From 9b24165aba663a92936705eeff4fcec52621e9a1 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Sun, 16 Jun 2024 16:19:09 +0200
Subject: [PATCH] Hotfix issue with alignment of data in AVX2 code
---
lightmotif/src/pli/platform/avx2.rs | 2 +-
lightmotif/src/pwm.rs | 16 ++++++++++++++--
2 files changed, 15 insertions(+), 3 deletions(-)
diff --git a/lightmotif/src/pli/platform/avx2.rs b/lightmotif/src/pli/platform/avx2.rs
index 4baa3d8..7fddb07 100644
--- a/lightmotif/src/pli/platform/avx2.rs
+++ b/lightmotif/src/pli/platform/avx2.rs
@@ -151,7 +151,7 @@ unsafe fn score_avx2_permute<A>(
let x3 = _mm256_shuffle_epi8(x, m3);
let x4 = _mm256_shuffle_epi8(x, m4);
// load row for current weight matrix position
- let t = _mm256_load_ps(pssmptr);
+ let t = _mm256_loadu_ps(pssmptr);
// index A/T/G/C/N lookup table with the bases
let b1 = _mm256_permutevar8x32_ps(t, x1);
let b2 = _mm256_permutevar8x32_ps(t, x2);
diff --git a/lightmotif/src/pwm.rs b/lightmotif/src/pwm.rs
index a56cabb..b1f6fc1 100644
--- a/lightmotif/src/pwm.rs
+++ b/lightmotif/src/pwm.rs
@@ -93,6 +93,12 @@ impl<A: Alphabet> CountMatrix<A> {
// }
}
+ /// The length of the motif encoded in this count matrix.
+ #[inline]
+ pub const fn len(&self) -> usize {
+ self.data.rows()
+ }
+
/// Create a new count matrix from the given sequences.
///
/// # Errors
@@ -233,6 +239,12 @@ impl<A: Alphabet> FrequencyMatrix<A> {
}
}
+ /// The length of the motif encoded in this frequency matrix.
+ #[inline]
+ pub const fn len(&self) -> usize {
+ self.data.rows()
+ }
+
/// Create a new frequency matrix.
///
/// The matrix must contain frequency data, i.e. rows should all sum to 1
@@ -331,7 +343,7 @@ impl<A: Alphabet> WeightMatrix<A> {
/// The length of the motif encoded in this weight matrix.
#[inline]
- pub fn len(&self) -> usize {
+ pub const fn len(&self) -> usize {
self.data.rows()
}
@@ -445,7 +457,7 @@ impl<A: Alphabet> ScoringMatrix<A> {
/// The length of the motif encoded in this scoring matrix.
#[inline]
- pub fn len(&self) -> usize {
+ pub const fn len(&self) -> usize {
self.data.rows()
}
--
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