From 7c7110db9e6fa4484dd5938d41a177ea8345936b Mon Sep 17 00:00:00 2001
From: Nils Homer <nilshomer@gmail.com>
Date: Thu, 30 Apr 2026 13:08:11 -0700
Subject: [PATCH 1/2] fix(clippy): address new lints from rust-1.95

Three new clippy errors started firing on `-D warnings` after the
rust-1.95 release:

- `clippy::manual_checked_ops` in src/catalog/builder.rs: rewrite
  the `pct` closure with `checked_div(total).unwrap_or(0)`, which
  is semantically identical to the existing `if total == 0 { 0 }
  else { (n * 100) / total }` form.
- `clippy::unnecessary_sort_by` in src/catalog/index.rs (x2):
  replace `sort_by(|a, b| b.1.cmp(&a.1))` with
  `sort_by_key(|b| std::cmp::Reverse(b.1))`. Both forms produce a
  stable sort by `.1` descending.

No behavioral change. Unblocks the pre-commit hook so README and
other commits can land again.
---
 src/catalog/builder.rs | 8 +-------
 src/catalog/index.rs   | 4 ++--
 2 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/src/catalog/builder.rs b/src/catalog/builder.rs
index 2d8769b..06ed703 100644
--- a/src/catalog/builder.rs
+++ b/src/catalog/builder.rs
@@ -987,13 +987,7 @@ impl std::fmt::Display for BuildSummary {
         writeln!(f)?;
 
         writeln!(f, "Coverage:")?;
-        let pct = |n: usize, total: usize| {
-            if total == 0 {
-                0
-            } else {
-                (n * 100) / total
-            }
-        };
+        let pct = |n: usize, total: usize| (n * 100).checked_div(total).unwrap_or(0);
         let check = |n: usize, total: usize| {
             if n == total {
                 "+"
diff --git a/src/catalog/index.rs b/src/catalog/index.rs
index 1106169..54046f1 100644
--- a/src/catalog/index.rs
+++ b/src/catalog/index.rs
@@ -30,7 +30,7 @@ impl<'a> CandidateFinder<'a> {
         }
 
         let mut candidates: Vec<_> = ref_counts.into_iter().collect();
-        candidates.sort_by(|a, b| b.1.cmp(&a.1)); // Sort by count descending
+        candidates.sort_by_key(|b| std::cmp::Reverse(b.1)); // Sort by count descending
         candidates
     }
 
@@ -68,7 +68,7 @@ impl<'a> CandidateFinder<'a> {
         }
 
         let mut candidates: Vec<_> = ref_counts.into_iter().collect();
-        candidates.sort_by(|a, b| b.1.cmp(&a.1));
+        candidates.sort_by_key(|b| std::cmp::Reverse(b.1));
         candidates
     }
 

From 55b1c4644cfaf475ee45f7057a7b1462975313fa Mon Sep 17 00:00:00 2001
From: Nils Homer <nilshomer@gmail.com>
Date: Thu, 30 Apr 2026 13:34:41 -0700
Subject: [PATCH 2/2] docs(readme): use absolute URLs for logo images

Use https://raw.githubusercontent.com/<org>/<repo>/main/... for logo
references so they render on crates.io. Relative paths render correctly
on GitHub but are dropped by the crates.io README sanitizer, leaving a
broken image at the top of every crate page.
---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 44df649..0ac1397 100644
--- a/README.md
+++ b/README.md
@@ -13,9 +13,9 @@ Identify which human reference genome was used to align a BAM/SAM/CRAM file.
 <p>
 <a href="https://fulcrumgenomics.com">
 <picture>
-  <source media="(prefers-color-scheme: dark)" srcset=".github/logos/fulcrumgenomics-dark.svg">
-  <source media="(prefers-color-scheme: light)" srcset=".github/logos/fulcrumgenomics-light.svg">
-  <img alt="Fulcrum Genomics" src=".github/logos/fulcrumgenomics-light.svg" height="100">
+  <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/fulcrumgenomics/ref-solver/main/.github/logos/fulcrumgenomics-dark.svg">
+  <source media="(prefers-color-scheme: light)" srcset="https://raw.githubusercontent.com/fulcrumgenomics/ref-solver/main/.github/logos/fulcrumgenomics-light.svg">
+  <img alt="Fulcrum Genomics" src="https://raw.githubusercontent.com/fulcrumgenomics/ref-solver/main/.github/logos/fulcrumgenomics-light.svg" height="100">
 </picture>
 </a>
 </p>