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.
Eric Coissac
coissac