This change adds the `obikseq` crate as a local dependency and inserts `set_k` and `set_m` calls across index creation and command modules. By synchronizing the runtime's global k-mer and minimizer dimensions with the loaded index parameters, downstream sequence processing and partitioning operations now consistently use the correct structural constraints.
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.
Refactors obikindex and obikpartitionner to delegate index construction to a new layered MPHF implementation. Adds resume-safe building with abundance filtering and count persistence, while introducing a PartitionMeta struct for JSON configuration persistence. Updates OKIError to wrap layer-specific errors, replaces single-path extraction with full path collection and logging, and registers new internal dependencies across the workspace.
Extracted core indexing logic, state tracking, and metadata management into a new `obikindex` crate. Refactored the `index` and `unitig` commands to leverage the `KmerIndex` abstraction and state-driven pipeline transitions. Removed obsolete CLI subcommands (`count`, `fasta`, `longtig`, `partition`) and their associated pipeline steps. Updated FASTA writing utilities for single-line output and deterministic identifiers, and refreshed workspace dependencies.
Eric Coissac