Introduces a new `obikselect` module to handle k-mer selection and column aggregation. Adds a `select` CLI command in `obikmer2` that supports group predicates, aggregate operators, and output column filtering. Implements operator parsing with case-insensitive matching and default rules, along with a centralized module for resolving group specifications from metadata or genome filters. Updates dependencies to include the new crate and its prerequisites.
Shifts the selection logic from a direct method into a dedicated `Select` struct implementing the `Algorithm` trait. Introduces a two-phase initialization pattern with explicit builder methods and closure-based progress callbacks. Updates the crate's dependency graph to include `obikalgorithm`, refactors layer processing with unified matrix dispatch, and implements dual directory routing for partition execution.
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