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.
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.
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.
Eric Coissac