Renames the reindex command to convert across all usage guides and navigation menus. Adds documentation for the newly introduced name-tree command. Updates flag references, such as replacing --metric with --distance in pack and phylo modules, and adjusts MkDocs configuration to match the revised structure. All changes are strictly limited to documentation and configuration files.
Introduces --iqtree-min-freq (default 0.001) to treat low-frequency nucleotide states as missing data during IQ-TREE alignment generation when --free-loss is active. This triggers a recoding pass that folds rare states into the missing symbol, followed by non-informative site removal and alphabet recomputation to maintain output consistency. The change also adds Sankoff model configuration files and updates related tests and documentation.
Generates a new CSV output that maps IQ-TREE's compact state symbols to canonical states alongside full-precision empirical frequencies. Updates documentation to clarify that state frequencies sum to 1.0 by design and documents conditional behavior under `--free-loss`. Includes unit tests verifying absent state exclusion, frequency summation, and CSV structure. Also restricts entropy annex resolution to non-monomorphic minorants to eliminate redundant per-genome checks.
Expands MkDocs navigation and documentation for evidence elimination, the merge command, and kmer filtering. Refactors kmer representation to a generic `KmerOf<L>` type with a bitwise reverse complement algorithm. Unifies MPHF construction, introduces approximate fingerprint-based indexing, and updates the pipeline, chunkreader, and storage layouts. Adds code coverage reports and clarifies architectural invariants for improved maintainability.
Formalize the two-phase MPHF indexing architecture and update Phase 6 to use `evidence.bin` for direct kmer extraction. Simplify the evidence and unitig storage layouts to flat packed formats enabling O(1) random access. Introduce aggregation traits (`ColumnWeights`, `CountPartials`, `BitPartials`) to support additive distance metric decomposition across partitions. Narrow the documented scope from metagenomic to individual genome datasets, and replace speculative open questions with concrete implementation specifications.
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.
Replace raw SuperkMer routing with a new RoutableSuperKimer type that embeds canonical sequences and precomputed minimizers, enabling direct partition routing via hash. Update the build pipeline to yield RoutableSuperKmers throughout (builder, scatterer), refactor FASTA/unitig export commands to use the new type and compressed outputs (.fasta.gz, .unitigs.fasta.zst), revise SuperKmer header to store n_kmers instead of seql (avoiding 256-byte wrap), and update documentation to reflect minimizer-based theory, two evidence-encoding strategies for unitig-MPHF indexing (global offset vs. ID+rank), and the new obipipeline library architecture with parallel workers, biased scheduling, and error handling.
Eric Coissac