Add in checks for n and case in revcomp

src/main.rs

@@ -118,6 +118,7 @@ fn update_with_vcf(
     if !fixed_genotype.is_empty() {
         genotype = parse_genotype(&fixed_genotype);
     }
+
     for result in reader.records() {
         let record = result.unwrap();
         let seq_name = record.reference_sequence_name().to_string();
@@ -127,6 +128,7 @@ fn update_with_vcf(
         let ref_end = record.variant_end(&header).unwrap().get();
         let alt_bases = record.alternate_bases();
         let alt_alleles: Vec<_> = alt_bases.iter().collect::<io::Result<_>>().unwrap();
+        // TODO: fix this duplication of handling an insert
         if !fixed_sample.is_empty() && !genotype.is_empty() {
             for (chromosome_index, genotype) in genotype.iter().enumerate() {
                 if let Some(gt) = genotype {

src/models/path.rs

@@ -22,11 +22,25 @@ pub fn revcomp(seq: &str) -> String {
         seq.chars()
             .rev()
             .map(|c| -> u8 {
+                let is_upper = c.is_ascii_uppercase();
                 let rc = c as u8;
-                if rc & 2 != 0 {
+                let v = if rc == 78 {
+                    // N
+                    rc
+                } else if rc == 110 {
+                    // n
+                    rc
+                } else if rc & 2 != 0 {
+                    // CG
                     rc ^ 4
                 } else {
+                    // AT
                     rc ^ 21
+                };
+                if is_upper {
+                    v
+                } else {
+                    v.to_ascii_lowercase()
                 }
             })
             .collect(),
@@ -324,4 +338,11 @@ mod tests {
         );
         assert_eq!(Path::sequence(conn, path.id), "GGGGGGGTTTTTTTCGATCGAT");
     }
+
+    #[test]
+    fn test_reverse_complement() {
+        assert_eq!(revcomp("ATCCGG"), "CCGGAT");
+        assert_eq!(revcomp("CNNNNA"), "TNNNNG");
+        assert_eq!(revcomp("cNNgnAt"), "aTncNNg");
+    }
 }