Restructure the benchmark pipeline to direct all simulated data, indices, statistics, and query outputs into a unified `run/` directory. Update Makefile targets, shell scripts, and Python utilities to resolve paths relative to this new base. Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.
Introduces a `batch_int_group_stats` API for computing presence counts, sums, minimums, and maximums across sparse and dense matrix representations. The selection layer now utilizes this batched approach to optimize aggregation semantics for boolean and numeric operations. Additionally, reorganizes the benchmarking infrastructure to support querying across presence and count index variants in both dense and sparse formats, including new packing scripts and updated statistics aggregation.
The `obikmer select` CLI no longer supports in-place index rewriting; the `--output` flag is now required, with benchmarks updated to use temporary directories for atomic replacement. Added `--dense` and `--force-copy` flags. Introduced `batch_presence_counts` to compute presence counts across multiple column groups in a single pass, eliminating redundant I/O. Refactored the aggregation pipeline to branch on layer content, applying the optimized batched counting for `Presence` layers. Enhanced the NUMA runner to catch worker panics, track them, and re-raise after thread join to prevent indefinite blocking.
Extends `KmerIndex::finalize_indexed` to accept a `sparse` boolean parameter, enabling control over whether output presence matrices are packed in a compact sparse format or stored densely. The merge command now exposes a `--dense` flag to invert this setting, defaulting to the existing sparse representation. Call sites in select and rebuild modules pass `false` to preserve current behavior. A benchmark lock file is also added for dependency tracking.
Introduces directory-level locking to prevent concurrent index operations from corrupting shared directories, along with explicit APIs for acquiring, probing, and releasing locks. Restructures the index cache crate to use a layered store architecture that eagerly initializes metadata and provides fast hierarchical lookups. Updates dependent modules, test suites, and CLI commands to align with the refactored API surface, and adds an end-to-end smoke test for validation.
Introduces a complete query benchmark track to evaluate performance and verify consistency between dense and sparse index formats. Adds scripts to simulate fixed-size paired-end reads, pack a sparse presence index, execute queries in both modes, and capture wall time and RSS metrics. Includes a verification step that compares outputs by read ID to ensure content identity across parallel processing. Updates build configuration, documentation, and ignore patterns to support the new pipeline for two microbial specimens.
Restructure the project by moving the standalone compare_sparse utility into an example directory, removing Sankoff parameter configurations and benchmark scripts, updating version control ignores, and expanding the test suite with diagnostic checks and performance benchmarks.
Adds a new binary that validates bit-level consistency between dense and sparse K-mer index representations by sampling slots across partitions and reporting discrepancies. Refactors sibling cache matrix initialization into a centralized factory method to simplify control flow and standardize error handling. Introduces diagnostic configurations, benchmark scripts, and an ignored test case to support k-mer resolution analysis.
Rename the distance CLI subcommand to phylo across the codebase, documentation, and build configurations. Relocate source files from cmd/distance/ to a dedicated cmd/phylo/ module, update all internal routing references, and adjust benchmark scripts and Makefile targets to reflect the new command name.
Introduces scripts to compute and validate pairwise genomic distance matrices across multiple metrics. Updates the Makefile with build and comparison targets, adds .gitignore rules for generated outputs, and includes test CSV matrices and a Newick phylogenetic tree for validating the distance computation pipeline.
Introduces a Make-based orchestration for simulating, indexing, merging, filtering, and verifying k-mer counts and presence. Exposes internal builder and iterator APIs publicly, enforces mandatory leading slashes for predicate patterns, registers the `obitaxonomy` crate, and updates tooling configurations alongside documentation.
Eric Coissac