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 `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

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 {
   |                  ~~~~~~~~

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 {
   |                    ~~~~~~~~

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: 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.
    |         ++

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: 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

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: 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.
    |         ++

warning: unneeded `return` statement
    --> src/bam/record.rs:2466:9
     |
2466 |         return Some(Ok(data));
     |         ^^^^^^^^^^^^^^^^^^^^^
     |
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
help: remove `return`
     |
2466 -         return Some(Ok(data));
2466 +         Some(Ok(data))
     |

warning: unneeded `return` statement
    --> src/bam/record.rs:2432:9
     |
2432 |         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`
     |
2432 -         return self.mod_state.query_type(code);
2432 +         self.mod_state.query_type(code)
     |

warning: this lifetime isn't used in the function definition
    --> src/bam/record.rs:2431:23
     |
2431 |     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:2419:12
     |
2419 |     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
     |
2419 -     fn new<'a>(r: &'a Record) -> Result<BaseModificationsIter<'a>> {
2419 +     fn new(r: &Record) -> Result<BaseModificationsIter<'_>> {
     |

warning: unneeded `return` statement
    --> src/bam/record.rs:2406:23
     |
2406 |             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`
     |
2406 |             Err(e) => Some(Err(e)),
     |                       ~~~~~~~~~~~~