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feat: add configurable presence threshold to kmer distance

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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.
This commit is contained in:
Eric Coissac
2026-06-08 20:13:07 +02:00
parent 1ec65922df
commit eb7805c747
2 changed files with 8 additions and 5 deletions
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src/obikindex/src/distance.rs
+3 -4
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@@ -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, 0),
DistanceMetric::Jaccard => CountPartials::threshold_jaccard_dist_matrix(&global, presence_threshold),
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