Extends the phylogenetic pipeline with exporters for TNT, PhyG, and IQ-TREE that generate executable scripts, cost matrices, and recoded alignments. Adds internal helpers for state indexing, floating-point matrix scaling, and Floyd-Warshall metric closure to satisfy external tool constraints. Adjusts visibility modifiers for sibling iterators and entropy annex structs, and updates design documentation for evolutionary distance metrics.
Introduce the --sankoff flag to generate subsampled calibration bundles and pairwise cost matrices. Expose internal sibling algorithm types as public to support external consumption. Implement YAML, CSV, and FASTA output serialization using serde, gated by a configurable substitution saturation ceiling and requiring the --subsample flag.
Replaces the previous two-pass design with a single-pass reduction that computes per-genome-pair substitution counts, cardinality and base-composition tallies, and transition cost matrices. Introduces internal APIs to derive downstream n×n matrices from reduced data and applies configurable filtering based on SNP ratios and exclusion masks. Adds a fused pipeline entry point aggregating alignment and distance outputs for downstream phylogenetic commands. Adjusts visibility of existing reduction functions to restrict external access while permitting sibling module invocation.
Replace per-family callbacks with a per-layer batch callback that accumulates surviving families into an Arc<Vec<SurvivingFamily>>. Update the alignment reduction routine to iterate over this batched structure, enabling zero-copy sharing for parallel operations and structuring the code for future extensibility.
Introduces `--sibling-stats` and `--sibling-hist` flags to compute and export family-size distributions from pre-built annexes. The new algorithms module implements parallel and sequential scanning routines, while the CLI layer handles CSV export with deduplication and standardized error handling.
Introduces configurable phylogenetic sampling and masking controls via new CLI flags (`--subsample`, `--entropy`, `--exclude-genome`, etc.). Adds a complete SNP pseudo-alignment pipeline featuring entropy-biased Gaussian sampling, post-hoc state masking, and proportional per-layer filtering. Extends the FASTA writer with a `write_plain_record` API for bare-header output without JSON annotations.
Introduces an entropy.pent persisted format and algorithms to compute per-family Shannon entropy across genomic partitions. Refactors IndexCache to use Arc-based layer sharing for efficient iteration and restructures the siblings module with extension traits for annex generation. Adds a --shannon CLI flag to export partition-level entropy metrics to CSV.
Refactors the `SiblingAnnexBuildExt` trait to `SiblingExt` across all imports, implementations, and documentation. Introduces new modules for streaming and batched iteration over sibling layers, along with a two-phase pipeline for resolving minorant families.
Introduces a new `--sibling-annex` CLI flag that triggers the construction of a sibling-count/minorant annex for multi-genome indices. The implementation adds a `FamilyMask` data structure with memory-mapped I/O, enabling lock-free concurrent updates via atomic bitwise operations. Batched processing improves cache locality and parallelism, while helper functions derive family presence and minorant flags dynamically. The feature is exposed through an `IndexCache` extension trait, protected by an exclusive directory lock to prevent index corruption during construction.
Implement an `obipipeline::Throttle` with an RAII guard to acquire and release concurrency slots. Expose new bounded parallel methods on `IndexCache` to process cached layers with a configurable cap. Refactor downstream aggregation logic to use single-pass parallel map-reduce instead of manual collect-map-reduce sequences, enforcing a maximum of 8 concurrent layer scans to bound memory usage.
Refactor phylogenetic algorithms (`neighbor_joining`, `upgma`) to return an explicit `Tree` struct instead of a serialized Newick string. This change makes serialization an explicit step for downstream consumers via the new public `Tree::to_newick()` method, decoupling tree construction from output formatting. The `siblings` module has also been moved to `siblings_old`.
Introduce the `obikphylo` crate to support genome-vs-genome distance matrix computation and phylogenetic tree inference via Neighbor-Joining and UPGMA algorithms. Extend the `obikmer2` CLI with a new `phylo` command that exposes configurable metrics, presence thresholds, and CSV/Newick output options. Refactor `obikindex` to expose trait-based partial aggregation for efficient distance metric finalization without full matrix materialization. Update dependency graphs and remove obsolete storage modules.
Update all matrix type references, imports, and instantiations across
the codebase to use the new PersistentIntMatrix name. The change also
includes standardizing code formatting, such as multi-line statements
and import ordering, without altering any behavioral logic or public
API contracts.
Relocate cardcomp into the siblings directory and update internal import paths to reflect the new hierarchy. Adjust the crate's public API surface by updating module declarations and re-exports. This is a purely structural change with no modifications to logic, data models, or runtime behavior.
Introduce a new CLI command that modifies existing indices to support exact, approximate, or hybrid evidence modes. This change enables the reindex module in obikrebuild, exposing an IndexReindex trait for evidence persistence and layer processing. It also refactors obikindexer to publicly expose an IndexBuilder trait for post-build evidence construction, while adding a set_evidence API in obikindex to safely update configuration fields without altering core parameters.
Replaces lifetime-bound references with runtime reference counting across multiple crates. This enables safe concurrent access across parallel workers without explicit cloning or manual lifetime management. Introduces the `query` and `utils` CLI commands in obikmer2, along with supporting modules for batch processing, sparse indexing, sliding-window findere logic, and output formatting. Updates dependency manifests and aligns test suites with the new ownership model.
Change the return type of `nonzero_iter` from an opaque `impl Iterator` to a `Box<dyn Iterator>`. This enables direct return coercion in the `Count` layer branch, removing an explicit `Box::new()` wrapper and aligning it with the existing `Presence` implementation. The modification shifts iterator construction to runtime dynamic dispatch while preserving the public API contract and iteration semantics.
Introduce a new `Sparse` format alongside existing `Columnar` and `Packed` variants, enabling optimized row-major pairwise counting for distance and similarity metrics via the `CountPartials` trait. Update storage detection priorities, extend matrix dispatch logic to sparse backends, and correct diagonal/off-diagonal formulas in bit matrix partial computations. Expand layer APIs with format-agnostic `nonzero_iter`, update usage documentation for the `--sparse` flag, and add comprehensive tests verifying roundtrip integrity and metric equivalence against dense implementations.
Adds the `pack` subcommand to `obikmer2` for persisting presence and count matrices in sparse or dense formats. Introduces the `compact_layer` module in `obikrebuild` to merge multiple partition layers into a single layer in-place via atomic operations. Updates dependencies across `obikdump`, `obikmer2`, and `obikrebuild` to resolve new local crate references. Shifts the architecture from multi-layer accumulation to in-place compaction, removing legacy rebuild modules.
Introduces a new unitig extraction feature that reads k-mers from an index, filters them by group metadata, and partitions the computation using rayon. The implementation constructs per-partition de Bruijn graphs, merges them, computes node degrees, and writes the resulting sequences as FASTA. A corresponding CLI command is added to obikmer2 to expose this functionality with configurable filtering and progress reporting.
Introduces a new `dump` CLI command to export index k-mers as a CSV table. Adds a reusable `GroupFilterArgs` struct for ingroup/outgroup metadata-predicate quorum filtering with configurable count and fraction thresholds. Refactors the filter command to use explicit flags and a `GenomeSelector`-based pipeline, improving error handling and predicate application order. Exposes `IndexDump` from the `obikdump` crate and updates local dependencies accordingly.
Introduces a new `obikselect` module to handle k-mer selection and column aggregation. Adds a `select` CLI command in `obikmer2` that supports group predicates, aggregate operators, and output column filtering. Implements operator parsing with case-insensitive matching and default rules, along with a centralized module for resolving group specifications from metadata or genome filters. Updates dependencies to include the new crate and its prerequisites.
Introduces a unified MatrixBuilder abstraction for persistent bit and integer matrices, replacing custom dispatch enums and boolean flags across consumers. Refactors index, merge, and select layers to adopt explicit merge modes and centralized lifecycle management. Adds a complete k-mer filtering implementation with partition-level processing, progress tracking, and a new CLI subcommand supporting configurable predicates and thresholds.
Introduces `PersistentSparseCompactIntMatrix`, a row-major sparse integer matrix combining a bitmatrix support layer with dual value streams for singleton and multi partitions. Adds builder and packing utilities to convert dense count matrices into the new on-disk format, featuring idempotency guards and crash-safe persistence workflows. Exposes core accessors, iterators, and column weight calculations while adjusting internal visibility for companion modules. Includes unit tests and diagnostic examples to validate equivalence with dense representations and measure compaction metrics.
Move the partition iterator implementation from obikdump to obikfilter, updating imports and exposing the type publicly. Add obikidxcache as a local dependency for obikfilter. In obikindexer, expose the new build_layer_from_kmers function to enable shared graph-building logic across pipelines without code duplication.
Move partition iteration logic to obikdump, introducing a FilteredPartitionIter trait over IndexCache for batch-oriented scanning with configurable data retrieval and early termination. Consolidate ingroup and outgroup index storage in GroupQuorumFilter into a unified Selection struct driven by predicate matching. Update dependency manifests to include obikidxcache, rayon, and obikentropy, and remove the deprecated dump_layer module while adjusting public API re-exports.
Extracts file creation, opening, and memory mapping logic into a new `mmap_file` module. This replaces repetitive unsafe operations across persistent data structures with standardized helper functions, ensuring consistent header validation, error handling, and data layout while keeping public APIs unchanged.
Update PersistentSparseBitMatrix documentation for clarity. Introduce select0 to the rank/select module, and add next_geq, contains, successor, and predecessor methods to the Elias-Fano implementation. Include naive reference implementations and unit tests to validate correctness and boundary conditions for all new APIs. All changes are strictly additive.
Shifts the selection logic from a direct method into a dedicated `Select` struct implementing the `Algorithm` trait. Introduces a two-phase initialization pattern with explicit builder methods and closure-based progress callbacks. Updates the crate's dependency graph to include `obikalgorithm`, refactors layer processing with unified matrix dispatch, and implements dual directory routing for partition execution.
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.
Extended `nonzero_triples` with a boolean flag to conditionally skip sorting when input slots are already ordered. Updated call sites to pass appropriate flags, enabling a single-pass columnar traversal in the sparse matrix builder. Refactored `build_from_dense` into a batched processing pipeline that reduces repeated file access and improves sequential read performance. Added a diagnostic example to validate the new builder against existing dense matrices.
Added a `col_weights` method to index layers for computing per-genome column sums or presence k-mer counts. Refactored `obikstats` to implement the `Algorithm` trait with a two-phase `new`/`run` model, replacing manual layer resolution with `IndexCache` for eager file I/O. Simplified per-genome counting logic and updated public exports and dependencies accordingly.
Introduces the `annotate` subcommand to apply genome metadata from an external CSV file to a pre-built k-mer index. The command supports configurable field separators, ID columns, and null markers, while providing a `--dump` option to export current index metadata as sorted CSV. Supporting changes include minor internal refactoring in `obikindex` to use object-level directory accessors and updates to the `csv` dependency.
Introduce `iter_unitigs` methods across the index cache, content layer, MphfLayer, and typed layer to stream whole reconstructed sequences directly from underlying storage without decomposing into k-mers. Add a corresponding low-level streaming iterator in obiskio for thread-safe, lazy reads from memory-mapped files. Include a new CLI subcommand to compute and display approximate false-positive rates based on provided indexing parameters.
Introduces a new `superkmer` command that implements a multi-stage pipeline for reading nucleotide pages and constructing superkmers with configurable parameters. The implementation uses partition-aware scatter writing via `obifastwrite` to distribute output batches across workers, and adds the necessary local dependencies to the project manifest.
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.
Replaces manual filesystem path handling and parallel iteration with dedicated internal utilities. Introduces `par_over_layer0` and `layer0()` to abstract partition layer access, enabling partition-driven initialization and centralized progress tracking. Removes disabled or internal methods (`rewrite_config`, `open_data`) no longer part of the active interface. Updates error propagation and metadata persistence to align with the new layer-centric workflow.
This commit partitions the obikindex crate into multiple focused subcrates (obikfilter, obikmerge, obikquery, obikrebuild, obikselect, obikstats, obikdump, and obikidxcache) to reduce coupling and clarify module boundaries. It standardizes error handling across the workspace using OKIError and OKIResult, updates index APIs to support lazy, disk-backed partition access, and migrates NUMA system utilities to a new obisys crate. All modifications are structural, focusing on dependency graph expansion, import path updates, and API surface reorganization without altering core runtime behavior.
The MphfLayer::open signature now accepts only a directory path. Mode configuration is resolved internally via disk-based auto-detection using LayerEvidence, eliminating the need for explicit arguments from callers. All internal query methods and external call sites have been updated accordingly, while TypedLayer::open temporarily retains the unused parameter for future cleanup.
Define a shared Algorithm trait with an associated Output type and a parameterless run(&mut self) method. Refactor PartitionRouter, Dereplicator, Counter, and LayerBuilder to implement the trait, standardizing receivers to &mut self and moving configuration and progress callbacks to dedicated builder setters. Decouple error handling using a generic boxed error type and update workspace dependencies accordingly.
Migrate index state tracking from filesystem sentinel files to an on-disk JSON schema within `index.meta`. The `IndexMeta` struct is now wrapped in an `Arc` with internal locking, exposing only fallible methods for genome and state access. In-memory mutation capabilities have been removed, requiring callers to handle I/O errors explicitly and pass immutable references to downstream components like `PartitionRouter`. Public sentinel constants have been removed from exports.
Extracts directory bookkeeping and construction methods into a new IndexBuilder trait, separating maintenance operations from scientific computation logic. Migrates relevant methods to the new trait, updates module imports across obikindex, and narrows the crate's public API surface. Adds an end-to-end CLI smoke test to verify multi-index merge workflows.
Moves pipeline state bookkeeping, including sentinel file marking and spectrum persistence, into the algorithms' run and close methods. Introduces a crate-private extension trait to satisfy Rust's orphan rule while implementing construction-only operations on KmerIndex. Updates helper function visibility for cross-crate access and removes the now-empty index_layer module.
This commit renames the `Layer` type to `KmerLayer` throughout the `obikindex` and `obikphylo` crates. All imports, struct fields, function signatures, pattern matches, and instantiation calls have been updated accordingly. The change is a purely structural refactor that tightens type constraints without altering runtime behavior or data models.
Introduce a dedicated LayerBuilder struct to orchestrate parallel layer 0 construction across partitions. The fluent API supports configurable abundance thresholds and intermediate artifact retention. Parallel execution is delegated to a NUMA-aware PartitionRunner scheduler, while progress reporting and stage timing are shifted to the command layer. A new mark_indexed method cleanly separates state tracking from orchestration by generating a completion sentinel.
The layer API has been updated to rename `index` and `index_batch` to `hash` and `hash_batch`, aligning with raw MPHF slot hashing behavior. New public methods have been added to directly expose kmer hashing and iteration, enforcing strict state validation on empty layers. All other modifications are consistent code formatting adjustments without functional changes.
Decouple k-mer counting from the partitioner by introducing a new `Counter` struct. The module exposes a fluent builder API with optional partial file retention, executes partition processing in parallel via Rayon with memory-aware chunk sizing, and integrates thread-safe progress callbacks. Update all callers to use the new counter, simplify test pipelines by removing serialization overhead, and clarify algorithm separation in module documentation.
Eric Coissac