feat: add entropy-driven k-mer complexity filtering

Introduces a MinComplexity filter driven by new CLI arguments, enabling sequence-aware threshold checks during index reconstruction and partitioning. Adds the kmer_entropy module for normalized complexity scoring, updates the KmerFilter trait to evaluate per-kmer context, and refactors test modules for better organization.
2026-07-08 12:48:25 +02:00
parent 165982fb07
commit e725523898
11 changed files with 350 additions and 192 deletions
@@ -6,7 +6,6 @@ edition = "2024"
 [dev-dependencies]
 tempfile = "3"
 obikseq   = { path = "../obikseq",   features = ["test-utils"] }
-obiskbuilder = { path = "../obiskbuilder" }
 obiread   = { path = "../obiread" }
 obikrope  = { path = "../obikrope" }

@@ -14,6 +13,7 @@ obikrope  = { path = "../obikrope" }
 niffler = "3.0.0"
 remove_dir_all = "0.8"
 obikseq      = { path = "../obikseq" }
+obiskbuilder = { path = "../obiskbuilder" }
 obiskio      = { path = "../obiskio" }
 obidebruinj  = { path = "../obidebruinj" }
 obilayeredmap = { path = "../obilayeredmap" }