pass lcp

sa-index/src/sa_searcher.rs

@@ -156,7 +156,7 @@ impl Searcher {
 
             // Calculate stricter starting bounds for the 3-mers
             // TODO: IL equality
-            let bounds = searcher.search_bounds_no_cache(&kmer, (0, searcher.sa.len()));
+            let bounds = searcher.search_bounds_no_cache(&kmer, (0, searcher.sa.len()), 0);
 
             if let BoundSearchResult::SearchResult((min_bound, max_bound)) = bounds {
                 let min_bound = if min_bound == 0 { 0 } else { min_bound - 1 };
@@ -245,10 +245,10 @@ impl Searcher {
     /// The first argument is true if a match was found
     /// The second argument indicates the index of the minimum or maximum bound for the match
     /// (depending on `bound`)
-    fn binary_search_bound(&self, bound: BoundSearch, search_string: &[u8], start_bounds: (usize, usize)) -> (bool, usize) {
+    fn binary_search_bound(&self, bound: BoundSearch, search_string: &[u8], start_bounds: (usize, usize), start_lcp: usize) -> (bool, usize) {
         let (mut left, mut right) = start_bounds;
-        let mut lcp_left: usize = 0;
-        let mut lcp_right: usize = 0;
+        let mut lcp_left: usize = start_lcp;
+        let mut lcp_right: usize = start_lcp;
         let mut found = false;
 
         // repeat until search window is minimum size OR we matched the whole search string last
@@ -309,7 +309,7 @@ impl Searcher {
         // to find the bounds of the entire string
         let max_mer_length = min(self.kmer_cache.k, search_string.len());
         if let Some(bounds) = self.kmer_cache.get_kmer(&search_string[..max_mer_length]) {
-            return self.search_bounds_no_cache(search_string, bounds);
+            return self.search_bounds_no_cache(search_string, bounds, max_mer_length);
         }
 
         // TODO: following code might be better on Trembl
@@ -323,14 +323,14 @@ impl Searcher {
         BoundSearchResult::NoMatches
     }
 
-    pub fn search_bounds_no_cache(&self, search_string: &[u8], start_bounds: (usize, usize)) -> BoundSearchResult {
-        let (found_min, min_bound) = self.binary_search_bound(Minimum, search_string, start_bounds);
+    pub fn search_bounds_no_cache(&self, search_string: &[u8], start_bounds: (usize, usize), start_lcp: usize) -> BoundSearchResult {
+        let (found_min, min_bound) = self.binary_search_bound(Minimum, search_string, start_bounds, start_lcp);
 
         if !found_min {
             return BoundSearchResult::NoMatches;
         }
 
-        let (_, max_bound) = self.binary_search_bound(Maximum, search_string, start_bounds);
+        let (_, max_bound) = self.binary_search_bound(Maximum, search_string, start_bounds, start_lcp);
 
         BoundSearchResult::SearchResult((min_bound, max_bound + 1))
     }

sa-server/src/main.rs

@@ -116,7 +116,7 @@ async fn start_server(args: Arguments) -> Result<(), Box<dyn Error>> {
     let proteins = Proteins::try_from_database_file(&database_file)?;
     eprintln!("✅ Successfully loaded the proteins!");
 
-    let searcher = Arc::new(SparseSearcher::new(suffix_array, proteins));
+    let searcher = Arc::new(SparseSearcher::new(suffix_array, proteins, 5));
 
     // build our application with a route
     let app = Router::new()