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perf(zipper): reduce serial-merge CPU and allocations at 1-2 threads - #971
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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 change adds allocation-free CIGAR encoding, fused auxiliary-tag rebuilding with integer normalization, and reusable scratch buffers across zipper merge paths. Mate MC-tag updates now encode CIGAR data directly. ChangesCIGAR and mate-tag encoding
Auxiliary-tag normalization and zipper integration
Priority: ⬇️ Low Estimated code review effort: 4 (Complex) | ~45 minutes Change: Refactor Sequence Diagram(s)sequenceDiagram
participant merge_zipper_batch
participant ZipperMergeStep
participant merge_one_template_with
participant RawTagsEditor
merge_zipper_batch->>ZipperMergeStep: reuse auxiliary scratch buffer
ZipperMergeStep->>merge_one_template_with: pass scratch storage
merge_one_template_with->>RawTagsEditor: rebuild and normalize AS/XS
RawTagsEditor-->>merge_one_template_with: return rebuilt tags
Suggested labels: Merge Risk: ⚪ Minimal · up to The previously identified normalization gaps are addressed in the current implementation, so no actionable merge-blocking risk remains. 🚥 Pre-merge checks | ✅ 3✅ Passed checks (3 passed)
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Inline comments:
In `@src/lib/commands/zipper.rs`:
- Around line 735-763: The AS/XS normalization coverage check around
Template::from_records_inner must handle mapped records not reached by
primary_reads() and collect_mapped_indices() in release builds. Track coverage
in all builds, then either return the established error for any uncovered record
or explicitly normalize every uncovered mapped record before output; do not rely
solely on debug_assert!.
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crates/fgumi-raw-bam/src/cigar.rscrates/fgumi-raw-bam/src/lib.rscrates/fgumi-raw-bam/src/tags.rssrc/lib/commands/zipper.rssrc/lib/pipeline/steps/align_and_merge.rssrc/lib/template.rs
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #971 +/- ##
==========================================
- Coverage 96.12% 96.09% -0.04%
==========================================
Files 293 293
Lines 146660 147093 +433
==========================================
+ Hits 140975 141344 +369
- Misses 5685 5749 +64 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Inline comments:
In `@crates/fgumi-raw-bam/src/tags.rs`:
- Around line 2355-2356: Update rebuild_with_int_normalized to remove the
64-entry assumption in its seen-state tracking: replace the u64 bitmask and i <
64 filtering with scalable tracking that captures normalized entries at every
index, preserving the documented sequential behavior for normalize lists longer
than 64.
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crates/fgumi-raw-bam/src/tags.rssrc/lib/commands/zipper.rs
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Inline comments:
In `@crates/fgumi-raw-bam/src/tags.rs`:
- Around line 2425-2427: Update the loop over normalize to skip keys that occur
later, then retrieve the value from the matching captured slot before calling
append_signed_int_tag. Ensure repeated keys such as AS are emitted only once at
their last position while preserving values from captured and adds.
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Inline comments:
In `@crates/fgumi-raw-bam/src/tags.rs`:
- Around line 2307-2310: Update the normalization flow around rebuild_with to
detect duplicate keys in normalize and use the sequential path: rebuild once,
then call normalize_int_tag_to_smallest_signed for each key in order. Preserve
the existing fast path for unique keys, and add a regression case covering
repeated normalization keys with duplicate integer auxiliary entries.
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Standalone zipper normalized the AS/XS alignment-score tags to the smallest signed width in a dedicated per-record pass that, for every mapped record, ran roughly four linear find_tag_position scans plus two Vec::drain memmoves and two appends. Fold that normalization into the single aux rebuild that the tag-copy step already performs per record, via a new RawTagsEditor::rebuild_with_int_normalized, so the smallest-signed re-encoding rides along on a walk that already happens instead of a second full pass. The new primitive is byte-identical to rebuild_with followed by normalize_int_tag_to_smallest_signed per tag, including first-key-occurrence semantics on degenerate duplicate-key aux (only the first occurrence is captured and relocated; later duplicates and a non-integer first occurrence are left verbatim, matching find_int_tag). Oracle and property tests cover the captured, relocated, left-in-place, spill, empty, and duplicate-key branches. Records whose unmapped read carries no copyable tags are normalized standalone in the existing empty-adds branch. A mapped record that no unmapped primary selects is reached by neither the fused copy nor the empty-adds branch: Template::from_records accepts a supplementary/secondary record whose segment has no primary, and primary_reads() x collect_mapped_indices only visits segments an unmapped primary selects. A final fallback pass therefore normalizes any mapped record the copy did not, tracked by a coverage bitset built in all builds, so such a record is never written with an un-normalized AS/XS in release rather than only tripping a debug_assert. A regression test drives that path (a supplementary R2 with no R2 primary, unmapped side carrying only an R1 primary). Also thread a reusable aux-rebuild scratch buffer through process_raw and merge_one_template_with so its allocation is reused across templates on the serial merge thread and across the align-and-merge / ZipperMerge pipeline loops. Output is byte-identical for well-formed input; the only behavioural change is that a malformed template's previously un-normalized AS/XS is now normalized. This is rebased onto #964, which independently reduced this path to single-pass walks, so the throughput figures from the original measurement (taken against the pre-#964 baseline: ~18% wall / ~9% CPU at two threads on a 60.1M-record synthetic set) need re-measuring against current main before merging.
Template::fix_mate_info sets the MC tag by rendering the mate's CIGAR via cigar_to_string_from_raw, which allocates an intermediate Vec<u32> of ops and one String per CIGAR op (u32::to_string) on every call. Since fix_mate_info runs once per template, that is a large amount of transient allocation on a shared hot path (group, consensus and dedup fix mate info too). Add cigar_to_bytes_into, which formats the CIGAR directly into a caller-provided byte buffer with no intermediate ops vector and no per-op allocation, and use it at fix_mate_info's five call sites. A differential oracle test asserts it is byte-identical to cigar_to_string_from_raw across simple, multi-op, multi-digit, zero-length-op and truncated (fail-closed) inputs. Output is unchanged.
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Summary
Optimizes
fgumi zipper's serial merge — the path it runs in production, at 1–2 threads between the aligner and the sorter, where both CPU efficiency and wall time matter. Three changes, all byte-identical to the previous output.Risk verdict: (1) Output — none; byte-identical across commands, verified with
fgumi compare bams(IDENTICAL) and a per-record on-disk-integer-width check over 60,116,876 records. (2)unsafe— none added. (3) Memory / thread / backpressure policy — unchanged; a single aux-rebuild scratch buffer is now reused across templates rather than reallocated per record, so steady-state memory stays a function of record size, not input size.What changed
Fold AS/XS normalization into the tag-copy rebuild. The old path normalized the AS/XS alignment-score tags to the smallest signed width in a dedicated per-record pass that ran roughly four linear tag scans plus two aux memmoves and two appends for every mapped record. A new
RawTagsEditor::rebuild_with_int_normalizedperforms that re-encoding during the single aux rebuild the tag-copy step already does, so it costs no extra scan or memmove. It is byte-identical torebuild_withfollowed bynormalize_int_tag_to_smallest_signedper tag — including first-key-occurrence semantics on degenerate duplicate-key aux — and is covered by oracle and property tests.Reuse the aux-rebuild buffer. A scratch
Vecis threaded throughprocess_rawandmerge_one_template_withso its allocation is reused across templates on the serial merge thread and across the align-and-merge / ZipperMerge pipeline loops.Stringify the mate CIGAR without per-op allocations.
Template::fix_mate_infoset theMCtag viacigar_to_string_from_raw, which allocates an intermediateVec<u32>of ops plus oneStringper CIGAR op. The newcigar_to_bytes_intoformats directly into a caller-provided buffer with no per-op allocation.fix_mate_infois shared infrastructure, so group, consensus and dedup benefit too.Performance
Synthetic 60.1M-record set (chr17), at the production thread counts:
zipper is I/O-codec-bound at these thread counts (input BGZF decompression dominates), so the merge-side win is single-digit at one thread and larger at two, where the serial merge thread is the wall-gating stage.
Validation
fgumi compare bams: IDENTICAL (0 content diffs, 60,116,876 records) against the pre-change binary.-D warnings -W pedantic, fmt, nextest plus doctests.Follow-on (not in this PR)
Scaling zipper beyond ~2 threads is a separate change: decompose the merge into a chain pipeline (parallel decode of the two inputs, a serial zip step, a parallel per-template merge step, parallel compress) so higher
--threadsfan out without raising per-record CPU. Left out deliberately — it trades CPU for wall and only helps the 4+ thread regime.Risk: No changes to grouping, consensus, sort order, corrected UMIs, or metrics output; byte-identical output was verified across 60,116,876 records. No
unsafechanges; noCLAUDE.mdallowlist update. No memory-bound, queue-capacity, thread, or backpressure policy changes.Fix: Reuse zipper scratch buffers and format mate CIGAR values without intermediate allocations.
cigar_to_bytes_into.Validation reports no on-disk differences and a passing workspace test suite. At two threads, wall time decreased 18% and CPU usage decreased 9%. At one thread, both decreased 3%.