refactor: extract index construction state tracking into extension trait

Moves pipeline state bookkeeping, including sentinel file marking and spectrum persistence, into the algorithms' run and close methods. Introduces a crate-private extension trait to satisfy Rust's orphan rule while implementing construction-only operations on KmerIndex. Updates helper function visibility for cross-crate access and removes the now-empty index_layer module.
2026-08-21 10:38:51 +02:00
parent 31bb324752
commit da3aa5a2cb
16 changed files with 527 additions and 254 deletions
@@ -6,6 +6,7 @@ edition = "2024"
 [dependencies]
 obikindex        = { path = "../obikindex" }
 obikseq          = { path = "../obikseq" }
+obidebruinj      = { path = "../obidebruinj" }
 obiskio          = { path = "../obiskio" }
 obisys           = { path = "../obisys" }
 obicompactvec    = { path = "../obicompactvec" }