feat: bring back short sequence branch in alignment

Let's use `kmer_length` instead of removed `seed_length` and adjust the coefficient to roughly match the old value.
nextstrain · Oct 12, 2023 · 9892aae · 9892aae
1 parent 6ed138e
commit 9892aae
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/packages_rs/nextclade/src/align/align.rs b/packages_rs/nextclade/src/align/align.rs
@@ -46,12 +46,12 @@ pub fn align_nuc(
     );
   }
 
-  // if ref_len + qry_len < (10 * params.seed_length) {
-  //   // for very short sequences, use full square
-  //   let stripes = full_matrix(ref_len, qry_len);
-  //   trace!("When processing sequence #{index} '{seq_name}': In nucleotide alignment: Band construction: short sequences, using full matrix");
-  //   return Ok(align_pairwise(qry_seq, ref_seq, gap_open_close, params, &stripes));
-  // }
+  if ref_len + qry_len < (20 * params.kmer_length) {
+    // for very short sequences, use full square
+    let stripes = full_matrix(ref_len, qry_len);
+    trace!("When processing sequence #{index} '{seq_name}': In nucleotide alignment: Band construction: short sequences, using full matrix");
+    return Ok(align_pairwise(qry_seq, ref_seq, gap_open_close, params, &stripes));
+  }
 
   // otherwise, determine seed matches roughly regularly spaced along the query sequence
   let SeedMatchesResult {