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.

This commit is contained in:

Eric Coissac

2026-05-05 18:08:19 +02:00

parent 602f414957

commit 8c17bf958b

37 changed files with 2641 additions and 2456 deletions

src/Cargo.lock

Generated

View File

@@ -1575,6 +1575,7 @@ dependencies = [
  "hashbrown 0.14.5",
  "obifastwrite",
  "obikseq",
  "xxhash-rust",
 ]
 [[package]]