Android

.github/workflows/build-test-rust-minimap2-sys.yml

@@ -32,7 +32,24 @@ jobs:
       run: cargo test
     - name: Run minimap2-sys simde tests
       run: cargo test --features simde
-
+
+  test-android:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Install Rust Cross
+      run: rustup target add aarch64-linux-android armv7-linux-androideabi i686-linux-android x86_64-linux-android
+    - run: cargo install cross --git https://github.com/cross-rs/cross
+    - run: cd minimap2-sys
+    - name: Run minimap2-sys tests on Android aarch64
+      run: cross test --target aarch64-linux-android
+    - name: Run minimap2-sys tests on Android armv7
+      run: cross test --target armv7-linux-androideabi
+    - name: Run minimap2-sys tests on Android i686
+      run: cross test --target i686-linux-android
+    - name: Run minimap2-sys tests on Android x86_64
+      run: cross test --target x86_64-linux-android
+
   test-macos-13:
     runs-on: macos-13
     steps:

minimap2-sys/build.rs

@@ -1,5 +1,5 @@
 use std::env;
-use std::path::PathBuf;
+use std::path::{Path, PathBuf};
 
 // Configure for minimap2
 fn configure(mut cc: &mut cc::Build) {
@@ -137,10 +137,11 @@ fn compile() {
 
     if !env::var("TARGET").unwrap().contains("android") {
         println!("cargo:rustc-link-lib=pthread");
+        cc.flag("-lpthread");
     }
 
-    if !env::var("TARGET").unwrap().contains("android") {
-        cc.flag("-lpthread");
+    if env::var("CARGO_CFG_TARGET_OS").unwrap() == "android" {
+        android();
     }
 
     cc.flag("-lm");
@@ -158,16 +159,17 @@ fn compile() {
     #[cfg(feature = "static")]
     cc.static_flag(true);
 
-    println!("cargo:rustc-cfg=link_libz");
+    // println!("cargo:rustc-cfg=link_libz");
 
     if let Some(include) = std::env::var_os("DEP_Z_INCLUDE") {
-        cc.include(include);
+        cc.include(include.clone());
         // Use env DEP_Z_ROOT to find the library
         if let Some(lib) = std::env::var_os("DEP_Z_ROOT") {
             let lib = lib.to_str().unwrap();
             println!("cargo:rustc-link-search=native={}", lib);
             println!("cargo:rustc-link-lib=static=z");
         }
+
     }
 
     if let Ok(lib) = pkg_config::find_library("zlib") {
@@ -220,6 +222,35 @@ fn gen_bindings() {
 #[cfg(not(feature = "bindgen"))]
 fn gen_bindings() {}
 
+fn android() {
+    println!("cargo:rustc-link-lib=z");
+
+    // If we are running via cross
+    if let Ok(sysroot) = env::var("CROSS_SYSROOT") {
+        let path = PathBuf::from(sysroot).join("usr/lib");
+        let path = path.join(&env::var("TARGET").unwrap());
+        println!("cargo:rustc-link-search=native={}", path.display());
+        let path = path.join("libz.so");
+        println!("cargo:rustc-link-search=native={}", path.display());
+        println!("cargo:rustc-link-lib=static=z");
+
+
+    }
+
+    if let Ok(output_path) = env::var("CARGO_NDK_OUTPUT_PATH") {
+        let sysroot_libs_path =
+            PathBuf::from(env::var_os("CARGO_NDK_SYSROOT_LIBS_PATH").unwrap());
+        let lib_path = sysroot_libs_path.join("libz.so");
+        std::fs::copy(
+            lib_path,
+            Path::new(&output_path)
+                .join(&env::var("CARGO_NDK_ANDROID_TARGET").unwrap())
+                .join("libz.so"),
+        )
+        .unwrap();
+    }
+}
+
 fn main() {
     compile();
     gen_bindings();

src/htslib.rs

@@ -166,7 +166,7 @@ impl Aligner {
                 mm_ffi::mm_map(
                     self.idx.unwrap() as *const mm_ffi::mm_idx_t,
                     query.inner.l_seq,
-                    query.inner.seq as *const i8,
+                    query.inner.seq as *const libc::c_char,
                     &mut n_regs,
                     buf.borrow_mut().buf,
                     &map_opt,