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.
Replace manual directory formatting and inline matrix opening with the newly introduced `layer_dir` and `open_data` helpers from the `obilayeredmap` crate. This standardizes filesystem access, encapsulates layer naming conventions, and simplifies error handling without altering computational behavior or test suites.
Refactor `pack_sparse_bit_matrix` to conditionally open either a packed or columnar dense representation based on file existence. This eliminates the previous unconditional pre-conversion step that forced a full packed copy. Update cleanup logic and add tests to verify direct transposition, proper file handling, and idempotency for both formats.
Consolidate row extraction and parallel column reduction into reusable generic utilities within the pairwise module. Replace manual iteration in builder and view methods with iterator-based zipped loops and deferred overflow processing to improve memory access patterns. Optimize distance functions by switching to bulk byte passes for branch-free SIMD vectorization, adding a merge-like helper to correct masked overflow values without secondary allocations. Add a comprehensive test validating the optimized distance paths against naive references across multiple thresholds and overflow scenarios.
Consolidate bit matrix operations by delegating pairwise metric calculations to IntSliceView and col_view implementations. Introduce chunked_presence_count in colgroup to handle threshold-based accumulation efficiently. Add a direct point lookup method to the sparse matrix representation to eliminate buffer allocations, and simplify match arms in persistent accessors accordingly. All public APIs and behavioral contracts remain unchanged.
Extract duplicated traversal logic into a shared `NonzeroSlotsView` trait and `nonzero_triples` helper. Update slice view iterators to consistently yield `(position, value)` tuples and use a temporary buffer with explicit permutation mapping for sorted access. Delegate manual slot sorting and column iteration to the new shared helper, eliminating per-format duplication and eager collection while preserving existing public API signatures.
Refactored `sub_matrix` to delegate column population to `fill_sub_matrix`, replacing manual buffer allocation and explicit permutation loops with direct value assignment via `enumerate_slots_values`. This eliminates intermediate allocations, reduces pipeline overhead, and simplifies control flow while preserving slot ordering and permutation semantics.
Renames `get_batch`, `fill_batch`, and `fill_batch_sorted` to `collect_slots_values`, `fill_slots_values`, and `fill_slots_values_sorted` to align with updated `common_traits 0.13` APIs. Introduces optimized batch retrieval that sorts input indices for sequential mmap access before reordering outputs to match the original query order. Updates test suites to reflect the new method signatures without altering validation logic or coverage.
Replaces nested column-major point lookups with a batched iterator that delegates to format-native traversal strategies. The implementation enforces a single pass per matrix type, using row-major iteration for sparse formats and eager collection for packed/columnar layouts while preserving original slot ordering. Memory allocation is optimized by removing `n_cols`-wide buffers in favor of per-row buffering or lazy iteration. Correctness tests verify iterator output against dense baselines across all supported layouts, and architecture documentation is updated to reflect the new format-agnostic query pattern.
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.
Bumps core dependencies including ndarray, rand, hashbrown, niffler, ureq, sysinfo, indicatif, lru, and remove_dir_all. Adapts source code to accommodate breaking changes by migrating RNG initialization, adjusting HTTP response handling, and replacing the fs4 crate with standard library file locking. Adds a planning document for query benchmarking and sparse index regression tests.
Updated core libraries and ecosystem packages, including the full serde suite and regex dependencies. Restructured syn dependency resolution by pinning 2.0.117 while introducing a standalone 3.0.3 entry for derive macros. Downgraded windows-sys to 0.59.0 and replaced the anes dependency in criterion2 with bpaf and walkdir. Removed an unused IntSliceView import from test modules.
Introduces raw mapping and iteration APIs that bypass membership checks, clarifies variant-specific storage layouts and auto-detection logic, and documents optimized batch access patterns with caller-provided buffers. Removes the outdated obicompactvector_reflexion.md specification to consolidate architectural details into current implementation docs.
This change removes precomputed model parameters, phylogenetic tree datasets, k-mer spectrum data, and compressed profile archives. It also deletes runtime logs and detailed pipeline documentation. The repository ignore list is updated to exclude the sandbox directory.
Removes the compressed JSON archive containing profile configuration and data model definitions. Build processes and runtime loaders referencing this path will require updates to prevent missing file errors.
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.
Introduce a `resume` method for persistent bit and int matrix builders to restore dimensions from persisted metadata. This enables incremental column appending across separate build sessions without requiring manual dimension tracking. Consolidate builder lifecycle management in the merge layer using a unified `MatrixBuilder` enum, simplify closure logic, and add instrumentation. Include tests verifying state preservation and data integrity across multiple resume cycles.
Update Cargo.lock to track the patch release of obikmer. This modification only adjusts the version in the lockfile and introduces no behavioral or API changes.
Updates the obikmer lockfile version to 1.2.1 and configures the obikindex dependency to explicitly disable default features. These are manifest and lockfile adjustments that do not modify source code or alter application behavior.
Explicitly sets `default-features = false` for the `obikindex` dependency to ensure no default features are activated during dependency resolution and compilation.
Adapts sibling k-mer tests to the updated canonical API by replacing string-based construction with direct byte conversion. Removes intermediate reverse complement steps and introduces a helper function to compute reverse complement strings directly from canonical k-mers, preserving existing test output while streamlining setup.
Updates the generated TNT script with configuration parameters and appends tree management commands for saving and exporting results. Modifications are strictly limited to string literals written to the output stream.
Introduce runtime dimension tracking, matrix shape validation, and per-layer diagnostics across multiple modules to improve execution observability. Extract intermediate computation results into local variables, standardize collection patterns in partial methods, and replace naive iteration with optimized pairwise counting. All modifications are strictly additive or structural; public APIs, data models, and core logic remain unchanged.
Introduce a `Sparse` variant for `PersistentBitMatrix` with full method dispatch and implementations of `ColumnWeights` and `BitPartials` traits. Refactor distance matrix computations in layered stores to eagerly collect results before reduction, enabling reliable dimension tracking. Add comprehensive debug logging across phylo commands and distance modules to report matrix shapes and flag out-of-bounds indices during CSV iteration.
Apply consistent multi-line formatting to iterator chains, struct initializations, function signatures, and CLI string literals. Convert sequence vector declarations to single-line format while expanding assertions and variable initializations across multiple lines. Reorder imports in the sankoff module and align test fixtures with updated line-length constraints. This change is purely syntactic with no functional or behavioral impact.
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.
Introduces --iqtree-min-freq (default 0.001) to treat low-frequency nucleotide states as missing data during IQ-TREE alignment generation when --free-loss is active. This triggers a recoding pass that folds rare states into the missing symbol, followed by non-informative site removal and alphabet recomputation to maintain output consistency. The change also adds Sankoff model configuration files and updates related tests and documentation.
Replaces premature exponentiation-based row normalization with log-sum-exp arithmetic to prevent tiny probabilities from collapsing to exactly zero. This eliminates spurious infinite costs for valid but rare transitions while preserving correct IEEE 754 semantics for genuinely unobserved pairs. Adds explicit guards against NaN in degenerate rows and includes a regression test verifying finite costs for probabilities as low as 1e-200.
Generates a new CSV output that maps IQ-TREE's compact state symbols to canonical states alongside full-precision empirical frequencies. Updates documentation to clarify that state frequencies sum to 1.0 by design and documents conditional behavior under `--free-loss`. Includes unit tests verifying absent state exclusion, frequency summation, and CSV structure. Also restricts entropy annex resolution to non-monomorphic minorants to eliminate redundant per-genome checks.
Shift monomorphism filtering from the entropy scan layer to a lightweight, annex-only pre-pass. By replacing `Selection::All` with a pre-filtered subset, expensive per-genome resolution is strictly limited to non-monomorphic families. This avoids processing ~98% of minorants that are known to be monomorphic, while preserving positional read speedups for subsequent runs. The change is an internal performance refinement with no public API modifications.
Documents architectural analysis, identified performance bottlenecks including hardcoded selection flags and redundant full-index scans causing I/O-bound stalls. Details planned pipeline refactoring to unify stages around a single shared selection for a fused single-pass scan, noting future dependencies on entropy-biased family selection.
Reworks `writeln!` macro invocations to multi-line syntax and adjusts whitespace for improved readability. Additionally, appends four commands to the generated phylogenetic script to explicitly export trees and manage taxon naming at runtime.
The index packing API now accepts a `sparse` parameter to generate `PersistentSparseBitMatrix` files alongside existing dense matrices. The sibling cache automatically detects this format via an `is_multi.prsb` marker file and routes queries identically to the dense variant. A new `--sparse` CLI flag exposes the option, with tests verifying end-to-end pipeline correctness and storage equivalence.
Implements a compact, row-major sparse bit matrix backed by memory-mapped components, introducing EliasFano, PersistentFixedIntVec, and PersistentRankSelectBitVec primitives for efficient storage and decoding. Adds a BinaryMatrix trait to unify row-level operations across dense and sparse implementations. Corrects edge-case behaviors for zero-width bit storage and cardinality-0 rows. Delivers reduced on-disk size and faster random row access, with column reads remaining dense-only. Test suites and benchmarks are included but currently marked as ignored.
Introduces `--subsample N` and `--shannon` CLI flags to cap retained variable families via proportional reservoir sampling and compute per-family Shannon entropy. Updates the family scanning API to support explicit selection filtering with early-exit optimization, resolving an indexing drift issue in monomorphic layers. Streams entropy metrics for 15-state and 4-nucleotide spaces directly to CSV while maintaining parallel processing across sibling layers.
Documents a proposed redesign for cross-partition batch resolution, shifting trigger logic to per-destination accumulator thresholds and introducing entropy-based pruning criteria. Adds an `n_layers_per_partition` method to the index, exposing partition metadata with consistent error handling and clarified documentation regarding build-time structural properties.
Adds compiler inlining hints to accessors, iterators, bitwise operations, and distance functions across multiple modules. This optimization aims to reduce call overhead for frequently invoked methods without modifying runtime behavior, API contracts, or data models.
Centralize the layer count validation into PartitionCache and track it via a new fast_mode flag. Extend query tuples to include a pre-resolved destination layer index, enabling a fast-path batch lookup that bypasses per-layer probing when enabled. Refactor neighbor iteration and hit resolution to eliminate duplication and conditionally dispatch to the optimized path based on the cache state.
Shift the sibling annex construction pipeline from an in-memory atomic mask to a memory-mapped file backend. This enables lock-free concurrent writes directly into the mapped region, streamlining the two-phase write process to accumulate bits atomically before finalization. Adjusted the cache lookup to return the specific matching layer index rather than a boolean flag, and added tests to verify correct layer tracking and cross-partition resolution in merged indexes.
Relocates `SiblingAnnex`, `FamilyMask`, and `SiblingAnnexBuilder` from `obicompactvec` to the local `obikphylo::siblings` module. Replaces the previous implementation with a memory-mapped version using `memmap2`, featuring a 2-byte-per-slot layout, explicit bitfield manipulation, and support for concurrent atomic writes. Updates all sibling module imports to local paths and adds the `memmap2` dependency to `obikphylo`.
Instruments the phylo command pipeline with structured execution timing, wrapping major computational blocks with stage hooks and printing aggregated metrics upon completion. Additionally, parallelizes sibling counting logic using Rayon to process independent layer directories concurrently, preserving identical functionality and public API contracts.
Shifts sibling annex construction from slot-indexed enumeration to iteration-order traversal by correcting cumulative k-mer offset tracking in batch enumeration. Replaces coarse per-partition parallelism with chunked work distribution to prevent thread starvation on skewed partitions. Decouples custom progress messages from ETA updates to eliminate display clobbering during high-frequency callbacks. Adds regression tests validating batch offset correctness, partial batch handling, and iterator-order consistency across layer builds.
Introduces timing constants and atomic fields to control ETA calculation intervals. Replaces the static template placeholder with dynamic messages, delegating formatting to a new helper that applies throttling thresholds and suppresses automatic updates during custom message hold periods.
Relocate the `siblings` and `cardcomp` modules from `obikindex` to a dedicated `obikphylo` workspace member. Convert inherent methods on `KmerIndex` into extension traits, update import paths across `obikmer`, and add supporting accessor methods to `obikseq` and `obilayeredmap`. This restructuring reduces the public API surface of `obikindex` while organizing phylogenetic iteration, caching, and distance calculation logic under a dedicated crate.
Transitions the index from MPHF slot-based to physical iteration-order indexing, aligning with the unitig layout. Introduces a streaming-only pipeline for k-mer iteration that adheres to memory constraints by avoiding full in-memory collections. Updates layer and sibling iterators to own an Arc clone of the file reader, making them Send + 'static and safe for concurrent use without borrowing the parent. Exposes batch and k-mer iterator types publicly while simplifying signature syntax with modern lifetime elision.
Introduces batch retrieval and sub-matrix extraction methods across vector, view, reader, and matrix types. These implementations optimize cache locality by sorting requested indices for sequential memory access before applying an inverse permutation to restore original order. Includes allocation-free variants that populate caller-provided buffers. Updates architecture documentation to define sibling annex persistence in iteration order and clarify pipeline separation.
Introduces `index` and `index_batch` methods for direct MPHF slot mapping without membership validation, alongside four public iterator methods for deterministic traversal of canonical kmers. These are backed by dedicated `KmerIter` and `KmerBatchIter` structs that wrap the underlying unitig file reader. Updates `LayerEvidence::Approx` to eagerly open the unitig reader during initialization, enforcing a clear separation between raw mapping and verified lookup workflows.
Transition the minorant flag from a derived value to a stored field within the family mask, resolving a performance regression where on-the-fly reconstruction consumed significant query time. This change introduces O(1) k-mer reconstruction APIs, shifts minorant computation to the index build phase, and enables direct annex-based statistics. Supporting updates include adopting shared ownership for partition caches and refactoring batch processing pipelines.
Refactor `scan_layer_families` across the siblings module to accept a closure callback instead of returning an intermediate collection. This eliminates eager materialization and per-layer buffering by streaming results directly into genome-specific buffers or tally matrices. The update introduces bounded batch processing and scratch buffer reuse to cap peak auxiliary memory, while preserving existing computational behavior, control flow, and error semantics.
The sibling calculation modules now process layer directories sequentially instead of in parallel. This eliminates concurrent processing overhead and prevents interleaved cache sweeps, improving disk I/O and page-cache locality for partition-grouped data access. Progress bar updates and result accumulation have been adapted to the sequential control flow, while core filtering logic and output structures remain unchanged.
Introduces a dedicated `family_scan` submodule to consolidate per-layer family traversal logic. Centralizes path validation, minorant filtering, and conditional matrix instantiation into a shared `scan_layer_families` function. Updates sibling-annex consumers to leverage the new abstraction, reducing inline scanning code. Adds a test fixture to verify numerical consistency across consumer methods for co-occurrence and base-pair metrics.
Restructure the output files section into categorized subsections with tables. Add explicit mappings between command-line options and generated files. Define CSV matrix conventions, clarify mathematical formulas for distance calculations, and document execution commands for external phylogenetic tools.
Extracts directory cleanup, partition initialization, and finalization into dedicated helper methods within KmerIndex. This centralizes force-flag handling and reduces boilerplate across merge, rebuild, and select workflows. Additionally updates the CLI progress bar template to display an ETA indicator following elapsed time.
Introduce the obikmer name-tree subcommand to map numeric leaf labels in phylogenetic tree exports back to taxon names using a reference FASTA file. Correct the --free-loss flag behavior by removing cardinality transition costs from pairwise cost calculations, ensuring sibling gains and losses are priced identically to whole-family events. Update documentation, configuration parameters, and add reference phylogenetic data files.
Introduces CLI flags for computing pairwise family overlap matrices and filtering genomes below a shared family threshold. Adds a free-loss mode that recodes locus non-detection states to missing data symbols in Sankoff-calibrated alignments, resolving ascertainment bias handling for IQ-TREE. Updates empirical transition parameters, removes the legacy model asset, and extends output writers for CSV diagnostics, FASTA pseudo-alignments, and Newick trees.
The index creation routine now uses the CLI `--force` argument instead of a hardcoded false value, enabling explicit overwrite control. Partition existence checks also verify for the designated subdirectory rather than the root path, ensuring conflict detection and cleanup only trigger when an actual partition layout exists.
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.
Establishes foundational infrastructure across multiple crates by introducing unified persistent bit matrix storage with columnar, packed, and implicit variants, alongside De Bruijn graph node encoding and unitig iteration logic. Adds a macro-driven parallel pipeline scheduler featuring NUMA-aware runners, bounded channels, and memory budgets to enforce concurrency limits. Implements streaming nucleotide parsers with pooled page buffers for FASTA, FASTQ, and Genbank formats, complemented by system resource monitoring, progress tracking, and stage profiling utilities. Collectively, these changes provide the core data models, execution frameworks, and I/O pipelines required for downstream k-mer indexing and analysis workloads.
Introduces a new predicate module in obikindex that implements genome metadata predicate parsing, evaluation, and group classification using three-valued logic. Extends the IndexMeta API with methods for single-predicate filtering and group quorum filtering. Updates obikmer command modules to delegate filter construction and matching to the centralized index API, removing local definitions and simplifying call sites.
Convert single-file modules to directory-based layouts across the cmd crate. Decompose the monolithic query command into dedicated submodules for batching, chunk processing, sparse finding, and output formatting. Introduce a new utils module to handle index management operations including statistics reporting, label renaming, and partition analysis.
Introduces a comprehensive documentation set covering theoretical foundations, CLI usage, installation, and system architecture. Adds MkDocs configuration and Makefile targets to generate, serve with live reload, and clean the documentation site. Includes citation styles and bibliography files for academic references.
Replaced the legacy Sankoff parsimony pipeline with a new cardinality-composition decomposition that constructs row-normalized transition probability matrices symmetrized via geometric mean. This ensures reversibility, reduces free parameters from 240 to 120, and guarantees a zero diagonal. Tallies are now explicitly restricted to variable families to align with +ASC-corrected alignment populations. Additionally, fixed `--exclude-genome` handling to re-scan surviving sequences and drop newly monomorphic columns, preventing silent data corruption in downstream tree inference tools.
Integrate in-memory row/column zeroing and alignment filtering across SNP, Sankoff, TNT, and IQ-TREE output paths. Add strict validation for missing labels, implement `write_iqtree` with empirical stationary frequencies, and introduce `--raw-snp-counts` diagnostic CSV output. Update documentation to reflect experimental validation of backbone resolution limits and theoretical considerations for CTMC rate matrices.
Introduce `--iqtree` and `--raw-snp-counts` flags to generate IQ-TREE model files, recoded FASTA alignments, and per-pair diagnostic counts. Centralize alphabet conversion by extracting a precomputed state index lookup table into the Sankoff module, eliminating redundant iterations across downstream adapters.
Replaces external Python glue with native Rust modules for Sankoff model calibration, exporting calibrated cost matrices, FASTA alignments, and YAML parameters. Adds dedicated writers for TNT and PhyG that apply integer scaling and Floyd-Warshall metric closure to enforce triangle inequality. Integrates these exporters into the distance command pipeline to streamline downstream tree inference workflows, while updating theory documentation to reflect IQ-TREE integration and state renumbering improvements.
Implements a calibrated 16-state Sankoff substitution cost matrix and CLI pipeline for evolutionary distance computation, including empirical calibration via saturation-filtered SNP counts. Refactors the sibling scanning stage to use batched transforms for improved synchronization efficiency. Introduces an OS-level advisory directory lock across all index-modifying commands to prevent concurrent write corruption. Updates dependencies and exposes new Sankoff utilities in the public API.
Re-enables the `numa` feature in CI workflows to prevent container/cgroup deadlocks while preserving validation correctness. Fixes concurrent test race conditions by replacing thread-local parameter storage with process-wide atomics and mutex locks. Integrates `tracing-subscriber` for structured logging and adds thread-ID tracking to debug worker lifecycles. Additionally bumps the crate version, updates `.gitignore`, documents experimental evolutionary distance pipelines, and refactors hardcoded test constants.
Disable the `numa` default feature in CI build and test steps to prevent container environment deadlocks, and add comments explaining the cache key salt bump (`v2`) to mitigate incremental compilation corruption. Document a 16-state Sankoff cost matrix derived from set-edit distances, including substitution, gain/loss, and context-disappearance costs compatible with TNT's interface. Bump `obikmer` crate version to 1.1.43.
Updated CI workflow cache keys with a `v2` salt and `Cargo.lock` hash to prevent stale incremental compilation caches and deadlocks, while updating restore keys and documenting interrupted job state. Introduced a 3-way ordinal distance metric framework that replaces ambiguous IUPAC encoding with explicit k-mer scoring, bridging pairwise methods to character-based phylogenetics via Sankoff parsimony. Bumped the `obikmer` crate version to 1.1.42.
Introduce `obisys::effective_parallelism()` to read Linux cgroup v1/v2 CPU quotas from sysfs, preventing thread pool oversubscription in containerized environments. Replace direct `std::thread::available_parallelism()` calls across `obikindex` and `obikmer` with this centralized function. Bump `obikmer` version to 1.1.41.
Introduces a `SnpAlignment` struct and helper methods to construct per-genome SNP pseudo-alignments from sibling k-mer data, filtering monomorphic families and encoding bases as IUPAC ambiguity codes. Exposes the type at the crate root for simplified imports. Adds a `--snp` CLI flag to compute and export these alignments as an IUPAC-coded FASTA file. Updates theory documentation to propose a multi-genome framing approach for joint phylogenetic inference, resolving pairwise correspondence ambiguities through positional homology and partial coverage thresholds. Bumps crate version to 1.1.40.
Exposes RawSnpDistanceOutput and implements KmerIndex::raw_snp_distance() to compute pairwise single-copy locus counts under a paralogy-aware rule. The implementation leverages ndarray for parallel matrix aggregation, producing raw p-distance matrices for sanity-checking. A --raw-snp-distance CLI flag is added to export results as CSV, mapping zero-eligible pairs to NA.
Replaces the explicit `SiblingInfo` struct and 3-bit minorant flags with a derived 4-bit presence mask (`FamilyMask`) that tracks observed bases per family. This eliminates redundant file I/O overhead by introducing a `PartitionCache` for batch lookups, simplifies serialization, and updates all downstream builders, stats computation, and tests to operate on the new bitmask representation. Adjusts CLI output to report deduplicated family sizes instead of histograms, ignores generated CSV files, and updates documentation to reflect the fixed canonical reference and new theory.
Add the `obipipeline` crate and replace sequential scatter/gather logic with a concurrent pipeline using `Flat` and `Transform` stages. Introduce `SiblingAnnexStats` API to compute distributions, and add CLI flags to `distance.rs` for constructing the annex and exporting statistics as CSV.
Introduce the siblingannex module in obicompactvec to store per-slot minorant flags and sibling counts in a memory-mapped annex file. Add a scatter-gather pipeline in obikindex to compute these values across index layers and write them to .psib files. Implement central_canonical_neighbors in obikseq for generating strand-aware k-mer variants around the middle base. Expose rolling statistics in obiskbuilder and update dependency graphs accordingly.
Updates CLI parsing to accept negative integers for count filters, interpreting them as offsets from the group size (e.g., `-1` means all but one). A resolution closure enforces a floor of 1 to prevent unconstrained filtering on small groups. Additionally, refines evolutionary distance documentation to condition comparisons on local homology, replacing union-based Jaccard with a self-contained `SnpTally`. This unified approach streamlines SNP and shared count computation, incorporates paralogy and heterozygosity handling, and enables direct derivation of corrected distance matrices without external dependencies.
Eric Coissac