Skip to content

Fix htslib include path for HTSLIB=system builds #119

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Maarten-vd-Sande wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Fix htslib include path for HTSLIB=system builds #119

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
e3b28f8
Fix htslib include path for HTSLIB=system builds
Maarten-vd-Sande Aug 17, 2026
17c8445
cleanup
Maarten-vd-Sande Aug 17, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion d4-hts/Cargo.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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"
19 changes: 12 additions & 7 deletions d4-hts/build.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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());
Expand All @@ -20,7 +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");
}
Expand Down Expand Up @@ -55,13 +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()
};
Expand Down
2 changes: 2 additions & 0 deletions d4-hts/build_htslib.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
Loading