m

src/lib.rs

@@ -411,7 +411,7 @@ impl Sam {
             query_range.end = query_range.end;
         }
 
-        let ref_sequence = fa.get_sequence(&ref_name, ref_range.start.clone(), ref_range.end.clone() + 1);
+        let ref_sequence = fa.get_sequence(&ref_name, ref_range.start.clone(), ref_range.end.clone());
         
         Sam {query_name, query_range, ref_name, ref_pos, ref_range, sequence, ref_sequence, ref_cigar}
     }
@@ -673,10 +673,10 @@ impl Fasta {
     fn get_sequence (&self, contig: &str, start: usize, end: usize) -> String { // end is included
         let chr_index = self.fa.fai().tid(contig).expect("Cannot find chr in index");
         if end < start {
-            let fv = self.fa.view(chr_index, end, start + 1).expect("Cannot get .fa view");
+            let fv = self.fa.view(chr_index, end + 2, start + 1).expect("Cannot get .fa view");
             revcomp(&fv.to_string().to_uppercase())
         } else {
-            let fv = self.fa.view(chr_index, start - 1, end).expect("Cannot get .fa view");
+            let fv = self.fa.view(chr_index, start - 1, end + 1).expect("Cannot get .fa view");
             fv.to_string().to_uppercase()
         }
     }