From 8048eb8ced2087659184f70bae9e0d91690aa212 Mon Sep 17 00:00:00 2001
From: Ragnar Groot Koerkamp <ragnar.grootkoerkamp@gmail.com>
Date: Wed, 9 Feb 2022 09:01:48 +0100
Subject: [PATCH] fix: overflow in `qgrams` for k=32 (#478)

* Fix undefined behaviour overflow for k=32

* Add a test to RankTransform ensuring `1<<(q*bits)` does not overflow

* Update MSRV to 1.53 for usize::BITS
---
 .github/workflows/rust.yml |  4 ++--
 README.md                  |  2 +-
 src/alphabets/mod.rs       | 11 ++++++++++-
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 41e1338696..fb6f2fb156 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -92,11 +92,11 @@ jobs:
       - name: Install MSRV toolchain
         uses: actions-rs/toolchain@v1
         with:
-          toolchain: 1.51.0
+          toolchain: 1.53.0
           override: true
 
       - name: check if README matches MSRV defined here
-        run: grep '1.51.0' README.md
+        run: grep '1.53.0' README.md
 
       - name: Run tests
         uses: actions-rs/cargo@v1
diff --git a/README.md b/README.md
index 2b6da77d53..e2192bd31d 100644
--- a/README.md
+++ b/README.md
@@ -57,7 +57,7 @@ For extra credit, feel free to familiarize yourself with:
 
 ## Minimum supported Rust version
 
-Currently the minimum supported Rust version is 1.51.0.
+Currently the minimum supported Rust version is 1.53.0.
 
 ## License
 
diff --git a/src/alphabets/mod.rs b/src/alphabets/mod.rs
index ad46bd5a3f..83b756dcde 100644
--- a/src/alphabets/mod.rs
+++ b/src/alphabets/mod.rs
@@ -326,7 +326,7 @@ impl RankTransform {
             text: text.into_iter(),
             ranks: self,
             bits,
-            mask: (1 << (q * bits)) - 1,
+            mask: 1usize.checked_shl(q * bits).unwrap_or(0).wrapping_sub(1),
             qgram: 0,
         };
 
@@ -448,4 +448,13 @@ mod tests {
         assert_eq!(Alphabet::new(b"ATCG"), Alphabet::new(b"TAGC"));
         assert_ne!(Alphabet::new(b"ATCG"), Alphabet::new(b"ATC"));
     }
+
+    /// When `q * bits == usize::BITS`, make sure that `1<<(1*bits)` does not overflow.
+    #[test]
+    fn test_qgram_shiftleft_overflow() {
+        let alphabet = Alphabet::new(b"ACTG");
+        let transform = RankTransform::new(&alphabet);
+        let text = b"ACTG".repeat(100);
+        transform.qgrams(usize::BITS / 2, text);
+    }
 }