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fix: build for macOS #431

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Merged
johanneskoester merged 14 commits into from
May 10, 2024
Merged

fix: build for macOS #431

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ad2b981
set host to macos-12
FelixMoelder May 3, 2024
53b11b1
set host to macos-13
FelixMoelder May 3, 2024
3b2daff
update hts-sys
FelixMoelder May 6, 2024
50f2396
set macos-latest
FelixMoelder May 6, 2024
0e24617
fix type
johanneskoester May 10, 2024
40793b8
fix internal insert size naming (isize vs isize_)
johanneskoester May 10, 2024
f9807c0
fix type
johanneskoester May 10, 2024
1c89f12
fix
johanneskoester May 10, 2024
2b901e0
fix
johanneskoester May 10, 2024
9bb53d1
fix
johanneskoester May 10, 2024
a4f3a2d
fmt
johanneskoester May 10, 2024
9a9b3d1
fix
johanneskoester May 10, 2024
77d7052
fmt
johanneskoester May 10, 2024
5eb729b
bump hts-sys
johanneskoester May 10, 2024
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42 changes: 18 additions & 24 deletions .github/workflows/rust.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -158,19 +157,14 @@ jobs:
- name: Install stable toolchain
uses: actions-rs/[email protected]
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/[email protected]
# with:
# toolchain: ${{ matrix.toolchain }}
# target: ${{ matrix.toolchain_target }}
# #override: true
# default: ${{ matrix.default }}

- name: Test
uses: actions-rs/[email protected]
with:
Expand Down
2 changes: 1 addition & 1 deletion Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"]}
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@sjackman sjackman Jul 8, 2024

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Was this an intentional change that bindgen changed from an optional dependency to a required dependency of rust-htslib?

ieee754 = "0.2"
lazy_static = "1.4"
libc = "0.2"
Expand Down
8 changes: 4 additions & 4 deletions src/bam/mod.rs
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Expand Up @@ -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
};

Expand Down Expand Up @@ -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
};

Expand Down Expand Up @@ -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
}
}
Expand Down
8 changes: 4 additions & 4 deletions src/bam/record.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -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 {
Expand Down Expand Up @@ -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 {
Expand Down
10 changes: 5 additions & 5 deletions src/bam/record_serde.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -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()
}
Expand Down Expand Up @@ -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
Expand All @@ -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);
Expand Down Expand Up @@ -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();
Expand All @@ -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);
Expand Down
2 changes: 1 addition & 1 deletion src/bcf/record.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -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 {
Expand Down
15 changes: 3 additions & 12 deletions src/bgzf/mod.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand Down Expand Up @@ -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,
Expand Down