Resolve dollar signs to gaps in refine_translation

tmaklin · Jan 8, 2025 · ac4bfed · ac4bfed
1 parent b6e4d25
commit ac4bfed
Showing 1 changed file with 7 additions and 1 deletion.
diff --git a/src/translate.rs b/src/translate.rs
@@ -386,7 +386,13 @@ pub fn refine_translation(
             for i in 1..(refined.len() - threshold) {
                 if refined[i - 1] == 'X' {
                     let midpoint = if i + k - 2 < n_elements && noisy_ms[i + k - 2].0 == k - 1 { k/2 } else { (threshold + 1)/2 };
-                    refined[i - 1] = sbwt.access_kmer(noisy_ms[i + k - 2 - midpoint].1.start)[midpoint] as char;
+                    let nucleotide = sbwt.access_kmer(noisy_ms[i + k - 2 - midpoint].1.start)[midpoint] as char;
+                    refined[i - 1] = if nucleotide == '$' {
+                        // SBWT does not contain this position
+                        '-'
+                    } else {
+                        nucleotide
+                    };
                 }
             }
         },