From e3b28f8d35ed1f7c7779d62043ce10833068556d Mon Sep 17 00:00:00 2001
From: "maarten.vandersande" <maartenvandersande@hotmail.com>
Date: Mon, 17 Aug 2026 10:19:28 +0200
Subject: [PATCH 1/2] Fix htslib include path for HTSLIB=system builds

---
 d4-hts/build.rs        | 8 +++++++-
 d4-hts/build_htslib.sh | 2 ++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/d4-hts/build.rs b/d4-hts/build.rs
index 8c36b9c..499b5ca 100644
--- a/d4-hts/build.rs
+++ b/d4-hts/build.rs
@@ -8,7 +8,13 @@ use std::process::Command;
 fn create_hts_bindings(includes: &[PathBuf], version: &str, system: bool) -> Result<(), ()> {
     let mut include_params: Vec<_> = includes
         .iter()
-        .map(|x| format!("-I{}/htslib", x.to_str().unwrap()))
+        .map(|x| {
+            if system {
+                format!("-I{}", x.to_str().unwrap())
+            } else {
+                format!("-I{}/htslib", x.to_str().unwrap())
+            }
+        })
         .collect();
     if system {
         include_params.push("-DUSE_SYSTEM_HTSLIB".to_string());
diff --git a/d4-hts/build_htslib.sh b/d4-hts/build_htslib.sh
index 80b540e..0721736 100644
--- a/d4-hts/build_htslib.sh
+++ b/d4-hts/build_htslib.sh
@@ -17,6 +17,8 @@ git clone -b ${HTSLIB_VERSION} http://github.com/samtools/htslib.git
 
 cd htslib
 
+git submodule update --init --recursive
+
 cat > config.h << CONFIG_H
 #define HAVE_LIBBZ2 1
 #define HAVE_DRAND48 1

From 17c84455394b26371588b3dbaebf6c4aa98f795a Mon Sep 17 00:00:00 2001
From: "maarten.vandersande" <maartenvandersande@hotmail.com>
Date: Mon, 17 Aug 2026 22:27:03 +0200
Subject: [PATCH 2/2] cleanup

---
 d4-hts/Cargo.toml |  2 +-
 d4-hts/build.rs   | 11 +++++------
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/d4-hts/Cargo.toml b/d4-hts/Cargo.toml
index 7822769..b244660 100644
--- a/d4-hts/Cargo.toml
+++ b/d4-hts/Cargo.toml
@@ -10,5 +10,5 @@ repository = "https://github.com/38/d4-format"
 [dependencies]
 
 [build-dependencies]
-bindgen = "0.55.1"
+bindgen = "0.72.1"
 pkg-config = "0.3.18"
diff --git a/d4-hts/build.rs b/d4-hts/build.rs
index 499b5ca..f130667 100644
--- a/d4-hts/build.rs
+++ b/d4-hts/build.rs
@@ -26,7 +26,8 @@ fn create_hts_bindings(includes: &[PathBuf], version: &str, system: bool) -> Res
             .layout_tests(false)
             .generate_comments(false)
             .generate_inline_functions(false)
-            .generate()?
+            .generate()
+            .map_err(|_| ())?
             .write_to_file("generated/hts.rs")
             .expect("Unable to write the generated file");
     }
@@ -61,13 +62,11 @@ fn main() -> Result<(), std::io::Error> {
     let link_system_lib = env::var("HTSLIB").map_or(false, |htslib| htslib == "system");
 
     let (htslib_includes, lib_version, system) = if link_system_lib {
-        pkg_config::Config::new()
+        let lib = pkg_config::Config::new()
             .atleast_version("1.6")
             .probe("htslib")
-            .map_or_else(
-                |_| build_own_htslib(),
-                |lib| (lib.include_paths, lib.version, true),
-            )
+            .expect("HTSLIB=system requested but htslib was not found via pkg-config");
+        (lib.include_paths, lib.version, true)
     } else {
         build_own_htslib()
     };