From 75ccc2ece420b08c99c2f7d4c514fb9e9f515aef Mon Sep 17 00:00:00 2001
From: ignatiuspang <IgnatiusPang@users.noreply.git.com>
Date: Fri, 25 Sep 2026 22:57:25 +1000
Subject: [PATCH 1/2] fix(bitkmer): correct reverse complement window size and
 length tag in minimizer

---
 src/bitkmer.rs | 35 ++++++++++++++++++++++++++++-------
 1 file changed, 28 insertions(+), 7 deletions(-)

diff --git a/src/bitkmer.rs b/src/bitkmer.rs
index ca0bf65..d90b5e5 100644
--- a/src/bitkmer.rs
+++ b/src/bitkmer.rs
@@ -144,21 +144,28 @@ pub fn canonical(kmer: BitKmer) -> (BitKmer, bool) {
 
 /// Find the lexicographically lowest substring of a given length in the `BitKmer`
 pub fn minimizer(kmer: BitKmer, minmer_size: u8) -> BitKmer {
+    if minmer_size == 0 || minmer_size > kmer.1 {
+        return (0, minmer_size);
+    }
     let mut new_kmer = kmer.0;
     let mut lowest = !0;
-    let bitmask = (BitKmerSeq::pow(2, u32::from(2 * minmer_size)) - 1) as BitKmerSeq;
+    let bitmask = if minmer_size >= 32 {
+        BitKmerSeq::MAX
+    } else {
+        (1u64 << (2 * minmer_size)) - 1
+    };
     for _ in 0..=(kmer.1 - minmer_size) {
         let cur = bitmask & new_kmer;
         if cur < lowest {
             lowest = cur;
         }
-        let cur_rev = reverse_complement((bitmask & new_kmer, kmer.1));
+        let cur_rev = reverse_complement((bitmask & new_kmer, minmer_size));
         if cur_rev.0 < lowest {
             lowest = cur_rev.0;
         }
         new_kmer >>= 2;
     }
-    (lowest, kmer.1)
+    (lowest, minmer_size)
 }
 
 pub fn bitmer_to_bytes(kmer: BitKmer) -> Vec<u8> {
@@ -260,10 +267,24 @@ mod tests {
 
     #[test]
     fn test_minimizer() {
-        assert_eq!(minimizer((0b00_1011, 3), 2).0, 0b0010);
-        assert_eq!(minimizer((0b00_1011, 3), 1).0, 0b00);
-        assert_eq!(minimizer((0b1100_0011, 4), 2).0, 0b0000);
-        assert_eq!(minimizer((0b11_0001, 3), 2).0, 0b0001);
+        // "AGT" has 2-mers "AG" (2) and "GT" (11).
+        // The reverse complement of "GT" is "AC" (1), which is the canonical minimizer.
+        assert_eq!(minimizer((0b00_1011, 3), 2), (0b0001, 2));
+        assert_eq!(minimizer((0b00_1011, 3), 1), (0b00, 1));
+        assert_eq!(minimizer((0b1100_0011, 4), 2), (0b0000, 2));
+        assert_eq!(minimizer((0b11_0001, 3), 2), (0b0001, 2));
+    }
+
+    #[test]
+    fn test_minimizer_matches_sequence_minimizer() {
+        let seq = b"AGTCAGTCAGT";
+        let kmer = bytes_to_bitmer(seq);
+        for minmer_size in 1..=seq.len() as u8 {
+            let bit_min = minimizer(kmer, minmer_size);
+            let seq_min = crate::sequence::minimizer(seq, minmer_size as usize);
+            assert_eq!(bit_min.1, minmer_size);
+            assert_eq!(bitmer_to_bytes(bit_min), seq_min.as_ref());
+        }
     }
 
     #[test]

From 16bbca7429c1e0156392ad4669d703d27af2d85a Mon Sep 17 00:00:00 2001
From: ignatiuspang <2321366+IgnatiusPang@users.noreply.github.com>
Date: Sat, 3 Oct 2026 15:43:03 +1000
Subject: [PATCH 2/2] fix(bitkmer): assert valid minmer_size in minimizer and
 add panic tests

---
 src/bitkmer.rs | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/src/bitkmer.rs b/src/bitkmer.rs
index d90b5e5..4c78f0f 100644
--- a/src/bitkmer.rs
+++ b/src/bitkmer.rs
@@ -144,9 +144,10 @@ pub fn canonical(kmer: BitKmer) -> (BitKmer, bool) {
 
 /// Find the lexicographically lowest substring of a given length in the `BitKmer`
 pub fn minimizer(kmer: BitKmer, minmer_size: u8) -> BitKmer {
-    if minmer_size == 0 || minmer_size > kmer.1 {
-        return (0, minmer_size);
-    }
+    assert!(
+        minmer_size > 0 && minmer_size <= kmer.1,
+        "minmer_size must be between 1 and the kmer length"
+    );
     let mut new_kmer = kmer.0;
     let mut lowest = !0;
     let bitmask = if minmer_size >= 32 {
@@ -287,6 +288,18 @@ mod tests {
         }
     }
 
+    #[test]
+    #[should_panic]
+    fn test_minimizer_zero_size() {
+        minimizer((0b00_1011, 3), 0);
+    }
+
+    #[test]
+    #[should_panic]
+    fn test_minimizer_size_greater_than_kmer() {
+        minimizer((0b00_1011, 3), 4);
+    }
+
     #[test]
     fn test_bytes_to_bitkmer() {
         let mut ikmer: BitKmer = bytes_to_bitmer(b"C");