From 500706995d4928646c34937f55408ae1e1437c2c Mon Sep 17 00:00:00 2001
From: Harinn <prinn.dev@pm.me>
Date: Wed, 20 May 2026 18:54:43 +0700
Subject: [PATCH] kallisto: fix build with gcc 15

---
 ...bifrost-fix-datastorage-sz_link-typo.patch | 26 +++++++++++++++++++
 pkgs/by-name/ka/kallisto/package.nix          |  7 ++++-
 2 files changed, 32 insertions(+), 1 deletion(-)
 create mode 100644 pkgs/by-name/ka/kallisto/bifrost-fix-datastorage-sz_link-typo.patch

diff --git a/pkgs/by-name/ka/kallisto/bifrost-fix-datastorage-sz_link-typo.patch b/pkgs/by-name/ka/kallisto/bifrost-fix-datastorage-sz_link-typo.patch
new file mode 100644
index 0000000000000..4aebfd351033d
--- /dev/null
+++ b/pkgs/by-name/ka/kallisto/bifrost-fix-datastorage-sz_link-typo.patch
@@ -0,0 +1,26 @@
+diff --git a/ext/bifrost/src/DataStorage.hpp b/ext/bifrost/src/DataStorage.hpp
+index 016775f..deb849d 100644
+--- a/ext/bifrost/src/DataStorage.hpp
++++ b/ext/bifrost/src/DataStorage.hpp
+@@ -67,6 +67,8 @@ class DataStorage {
+ 
+         inline size_t getNbColors() const { return color_names.size(); }
+ 
++        inline vector<string> const& getColorNames() const { return color_names; }
++
+         size_t getUnitigColorsSize(const size_t nb_threads = 1) const;
+ 
+         uint64_t getHash(const UnitigColorMap<U>& um) const;
+diff --git a/ext/bifrost/src/DataStorage.tcc b/ext/bifrost/src/DataStorage.tcc
+index 02929d9..10b844e 100644
+--- a/ext/bifrost/src/DataStorage.tcc
++++ b/ext/bifrost/src/DataStorage.tcc
+@@ -78,7 +78,7 @@ DataStorage<U>::DataStorage(const DataStorage& o) : color_sets(nullptr), shared_
+ 
+         unitig_cs_link = new atomic<uint64_t>[sz_link];
+ 
+-        for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load();
++        for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.unitig_cs_link[i].load();
+     }
+ 
+     if ((o.data != nullptr) && (o.sz_cs != 0)){
diff --git a/pkgs/by-name/ka/kallisto/package.nix b/pkgs/by-name/ka/kallisto/package.nix
index 63ed552052cb9..e772852c46422 100644
--- a/pkgs/by-name/ka/kallisto/package.nix
+++ b/pkgs/by-name/ka/kallisto/package.nix
@@ -18,9 +18,14 @@ stdenv.mkDerivation (finalAttrs: {
     repo = "kallisto";
     owner = "pachterlab";
     rev = "v${finalAttrs.version}";
-    sha256 = "sha256-hfdeztEyHvuOnLS71oSv8sPqFe2UCX5KlANqrT/Gfx8=";
+    hash = "sha256-hfdeztEyHvuOnLS71oSv8sPqFe2UCX5KlANqrT/Gfx8=";
   };
 
+  patches = [
+    # https://github.com/pmelsted/bifrost/pull/18
+    ./bifrost-fix-datastorage-sz_link-typo.patch
+  ];
+
   postPatch = ''
     substituteInPlace CMakeLists.txt ext/bifrost/CMakeLists.txt \
       --replace-fail "cmake_minimum_required(VERSION 3.0.0)" "cmake_minimum_required(VERSION 3.10)"