This commit introduces a new `distance` CLI subcommand that computes pairwise genomic distance matrices using configurable metrics (Jaccard, Hamming, Bray-Curtis, Euclidean, and Hellinger). It optionally generates phylogenetic trees (NJ or UPGMA) in Newick format and outputs results as CSV. The implementation adds a robust distance computation backend that dynamically routes to optimized backends based on index configuration, supports parallel iteration, and gracefully handles missing data. Additionally, it adds a `dump` task for exporting k-mer to genome mappings as CSV, introduces an `InvalidInput` error variant, updates dependencies to support numerical operations and tree construction, and performs minor module reorganizations.
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.
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.
Add comprehensive documentation for the `obilayeredmap` crate, `PersistentCompactIntVec`, `PersistentBitVec`, and the hierarchical k-mer index architecture, including sidebar navigation updates across all documentation pages. Refactor the Bray-Curtis distance computation in `obicompactvec` to decouple numerator and denominator calculations, replacing direct pairwise calls with explicit loops over precomputed sums. Update tests to verify column sum accuracy and align with the simplified API.
Introduces parallel `count_ones` for `BitMatrix` and parallel column-sum aggregation alongside three pairwise distance constructors (Bray-Curtis, Euclidean, Hellinger) for `IntMatrix`. These methods support partial, layer-wise data by accepting precomputed global column sums for normalization, enabling additive decomposition across partitions. Includes unit tests verifying mathematical equivalence and partition additivity.
Introduce parallel distance matrix generation using `ndarray` and `rayon` for both `BitMatrix` and `IntMatrix`. Adds full and additive-partial variants for Jaccard, Hamming, Bray-Curtis, Euclidean, and Hellinger metrics. Includes comprehensive unit tests verifying matrix symmetry, zero diagonals, and numerical correctness against pairwise calculations.
Introduces `partial_jaccard_dist` to return raw intersection and union counts, improving Jaccard distance flexibility. Corrects `not()` to explicitly zero padding bits in the final word, ensuring accurate bit-counting for partially-filled words. Adds an optimized `build_from_counts` constructor.
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.
Introduces PersistentBitVec, a dense, memory-mapped bit vector optimized for bulk u64-word operations and SIMD acceleration, complete with bitwise operators and Jaccard/Hamming distance metrics. Upgrades PersistentCompactIntVec to a unified .pciv format using 64-bit indices and offsets, consolidating the binary layout and updating builder/reader lifecycles accordingly. Adds corresponding documentation, updates MkDocs navigation, and implements a comprehensive test suite for persistence round-trips, edge cases, and metric accuracy.
Adds a `sum()` method to compute the aggregate of all elements using u64 arithmetic to safely handle potential overflows. Introduces a `sumadd()` method for element-wise addition into the builder, enforcing strict length equality and using `checked_add` for safe accumulation. Includes unit tests to verify correct aggregation and overflow safety.
Refactor `PersistentCompactIntVecBuilder` to replace in-memory `Vec<u8>` with `MmapMut` for primary storage. Decouples initialization from finalization by updating `finalize_pciv` to truncate, append overflow data, and overwrite the header placeholder. Adds file path tracking via a new `path()` accessor, implements `build_from` for efficient copying, and introduces arithmetic/set operations (`min`, `max`, `sum`, `diff`). Expands test coverage for persistence roundtrips, mutations, iteration, and the new vector operations.
Add an `Iter` struct that implements `Iterator` and `ExactSizeIterator` to enable idiomatic traversal of `&PersistentCompactIntVec`. The iterator maintains `slot` and `overflow_pos` state to correctly yield `u32` values from both primary and overflow memory regions. Includes three unit tests validating iteration correctness against direct indexing, accurate `len()` tracking, and proper reference-based iteration.
Refactors the storage format to separate primary and overflow data into distinct files. Introduces a cache-friendly sparse index with dynamically computed step and entry counts. Consolidates dual memory-mapped regions into a single file with explicit header parsing and validation, replacing unsafe slice casting with direct byte-offset indexing. Updates the test suite to accommodate the new file structure.
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.
Eric Coissac