m

src/lib.rs

@@ -573,7 +573,7 @@ impl NeoContig {
         }
     }
     
-    pub fn get_hgvs(self, centromere_pos: Vec<(String, i64)>) -> Option<String> {
+    pub fn get_hgvs(&self, centromere_pos: Vec<(String, i64)>) -> Option<String> {
         fn get_hgvs_part(aln: Sam, centro_pos: i64) -> String {
             let mut part = "".to_string();
             if aln.ref_pos < centro_pos {
@@ -606,12 +606,13 @@ impl NeoContig {
                     b_part = get_hgvs_part(self.alignments[1].clone(), *pos);
                 }
             });
-
-            let mut added_nt = self.alignments[0].sequence[
-                self.alignments[0].query_range.end..(self.alignments[1].query_range.start - 1)
-            ].to_string();
-
-            if added_nt.len() > 0 { added_nt.push(';'); }
+            let mut added_nt = String::new();
+            if self.alignments[0].query_range.end < self.alignments[1].query_range.start {
+                added_nt = self.alignments[0].sequence[
+                    self.alignments[0].query_range.end..(self.alignments[1].query_range.start - 1)
+                ].to_string();
+                added_nt.push(';');
+            }
 
             res = Some(format!(
                 "{}:g.{}[{}{}:g.{}]",
@@ -624,6 +625,9 @@ impl NeoContig {
         }
         res
     }
+    pub fn get_fasta(&self) -> String {
+        String::new()
+    }
 }
 pub struct Fasta {
     fa: IndexedFasta