From 3489e6ab493b5191b879b4405b868a4004bbb88e Mon Sep 17 00:00:00 2001
From: Christian Heide <11767963+jch-13@users.noreply.github.com>
Date: Mon, 4 Oct 2021 09:23:50 +0200
Subject: [PATCH] fix: backward search yielding potentially incorrect positions
 on FM-Index (#454) (#455)

---
 src/data_structures/fmindex.rs | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/src/data_structures/fmindex.rs b/src/data_structures/fmindex.rs
index 124f5a898..370c9fc18 100644
--- a/src/data_structures/fmindex.rs
+++ b/src/data_structures/fmindex.rs
@@ -127,7 +127,7 @@ pub trait FMIndexable {
 
             // The symbol was not found if we end up with an empty interval.
             // Terminate the LF-mapping process.
-            if l == r {
+            if l > r {
                 break;
             }
         }
@@ -540,6 +540,24 @@ mod tests {
         assert_eq!(positions, []);
     }
 
+    #[test]
+    fn test_fmindex_backward_search_optimization() {
+        let text = b"GATTACA$";
+        let pattern = &text[..text.len() - 1];
+        let alphabet = dna::n_alphabet();
+        let sa = suffix_array(text);
+        let bwt = bwt(text, &sa);
+        let less = less(&bwt, &alphabet);
+        let occ = Occ::new(&bwt, 3, &alphabet);
+        let fm = FMIndex::new(&bwt, &less, &occ);
+
+        let sai = fm.backward_search(pattern.iter());
+
+        let positions = sai.occ(&sa);
+
+        assert_eq!(positions, [0]);
+    }
+
     #[test]
     fn test_smems() {
         let orig_text = b"GCCTTAACAT";