Phase B4a — ReferenceView (self-contained reference access) - #18
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…w) design First sub-stage of B4 (wire consumers onto the persisted index). A borrowed zero-copy ReferenceView over the Reference2bit section (base_at + decode_window, on-demand decode, no full-reference Vec), via ReferenceIndex::reference_view(). The shared reference-access foundation B4b (aligner DP window) and B4c (variants ref_base/pileup) need. Gated by decode==original over an N-bearing multi-contig reference. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…s) plan Single TDD task: a borrowed zero-copy ReferenceView over Reference2bit (base_at + decode_window) + ReferenceIndex::reference_view() + re-exports, gated by decode==original over an N-bearing multi-contig index. Reuses view.rs section/align_to helpers. Derived from spec 913b993. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
… from the index A borrowed ReferenceView over the persisted Reference2bit section (base_at + decode_window, on-demand 2-bit decode mirroring CompressedDNA::base_at, no full-reference Vec), via ReferenceIndex::reference_view(). Gated by base_at/decode_window == the original reference over an N-bearing multi-contig index. The shared reference-access foundation B4b (aligner DP window) and B4c (variants ref_base) consume. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
First sub-stage of B4 (wire the consumers onto the persisted multi-contig index). B3b stored the 2-bit forward reference into the index (the
Reference2bitsection) but gave it no read path; B4a adds one.ReferenceView<'a>— a borrowed, zero-copy view over theReference2bitsection.base_at(global) -> u8decodes one ASCII base on demand (ambiguity bit →N, else 2-bit code → A/C/G/T), mirroringCompressedDNA::base_at;decode_window(start, end, &mut Vec<u8>)fills a bounded caller buffer (endclamped tolen). Obtained viaReferenceIndex::reference_view()(checkedalign_to, little-endian host, section-extent validation — same discipline asFmIndexView).&[u64]slices + a length (40 bytes), decoding only the windows a consumer asks for — no O(reference)Vec, preserving the persisted index's bounded-query guarantee.ref_base/ pileup) consume — after B4a they read the reference from the.idxalone, no separate--referenceFASTA.Scope: the reader only. Deferred: wiring it into the aligner (B4b) and into
variants/pileup (B4c).Test plan
base_at(i)over the whole reference, anddecode_windowover several ranges (boundary-spanning, N-bearing, full, and an over-range clamp case), are byte-identical to the originalindex.reference()over anN-bearing multi-contig index.ReferenceViewis a small borrow (size_of <= 64), not an owned copy.base_atreviewed byte-equivalent toCompressedDNA::base_at(ambiguity word/bit + 2-bit word/shift + 0/1/2/3 → A/C/G/T).cargo test— full suite green (151 lib tests + integration), 0 warnings,cargo fmt --all -- --checkclean, MSRV 1.72 (nodiv_ceil).Design spec:
docs/superpowers/specs/2026-05-27-phase-b4a-reference-view-design.md. Plan:docs/superpowers/plans/2026-05-27-phase-b4a-reference-view.md.🤖 Generated with Claude Code