4 Commits

Include renames

Author	SHA1	Message	Date
Eric Coissac	8bb1d52514	disable default features for obisys dependency ... Update obisys dependency configuration across multiple crates to explicitly set default-features = false. This restricts compilation to only explicitly enabled feature flags, affecting build resolution and potentially compile-time paths or binary size. Also updates the obikmer package version to 1.3.1.	2026-08-29 08:13:49 +02:00
Eric Coissac	737966899f	Add obikselect crate for k-mer selection and aggregation ... 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.	2026-08-26 14:27:19 +02:00
Eric Coissac	5dc16b0127	refactor(obikselect): implement Algorithm trait for selection ... 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.	2026-08-26 09:17:48 +02:00
Eric Coissac	fc4464a0ef	Extract index modules into specialized workspace subcrates ... 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.	2026-08-22 06:25:28 +02:00