chore(master): release 0.44.1 (#399) #747

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Formatting

Testing-Features (no-default-features): src/bcf/record.rs#L134

field `buffer` is never read

Testing-Features (no-default-features): src/tbx/mod.rs#L94

field `hts_format` is never read

Testing-Features (no-default-features): src/bam/record.rs#L128

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

Testing-Features (no-default-features)

`rust-htslib` (lib) generated 3 warnings

Testing-Features (no-default-features)

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Testing-Features (no-default-features)

the type `hts_sys::bam1_t` does not permit being left uninitialized: src/bam/record.rs#L128

warning: the type `hts_sys::bam1_t` does not permit being left uninitialized --> src/bam/record.rs:128:42 | 128 | 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

unneeded `return` statement: src/bgzf/mod.rs#L235

warning: unneeded `return` statement --> src/bgzf/mod.rs:235:9 | 235 | 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`

redundant closure: src/bcf/record.rs#L1471

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

redundant closure: src/bcf/record.rs#L1448

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

very complex type used. Consider factoring parts into `type` definitions: src/bcf/record.rs#L1329

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

dereferencing a tuple pattern where every element takes a reference: src/bcf/record.rs#L1196

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; |

returning the result of a `let` binding from a block: src/bcf/record.rs#L1097

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) |

you should consider adding a `Default` implementation for `Buffer`: src/bcf/record.rs#L115

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 + } |

this expression creates a reference which is immediately dereferenced by the compiler: src/bam/mod.rs#L1289

warning: this expression creates a reference which is immediately dereferenced by the compiler --> src/bam/mod.rs:1289:32 | 1289 | 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

casting to the same type is unnecessary (`usize` -> `usize`): src/bam/mod.rs#L1123

warning: casting to the same type is unnecessary (`usize` -> `usize`) --> src/bam/mod.rs:1123:17 | 1123 | ((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 = note: `#[warn(clippy::unnecessary_cast)]` on by default

unneeded `return` statement: src/bam/record.rs#L2447

warning: unneeded `return` statement --> src/bam/record.rs:2447:9 | 2447 | return Some(Ok(data)); | ^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return = help: remove `return`

unneeded `return` statement: src/bam/record.rs#L2413

warning: unneeded `return` statement --> src/bam/record.rs:2413:9 | 2413 | 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`

this lifetime isn't used in the function definition: src/bam/record.rs#L2412

warning: this lifetime isn't used in the function definition --> src/bam/record.rs:2412:23 | 2412 | 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

the following explicit lifetimes could be elided: 'a: src/bam/record.rs#L2400

warning: the following explicit lifetimes could be elided: 'a --> src/bam/record.rs:2400:5 | 2400 | 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 | 2400 - fn new<'a>(r: &'a Record) -> Result<BaseModificationsIter<'a>> { 2400 + fn new(r: &Record) -> Result<BaseModificationsIter<'_>> { |

unneeded `return` statement: src/bam/record.rs#L2387

warning: unneeded `return` statement --> src/bam/record.rs:2387:23 | 2387 | 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`

unneeded `return` statement: src/bam/record.rs#L2384

warning: unneeded `return` statement --> src/bam/record.rs:2384:21 | 2384 | return Some(Ok(data)); | ^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return = help: remove `return`

unneeded `return` statement: src/bam/record.rs#L2381

warning: unneeded `return` statement --> src/bam/record.rs:2381:21 | 2381 | return None; | ^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return = help: remove `return`

unneeded `return` statement: src/bam/record.rs#L2364

warning: unneeded `return` statement --> src/bam/record.rs:2364:9 | 2364 | 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`

this lifetime isn't used in the function definition: src/bam/record.rs#L2363

warning: this lifetime isn't used in the function definition --> src/bam/record.rs:2363:23 | 2363 | 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

the following explicit lifetimes could be elided: 'a: src/bam/record.rs#L2354

warning: the following explicit lifetimes could be elided: 'a --> src/bam/record.rs:2354:5 | 2354 | 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 | 2354 - fn new<'a>(r: &'a Record) -> Result<BaseModificationsPositionIter<'a>> { 2354 + fn new(r: &Record) -> Result<BaseModificationsPositionIter<'_>> { |

unneeded `return` statement: src/bam/record.rs#L2329

warning: unneeded `return` statement --> src/bam/record.rs:2329:17 | 2329 | / return Ok(BaseModificationMetadata { 2330 | | strand, 2331 | | implicit, 2332 | | canonical, 2333 | | }); | |__________________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return = help: remove `return`

unneeded `return` statement: src/bam/record.rs#L2327

warning: unneeded `return` statement --> src/bam/record.rs:2327:17 | 2327 | return Err(Error::BamBaseModificationTypeNotFound); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return = help: remove `return`

this lifetime isn't used in the function definition: src/bam/record.rs#L2313

warning: this lifetime isn't used in the function definition --> src/bam/record.rs:2313:23 | 2313 | 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

unneeded `return` statement: src/bam/record.rs#L2288

warning: unneeded `return` statement --> src/bam/record.rs:2288:13 | 2288 | 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`

unneeded `return` statement: src/bam/record.rs#L2260

warning: unneeded `return` statement --> src/bam/record.rs:2260:9 | 2260 | 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`

the following explicit lifetimes could be elided: 'a: src/bam/record.rs#L2236

warning: the following explicit lifetimes could be elided: 'a --> src/bam/record.rs:2236:5 | 2236 | 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 | 2236 - fn new<'a>(r: &'a Record) -> Result<BaseModificationState<'a>> { 2236 + fn new(r: &Record) -> Result<BaseModificationState<'_>> { |

unsafe function's docs miss `# Safety` section: src/bam/record.rs#L1619

warning: unsafe function's docs miss `# Safety` section --> src/bam/record.rs:1619:5 | 1619 | 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

unsafe function's docs miss `# Safety` section: src/bam/record.rs#L1611

warning: unsafe function's docs miss `# Safety` section --> src/bam/record.rs:1611:5 | 1611 | 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

field `hts_format` is never read: src/tbx/mod.rs#L94

warning: field `hts_format` is never read --> src/tbx/mod.rs:94:5 | 87 | pub struct Reader { | ------ field in this struct ... 94 | hts_format: htslib::htsExactFormat, | ^^^^^^^^^^ | = note: `Reader` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis

field `buffer` is never read: src/bcf/record.rs#L134

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

Linting