Push vqmnuyrkpxot #9

2026-05-26T09:05:12Z

coissac commented

2026-05-26 09:05:12 +00:00

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coissac added 4 commits 2026-05-26 09:05:12 +00:00

refactor: update core types and add approximate evidence support 036d044291

Refactor `Kmer`, `SuperKmer`, and chunk reader into optimized, generic representations with compile-time length parameters and bitwise operations. Update the pipeline and scheduler to support batch processing, 1→N flat transformations, and multi-source merging. Introduce an approximate evidence mode using b-bit fingerprints and `.idx` files, alongside existing exact mode. Update CLI documentation, minimizer selection, and query output schema accordingly.

feat: support exact and approximate evidence in layer construction 9d46400898

Refactored `MphfLayer::build` to accept an `EvidenceKind` parameter, routing to exact (index-based, parallel MPHF, writes `evidence.bin`) or approximate (sequential mmap iterator, writes `fingerprint.bin`) pipelines. Introduced `CanonicalKmerIter` for memory-mapped, chunked k-mer iteration with O(1) resets via `Arc<Mmap>`. Updated layer and map APIs to forward evidence kind, added `push_layer` for count matrices, and adjusted tests and public exports accordingly.

refactor: handle kmer deduplication and layer initialization concurrently 009a328c58

Introduce a secondary layer iteration to open `SrcLayerData` alongside the unitig reader for concurrent metadata access. This refactors the merge routine to handle kmer deduplication and per-layer data initialization simultaneously. Also corrects a typo in `rebuild_layer.rs` where `openopen_sequential` is renamed to `open_sequential`.

refactor: optimize MPHF construction and update legacy guidelines 1d880fdc5f

Replaces parallel random-access unitig iteration with a sequential mmap-based iterator for MPHF construction, eliminating the build-time `.idx` dependency by deferring index generation until after persistence. Updates `CLAUDE.md` to treat existing code as a hypothesis, mandating proactive removal of obsolete legacy constructs rather than preserving them out of inertia.

coissac merged commit 6f7abddeaf into main

2026-05-26 09:05:51 +00:00

coissac deleted branch push-vqmnuyrkpxot

2026-05-26 09:05:51 +00:00

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Reference: OBIKmers/obikmer#9