fix: build for macOS (#431)

* set host to macos-12

* set host to macos-13

* update hts-sys

* set macos-latest

* fix type

* fix internal insert size naming (isize vs isize_)

* fix type

* fix

* fix

* fix

* fmt

* fix

* fmt

* bump hts-sys

---------

Co-authored-by: Johannes Koester <johannes.koester@uni-due.de>

.github/workflows/rust.yml

@@ -125,29 +125,28 @@ jobs:
     strategy:
       matrix:
         target:
-          - intel-catalina
-          - intel-bigsur
-          - m1-bigsur
+          - intel-monterey
+          - intel-ventura
+          - silicon-sonoma
         include:
-          - target: intel-catalina
-            os: macOS-10.15
+          - target: intel-monterey
+            os: macOS-12.0
             toolchain_target: x86_64-apple-darwin
             toolchain: stable
-            aux_args: ""
-            default: false
-          - target: intel-bigsur
-            os: macOS-11.0
+            aux_args: --target x86_64-apple-darwin
+            default: true
+          - target: intel-ventura
+            os: macOS-13.0
             toolchain_target: x86_64-apple-darwin
             toolchain: stable
+            aux_args: --target x86_64-apple-darwin
+            default: true
+          - target: silicon-sonoma
+            os: macOS-14.0
+            toolchain_target: aarch64-apple-darwin
+            toolchain: stable
             aux_args: ""
             default: false
-          # TODO enable again and try to find out why this fails
-          # - target: m1-bigsur
-          #   os: macOS-11.0
-          #   toolchain_target: aarch64-apple-darwin
-          #   toolchain: nightly
-          #   aux_args: --target aarch64-apple-darwin
-          #   default: true
 
     steps:
       - name: Checkout repository
@@ -158,19 +157,14 @@ jobs:
       - name: Install stable toolchain
         uses: actions-rs/toolchain@v1.0.6
         with:
-          toolchain: stable
+          toolchain: ${{ matrix.toolchain }}
+          target: ${{ matrix.toolchain_target }}
           override: true
+          default: ${{ matrix.default }}
 
       - name: Install htslib dependencies
         run: brew install bzip2 zlib xz curl-openssl
 
-      #- uses: actions-rs/toolchain@v1.0.6
-      #  with:
-      #    toolchain: ${{ matrix.toolchain }}
-      #    target: ${{ matrix.toolchain_target }}
-      #    #override: true
-      #    default: ${{ matrix.default }}
-
       - name: Test
         uses: actions-rs/cargo@v1.0.1
         with:

Cargo.toml

@@ -21,7 +21,7 @@ bio-types = ">=0.9"
 byteorder = "1.3"
 custom_derive = "0.1"
 derive-new = "0.5"
-hts-sys = {version = "2.1.1", default-features = false}
+hts-sys = {version = "2.1.4", default-features = false, features = ["bindgen"]}
 ieee754 = "0.2"
 lazy_static = "1.4"
 libc = "0.2"

src/bam/mod.rs

@@ -1127,7 +1127,7 @@ impl Writer {
             );
 
             (*rec).text = text as *mut c_char;
-            (*rec).l_text = l_text as u64;
+            (*rec).l_text = l_text;
             rec
         };
 
@@ -1392,9 +1392,9 @@ impl HeaderView {
                 header_string.len(),
             );
 
-            let rec = htslib::sam_hdr_parse((l_text + 1) as u64, text as *const c_char);
+            let rec = htslib::sam_hdr_parse((l_text + 1), text as *const c_char);
             (*rec).text = text as *mut c_char;
-            (*rec).l_text = l_text as u64;
+            (*rec).l_text = l_text;
             rec
         };
 
@@ -1580,7 +1580,7 @@ CCCCCCCCCCCCCCCCCCC"[..],
             assert_eq!(c1.inner().core.l_qname, b1.inner().core.l_qname);
             assert_eq!(c1.inner().core.n_cigar, b1.inner().core.n_cigar);
             assert_eq!(c1.inner().core.l_qseq, b1.inner().core.l_qseq);
-            assert_eq!(c1.inner().core.isize, b1.inner().core.isize);
+            assert_eq!(c1.inner().core.isize_, b1.inner().core.isize_);
             //... except m_data
         }
     }

src/bam/record.rs

@@ -152,8 +152,8 @@ impl Record {
 
         let mut sam_string = htslib::kstring_t {
             s: sam_copy.as_ptr() as *mut c_char,
-            l: sam_copy.len() as u64,
-            m: sam_copy.len() as u64,
+            l: sam_copy.len(),
+            m: sam_copy.len(),
         };
 
         let succ = unsafe {
@@ -286,12 +286,12 @@ impl Record {
 
     /// Get insert size.
     pub fn insert_size(&self) -> i64 {
-        self.inner().core.isize
+        self.inner().core.isize_
     }
 
     /// Set insert size.
     pub fn set_insert_size(&mut self, insert_size: i64) {
-        self.inner_mut().core.isize = insert_size;
+        self.inner_mut().core.isize_ = insert_size;
     }
 
     fn qname_capacity(&self) -> usize {

src/bam/record_serde.rs

@@ -29,7 +29,7 @@ impl Serialize for Record {
         state.serialize_field("seq_len", &core.l_qseq)?;
         state.serialize_field("mtid", &core.mtid)?;
         state.serialize_field("mpos", &core.mpos)?;
-        state.serialize_field("isize", &core.isize)?;
+        state.serialize_field("isize", &core.isize_)?;
         state.serialize_field("data", Bytes::new(self.data()))?;
         state.end()
     }
@@ -138,7 +138,7 @@ impl<'de> Deserialize<'de> for Record {
                 let mpos = seq
                     .next_element()?
                     .ok_or_else(|| de::Error::invalid_length(0, &self))?;
-                let isize = seq
+                let isize_ = seq
                     .next_element()?
                     .ok_or_else(|| de::Error::invalid_length(0, &self))?;
                 let data = seq
@@ -159,7 +159,7 @@ impl<'de> Deserialize<'de> for Record {
                     m.l_qseq = seq_len;
                     m.mtid = mtid;
                     m.mpos = mpos;
-                    m.isize = isize;
+                    m.isize_ = isize_;
                 }
 
                 rec.set_data(&data);
@@ -271,7 +271,7 @@ impl<'de> Deserialize<'de> for Record {
                 let seq_len = seq_len.ok_or_else(|| de::Error::missing_field("seq_len"))?;
                 let mtid = mtid.ok_or_else(|| de::Error::missing_field("mtid"))?;
                 let mpos = mpos.ok_or_else(|| de::Error::missing_field("mpos"))?;
-                let isize = isize.ok_or_else(|| de::Error::missing_field("isize"))?;
+                let isize_ = isize.ok_or_else(|| de::Error::missing_field("isize"))?;
                 let data = data
                     .ok_or_else(|| de::Error::missing_field("data"))?
                     .into_vec();
@@ -289,7 +289,7 @@ impl<'de> Deserialize<'de> for Record {
                     m.l_qseq = seq_len;
                     m.mtid = mtid;
                     m.mpos = mpos;
-                    m.isize = isize;
+                    m.isize_ = isize_;
                 }
 
                 rec.set_data(&data);

src/bcf/record.rs

@@ -1008,7 +1008,7 @@ impl Record {
     }
 
     pub fn remove_alleles(&mut self, remove: &[bool]) -> Result<()> {
-        let rm_set = unsafe { htslib::kbs_init(remove.len() as u64) };
+        let rm_set = unsafe { htslib::kbs_init(remove.len()) };
 
         for (i, &r) in remove.iter().enumerate() {
             if r {

src/bgzf/mod.rs

@@ -112,11 +112,7 @@ impl Reader {
 impl std::io::Read for Reader {
     fn read(&mut self, buf: &mut [u8]) -> std::io::Result<usize> {
         let nbytes = unsafe {
-            htslib::bgzf_read(
-                self.inner,
-                buf.as_mut_ptr() as *mut libc::c_void,
-                buf.len() as u64,
-            )
+            htslib::bgzf_read(self.inner, buf.as_mut_ptr() as *mut libc::c_void, buf.len())
         };
         if nbytes < 0 {
             Err(std::io::Error::new(
@@ -257,13 +253,8 @@ impl Writer {
 
 impl std::io::Write for Writer {
     fn write(&mut self, buf: &[u8]) -> std::io::Result<usize> {
-        let nbytes = unsafe {
-            htslib::bgzf_write(
-                self.inner,
-                buf.as_ptr() as *mut libc::c_void,
-                buf.len() as u64,
-            )
-        };
+        let nbytes =
+            unsafe { htslib::bgzf_write(self.inner, buf.as_ptr() as *mut libc::c_void, buf.len()) };
         if nbytes < 0 {
             Err(std::io::Error::new(
                 std::io::ErrorKind::Other,