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fix: build for macOS #431

Merged
merged 14 commits into from
May 10, 2024
42 changes: 18 additions & 24 deletions .github/workflows/rust.yml
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
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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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
Original file line number Diff line number Diff line change
Expand Up @@ -1122,12 +1122,12 @@

//println!("{}", str::from_utf8(&header_string).unwrap());
let rec = htslib::sam_hdr_parse(
((l_text + 1) as usize).try_into().unwrap(),

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casting to the same type is unnecessary (`usize` -> `usize`)

warning: casting to the same type is unnecessary (`usize` -> `usize`) --> src/bam/mod.rs:1125:17 | 1125 | ((l_text + 1) as usize).try_into().unwrap(), | ^^^^^^^^^^^^^^^^^^^^^^^ help: try: `(l_text + 1)` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

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useless conversion to the same type: `usize`

warning: useless conversion to the same type: `usize` --> src/bam/mod.rs:1125:17 | 1125 | ((l_text + 1) as usize).try_into().unwrap(), | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = help: consider removing `.try_into()` = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_conversion = note: `#[warn(clippy::useless_conversion)]` on by default
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 @@ -1288,7 +1288,7 @@
}
};

match self.reader.read(&mut record) {

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this expression creates a reference which is immediately dereferenced by the compiler

warning: this expression creates a reference which is immediately dereferenced by the compiler --> src/bam/mod.rs:1291:32 | 1291 | match self.reader.read(&mut record) { | ^^^^^^^^^^^ help: change this to: `record` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow = note: `#[warn(clippy::needless_borrow)]` on by default
None => None,
Some(Ok(_)) => Some(Ok(Rc::clone(&self.record))),
Some(Err(err)) => Some(Err(err)),
Expand Down Expand Up @@ -1392,9 +1392,9 @@
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);

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unnecessary parentheses around function argument

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unnecessary parentheses around function argument

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unnecessary parentheses around function argument

warning: unnecessary parentheses around function argument --> src/bam/mod.rs:1395:45 | 1395 | let rec = htslib::sam_hdr_parse((l_text + 1), text as *const c_char); | ^ ^ | = note: `#[warn(unused_parens)]` on by default help: remove these parentheses | 1395 - let rec = htslib::sam_hdr_parse((l_text + 1), text as *const c_char); 1395 + let rec = htslib::sam_hdr_parse(l_text + 1, text as *const c_char); |

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unnecessary parentheses around function argument

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unnecessary parentheses around function argument
(*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 @@
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
Original file line number Diff line number Diff line change
Expand Up @@ -126,7 +126,7 @@
Record {
inner: {
#[allow(clippy::uninit_assumed_init)]
let mut inner = unsafe { MaybeUninit::uninit().assume_init() };

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the type `hts_sys::bam1_t` does not permit being left uninitialized

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the type `hts_sys::bam1_t` does not permit being left uninitialized

warning: the type `hts_sys::bam1_t` does not permit being left uninitialized --> src/bam/record.rs:129:42 | 129 | let mut inner = unsafe { MaybeUninit::uninit().assume_init() }; | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | | | this code causes undefined behavior when executed | help: use `MaybeUninit<T>` instead, and only call `assume_init` after initialization is done | = note: integers must be initialized = note: `#[warn(invalid_value)]` on by default

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the type `hts_sys::bam1_t` does not permit being left uninitialized
unsafe {
::libc::memcpy(
&mut inner as *mut htslib::bam1_t as *mut ::libc::c_void,
Expand All @@ -152,8 +152,8 @@

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 @@

/// 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 Expand Up @@ -800,7 +800,7 @@
ctag,
b'A' as c_char,
size_of::<u8>() as i32,
[v].as_mut_ptr() as *mut u8,

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casting raw pointers to the same type and constness is unnecessary (`*mut u8` -> `*mut u8`)

warning: casting raw pointers to the same type and constness is unnecessary (`*mut u8` -> `*mut u8`) --> src/bam/record.rs:803:21 | 803 | [v].as_mut_ptr() as *mut u8, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `[v].as_mut_ptr()` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast = note: `#[warn(clippy::unnecessary_cast)]` on by default
),
Aux::I8(v) => htslib::bam_aux_append(
self.inner_ptr_mut(),
Expand All @@ -814,7 +814,7 @@
ctag,
b'C' as c_char,
size_of::<u8>() as i32,
[v].as_mut_ptr() as *mut u8,

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casting raw pointers to the same type and constness is unnecessary (`*mut u8` -> `*mut u8`)

warning: casting raw pointers to the same type and constness is unnecessary (`*mut u8` -> `*mut u8`) --> src/bam/record.rs:817:21 | 817 | [v].as_mut_ptr() as *mut u8, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `[v].as_mut_ptr()` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast
),
Aux::I16(v) => htslib::bam_aux_append(
self.inner_ptr_mut(),
Expand Down Expand Up @@ -1609,7 +1609,7 @@

/// Return encoded base. Complexity: O(1).
#[inline]
pub unsafe fn encoded_base_unchecked(&self, i: usize) -> u8 {

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unsafe function's docs miss `# Safety` section

warning: unsafe function's docs miss `# Safety` section --> src/bam/record.rs:1612:5 | 1612 | pub unsafe fn encoded_base_unchecked(&self, i: usize) -> u8 { | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#missing_safety_doc = note: `#[warn(clippy::missing_safety_doc)]` on by default
encoded_base_unchecked(self.encoded, i)
}

Expand All @@ -1617,7 +1617,7 @@
/// Use index based access seq()[i], for checked, safe access.
/// Complexity: O(1).
#[inline]
pub unsafe fn decoded_base_unchecked(&self, i: usize) -> u8 {

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unsafe function's docs miss `# Safety` section

warning: unsafe function's docs miss `# Safety` section --> src/bam/record.rs:1620:5 | 1620 | pub unsafe fn decoded_base_unchecked(&self, i: usize) -> u8 { | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#missing_safety_doc
*decode_base_unchecked(self.encoded_base_unchecked(i))
}

Expand Down Expand Up @@ -2234,7 +2234,7 @@
/// This function allocates memory for the state structure
/// and initializes the iterator to the start of the modification
/// records.
fn new<'a>(r: &'a Record) -> Result<BaseModificationState<'a>> {

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the following explicit lifetimes could be elided: 'a

warning: the following explicit lifetimes could be elided: 'a --> src/bam/record.rs:2237:12 | 2237 | fn new<'a>(r: &'a Record) -> Result<BaseModificationState<'a>> { | ^^ ^^ ^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes = note: `#[warn(clippy::needless_lifetimes)]` on by default help: elide the lifetimes | 2237 - fn new<'a>(r: &'a Record) -> Result<BaseModificationState<'a>> { 2237 + fn new(r: &Record) -> Result<BaseModificationState<'_>> { |
let mut bm = unsafe {
BaseModificationState {
record: r,
Expand All @@ -2258,7 +2258,7 @@

let types = bm.recorded();
bm.buffer.reserve(types.len());
return Ok(bm);

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unneeded `return` statement

warning: unneeded `return` statement --> src/bam/record.rs:2261:9 | 2261 | return Ok(bm); | ^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return = note: `#[warn(clippy::needless_return)]` on by default help: remove `return` | 2261 - return Ok(bm); 2261 + Ok(bm) |
}

pub fn buffer_next_mods(&mut self) -> Result<usize> {
Expand Down Expand Up @@ -2286,7 +2286,7 @@
// not update the length so needs to be manually set
self.buffer.set_len(ret as usize);

return Ok(ret as usize);

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unneeded `return` statement

warning: unneeded `return` statement --> src/bam/record.rs:2289:13 | 2289 | return Ok(ret as usize); | ^^^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2289 - return Ok(ret as usize); 2289 + Ok(ret as usize) |
}
}

Expand All @@ -2311,7 +2311,7 @@
/// and the ascii code for the canonical base.
/// If there are multiple modifications with the same code this will return the data
/// for the first mod. See https://github.com/samtools/htslib/issues/1635
pub fn query_type<'a>(&self, code: i32) -> Result<BaseModificationMetadata> {

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this lifetime isn't used in the function definition

warning: this lifetime isn't used in the function definition --> src/bam/record.rs:2314:23 | 2314 | pub fn query_type<'a>(&self, code: i32) -> Result<BaseModificationMetadata> { | ^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#extra_unused_lifetimes = note: `#[warn(clippy::extra_unused_lifetimes)]` on by default
unsafe {
let mut strand: i32 = 0;
let mut implicit: i32 = 0;
Expand All @@ -2326,13 +2326,13 @@
&mut canonical,
);
if ret == -1 {
return Err(Error::BamBaseModificationTypeNotFound);

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unneeded `return` statement

warning: unneeded `return` statement --> src/bam/record.rs:2329:17 | 2329 | return Err(Error::BamBaseModificationTypeNotFound); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2329 - return Err(Error::BamBaseModificationTypeNotFound); 2329 + Err(Error::BamBaseModificationTypeNotFound) |
} else {
return Ok(BaseModificationMetadata {
strand,
implicit,
canonical: canonical.try_into().unwrap(),
});

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unneeded `return` statement

warning: unneeded `return` statement --> src/bam/record.rs:2331:17 | 2331 | / return Ok(BaseModificationMetadata { 2332 | | strand, 2333 | | implicit, 2334 | | canonical: canonical.try_into().unwrap(), 2335 | | }); | |__________________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2331 ~ Ok(BaseModificationMetadata { 2332 + strand, 2333 + implicit, 2334 + canonical: canonical.try_into().unwrap(), 2335 ~ }) |
}
}
}
Expand All @@ -2353,7 +2353,7 @@
}

impl BaseModificationsPositionIter<'_> {
fn new<'a>(r: &'a Record) -> Result<BaseModificationsPositionIter<'a>> {

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the following explicit lifetimes could be elided: 'a

warning: the following explicit lifetimes could be elided: 'a --> src/bam/record.rs:2356:12 | 2356 | fn new<'a>(r: &'a Record) -> Result<BaseModificationsPositionIter<'a>> { | ^^ ^^ ^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 2356 - fn new<'a>(r: &'a Record) -> Result<BaseModificationsPositionIter<'a>> { 2356 + fn new(r: &Record) -> Result<BaseModificationsPositionIter<'_>> { |
let state = BaseModificationState::new(r)?;
Ok(BaseModificationsPositionIter { mod_state: state })
}
Expand All @@ -2362,8 +2362,8 @@
return self.mod_state.recorded();
}

pub fn query_type<'a>(&self, code: i32) -> Result<BaseModificationMetadata> {

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this lifetime isn't used in the function definition

warning: this lifetime isn't used in the function definition --> src/bam/record.rs:2365:23 | 2365 | pub fn query_type<'a>(&self, code: i32) -> Result<BaseModificationMetadata> { | ^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#extra_unused_lifetimes
return self.mod_state.query_type(code);

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unneeded `return` statement

warning: unneeded `return` statement --> src/bam/record.rs:2366:9 | 2366 | return self.mod_state.query_type(code); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2366 - return self.mod_state.query_type(code); 2366 + self.mod_state.query_type(code) |
}
}

Expand All @@ -2380,13 +2380,13 @@
match ret {
Ok(num_mods) => {
if num_mods == 0 {
return None;

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unneeded `return` statement

warning: unneeded `return` statement --> src/bam/record.rs:2383:21 | 2383 | return None; | ^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2383 - return None; 2383 + None |
} else {
let data = (self.mod_state.buffer_pos, self.mod_state.buffer.clone());
return Some(Ok(data));

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unneeded `return` statement

warning: unneeded `return` statement --> src/bam/record.rs:2386:21 | 2386 | return Some(Ok(data)); | ^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2386 - return Some(Ok(data)); 2386 + Some(Ok(data)) |
}
}
Err(e) => return Some(Err(e)),

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unneeded `return` statement

warning: unneeded `return` statement --> src/bam/record.rs:2389:23 | 2389 | Err(e) => return Some(Err(e)), | ^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2389 | Err(e) => Some(Err(e)), | ~~~~~~~~~~~~
}
}
}
Expand All @@ -2399,7 +2399,7 @@
}

impl BaseModificationsIter<'_> {
fn new<'a>(r: &'a Record) -> Result<BaseModificationsIter<'a>> {

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the following explicit lifetimes could be elided: 'a

warning: the following explicit lifetimes could be elided: 'a --> src/bam/record.rs:2402:12 | 2402 | fn new<'a>(r: &'a Record) -> Result<BaseModificationsIter<'a>> { | ^^ ^^ ^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 2402 - fn new<'a>(r: &'a Record) -> Result<BaseModificationsIter<'a>> { 2402 + fn new(r: &Record) -> Result<BaseModificationsIter<'_>> { |
let state = BaseModificationState::new(r)?;
Ok(BaseModificationsIter {
mod_state: state,
Expand All @@ -2411,8 +2411,8 @@
return self.mod_state.recorded();
}

pub fn query_type<'a>(&self, code: i32) -> Result<BaseModificationMetadata> {

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this lifetime isn't used in the function definition

warning: this lifetime isn't used in the function definition --> src/bam/record.rs:2414:23 | 2414 | pub fn query_type<'a>(&self, code: i32) -> Result<BaseModificationMetadata> { | ^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#extra_unused_lifetimes
return self.mod_state.query_type(code);

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unneeded `return` statement

warning: unneeded `return` statement --> src/bam/record.rs:2415:9 | 2415 | return self.mod_state.query_type(code); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2415 - return self.mod_state.query_type(code); 2415 + self.mod_state.query_type(code) |
}
}

Expand Down Expand Up @@ -2446,7 +2446,7 @@
self.mod_state.buffer[self.buffer_idx],
);
self.buffer_idx += 1;
return Some(Ok(data));

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unneeded `return` statement

warning: unneeded `return` statement --> src/bam/record.rs:2449:9 | 2449 | return Some(Ok(data)); | ^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2449 - return Some(Ok(data)); 2449 + Some(Ok(data)) |
}
}

Expand Down
10 changes: 5 additions & 5 deletions src/bam/record_serde.rs
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
Original file line number Diff line number Diff line change
Expand Up @@ -112,18 +112,18 @@
}

impl Buffer {
pub fn new() -> Self {
Buffer {
inner: ptr::null_mut(),
len: 0,
}
}

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you should consider adding a `Default` implementation for `Buffer`

warning: you should consider adding a `Default` implementation for `Buffer` --> src/bcf/record.rs:115:5 | 115 | / pub fn new() -> Self { 116 | | Buffer { 117 | | inner: ptr::null_mut(), 118 | | len: 0, 119 | | } 120 | | } | |_____^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#new_without_default = note: `#[warn(clippy::new_without_default)]` on by default help: try adding this | 114 + impl Default for Buffer { 115 + fn default() -> Self { 116 + Self::new() 117 + } 118 + } |
}

impl Drop for Buffer {
fn drop(&mut self) {
unsafe {
::libc::free(self.inner as *mut ::libc::c_void);

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casting raw pointers to the same type and constness is unnecessary (`*mut libc::c_void` -> `*mut libc::c_void`)

warning: casting raw pointers to the same type and constness is unnecessary (`*mut libc::c_void` -> `*mut libc::c_void`) --> src/bcf/record.rs:126:26 | 126 | ::libc::free(self.inner as *mut ::libc::c_void); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `self.inner` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast
}
}
}
Expand All @@ -131,7 +131,7 @@
#[derive(new, Debug)]
pub struct BufferBacked<'a, T: 'a + fmt::Debug, B: Borrow<Buffer> + 'a> {
value: T,
buffer: B,

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field `buffer` is never read

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field `buffer` is never read

warning: field `buffer` is never read --> src/bcf/record.rs:134:5 | 132 | pub struct BufferBacked<'a, T: 'a + fmt::Debug, B: Borrow<Buffer> + 'a> { | ------------ field in this struct 133 | value: T, 134 | buffer: B, | ^^^^^^ | = note: `BufferBacked` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis = note: `#[warn(dead_code)]` on by default

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field `buffer` is never read
#[new(default)]
phantom: PhantomData<&'a B>,
}
Expand Down Expand Up @@ -1008,7 +1008,7 @@
}

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 Expand Up @@ -1094,7 +1094,7 @@
fn clone(&self) -> Self {
let inner = unsafe {
let inner = htslib::bcf_dup(self.inner);
inner

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returning the result of a `let` binding from a block

warning: returning the result of a `let` binding from a block --> src/bcf/record.rs:1097:13 | 1096 | let inner = htslib::bcf_dup(self.inner); | ---------------------------------------- unnecessary `let` binding 1097 | inner | ^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#let_and_return = note: `#[warn(clippy::let_and_return)]` on by default help: return the expression directly | 1096 ~ 1097 ~ htslib::bcf_dup(self.inner) |
};
Record {
inner,
Expand Down Expand Up @@ -1193,7 +1193,7 @@

impl fmt::Display for Genotype {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
let &Genotype(ref alleles) = self;

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dereferencing a tuple pattern where every element takes a reference

warning: dereferencing a tuple pattern where every element takes a reference --> src/bcf/record.rs:1196:13 | 1196 | let &Genotype(ref alleles) = self; | ^^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrowed_reference = note: `#[warn(clippy::needless_borrowed_reference)]` on by default help: try removing the `&` and `ref` parts | 1196 - let &Genotype(ref alleles) = self; 1196 + let Genotype(alleles) = self; |
write!(f, "{}", alleles[0])?;
for a in &alleles[1..] {
let sep = match a {
Expand Down Expand Up @@ -1326,7 +1326,7 @@
/// as along as the data is accessed. If parts of the data are accessed while
/// the BufferBacked object is already dropped, you will access unallocated
/// memory.
pub fn string(mut self) -> Result<Option<BufferBacked<'b, Vec<&'b [u8]>, B>>> {

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very complex type used. Consider factoring parts into `type` definitions

warning: very complex type used. Consider factoring parts into `type` definitions --> src/bcf/record.rs:1329:32 | 1329 | pub fn string(mut self) -> Result<Option<BufferBacked<'b, Vec<&'b [u8]>, B>>> { | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#type_complexity = note: `#[warn(clippy::type_complexity)]` on by default
self.data(htslib::BCF_HT_STR).map(|data| {
data.map(|ret| {
BufferBacked::new(
Expand Down Expand Up @@ -1445,7 +1445,7 @@
)
}
.chunks(self.values_per_sample())
.map(|s| trim_slice(s))

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redundant closure

warning: redundant closure --> src/bcf/record.rs:1448:22 | 1448 | .map(|s| trim_slice(s)) | ^^^^^^^^^^^^^^^^^ help: replace the closure with the function itself: `trim_slice` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_closure = note: `#[warn(clippy::redundant_closure)]` on by default
.collect(),
self.buffer,
)
Expand All @@ -1468,7 +1468,7 @@
)
}
.chunks(self.values_per_sample())
.map(|s| trim_slice(s))

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redundant closure

warning: redundant closure --> src/bcf/record.rs:1471:22 | 1471 | .map(|s| trim_slice(s)) | ^^^^^^^^^^^^^^^^^ help: replace the closure with the function itself: `trim_slice` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_closure
.collect(),
self.buffer,
)
Expand Down
15 changes: 3 additions & 12 deletions src/bgzf/mod.rs
Original file line number Diff line number Diff line change
Expand Up @@ -112,11 +112,7 @@
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 @@ -232,7 +228,7 @@
// This should be unreachable
Ok(i) => return Err(Error::BgzfInvalidCompressionLevel { level: i }),
};
return Ok(ffi::CString::new(write_string).unwrap());

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unneeded `return` statement

warning: unneeded `return` statement --> src/bgzf/mod.rs:231:9 | 231 | return Ok(ffi::CString::new(write_string).unwrap()); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 231 - return Ok(ffi::CString::new(write_string).unwrap()); 231 + Ok(ffi::CString::new(write_string).unwrap()) |
}

/// Set the thread pool to use for parallel compression.
Expand All @@ -257,13 +253,8 @@

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
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