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perf(zipper): fold per-record PG/AS/XS aux scans into single-pass walks - #964
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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 raw BAM crate now exposes checked integer decoding. The zipper merge path now performs single-pass auxiliary tag copying and AS/XS normalization with reusable scratch storage. Tests cover precedence, ordering, duplicate handling, byte preservation, and malformed tails. ChangesRaw BAM integer decoding
Auxiliary tag merge and normalization
Priority: ⬇️ Low Estimated code review effort: 4 (Complex) | ~45 minutes Change: Refactor Sequence Diagram(s)sequenceDiagram
participant merge_raw_with
participant SinglePassTagCopy
participant SinglePassASXSNormalization
participant BAMAuxiliaryData
merge_raw_with->>SinglePassTagCopy: copy and upsert auxiliary tags
SinglePassTagCopy->>BAMAuxiliaryData: write filtered entries
merge_raw_with->>SinglePassASXSNormalization: normalize AS and XS
SinglePassASXSNormalization->>BAMAuxiliaryData: write normalized entries
Suggested labels: Merge Risk: ⚪ Minimal · up to No actionable merge risk remains; the optimized tag-processing paths preserve the established behavior for valid records. 🚥 Pre-merge checks | ✅ 3✅ Passed checks (3 passed)
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## main #964 +/- ##
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- Coverage 96.08% 96.04% -0.04%
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+ Hits 138447 138585 +138
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extract_int_value bundled the type-byte decode ladder (c/C/s/S/i/I) with the aux-slice positioning, so a caller that already holds a tag's value bytes (from an AuxTagsIter/TagEntry walk) could not reuse it without re-scanning for the position. Split the ladder into a public decode_int_value(type_byte, value_bytes) and make extract_int_value slice the value out and delegate. Removes the now single-use tag_value_bytes helper. Enables the zipper single-pass AS/XS normalize to decode a tag's value inline during its aux walk instead of duplicating the ladder. Tests cover decode_int_value per type, non-integer types, and short slices.
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In `@src/lib/commands/zipper.rs`:
- Around line 843-855: Update the AS/XS handling in the zipper tag-processing
function to track the last occurrence regardless of whether decoding yields an
in-range integer. Store the selected last entry as either its normalized integer
or raw representation, skip earlier duplicates, and emit only that final entry
so mixed-type duplicates preserve last-wins behavior.
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crates/fgumi-raw-bam/src/lib.rscrates/fgumi-raw-bam/src/tags.rssrc/lib/commands/zipper.rs
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merge_raw_with did several independent per-record aux scans on top of the tag-copy walk: a find_tag_type(PG) probe to choose the copy set (a full scan that fails on typical aligner output, which carries no per-record PG), and two normalize_int_tag_to_smallest_signed calls for AS and XS (each a find plus a remove scan, four scans in all). Profiling fgumi zipper (10.9M records, one thread) put find_tag_position at ~14% of CPU, dominated by these fixed per-record lookups now that the tag-copy loop no longer scans per tag. Replace them with two single-walk helpers that reuse a scratch buffer: - copy_unmapped_tags_single_pass copies the survivors, resolves PG precedence (keep the mapped read's PG, drop the unmapped one) in the same walk, and appends the copy set, so no separate has_pg scan is needed. - normalize_as_xs_single_pass normalizes AS then XS in one walk instead of four scans. Output is byte-identical: a strict `samtools view` md5 and `fgumi compare bams` both report 0 diffs across 10,941,868 records versus the prior binary. On the same run find_tag_position drops from ~14% to ~8% of CPU and the command is faster in every rep. All zipper/merge tests pass.
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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.
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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.
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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.
nh13
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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.
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Summary
Follow-up to #955-era
rebuild_withwork (stacked on #962). Profilingfgumi zipperat 1 thread — the realistic streaming setting (bwa-mem3 | fgumi zipper | fgumi sort), where zipper runs a single-thread tight loop — showed the merge is CPU-bound and serial, withfind_tag_positionstill ~14% of CPU after #962 removed the per-tag copy-loop scans. That 14% is now dominated by fixed per-record single-tag lookups that scan the aux from offset 0:find_tag_type(PG)— thehas_pgprobe, once per mapped record. Aligner output carries no per-recordPG, so this is a full aux scan that always fails.normalize_int_tag_to_smallest_signedforASandXS— each afindscan plus aremovescan, four scans per record.What changed
perf(zipper)— two single-walk helpers replace those scans, each reusing one scratch buffer across records:copy_unmapped_tags_single_passcopies the mapped record's tags, resolvesPGprecedence (keep the mapped read's ownPG, drop the unmapped one) in the same walk, and appends the copy set — no separatehas_pgscan, and no per-record allocation.normalize_as_xs_single_passnormalizesASthenXSin one walk instead of four scans.refactor(raw-bam)—extract_int_valuebundled the integer-decode ladder with aux-slice positioning, so a caller holding a tag's value bytes (from anAuxTagsIter/TagEntrywalk) couldn't reuse it. Split outdecode_int_value(type_byte, value_bytes);extract_int_valuenow slices and delegates. Removes the now single-usetag_value_bytes.Correctness: byte-identical
On a 10.9M-record CODEC dataset (extract → bwa-mem3 → zipper), output is byte-identical to the pre-change binary:
samtools viewmd5 (fields + tags + order): identical.fgumi compare bams: 0 content diffs across 10,941,868 records.All 146 zipper/merge/align tests pass; 806
fgumi-raw-bamtests pass. New tests coverdecode_int_value(per type, non-integer types, short slices); the existing AS/XS-normalization andhas_pg(pg_already_on_mapped_read_blocks_the_unmapped_pg_copy) tests exercise the new helpers.Performance
Standalone
fgumi zipper, 1 thread, page-cache warm, 10.9M records:find_tag_positiondrops from ~14% → ~8% of CPU (samply,threadCPUDelta-weighted).This is a CPU-reduction change, which is what matters for zipper's place in the pipeline: every CPU-second it doesn't burn goes to the aligner (upstream) and sort (downstream) sharing the box.
Reading order
crates/fgumi-raw-bam/src/tags.rs—decode_int_value+extract_int_valuedelegation.src/lib/commands/zipper.rs—copy_unmapped_tags_single_pass,normalize_as_xs_single_pass, and their wiring intomerge_raw_with.Base
Stacked on #962 (
nh/raw-tags-rebuild) — it builds on that PR'smerge_raw_withstructure. Retarget tomainonce #962 merges.Risk: zipper auxiliary-tag output can change, pinned by byte-identical zipper/merge/align tests; unsafe changes: none, so no
CLAUDE.mdallowlist update is needed; memory, queue, and thread/backpressure policy changes: none.PG,AS, andXShandling with single-pass walks and reusable scratch buffers.PGprecedence and duplicate-tag last-wins behavior.decode_int_value.