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fix: overflow in qgrams for k=32 #478

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merged 3 commits into from Feb 9, 2022
Merged

fix: overflow in qgrams for k=32 #478

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27d5807
Fix undefined behaviour overflow for k=32
RagnarGrootKoerkamp Feb 2, 2022
74a25c2
Add a test to RankTransform ensuring `1<<(q*bits)` does not overflow
RagnarGrootKoerkamp Feb 2, 2022
d31f971
Update MSRV to 1.53 for usize::BITS
RagnarGrootKoerkamp Feb 8, 2022
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11 changes: 10 additions & 1 deletion src/alphabets/mod.rs
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Expand Up @@ -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,
};

Expand Down Expand Up @@ -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);
}
}