Merge pull request #1332 from nextstrain/feat/optimize-minimizer-storage

packages_rs/nextclade/src/sort/minimizer_index.rs

@@ -14,7 +14,7 @@ pub const MINIMIZER_INDEX_SCHEMA_VERSION_FROM: &str = "3.0.0";
 pub const MINIMIZER_INDEX_SCHEMA_VERSION_TO: &str = "3.0.0";
 pub const MINIMIZER_INDEX_ALGO_VERSION: &str = "1";
 
-pub type MinimizerMap = BTreeMap<u64, String>;
+pub type MinimizerMap = BTreeMap<u64, Vec<usize>>;
 
 /// Contains external configuration and data specific for a particular pathogen
 #[derive(Debug, Clone, Serialize, Deserialize, JsonSchema)]
@@ -43,24 +43,22 @@ pub struct MinimizerIndexJson {
   pub other: serde_json::Value,
 }
 
-/// Serde serializer for Letter sequences
 pub fn serde_serialize_minimizers<S: Serializer>(minimizers: &MinimizerMap, s: S) -> Result<S::Ok, S::Error> {
   let mut map = s.serialize_map(Some(minimizers.len()))?;
   for (k, v) in minimizers {
-    map.serialize_entry(&k.to_string(), &v.to_string())?;
+    map.serialize_entry(&k.to_string(), &v)?;
   }
   map.end()
 }
 
-/// Serde deserializer for Letter sequences
 pub fn serde_deserialize_minimizers<'de, D: Deserializer<'de>>(deserializer: D) -> Result<MinimizerMap, D::Error> {
-  let map = BTreeMap::<String, String>::deserialize(deserializer)?;
+  let map = BTreeMap::<String, Vec<usize>>::deserialize(deserializer)?;
 
   let res = map
     .into_iter()
     .map(|(k, v)| Ok((u64::from_str(&k)?, v)))
     .collect::<Result<MinimizerMap, Report>>()
-    .unwrap();
+    .map_err(serde::de::Error::custom)?;
 
   Ok(res)
 }
@@ -121,6 +119,6 @@ impl MinimizerIndexJson {
       warn!("Version of the minimizer index data ({version}) is greater than maximum supported by this version of Nextclade ({MINIMIZER_INDEX_ALGO_VERSION}). This may lead to errors or incorrect results. Please try to update your version of Nextclade and/or contact dataset maintainers for more details.");
     }
 
-    json_parse(s)
+    json_parse(s).wrap_err("When parsing minimizer index")
   }
 }

packages_rs/nextclade/src/sort/minimizer_search.rs

@@ -45,8 +45,10 @@ pub fn run_minimizer_search(
   let mut hit_counts = vec![0; n_refs];
   for m in minimizers {
     if let Some(mz) = index.minimizers.get(&m) {
-      for i in 0..n_refs {
-        hit_counts[i] += u64::from_str(&mz[i..=i])?;
+      for (ri, hit_count) in hit_counts.iter_mut().enumerate() {
+        if mz.contains(&ri) {
+          *hit_count += 1;
+        }
       }
     }
   }