params,OperationTimer, query-grouped rejection,@HD/@PG, kept/rejected/masked summary, the--rejectsBAM, the success-only--statsTSV, and the per-batch heartbeat. Nothing needed adding.Restoring the name_hash_only guard
Before this PR,
test_filter_chain_matches_single_threaded_with_rg_and_cb_variationcompared the chain'sname_hash_onlydecode key against the legacy path's full-key decode — the contrast that proved the RG/position skip was invisible to filtering. With the legacy path gone, both sides now usename_hash_only, so that test only proves worker-count invariance (its docstring was corrected to say so). To keep the skip guarded in-repo (withoutFGUMI_BASELINE_BIN), a new unit testdecode::tests::name_hash_only_matches_full_key_grouping_when_rg_and_position_varyassertsname_hash_onlyvs a fullGroupKeyConfigyield identical grouping for records whose RG/position vary (and that the full key genuinely varies, so the check is non-vacuous).Tests
tests/integration/test_filter_cutover_parity.rs— pins chain output == the pre-removal serial baseline viaFGUMI_BASELINE_BIN(kept records +--rejectsBAM byte-identical modulo@PG, plus the--statsTSV) across template, single-read, with-rejects, with-stats, single-read+rejects, single-read+stats. The corpus now includes a real paired template so thetemplatecase exercises template-drop (whole template rejected) distinct from single-read. The self-consistency oracle (default CI) is mode-aware and asserts the masked-base position + regeneratedNM.Full gate green (
cargo ci-test9958 passed / 31 skipped withFGUMI_BASELINE_BINset proving 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 shared--threadshelp text is reworded generically by the retag cutover PR (not re-touched here to avoid a merge conflict).Risk:
filteroutput may change; parity tests and the optional pre-removal baseline pin records, grouping, rejects, headers, and metrics. Consensus, sort order, and corrected UMIs: none.unsafe: none; CLAUDE.md allowlist: unchanged. Memory bounds and queue capacity: none; thread and backpressure policy: changed to declarative-chain scheduling with one worker when--threadsis absent.Fix: route all
filterexecutions through the declarative chain.NM, and grouping.