feat: add kmer iterators and optimize layered map performance

Replace `ph` with `ptr_hash` and introduce `epserde` and `rayon` dependencies. Refactor MPHF construction to leverage parallel iteration, eliminating intermediate `Vec<u64>` allocations and reducing memory footprint. Add a `n_kmers` field to track and serialize total kmer counts, alongside three zero-allocation iterators for efficient chunk traversal. Include comprehensive unit tests for the new iterators and update CLAUDE.md to enforce explicit dependency validation policies.
2026-05-12 22:28:01 +08:00
parent 9c41891cc8
commit ff75c9198d
7 changed files with 359 additions and 61 deletions
@@ -6,7 +6,9 @@ edition = "2024"
 [dependencies]
 obikseq  = { path = "../obikseq" }
 obiskio  = { path = "../obiskio" }
-ph = "0.11"
+ptr_hash = "1.1"
+epserde  = "0.8"
+rayon    = "1"
 memmap2  = "0.9"
 serde      = { version = "1", features = ["derive"] }
 serde_json = "1"