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.
The command now supports reopening existing indexes instead of failing when the output file exists. Control flow branches between opening an existing index and constructing a new one, moving configuration setup exclusively to the creation path. Directory existence is enforced upfront with proper I/O error propagation. The --force flag retains its original semantics by removing the target directory before proceeding with a fresh build.
Move partition dereplication logic into a dedicated `obikderep` crate that implements a two-phase hash-split/merge strategy with Rayon for parallel processing. Centralize superkmer file path construction in `obilayeredmap` and update dependent crates to use the new pipeline and shared path helpers. Adjust test suites to explicitly invoke the dereplication step.
Invert dependencies by moving partition path primitives to a dedicated module and updating the index crate accordingly. Reshape the partition router to accept a mutable index reference, enabling chainable configuration and resolving lifetime issues with explicit drops. Shift orchestration logic from the index crate to the CLI, replacing monolithic scatter calls with discrete dereplication and counting steps. Introduce a generic progress callback API to decouple rate calculation from UI rendering, and correct file I/O paths to route layer-0 artifacts under the partition index directory.
Introduces the `obikpartition` crate containing the `KmerPartition` struct to manage open layers in sequential order. The `open` constructor eagerly initializes layers under a specified directory, while the `find` method returns the index of the first layer containing a given k-mer. Dependencies are strictly scoped to `obilayeredmap` and `obikseq`, with unit tests validating layer ingestion and single-kmer lookup behavior. Batch lookups and further migration are deferred to a subsequent phase.
The `Layer` enum is transformed into a lifecycle-aware state machine with an `Empty` variant representing an unconstructed directory. Read and query operations now explicitly panic when invoked on this state, enforcing explicit progression through `create()` before use. Iterator methods are updated to handle the new variant exhaustively, and module visibility constants are adjusted to support the refactored structure.
Renames `Layer<D>` to `TypedLayer<D>` to establish a distinct typed abstraction. Introduces a new heterogeneous `Layer` enum that unifies count and presence storage with runtime dispatch, delegating operations to the underlying typed variants. Updates cache, index, and phylo consumers to align with the renamed type and new extension traits, preserving full test suite stability while preparing the foundation for multi-partition caching.
Consolidates partition logic, metadata storage, and layer management directly into KmerIndex. Renames obikpartitionner to obikpartition, retaining only PartitionRouter for superkmer routing. Removes intermediate .partition() accessors in favor of direct methods on the index and updates PartitionCache::build to accept &KmerIndex directly. Derives n_partitions from config.n_bits and consolidates k-mer/minimizer sizes into IndexMeta.config. Fixes a regression where PartitionRouter::open incorrectly defaulted to closed.
Update all dependent crates and internal imports to reference the renamed module. Expose configuration parameters and genome metadata through new public accessor methods in the index API, and update documentation comments to align with the new package name.
Adjusts the visibility of the COUNTS_DIR constant to pub(crate), enabling internal crate-wide access without altering runtime behavior or data structures.
Update Cargo manifests, dependency paths, and Rust imports across the workspace to reflect the `obikpartitionner` to `obikpartition` rename. Synchronize architecture and implementation documentation with the new module structure. Fix minor syntax issues in test assertions to ensure compilation compatibility. No behavioral or API changes are introduced.
Rename the KmerPartition type to KmerPartitions across obikindex, obikpartitionner, and obikphylo/siblings to reflect an updated data model. Update the Mat enum in siblings/cache.rs to add a SparsePresence variant and simplify opening logic by delegating sparse versus dense detection to PersistentBitMatrix. Apply consistent code formatting, import reordering, and multi-line refactoring throughout the affected modules.
Replaced scattered direct metadata loading with centralized instance methods on `KmerPartition` to guarantee consistent error mapping and legacy recovery. Introduced `StorageKind`, `LayerContent`, and `EvidenceKind` enums alongside lightweight disk-probe methods that inspect file presence without opening heavy data structures. Updated callers across the index, partitioner, and phylo modules to use the new partition API, and added unit tests validating the introspection behavior.
Introduce a design specification outlining performance bottlenecks in layer data access and an agreed-upon implementation direction for caching. Refactor the codebase to centralize index and layer directory path resolution within the partition object, replacing manual string joining and external helper functions with dedicated accessor methods.
Standardizes layer directory path resolution across obikindex, obikpartitionner, and obikphylo by replacing inline string formatting and join calls with the centralized obilayeredmap::layer_dir utility. This refactoring removes redundant path construction logic while preserving existing iteration bounds, control flow, and public APIs.
Eric Coissac