m

src/lib.rs

@@ -391,7 +391,7 @@ impl Sam {
         if is_reverse(flag) {
             let len = ref_range.len();
             ref_range.end = (ref_pos as usize) - 1;
-            ref_range.start = ref_pos as usize + len - 1;
+            ref_range.start = ref_pos as usize + len;
             query_range.end = query_range.end + 1;
         } else {
             let len = ref_range.len(); 
@@ -586,10 +586,10 @@ impl Fasta {
     }
     fn get_sequence (&self, contig: &str, start: usize, end: usize) -> String { // end is included
         // let start = start - 1;
-        let end = end - 1;
+        
         let chr_index = self.fa.fai().tid(contig).expect("Cannot find chr in index");
         if (end as i64 - start as i64) < (0 as i64) {
-            let fv = self.fa.view(chr_index, end, start).expect("Cannot get .fa view");
+            let fv = self.fa.view(chr_index, end - 1, start + 1).expect("Cannot get .fa view");
             revcomp(&fv.to_string().to_uppercase())
         } else {
             let fv = self.fa.view(chr_index, start, end).expect("Cannot get .fa view");