feat: fuse annotated+spliced haplotype reconstruction (Phase 5 W3)#258
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…sized plan) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…FFI crossing (Phase 5 W3) Add reconstruct_annotated_haplotypes_spliced_fused — the annotated counterpart of reconstruct_haplotypes_spliced_fused. Folds RC in-kernel (bytes RC'd, annotation rows reversed) so the Python _FlatAnnotatedHaps.reverse_masked post-pass is dropped on the rust backend. Byte-identical to the composed numba oracle (new parity backstop). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…combos now single-FFI (Phase 5 W3) Also applies ruff formatting to _haps.py (post-Task-1 residual). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Phase 5 W3 — fuse the deferred annotated+spliced reconstruction path
Closes the last un-fused FFI seam in haplotype reconstruction. Three of the four annotated×spliced combinations were already single-FFI-crossing fused kernels; the fourth — annotated AND spliced — was deferred to Phase 5. On the rust backend it ran the un-fused dispatched core plus a Python RC post-pass (
_FlatAnnotatedHaps.reverse_masked).What changed
reconstruct_annotated_haplotypes_spliced_fused(src/ffi/mod.rs) — a faithful merge of the two existing parity-proven kernels: the spliced scaffolding (reconstruct_haplotypes_spliced_fused: precomputedout_offsets, permuted ploidy-1 inputs, noget_diffs_sparse) + the annotation buffers and RC triple (reconstruct_annotated_haplotypes_fused). Registered insrc/lib.rs, imported in_haps.py._dataset/_haps.py): the splice branch of_reconstruct_annotated_haplotypesnow calls the fused kernel on the rust backend (RC folded in-kernel) and drops the Pythonreverse_maskedpost-pass; the numba branch is retained unchanged as the oracle.RC invariant (the parity-critical detail)
For the spliced path RC is per permuted element. Rust folds RC in-kernel:
rc_flat_rows_inplaceon the sequence bytes (reverse+complement) andreverse_flat_rows_inplaceon both annotation arrays (reverse only, no complement) — byte-identical to_FlatAnnotatedHaps.reverse_masked(mask, _COMP). Numba RCs externally in_query.py::_getitem_spliced(numba-only guard);_query.pyis untouched. No double-RC, no missed-RC.Parity gate
New
tests/parity/test_annotated_spliced_haplotypes_parity.py: spy proves the fused entry fires on rust only; all three arrays (haps,var_idxs,ref_coords) + offsets compared byte-identically to the composed numba oracle; a negative-strand transcript with anrc_negTrue-vs-False difference check exercises the in-kernel RC path. Full parity suite green on both backends (78p/1s each); dataset+unit 632p; ruff/format/typecheck/clippy clean; 17 cargo reconstruct tests pass.numba remains the oracle (deletion is W5/W6). Phase 5 stays 🚧 (W4–W9 remain).
Plan:
docs/superpowers/plans/2026-06-26-rust-migration-phase-5-w3.md🤖 Generated with Claude Code