Update documentation to reflect architectural fixes in the NUMA partition runner and implementation changes in the merge and select modules. The partition runner now wraps task execution in `catch_unwind`, emitting panic events that count toward completion thresholds to prevent controller deadlocks, while re-raising the first payload on return. CLI documentation for select has been updated to mandate output directories, introduce default hard-linking with automatic fallback, and document presence aggregation optimizations. Known issues such as self-merge crashes and sparse-packed index gaps are now documented as failing fast due to these improvements.
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.
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.
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.
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.
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.
Eric Coissac