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.
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