From 79e197b0eeb4baed2c6bb7245d9b8beed3c19e65 Mon Sep 17 00:00:00 2001
From: Benjamin Demaille <benjamin.demaille@icloud.com>
Date: Mon, 24 Aug 2026 00:18:48 +0200
Subject: [PATCH] chore(lint): fix clippy 1.98 pedantic lints on the CI
 toolchain

Stable clippy 1.98 adds chunks_exact_to_as_chunks and manual_midpoint, both
pedantic, both firing on existing code. CI runs clippy with -D warnings, so
every PR opened today fails on unrelated files.

- simd_scan::find_stop: as_chunks::<16>() instead of chunks_exact(16) plus
  try_into().unwrap(); the remainder now comes from the same destructuring.
- bam_dedup: as_chunks::<2>() for the (mate1, mate2) pairing.
- quant: usize::midpoint for the segment-tree split point.

Behaviour is unchanged: as_chunks yields the same chunks and remainder as
chunks_exact, and midpoint equals (a + b) >> 1 for the non-overflowing
indices here. MSRV 1.89 covers as_chunks (1.88) and usize::midpoint (1.85).

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
---
 src/align/simd_scan.rs | 10 +++-------
 src/bam_dedup.rs       |  7 ++++++-
 src/quant/mod.rs       |  2 +-
 3 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/src/align/simd_scan.rs b/src/align/simd_scan.rs
index 3bf4833e..2511570e 100644
--- a/src/align/simd_scan.rs
+++ b/src/align/simd_scan.rs
@@ -28,11 +28,9 @@ pub fn find_stop(read: &[u8], genome: &[u8]) -> Option<usize> {
     debug_assert_eq!(read.len(), genome.len());
 
     let mut base = 0usize;
-    let mut r_chunks = read.chunks_exact(16);
-    let mut g_chunks = genome.chunks_exact(16);
-    while let (Some(rc), Some(gc)) = (r_chunks.next(), g_chunks.next()) {
-        let rc: &[u8; 16] = rc.try_into().unwrap();
-        let gc: &[u8; 16] = gc.try_into().unwrap();
+    let (r_chunks, r_rem) = read.as_chunks::<16>();
+    let (g_chunks, g_rem) = genome.as_chunks::<16>();
+    for (rc, gc) in r_chunks.iter().zip(g_chunks) {
         if !chunk_all_match(rc, gc) {
             for k in 0..16 {
                 if gc[k] >= 5 || rc[k] != gc[k] {
@@ -45,8 +43,6 @@ pub fn find_stop(read: &[u8], genome: &[u8]) -> Option<usize> {
     }
 
     // Tail shorter than 16 bytes: plain scalar scan.
-    let r_rem = r_chunks.remainder();
-    let g_rem = g_chunks.remainder();
     for (k, (&r, &g)) in r_rem.iter().zip(g_rem.iter()).enumerate() {
         if g >= 5 || r != g {
             return Some(base + k);
diff --git a/src/bam_dedup.rs b/src/bam_dedup.rs
index 07658c90..57170391 100644
--- a/src/bam_dedup.rs
+++ b/src/bam_dedup.rs
@@ -314,7 +314,12 @@ fn collapse_group(recs: &mut [DedupRec], group: &[usize], mate2_bases_n: u32) ->
             .then_with(|| (ra.flag & 0x80).cmp(&(rb.flag & 0x80)))
     });
     // Pairs of adjacent (mate1, mate2) indices.
-    let mut pairs: Vec<(usize, usize)> = sorted.chunks_exact(2).map(|c| (c[0], c[1])).collect();
+    let mut pairs: Vec<(usize, usize)> = sorted
+        .as_chunks::<2>()
+        .0
+        .iter()
+        .map(|&[m1, m2]| (m1, m2))
+        .collect();
     // Sort pairs by the coordinate/flag/CIGAR key.
     pairs.sort_by(|&(a1, a2), &(b1, b2)| {
         cmp_pair(&recs[a1], &recs[a2], &recs[b1], &recs[b2], mate2_bases_n)
diff --git a/src/quant/mod.rs b/src/quant/mod.rs
index 7df5ddc5..efd0694f 100644
--- a/src/quant/mod.rs
+++ b/src/quant/mod.rs
@@ -320,7 +320,7 @@ impl GeneAnnotation {
                     out.push(chr[nlo].2);
                     continue;
                 }
-                let mid = (nlo + nhi) >> 1;
+                let mid = usize::midpoint(nlo, nhi);
                 stack[sp] = (2 * node, nlo, mid);
                 sp += 1;
                 stack[sp] = (2 * node + 1, mid, nhi);