skip clustering when both are skani

src/cluster_argument_parsing.rs

@@ -901,7 +901,7 @@ pub fn generate_galah_clusterer<'a>(
 ) -> std::result::Result<GalahClusterer<'a>, String> {
     crate::external_command_checker::check_for_fastani();
 
-    let repeat_clusterer = {
+    let skip_clusterer = {
         clap_matches
             .get_one::<String>(&argument_definition.dereplication_precluster_method_argument)
             .unwrap()
@@ -982,7 +982,7 @@ pub fn generate_galah_clusterer<'a>(
                     }),
                     "skani" => Preclusterer::Skani(SkaniPreclusterer {
                         threshold: {
-                            if repeat_clusterer {
+                            if skip_clusterer {
                                 parse_percentage(
                                     clap_matches,
                                     &argument_definition.dereplication_ani_argument,

src/clusterer.rs

@@ -26,6 +26,12 @@ pub fn cluster<P: PreclusterDistanceFinder, C: ClusterDistanceFinder + std::mark
         preclusterer_name, clusterer_name
     );
 
+    let mut skip_clusterer = false;
+    if clusterer_name == preclusterer_name {
+        info!("Preclustering and clustering methods are the same, so skipping preclustering");
+        skip_clusterer = true;
+    }
+
     // Dashing all the genomes together
     let dashing_cache = preclusterer.distances(genomes);
 
@@ -83,6 +89,7 @@ pub fn cluster<P: PreclusterDistanceFinder, C: ClusterDistanceFinder + std::mark
                 clusterer,
                 &precluster_dashing_cache,
                 precluster_genomes.as_slice(),
+                skip_clusterer,
             );
             debug!(
                 "In precluster {}, found {} genome representatives",
@@ -149,6 +156,7 @@ fn find_dashing_fastani_representatives(
     clusterer: &(impl ClusterDistanceFinder + std::marker::Sync),
     dashing_cache: &SortedPairGenomeDistanceCache,
     genomes: &[&str],
+    skip_clusterer: bool,
 ) -> (BTreeSet<usize>, SortedPairGenomeDistanceCache) {
     let mut clusters_to_return: BTreeSet<usize> = BTreeSet::new();
     let mut fastani_cache = SortedPairGenomeDistanceCache::new();
@@ -169,15 +177,23 @@ fn find_dashing_fastani_representatives(
             .collect();
 
         // FastANI all potential reps against the current genome
-        let fastanis = calculate_fastani_many_to_one_pairwise_stop_early(
-            clusterer,
-            potential_refs
-                .iter()
-                .map(|ref_index| genomes[*ref_index])
-                .collect::<Vec<_>>()
-                .as_slice(),
-            genomes[i],
-        );
+        let fastanis = if skip_clusterer {
+            compute_ani_from_preclusterer(
+                dashing_cache,
+                potential_refs.iter().collect::<Vec<_>>().as_slice(),
+                &i,
+            )
+        } else {
+            calculate_fastani_many_to_one_pairwise_stop_early(
+                clusterer,
+                potential_refs
+                    .iter()
+                    .map(|ref_index| genomes[*ref_index])
+                    .collect::<Vec<_>>()
+                    .as_slice(),
+                genomes[i],
+            )
+        };
         let mut is_rep = true;
         for (potential_ref, fastani) in potential_refs.into_iter().zip(fastanis.iter()) {
             debug!(
@@ -245,6 +261,23 @@ fn calculate_fastani_many_to_one_pairwise_stop_early(
     to_return.into_inner().unwrap()
 }
 
+fn compute_ani_from_preclusterer(
+    dashing_cache: &SortedPairGenomeDistanceCache,
+    query_genome_indexes: &[&usize],
+    ref_genome_index: &usize,
+) -> Vec<Option<f32>> {
+    query_genome_indexes
+        .iter()
+        .map(|query_genome| {
+            let ani = dashing_cache.get(&(**query_genome, *ref_genome_index));
+            ani.copied()
+        })
+        .collect::<Vec<_>>()
+        .into_iter()
+        .flatten()
+        .collect()
+}
+
 // /// For each genome (sketch) assign it to the closest representative genome:
 // fn find_minhash_memberships(
 //     representatives: &BTreeSet<usize>,