feat: Add to_vcf_string method for bcf::Record (#443) #862

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/toolchain@v1.0.6, Swatinem/rust-cache@v1.3.0, 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/

Testing-Features (no-default-features)

The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2, actions-rs/toolchain@v1.0.6, Swatinem/rust-cache@v1.3.0, actions-rs/cargo@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Testing-Features (no-default-features): src/bam/mod.rs#L1395

unnecessary parentheses around function argument

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#L140

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

Testing-Features (no-default-features)

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

Testing-Features (no-default-features)

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

Testing-Features (no-default-features): src/bam/mod.rs#L1395

unnecessary parentheses around function argument

Testing-Features (no-default-features)

1 warning emitted

Testing-Features (no-default-features)

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/

Testing-Features (no-default-features)

Testing-MacOS (silicon-sonoma)

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/toolchain@v1.0.6, actions-rs/cargo@v1.0.1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

Testing-MacOS (silicon-sonoma)

The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2, actions-rs/toolchain@v1.0.6, actions-rs/cargo@v1.0.1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Testing-MacOS (silicon-sonoma)

Formula curl-openssl was renamed to curl.

Testing-MacOS (silicon-sonoma)

xz 5.6.3 is already installed and up-to-date. To reinstall 5.6.3, run: brew reinstall xz

Testing-MacOS (silicon-sonoma)

curl 8.10.1 is already installed and up-to-date. To reinstall 8.10.1, run: brew reinstall curl

the type `hts_sys::bam1_t` does not permit being left uninitialized: src/bam/record.rs#L140

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

usage of an `Arc` that is not `Send` and `Sync`: src/tpool.rs#L33

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 `RefCell<InnerThreadPool>` is neither `Send` nor `Sync` = help: if the `Arc` will not used be across threads replace it with an `Rc` = help: otherwise make `RefCell<InnerThreadPool>` `Send` and `Sync` or consider a wrapper type such as `Mutex` = 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

usage of a legacy numeric constant: src/faidx/mod.rs#L92

warning: usage of a legacy numeric constant --> src/faidx/mod.rs:92:18 | 92 | if end > std::i64::MAX as usize { | ^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#legacy_numeric_constants help: use the associated constant instead | 92 | if end > i64::MAX as usize { | ~~~~~~~~

usage of a legacy numeric constant: src/faidx/mod.rs#L89

warning: usage of a legacy numeric constant --> src/faidx/mod.rs:89:20 | 89 | if begin > std::i64::MAX as usize { | ^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#legacy_numeric_constants help: use the associated constant instead | 89 | if begin > i64::MAX as usize { | ~~~~~~~~

unneeded `return` statement: src/bgzf/mod.rs#L243

warning: unneeded `return` statement --> src/bgzf/mod.rs:243:9 | 243 | 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` | 243 - return Ok(ffi::CString::new(write_string).unwrap()); 243 + Ok(ffi::CString::new(write_string).unwrap()) |

comparing with null is better expressed by the `.is_null()` method: src/bgzf/mod.rs#L220

warning: comparing with null is better expressed by the `.is_null()` method --> src/bgzf/mod.rs:220:12 | 220 | if inner != std::ptr::null_mut() { | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cmp_null

comparing with null is better expressed by the `.is_null()` method: src/bgzf/mod.rs#L90

warning: comparing with null is better expressed by the `.is_null()` method --> src/bgzf/mod.rs:90:12 | 90 | if inner != std::ptr::null_mut() { | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cmp_null = note: `#[warn(clippy::cmp_null)]` on by default

doc list item without indentation: src/bcf/mod.rs#L324

warning: doc list item without indentation --> src/bcf/mod.rs:324:9 | 324 | /// is given, records are fetched from `start` until the end of the contig. | ^ | = help: if this is supposed to be its own paragraph, add a blank line = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation help: indent this line | 324 | /// is given, records are fetched from `start` until the end of the contig. | ++

redundant closure: src/bcf/record.rs#L1503

warning: redundant closure --> src/bcf/record.rs:1503:22 | 1503 | .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#L1480

warning: redundant closure --> src/bcf/record.rs:1480:22 | 1480 | .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#L1361

warning: very complex type used. Consider factoring parts into `type` definitions --> src/bcf/record.rs:1361:32 | 1361 | 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#L1228

warning: dereferencing a tuple pattern where every element takes a reference --> src/bcf/record.rs:1228:13 | 1228 | 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 | 1228 - let &Genotype(ref alleles) = self; 1228 + let Genotype(alleles) = self; |

returning the result of a `let` binding from a block: src/bcf/record.rs#L1129

warning: returning the result of a `let` binding from a block --> src/bcf/record.rs:1129:13 | 1128 | let inner = htslib::bcf_dup(self.inner); | ---------------------------------------- unnecessary `let` binding 1129 | 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 | 1128 ~ 1129 ~ htslib::bcf_dup(self.inner) |

casting raw pointers to the same type and constness is unnecessary (`*mut libc::c_void` -> `*mut libc::c_void`): src/bcf/record.rs#L126

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

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 + } |

importing legacy numeric constants: src/bcf/record.rs#L10

warning: importing legacy numeric constants --> src/bcf/record.rs:10:5 | 10 | use std::i32; | ^^^^^^^^ | = help: remove this import = note: then `i32::<CONST>` will resolve to the respective associated constant = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#legacy_numeric_constants

casting raw pointers to the same type and constness is unnecessary (`*mut i32` -> `*mut i32`): src/bcf/header.rs#L120

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

casting raw pointers to the same type and constness is unnecessary (`*const *mut i8` -> `*const *mut i8`): src/bcf/header.rs#L119

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

this expression creates a reference which is immediately dereferenced by the compiler: src/bam/mod.rs#L1291

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

casting to the same type is unnecessary (`usize` -> `usize`): src/bam/mod.rs#L1125

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

useless conversion to the same type: `usize`: src/bam/mod.rs#L1125

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

doc list item without indentation: src/bam/mod.rs#L325

warning: doc list item without indentation --> src/bam/mod.rs:325:9 | 325 | /// a valid virtual offset. | ^ | = help: if this is supposed to be its own paragraph, add a blank line = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation = note: `#[warn(clippy::doc_lazy_continuation)]` on by default help: indent this line | 325 | /// a valid virtual offset. | ++

unneeded `return` statement: src/bam/record.rs#L2471

warning: unneeded `return` statement --> src/bam/record.rs:2471:9 | 2471 | return Some(Ok(data)); | ^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2471 - return Some(Ok(data)); 2471 + Some(Ok(data)) |

unneeded `return` statement: src/bam/record.rs#L2437

warning: unneeded `return` statement --> src/bam/record.rs:2437:9 | 2437 | 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` | 2437 - return self.mod_state.query_type(code); 2437 + self.mod_state.query_type(code) |

this lifetime isn't used in the function definition: src/bam/record.rs#L2436

warning: this lifetime isn't used in the function definition --> src/bam/record.rs:2436:23 | 2436 | 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#L2424

warning: the following explicit lifetimes could be elided: 'a --> src/bam/record.rs:2424:12 | 2424 | 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 | 2424 - fn new<'a>(r: &'a Record) -> Result<BaseModificationsIter<'a>> { 2424 + fn new(r: &Record) -> Result<BaseModificationsIter<'_>> { |

unneeded `return` statement: src/bam/record.rs#L2411

warning: unneeded `return` statement --> src/bam/record.rs:2411:23 | 2411 | 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` | 2411 | Err(e) => Some(Err(e)), | ~~~~~~~~~~~~

unneeded `return` statement: src/bam/record.rs#L2408

warning: unneeded `return` statement --> src/bam/record.rs:2408:21 | 2408 | return Some(Ok(data)); | ^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2408 - return Some(Ok(data)); 2408 + Some(Ok(data)) |

unneeded `return` statement: src/bam/record.rs#L2405

warning: unneeded `return` statement --> src/bam/record.rs:2405:21 | 2405 | return None; | ^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2405 - return None; 2405 + None |

unneeded `return` statement: src/bam/record.rs#L2388

warning: unneeded `return` statement --> src/bam/record.rs:2388:9 | 2388 | 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` | 2388 - return self.mod_state.query_type(code); 2388 + self.mod_state.query_type(code) |

this lifetime isn't used in the function definition: src/bam/record.rs#L2387

warning: this lifetime isn't used in the function definition --> src/bam/record.rs:2387:23 | 2387 | 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#L2378

warning: the following explicit lifetimes could be elided: 'a --> src/bam/record.rs:2378:12 | 2378 | 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 | 2378 - fn new<'a>(r: &'a Record) -> Result<BaseModificationsPositionIter<'a>> { 2378 + fn new(r: &Record) -> Result<BaseModificationsPositionIter<'_>> { |

unneeded `return` statement: src/bam/record.rs#L2353

warning: unneeded `return` statement --> src/bam/record.rs:2353:17 | 2353 | / return Ok(BaseModificationMetadata { 2354 | | strand, 2355 | | implicit, 2356 | | canonical: canonical.try_into().unwrap(), 2357 | | }); | |__________________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2353 ~ Ok(BaseModificationMetadata { 2354 + strand, 2355 + implicit, 2356 + canonical: canonical.try_into().unwrap(), 2357 ~ }) |

unneeded `return` statement: src/bam/record.rs#L2351

warning: unneeded `return` statement --> src/bam/record.rs:2351:17 | 2351 | return Err(Error::BamBaseModificationTypeNotFound); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return help: remove `return` | 2351 - return Err(Error::BamBaseModificationTypeNotFound); 2351 + Err(Error::BamBaseModificationTypeNotFound) |

this lifetime isn't used in the function definition: src/bam/record.rs#L2336

warning: this lifetime isn't used in the function definition --> src/bam/record.rs:2336:23 | 2336 | 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#L2311

warning: unneeded `return` statement --> src/bam/record.rs:2311:13 | 2311 | 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` | 2311 - return Ok(ret as usize); 2311 + Ok(ret as usize) |

unneeded `return` statement: src/bam/record.rs#L2283

warning: unneeded `return` statement --> src/bam/record.rs:2283:9 | 2283 | 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` | 2283 - return Ok(bm); 2283 + Ok(bm) |

the following explicit lifetimes could be elided: 'a: src/bam/record.rs#L2259

warning: the following explicit lifetimes could be elided: 'a --> src/bam/record.rs:2259:12 | 2259 | 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 | 2259 - fn new<'a>(r: &'a Record) -> Result<BaseModificationState<'a>> { 2259 + fn new(r: &Record) -> Result<BaseModificationState<'_>> { |

unsafe function's docs are missing a `# Safety` section: src/bam/record.rs#L1637

warning: unsafe function's docs are missing a `# Safety` section --> src/bam/record.rs:1637:5 | 1637 | 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 are missing a `# Safety` section: src/bam/record.rs#L1629

warning: unsafe function's docs are missing a `# Safety` section --> src/bam/record.rs:1629:5 | 1629 | 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

using `map_err` over `inspect_err`: src/bam/record.rs#L1574

warning: using `map_err` over `inspect_err` --> src/bam/record.rs:1574:18 | 1574 | .map_err(|e| { | ^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_inspect = note: `#[warn(clippy::manual_inspect)]` on by default help: try | 1574 ~ .inspect_err(|e| { 1575 | // In the case of an error, we can not safely advance in the aux data, so we terminate the Iteration 1576 ~ self.aux = &[]; |

casting raw pointers to the same type and constness is unnecessary (`*mut u8` -> `*mut u8`): src/bam/record.rs#L828

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

casting raw pointers to the same type and constness is unnecessary (`*mut u8` -> `*mut u8`): src/bam/record.rs#L814

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

importing legacy numeric constants: src/bam/record.rs#L17

warning: importing legacy numeric constants --> src/bam/record.rs:17:5 | 17 | use std::u32; | ^^^^^^^^ | = help: remove this import = note: then `u32::<CONST>` will resolve to the respective associated constant = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#legacy_numeric_constants

usage of a legacy numeric method: src/bam/pileup.rs#L145

warning: usage of a legacy numeric method --> src/bam/pileup.rs:145:22 | 145 | i32::max_value(), | ^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#legacy_numeric_constants help: use the associated constant instead | 145 | i32::MAX, | ~~~

usage of a legacy numeric method: src/bam/pileup.rs#L142

warning: usage of a legacy numeric method --> src/bam/pileup.rs:142:25 | 142 | if depth > i32::max_value() as u32 { | ^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#legacy_numeric_constants = note: `#[warn(clippy::legacy_numeric_constants)]` on by default help: use the associated constant instead | 142 | if depth > i32::MAX as u32 { | ~~~

this item has comments with 4 forward slashes (`////`). These look like doc comments, but they aren't: src/bam/ext.rs#L1

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. |

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

unnecessary parentheses around function argument: src/bam/mod.rs#L1395

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); |

Linting

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/toolchain@v1.0.6, actions-rs/clippy-check@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

Linting

The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2, actions-rs/toolchain@v1.0.6, actions-rs/clippy-check@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Linting

Testing-MacOS (intel-ventura)

Formula curl-openssl was renamed to curl.

Testing-MacOS (intel-ventura)

xz 5.6.3 is already installed and up-to-date. To reinstall 5.6.3, run: brew reinstall xz

Testing-MacOS (intel-ventura)

curl 8.10.1 is already installed and up-to-date. To reinstall 8.10.1, run: brew reinstall curl

Testing-MacOS (intel-ventura)

Testing-Features (all-features)

Testing-Features (all-features): src/bam/mod.rs#L1395

unnecessary parentheses around function argument

Testing-Features (all-features): src/bcf/record.rs#L134

field `buffer` is never read

Testing-Features (all-features): src/tbx/mod.rs#L94

field `hts_format` is never read

Testing-Features (all-features): src/bam/record.rs#L140

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

Testing-Features (all-features)

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

Testing-Features (all-features)

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

Testing-Features (all-features): src/bam/mod.rs#L1395

unnecessary parentheses around function argument

Testing-Features (all-features)

1 warning emitted

Testing-Features (all-features)

Testing-MacOS (intel-monterey)

Formula curl-openssl was renamed to curl.

Testing-MacOS (intel-monterey)

xz 5.6.3 is already installed and up-to-date. To reinstall 5.6.3, run: brew reinstall xz

Testing-MacOS (intel-monterey)

curl 8.10.1 is already installed and up-to-date. To reinstall 8.10.1, run: brew reinstall curl

Testing-MacOS (intel-monterey)

Testing

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/toolchain@v1.0.6, Swatinem/rust-cache@v1.3.0, actions-rs/tarpaulin@v0.1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

Testing

The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2, actions-rs/toolchain@v1.0.6, Swatinem/rust-cache@v1.3.0, actions-rs/tarpaulin@v0.1, coverallsapp/github-action@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

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feat: Add to_vcf_string method for bcf::Record (#443) #862

Summary

feat: Add to_vcf_string method for bcf::Record (#443) #862

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