feat: add configurable presence threshold to kmer distance

Introduce a `--presence-threshold` CLI argument (default: 1) and update `KmerIndex::distance` to accept a `presence_threshold` parameter. This replaces hardcoded zero thresholds, enabling configurable filtering of low-abundance kmers during Jaccard distance calculations.

src/obikindex/src/distance.rs

@@ -52,7 +52,7 @@ impl DistanceMetric {
 // ── KmerIndex::distance ───────────────────────────────────────────────────────
 
 impl KmerIndex {
-    pub fn distance(&self, metric: DistanceMetric, shared_kmers: bool) -> OKIResult<DistanceOutput> {
+    pub fn distance(&self, metric: DistanceMetric, shared_kmers: bool, presence_threshold: u32) -> OKIResult<DistanceOutput> {
         let n_genomes = self.meta.genomes.len();
         if n_genomes < 2 {
             return Err(OKIError::InvalidInput(
@@ -83,8 +83,7 @@ impl KmerIndex {
                 DistanceMetric::RelfreqEuclidean  => CountPartials::relfreq_euclidean_dist_matrix(&global),
                 DistanceMetric::Hellinger         => CountPartials::hellinger_dist_matrix(&global),
                 DistanceMetric::HellingerEuclidean => CountPartials::hellinger_euclidean_dist_matrix(&global),
-                // Jaccard on count data: threshold at 0 (present if count > 0)
+                DistanceMetric::Jaccard           => CountPartials::threshold_jaccard_dist_matrix(&global, presence_threshold),
-                DistanceMetric::Jaccard           => CountPartials::threshold_jaccard_dist_matrix(&global, 0),
                 DistanceMetric::Hamming           => {
                     return Err(OKIError::InvalidInput(
                         "Hamming is only available for presence/absence indexes".into(),
@@ -93,7 +92,7 @@ impl KmerIndex {
             };
 
             let shared = if shared_kmers {
-                let (inter, _) = CountPartials::partial_threshold_jaccard(&global, 0);
+                let (inter, _) = CountPartials::partial_threshold_jaccard(&global, presence_threshold);
                 Some(inter)
             } else {
                 None

src/obikmer/src/cmd/distance.rs

@@ -46,6 +46,10 @@ pub struct DistanceArgs {
     #[arg(long, value_enum, default_value = "jaccard")]
     pub metric: MetricArg,
 
+    /// Minimum count to consider a kmer present when computing Jaccard on count indexes
+    #[arg(long, default_value = "1")]
+    pub presence_threshold: u32,
+
     /// Also output the shared-kmer count matrix (CSV)
     #[arg(long)]
     pub shared_kmers: bool,
@@ -81,7 +85,7 @@ pub fn run(args: DistanceArgs) {
 
     let need_shared = args.shared_kmers || args.nj || args.upgma;
     let result = idx
-        .distance(args.metric.into(), need_shared)
+        .distance(args.metric.into(), need_shared, args.presence_threshold)
         .unwrap_or_else(|e| {
             eprintln!("error computing distances: {e}");
             std::process::exit(1);