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