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perf(filter): decode-free BAM fast path for single-record filter - #961
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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. WalkthroughThe pipeline adds a decode-free BAM path for eligible single-record filters. It processes borrowed ChangesBAM raw-record filtering
Priority: ⬇️ Low Estimated code review effort: 4 (Complex) | ~45 minutes Change: Refactor Sequence Diagram(s)sequenceDiagram
participant BAMInput
participant PipelineBuilder
participant RawFilterStep
participant KeptBAM
participant RejectedBAM
BAMInput->>PipelineBuilder: construct eligible single-record filter chain
PipelineBuilder->>RawFilterStep: pass RecordBatch
RawFilterStep->>KeptBAM: emit kept records
RawFilterStep->>RejectedBAM: emit rejected records
Merge Risk: ⚪ Minimal · up to The BAM fast path preserves validated record handling and kept/rejected output routing, with template filtering retained on its decoded path. No actionable merge risk remains. 🚥 Pre-merge checks | ✅ 2 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (2 passed)
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #961 +/- ##
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- Coverage 96.09% 96.08% -0.02%
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Files 292 292
Lines 145174 145437 +263
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+ Hits 139510 139747 +237
- Misses 5664 5690 +26 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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In `@tests/integration/test_filter_command.rs`:
- Around line 947-950: Strengthen each new filter parity case by comparing
normalized BAM headers for both kept and rejects outputs using read_bam_output,
alongside the existing read_filter_records assertions. Preserve the existing `@PG`
normalization so differing --threads values do not cause false mismatches, and
apply this consistently to all newly added parity cases.
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tests/integration/test_filter_command.rs
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Route single-record `fgumi filter` (not --filter-by-template) over a BAM source through a borrowed RecordBatch instead of the owned DecodedRecordBatch decode, eliminating the per-record heap allocation and the dead GroupKey/name_hash computation the filter transform never reads. - Add `for_each_raw_record`: iterates a RecordBatch's borrowed record byte-ranges into one reused scratch RawRecord, validating each with `validate_record_for_decode` first so a truncated record still surfaces as a clean error (the fast path drops DecodeRecords, which otherwise ran that guard before the unchecked field accessors the transform uses). - Add `ChainTailKind::RecordBatch`, `first_stage_uses_raw_record_fast_path` (single-record filter only; --filter-by-template keeps the DecodedRecordBatch path its GroupByQueryname grouper needs), and a ParseBamRecords BAM preamble. - Add RecordBatch filter step builders reusing the identical process_record_raw_call transform and metric tally; add_filter selects them on the fast path and keeps the DecodedRecordBatch builders for SAM input. Output is byte-identical: the discarded key never reached the encoder. Covered by seam unit tests (scratch reuse, fail-closed, raw-vs-decoded framing parity), the fast-path selection tests, and the existing filter integration + cutover parity suites, which exercise single-record BAM filter end-to-end.
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First of three stacked PRs extending the decode-free path (from the
fgumi fastqno-key work) to the per-record-transform stages. This one converts single-recordfgumi filterand lands the shared seam the latercopy_umi/retagPRs reuse.What and why
A single-record filter (not
--filter-by-template) reads only the raw record — it never touches aGroupKey— yet its source decode was building an ownedVec<DecodedRecord>(one heap allocation per record) and computing aname_hashthat is immediately discarded. On a BAM source this now takes the borrowedRecordBatchfast path (ParseBamRecords) instead ofDecodeRecords, eliminating the per-record heap allocation and the dead key computation. The per-record copy count is unchanged; the win is allocation-elimination (themi_*malloc/free slice from the earlier profiling), so it is framed as a mechanism, not a benchmarked percentage — a representative benchmark is a follow-up.Output is byte-identical: the discarded key never reached the encoder, and the per-record transform is the same
process_record_raw_callon both paths.How
for_each_raw_record(commands/mod.rs): iterates aRecordBatch's borrowed record byte-ranges into one reused scratchRawRecord(cleared, not truncated, each record), callingvalidate_record_for_decodefirst — the fast path dropsDecodeRecords, which otherwise ran that guard, so without it a truncated record would panic the unchecked field accessors instead of erroring cleanly.filter_one_record(commands/filter.rs): the single per-record body — transform, masked-bases tally, keep/reject routing — shared by all four single-record filter builders (decoded/raw × no-rejects/with-rejects), so the owned and borrowed paths cannot drift.builder.rs):ChainTailKind::RecordBatch,first_stage_uses_raw_record_fast_path(single-record filter only;--filter-by-templatekeeps theDecodedRecordBatchpath itsGroupByQuerynamegrouper needs, with a defensive bail if that pairing is ever reached), aParseBamRecordsBAM preamble, andadd_filterselecting the raw builders on theRecordBatchtail. SAM source keeps theDecodedRecordBatchpath unchanged.Scope
Out of scope (later PRs / deliberate): the SAM-source fast path,
--filter-by-template, andcopy_umi/retag.Tests
cargo ci-test: 10200 passed, 0 failed. New coverage: thefor_each_raw_recordseam (scratch reuse without stale tail; fail-closed on a truncated record; raw-vs-decoded framing/routing byte-parity under a length-changing mutation), the fast-path selection predicate, and a single-record--rejectschain-vs-single-worker parity test exercising the with-rejects fast path end-to-end. The existing filter integration + cutover-parity suites (single-record BAM, no-rejects) stay green.Reviewed with a CodeRabbit-style pass and a multi-agent gauntlet (10 findings, all addressed): the doc-placement fix, the
filter_one_recordde-duplication, the scratch-reuse doc correction, and the with-rejects test.Risk: output changes none;
unsafechanges none and CLAUDE.md allowlist changes none; memory bounds, queue capacity, and thread/backpressure policy changes none. Fix: add a validated raw BAM fast path with scratch-buffer reuse while preserving decoded paths where required.RecordBatchdata.