fix: error on sequence complement when lowercase

nt in fasta file
zaeleus · May 26, 2024 · b782045 · b782045
1 parent 052db76
commit b782045
Showing 1 changed file with 33 additions and 0 deletions.
diff --git a/noodles-fasta/src/record/sequence/complement.rs b/noodles-fasta/src/record/sequence/complement.rs
@@ -61,6 +61,23 @@ fn complement(b: u8) -> Result<u8, ComplementError> {
         b'H' => Ok(b'D'),
         b'V' => Ok(b'B'),
         b'N' => Ok(b'N'),
+        b'a' => Ok(b't'),
+        b'c' => Ok(b'g'),
+        b'g' => Ok(b'c'),
+        b't' => Ok(b'a'),
+        b'u' => Ok(b'a'),
+        b'w' => Ok(b'w'),
+        b's' => Ok(b's'),
+        b'm' => Ok(b'k'),
+        b'k' => Ok(b'm'),
+        b'r' => Ok(b'y'),
+        b'y' => Ok(b'r'),
+        b'b' => Ok(b'v'),
+        b'd' => Ok(b'h'),
+        b'h' => Ok(b'd'),
+        b'v' => Ok(b'b'),
+        b'n' => Ok(b'n'),
+
         _ => Err(ComplementError(b)),
     }
 }
@@ -96,6 +113,22 @@ mod tests {
         assert_eq!(complement(b'H'), Ok(b'D'));
         assert_eq!(complement(b'V'), Ok(b'B'));
         assert_eq!(complement(b'N'), Ok(b'N'));
+        assert_eq!(complement(b'a'), Ok(b't'));
+        assert_eq!(complement(b'c'), Ok(b'g'));
+        assert_eq!(complement(b'g'), Ok(b'c'));
+        assert_eq!(complement(b't'), Ok(b'a'));
+        assert_eq!(complement(b'u'), Ok(b'a'));
+        assert_eq!(complement(b'w'), Ok(b'w'));
+        assert_eq!(complement(b's'), Ok(b's'));
+        assert_eq!(complement(b'm'), Ok(b'k'));
+        assert_eq!(complement(b'k'), Ok(b'm'));
+        assert_eq!(complement(b'r'), Ok(b'y'));
+        assert_eq!(complement(b'y'), Ok(b'r'));
+        assert_eq!(complement(b'b'), Ok(b'v'));
+        assert_eq!(complement(b'd'), Ok(b'h'));
+        assert_eq!(complement(b'h'), Ok(b'd'));
+        assert_eq!(complement(b'v'), Ok(b'b'));
+        assert_eq!(complement(b'n'), Ok(b'n'));
         assert_eq!(complement(b'X'), Err(ComplementError(b'X')));
     }
 }