refactor: centralize k-mer config and introduce packed sequences

Centralize k-mer and minimizer configuration using a thread-safe global module, and replace manual bit-packing with a memory-efficient `PackedSeq` type. Refactor core sequence and k-mer types to use compile-time length enforcement and centralized hashing. Introduce a new De Bruijn graph implementation with compact node encoding and traversal iterators. Update I/O, partitioning, and builder modules to align with the new architecture, and add the `xxhash-rust` dependency.
2026-05-05 18:08:19 +02:00
parent 602f414957
commit 8c17bf958b
37 changed files with 2641 additions and 2456 deletions
@@ -6,3 +6,6 @@ edition = "2024"
 [dependencies]
 obikseq = { path = "../obikseq" }
 xxhash-rust = { version = "0.8", features = ["xxh64"] }
+
+[dev-dependencies]
+obikseq = { path = "../obikseq", features = ["test-utils"] }