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.
This change introduces the `query` CLI command and its supporting infrastructure for sequence-to-genome mapping and k-mer matching. It adds a `QueryLayer` abstraction backed by MPHF and persistent matrices, exposes the index partition for direct querying, and implements `Hash`/`Eq` for `RoutableSuperKmer`. The command ingests sequence batches, deduplicates superkmers, routes them to index partitions for parallel exact or 1-mismatch matching, and outputs results as FASTA records annotated with JSON metadata. Includes `serde_json` dependency addition, module exports, and documentation updates.
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.
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.
Added implementation specifications for the `merge` operation, detailing parallel partition processing, I/O paths, and kmer matrix aggregation across multiple indexes. Integrated an `indicatif` progress bar into the `rayon` parallel loop to monitor processing position, throughput, ETA, and recent partition duration.
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.
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