5 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	904d85f33b	Implement pack CLI command for matrix packing and layer compaction ... Adds the `pack` subcommand to `obikmer2` for persisting presence and count matrices in sparse or dense formats. Introduces the `compact_layer` module in `obikrebuild` to merge multiple partition layers into a single layer in-place via atomic operations. Updates dependencies across `obikdump`, `obikmer2`, and `obikrebuild` to resolve new local crate references. Shifts the architecture from multi-layer accumulation to in-place compaction, removing legacy rebuild modules.	2026-08-26 14:48:44 +02:00
Eric Coissac	96dfb5300b	Add unitig extraction command to obikdump and obikmer2 ... Introduces a new unitig extraction feature that reads k-mers from an index, filters them by group metadata, and partitions the computation using rayon. The implementation constructs per-partition de Bruijn graphs, merges them, computes node degrees, and writes the resulting sequences as FASTA. A corresponding CLI command is added to obikmer2 to expose this functionality with configurable filtering and progress reporting.	2026-08-26 14:40:02 +02:00
Eric Coissac	16ade823d6	refactor: extract partition iteration and unify group selection ... 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.	2026-08-26 09:33:37 +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