feat: add benchmark pipeline, expose APIs, and enforce strict paths

Introduces a Make-based orchestration for simulating, indexing, merging, filtering, and verifying k-mer counts and presence. Exposes internal builder and iterator APIs publicly, enforces mandatory leading slashes for predicate patterns, registers the `obitaxonomy` crate, and updates tooling configurations alongside documentation.
2026-06-19 09:55:41 +02:00
parent 280ca1f5a3
commit c694e1f2b0
42 changed files with 2585 additions and 84 deletions
@@ -9,3 +9,13 @@ data-stress
 ./**/*.json
 *.bin
 Betula_exilis--IGA-24-33
+benchmark/genomes
+benchmark/simulated_data
+benchmark/specimen_index_presence
+benchmark/specimen_index_count
+benchmark/global_index_presence
+benchmark/global_index_count
+benchmark/stats
+benchmark/reference_index
+benchmark/specific_index_count
+benchmark/specific_index_presence