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`/home/runner/work/rust-htslib/rust-htslib/.cargo/config` is deprecated in favor of `config.toml`

unnecessary parentheses around function argument

field `buffer` is never read

field `hts_format` is never read

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

`rust-htslib` (lib) generated 4 warnings (run `cargo fix --lib -p rust-htslib` to apply 1 suggestion)

`rust-htslib` (lib test) generated 5 warnings (4 duplicates) (run `cargo fix --lib -p rust-htslib --tests` to apply 1 suggestion)

unnecessary parentheses around function argument

1 warning emitted

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warning: the type `hts_sys::bam1_t` does not permit being left uninitialized --> src/bam/record.rs:140:42 | 140 | 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

warning: usage of an `Arc` that is not `Send` and `Sync` --> src/tpool.rs:33:26 | 33 | let handle = Arc::new(RefCell::new(inner)); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = note: `Arc<RefCell<InnerThreadPool>>` is not `Send` and `Sync` as: = note: - the trait `Send` is not implemented for `RefCell<InnerThreadPool>` = note: - the trait `Sync` is not implemented for `RefCell<InnerThreadPool>` = help: consider using an `Rc` instead. `Arc` does not provide benefits for non `Send` and `Sync` types = note: if you intend to use `Arc` with `Send` and `Sync` traits = note: wrap the inner type with a `Mutex` or implement `Send` and `Sync` for `RefCell<InnerThreadPool>` = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#arc_with_non_send_sync = note: `#[warn(clippy::arc_with_non_send_sync)]` on by default

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()) |

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

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

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

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; |

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) |

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

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 + } |

warning: casting raw pointers to the same type and constness is unnecessary (`*mut i32` -> `*mut i32`) --> src/bcf/header.rs:120:17 | 120 | imap.as_mut_ptr() as *mut i32, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `imap.as_mut_ptr()` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

warning: casting raw pointers to the same type and constness is unnecessary (`*const *mut i8` -> `*const *mut i8`) --> src/bcf/header.rs:119:17 | 119 | name_pointers.as_ptr() as *const *mut c_char, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `name_pointers.as_ptr()` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

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

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

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

warning: unneeded `return` statement --> src/bam/record.rs:2460:9 | 2460 | return Some(Ok(data)); | ^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2460 - return Some(Ok(data)); 2460 + Some(Ok(data)) |

warning: unneeded `return` statement --> src/bam/record.rs:2426:9 | 2426 | 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` | 2426 - return self.mod_state.query_type(code); 2426 + self.mod_state.query_type(code) |

warning: this lifetime isn't used in the function definition --> src/bam/record.rs:2425:23 | 2425 | 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

warning: the following explicit lifetimes could be elided: 'a --> src/bam/record.rs:2413:12 | 2413 | 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 | 2413 - fn new<'a>(r: &'a Record) -> Result<BaseModificationsIter<'a>> { 2413 + fn new(r: &Record) -> Result<BaseModificationsIter<'_>> { |

warning: unneeded `return` statement --> src/bam/record.rs:2400:23 | 2400 | 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` | 2400 | Err(e) => Some(Err(e)), | ~~~~~~~~~~~~

warning: unneeded `return` statement --> src/bam/record.rs:2397:21 | 2397 | return Some(Ok(data)); | ^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2397 - return Some(Ok(data)); 2397 + Some(Ok(data)) |

warning: unneeded `return` statement --> src/bam/record.rs:2394:21 | 2394 | return None; | ^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2394 - return None; 2394 + None |

warning: unneeded `return` statement --> src/bam/record.rs:2377:9 | 2377 | 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` | 2377 - return self.mod_state.query_type(code); 2377 + self.mod_state.query_type(code) |

warning: this lifetime isn't used in the function definition --> src/bam/record.rs:2376:23 | 2376 | 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

warning: the following explicit lifetimes could be elided: 'a --> src/bam/record.rs:2367:12 | 2367 | 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 | 2367 - fn new<'a>(r: &'a Record) -> Result<BaseModificationsPositionIter<'a>> { 2367 + fn new(r: &Record) -> Result<BaseModificationsPositionIter<'_>> { |

warning: unneeded `return` statement --> src/bam/record.rs:2342:17 | 2342 | / return Ok(BaseModificationMetadata { 2343 | | strand, 2344 | | implicit, 2345 | | canonical: canonical.try_into().unwrap(), 2346 | | }); | |__________________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2342 ~ Ok(BaseModificationMetadata { 2343 + strand, 2344 + implicit, 2345 + canonical: canonical.try_into().unwrap(), 2346 ~ }) |

warning: unneeded `return` statement --> src/bam/record.rs:2340:17 | 2340 | return Err(Error::BamBaseModificationTypeNotFound); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2340 - return Err(Error::BamBaseModificationTypeNotFound); 2340 + Err(Error::BamBaseModificationTypeNotFound) |

warning: this lifetime isn't used in the function definition --> src/bam/record.rs:2325:23 | 2325 | 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

warning: unneeded `return` statement --> src/bam/record.rs:2300:13 | 2300 | 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` | 2300 - return Ok(ret as usize); 2300 + Ok(ret as usize) |

warning: unneeded `return` statement --> src/bam/record.rs:2272:9 | 2272 | 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` | 2272 - return Ok(bm); 2272 + Ok(bm) |

warning: the following explicit lifetimes could be elided: 'a --> src/bam/record.rs:2248:12 | 2248 | 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 | 2248 - fn new<'a>(r: &'a Record) -> Result<BaseModificationState<'a>> { 2248 + fn new(r: &Record) -> Result<BaseModificationState<'_>> { |

warning: unsafe function's docs miss `# Safety` section --> src/bam/record.rs:1631:5 | 1631 | 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

warning: unsafe function's docs miss `# Safety` section --> src/bam/record.rs:1623:5 | 1623 | 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

warning: casting raw pointers to the same type and constness is unnecessary (`*mut u8` -> `*mut u8`) --> src/bam/record.rs:828:21 | 828 | [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

warning: casting raw pointers to the same type and constness is unnecessary (`*mut u8` -> `*mut u8`) --> src/bam/record.rs:814:21 | 814 | [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

warning: this item has comments with 4 forward slashes (`////`). These look like doc comments, but they aren't --> src/bam/ext.rs:1:1 | 1 | / //// Copyright 2019 Johannes Köster and Florian Finkernagel. 2 | | // Licensed under the MIT license (http://opensource.org/licenses/MIT) 3 | | // This file may not be copied, modified, or distributed 4 | | // except according to those terms. ... | 7 | | 8 | | use crate::bam; | |_ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#four_forward_slashes = note: `#[warn(clippy::four_forward_slashes)]` on by default help: make this a doc comment by removing one `/` | 1 + /// Copyright 2019 Johannes Köster and Florian Finkernagel. |

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

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

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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Formula curl-openssl was renamed to curl.

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curl 8.7.1 is already installed and up-to-date. To reinstall 8.7.1, run: brew reinstall curl

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2, actions-rs/[email protected], Swatinem/[email protected], actions-rs/cargo@v1. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/[email protected], Swatinem/[email protected], actions-rs/cargo@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

`/home/runner/work/rust-htslib/rust-htslib/.cargo/config` is deprecated in favor of `config.toml`

unnecessary parentheses around function argument

field `buffer` is never read

field `hts_format` is never read

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

`rust-htslib` (lib) generated 4 warnings (run `cargo fix --lib -p rust-htslib` to apply 1 suggestion)

`rust-htslib` (lib test) generated 5 warnings (4 duplicates) (run `cargo fix --lib -p rust-htslib --tests` to apply 1 suggestion)

unnecessary parentheses around function argument

1 warning emitted

The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2, actions-rs/[email protected], Swatinem/[email protected], actions-rs/[email protected], coverallsapp/github-action@v1. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/[email protected], Swatinem/[email protected], actions-rs/[email protected]. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/