feat: integrate obikseq to configure global k-mer and minimizer sizes

This change adds the `obikseq` crate as a local dependency and inserts `set_k` and `set_m` calls across index creation and command modules. By synchronizing the runtime's global k-mer and minimizer dimensions with the loaded index parameters, downstream sequence processing and partitioning operations now consistently use the correct structural constraints.

src/Cargo.lock

@@ -1507,6 +1507,7 @@ dependencies = [
  "ndarray",
  "obicompactvec",
  "obikpartitionner",
+ "obikseq",
  "obilayeredmap",
  "obiskio",
  "obisys",

src/obikindex/Cargo.toml

@@ -4,6 +4,7 @@ version = "0.1.0"
 edition = "2024"
 
 [dependencies]
+obikseq          = { path = "../obikseq" }
 obikpartitionner = { path = "../obikpartitionner" }
 obiskio          = { path = "../obiskio" }
 obisys           = { path = "../obisys" }

src/obikindex/src/index.rs

@@ -11,6 +11,8 @@ use obisys::{Reporter, Stage};
 use rayon::prelude::*;
 use tracing::info;
 
+use obikseq::{set_k, set_m};
+
 use crate::error::{OKIError, OKIResult};
 use crate::meta::{GenomeInfo, IndexConfig, IndexMeta};
 use crate::state::{IndexState, SENTINEL_COUNTED, SENTINEL_INDEXED, SENTINEL_SCATTERED};
@@ -40,6 +42,8 @@ impl KmerIndex {
             config.minimizer_size,
             force,
         )?;
+        set_k(config.kmer_size);
+        set_m(config.minimizer_size);
         let mut meta = IndexMeta::new(config);
         if let Some(info) = genome_info {
             meta.genomes.push(info);
@@ -51,6 +55,8 @@ impl KmerIndex {
     pub fn open<P: AsRef<Path>>(path: P) -> OKIResult<Self> {
         let root_path = path.as_ref().to_owned();
         let meta = IndexMeta::read(&root_path).map_err(OKIError::Io)?;
+        set_k(meta.config.kmer_size);
+        set_m(meta.config.minimizer_size);
         let partition = KmerPartition::open_with_config(
             &root_path,
             meta.config.kmer_size,

src/obikmer/src/cmd/distance.rs

@@ -4,7 +4,6 @@ use std::path::PathBuf;
 use clap::Args;
 use kodama::{Method, linkage};
 use obikindex::{DistanceMetric, KmerIndex};
-use obikseq::{set_k, set_m};
 use speedytree::{DistanceMatrix, Hybrid, NeighborJoiningSolver, to_newick};
 use tracing::info;
 
@@ -72,8 +71,6 @@ pub fn run(args: DistanceArgs) {
         std::process::exit(1);
     });
 
-    set_k(idx.kmer_size());
-    set_m(idx.minimizer_size());
 
     let labels: Vec<String> = idx.meta().genomes.iter().map(|g| g.label.clone()).collect();
     let n = labels.len();

src/obikmer/src/cmd/dump.rs

@@ -3,7 +3,6 @@ use std::path::PathBuf;
 
 use clap::Args;
 use obikindex::KmerIndex;
-use obikseq::set_k;
 use tracing::info;
 
 #[derive(Args)]
@@ -26,7 +25,6 @@ pub fn run(args: DumpArgs) {
         std::process::exit(1);
     });
 
-    set_k(idx.kmer_size());
     info!(
         "dumping {} partitions, {} genome(s)",
         idx.n_partitions(),

src/obikmer/src/cmd/index.rs

@@ -8,7 +8,6 @@ fn parse_key_value(s: &str) -> Result<(String, String), String> {
     let pos = s.find('=').ok_or_else(|| format!("invalid key=value: no '=' in '{s}'"))?;
     Ok((s[..pos].to_string(), s[pos + 1..].to_string()))
 }
-use obikseq::{set_k, set_m};
 use obisys::Reporter;
 use tracing::info;
 
@@ -222,8 +221,6 @@ pub fn run(args: IndexArgs) {
         })
     };
 
-    set_k(idx.kmer_size());
-    set_m(idx.minimizer_size());
 
     // ── Stage 1: scatter ─────────────────────────────────────────────────────
     if idx.state() < IndexState::Scattered {

src/obikmer/src/cmd/merge.rs

@@ -2,7 +2,6 @@ use std::path::PathBuf;
 
 use clap::Args;
 use obikindex::{KmerIndex, MergeMode};
-use obikseq::{set_k, set_m};
 use obisys::Reporter;
 use tracing::info;
 
@@ -53,8 +52,6 @@ pub fn run(args: MergeArgs) {
 
     let source_refs: Vec<&KmerIndex> = sources.iter().collect();
 
-    set_k(sources[0].kmer_size());
-    set_m(sources[0].minimizer_size());
 
     let n_genomes: usize = sources.iter().map(|s| s.meta().genomes.len()).sum();
     info!(

src/obikmer/src/cmd/query.rs

@@ -6,7 +6,7 @@ use std::sync::Arc;
 use clap::Args;
 use obikindex::KmerIndex;
 use obikrope::Rope;
-use obikseq::{RoutableSuperKmer, set_k, set_m};
+use obikseq::RoutableSuperKmer;
 use obilayeredmap::IndexMode;
 use obiread::chunk::read_sequence_chunks_sized;
 use obiread::record::{SeqRecord, parse_chunk};
@@ -427,9 +427,6 @@ pub fn run(args: QueryArgs) {
         std::process::exit(1);
     }));
 
-    set_k(idx.kmer_size());
-    set_m(idx.minimizer_size());
-
     let k = idx.kmer_size();
     let n_genomes = idx.meta().genomes.len();
     let n_partitions = idx.n_partitions();

src/obikmer/src/cmd/rebuild.rs

@@ -7,7 +7,6 @@ use obikpartitionner::filter::{
     MinGenomeCount, MinGenomeFraction, MinTotalCount,
 };
 use obisys::Reporter;
-use obikseq::{set_k, set_m};
 use tracing::info;
 
 #[derive(Args)]
@@ -62,8 +61,6 @@ pub fn run(args: RebuildArgs) {
         std::process::exit(1);
     });
 
-    set_k(src.kmer_size());
-    set_m(src.minimizer_size());
 
     let n_genomes = src.meta().genomes.len();
     let mode = if args.presence || !src.meta().config.with_counts {

src/obikmer/src/cmd/utils.rs

@@ -2,7 +2,6 @@ use std::path::PathBuf;
 
 use clap::Args;
 use obikindex::{validate_label, KmerIndex};
-use obikseq::set_k;
 use tracing::info;
 
 #[derive(Args)]
@@ -43,7 +42,6 @@ fn run_upgrade_index(index_path: &PathBuf) {
         eprintln!("error opening index: {e}");
         std::process::exit(1);
     });
-    set_k(idx.kmer_size());
     idx.upgrade_layer_meta().unwrap_or_else(|e| {
         eprintln!("upgrade error: {e}");
         std::process::exit(1);