Replace EvidenceKind with IndexMode (Exact, Approx, Hybrid) across layer construction and query dispatch. Update PartitionMeta and LayerMeta serialization to centralize index-wide configuration. Add flexible push_layer overloads to LayeredMap for dynamic index expansion without full rebuilds. Improve UnitigFileReader to gracefully fallback to sequential scanning when indexes are missing, eliminating panics.
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.
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.
Propagate configurable block size (`block_bits`) through index and layer construction to control unitig chunking and optimize memory/performance trade-offs. Introduce an in-place `reindex` command and library method to convert indices between exact and approximate evidence formats. Add validation to reject merging indexes with mismatched evidence types, and update parallel kmer counting to use `AtomicUsize` for thread-safe aggregation. Includes CLI argument parsing, metadata persistence, and updated tests.
Introduces a new `estimate` CLI subcommand to calculate bloom filter size, evidence bits, and false-positive rates for approximate indexing. Updates the index building and querying pipelines to support both exact and approximate evidence types via a unified `EvidenceKind` abstraction. Refactors `MphfLayer` and partition index builders to route operations based on the selected evidence mode, and adds the required `obilayeredmap` dependency.
Introduces `EvidenceKind` and `LayerMeta` structs to manage per-layer evidence configuration and false-positive parameters. Adds JSON serialization for layer metadata persistence and updates `build_approx_evidence` to accept a `z` parameter for consecutive k-mer thresholds. Exposes these types publicly and documents a future `aggregate` command for merging index matrix columns.
Introduce a new `fingerprint` module that stores packed B-bit vectors via memory-mapped files. Expose the module publicly and add `build_approx_evidence` to `Layer` and `MphfLayer` for generating compact `fingerprint.bin` files. Implement `find_approx` for fast, probabilistic kmer lookups using configurable bit-widths. Update dependencies to `bitvec` v1 and add `cacheline-ef`, `epserde`, and `memmap2` to support the new storage and serialization logic.
Decouple index generation by introducing `build_unitig_idx()` for retroactive `.idx` creation and optional immediate writing on close. Add `open_sequential()` for index-less iteration while enforcing index requirements for random access. Refactor the MPHF layer to pre-generate the unitig index for parallel random access, integrate `rayon` for k-mer processing, and enforce mapping integrity via duplicate slot validation. Additionally, implement `build_exact_evidence()` to reconstruct evidence from existing artifacts, and update tests to leverage the new index generation and simplified k-mer iteration helpers.
Implements a new `merge` command that aggregates k-mer counts and presence/absence matrices from multiple source indices using a parallelized, partition-based algorithm. Adds CLI progress bars and execution timing across the bootstrap, spectrum rebuild, and merge phases. Updates logging to report the aggregate genome count and introduces a bounds check in the perfect hash layer to safely return `None` for unknown k-mers, preventing out-of-bounds access in downstream operations.
Introduces a new `merge` CLI subcommand and underlying implementation to consolidate multiple pre-indexed k-mer indexes into a single output. Adds `append_column` methods to persistent bit and int matrices to enable incremental genome column expansion without rebuilding the MPHF. Includes new error variants for index readiness and configuration mismatches, adds a `--force` flag to the index command, and updates documentation and navigation structure accordingly.
Extracts MPHF construction, evidence encoding, and unitig I/O into a new `MphfLayer` module. This removes direct dependencies on `Evidence`, `PersistentBitMatrix`, and `PersistentCompactIntMatrix` from `Layer`. The `query` method is simplified to perform direct MPHF lookups, while build logic and serialization are consolidated within the new module.
Introduces ColumnWeights, CountPartials, and BitPartials traits to compute and finalize partial distance matrices. Implements these traits for PersistentBitMatrix, PersistentCompactIntMatrix, and a new LayeredStore<S> wrapper that aggregates metrics across layers via parallel reduction. Adds ndarray for numerical aggregation and updates architecture documentation to reflect the trait-driven design and pending refactoring roadmap.
Introduces `PersistentBitMatrix` and `PersistentCompactIntMatrix` to replace single-file vector storage with a column-major, directory-based layout. Each column is persisted as an individual file alongside a lightweight `meta.json` for dimension tracking. Migrates `obilayeredmap` to use these multi-column structures, updating Rust APIs, query return types, and build signatures. Includes comprehensive documentation, unit and integration tests for persistence and accessors, and refactors distance calculation helpers.
Replace the hardcoded `Counts` module with a generic `LayerData` trait, parameterizing `Layer` and `LayeredMap` over arbitrary payload types. This decouples read-path access from build-path logic, enabling both set membership and count-based indexing via `PersistentCompactIntVec`. Adds the `obicompactvec` dependency, implements streaming layer construction, and expands test coverage for persistence and multi-layer resolution.
Introduce the `obicompactvec` crate, featuring a two-tier, memory-mapped integer vector that uses a primary `u8` array with a sentinel for overflow dispatch and a sparse L1-resident index for fast random access. Implement builder and reader modules with zero-copy serialization and comprehensive test coverage. Update `obilayeredmap` to replace the default hash function with a cache-line-optimized `Mphf`, adding explicit bounds checking and duplicate-slot detection. Add documentation for both modules and update project configuration files accordingly.
Replace `ph` with `ptr_hash` and introduce `epserde` and `rayon` dependencies. Refactor MPHF construction to leverage parallel iteration, eliminating intermediate `Vec<u64>` allocations and reducing memory footprint. Add a `n_kmers` field to track and serialize total kmer counts, alongside three zero-allocation iterators for efficient chunk traversal. Include comprehensive unit tests for the new iterators and update CLAUDE.md to enforce explicit dependency validation policies.
Introduces the `obilayeredmap` crate (v0.1.0), implementing an append-only, disk-backed k-mer index using a minimal perfect hash function (MPHF). The module features memory-mapped reads, buffered writes, custom error handling, partition metadata persistence, and comprehensive unit tests. Also adds a reverse complement benchmark for `obikseq` and updates `Cargo.lock` with the new dependencies.
Eric Coissac