Extract dereplication logic into obikderep crate and centralize paths

Move partition dereplication logic into a dedicated `obikderep` crate that implements a two-phase hash-split/merge strategy with Rayon for parallel processing. Centralize superkmer file path construction in `obilayeredmap` and update dependent crates to use the new pipeline and shared path helpers. Adjust test suites to explicitly invoke the dereplication step.
2026-08-20 22:30:03 +02:00
parent 616cb76af3
commit abc51c2add
17 changed files with 534 additions and 97 deletions
@@ -0,0 +1,21 @@
+[package]
+name = "obikderep"
+version = "0.1.0"
+edition = "2024"
+
+[dependencies]
+niffler = "3.0.0"
+obikseq       = { path = "../obikseq" }
+obikindex     = { path = "../obikindex" }
+obilayeredmap = { path = "../obilayeredmap" }
+obiskio       = { path = "../obiskio" }
+obisys        = { path = "../obisys" }
+rayon = "1"
+sysinfo = "0.39"
+tracing = "0.1.44"
+
+[dev-dependencies]
+tempfile = "3"
+obikseq  = { path = "../obikseq", features = ["test-utils"] }
+obikrope = { path = "../obikrope" }
+obiskbuilder = { path = "../obiskbuilder" }