warning: module has the same name as its containing module
   --> src/stats/pairhmm/mod.rs:106:1
    |
106 | mod pairhmm;
    | ^^^^^^^^^^^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#module_inception
    = note: `#[warn(clippy::module_inception)]` on by default

warning: casting to the same type is unnecessary (`u8` -> `u8`)
  --> src/seq_analysis/orf.rs:65:44
   |
65 |                 .map(|x| x.iter().map(|&x| x as u8).collect::<VecDeque<u8>>())
   |                                            ^^^^^^^ help: try: `x`
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

warning: casting to the same type is unnecessary (`u8` -> `u8`)
  --> src/seq_analysis/orf.rs:61:44
   |
61 |                 .map(|x| x.iter().map(|&x| x as u8).collect::<VecDeque<u8>>())
   |                                            ^^^^^^^ help: try: `x`
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

warning: casting to the same type is unnecessary (`i8` -> `i8`)
   --> src/pattern_matching/myers/long.rs:231:28
    |
231 |             self.add_state(-carry as i8);
    |                            ^^^^^^^^^^^^ help: try: `-carry`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

warning: the borrowed expression implements the required traits
   --> src/io/fasta.rs:417:24
    |
417 |         fs::File::open(&path)
    |                        ^^^^^ help: change this to: `path`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow

warning: the borrowed expression implements the required traits
   --> src/io/fasta.rs:374:24
    |
374 |         fs::File::open(&path)
    |                        ^^^^^ help: change this to: `path`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow

warning: the borrowed expression implements the required traits
   --> src/io/bed.rs:115:28
    |
115 |                 .serialize(&(&record.chrom, record.start, record.end, &record.aux))
    |                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: change this to: `(&record.chrom, record.start, record.end, &record.aux)`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow

warning: the borrowed expression implements the required traits
   --> src/io/bed.rs:112:28
    |
112 |                 .serialize(&(&record.chrom, record.start, record.end))
    |                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: change this to: `(&record.chrom, record.start, record.end)`
    |
    = 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/data_structures/wavelet_matrix.rs:137:22
    |
137 |         let height = self.height as usize;
    |                      ^^^^^^^^^^^^^^^^^^^^ help: try: `self.height`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

warning: implicitly performing saturating subtraction
   --> src/data_structures/rank_select.rs:174:9
    |
174 | /         if superblock > 0 {
175 | |             superblock -= 1;
176 | |         }
    | |_________^ help: try: `superblock = superblock.saturating_sub(1);`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#implicit_saturating_sub
    = note: `#[warn(clippy::implicit_saturating_sub)]` on by default

warning: casting to the same type is unnecessary (`usize` -> `usize`)
   --> src/data_structures/qgram_index.rs:100:28
    |
100 |                     offset[qgram as usize] += 1;
    |                            ^^^^^^^^^^^^^^ help: try: `qgram`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

warning: casting to the same type is unnecessary (`usize` -> `usize`)
  --> src/data_structures/qgram_index.rs:99:36
   |
99 |                     pos[a + offset[qgram as usize]] = i;
   |                                    ^^^^^^^^^^^^^^ help: try: `qgram`
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

warning: casting to the same type is unnecessary (`usize` -> `usize`)
  --> src/data_structures/qgram_index.rs:97:28
   |
97 |                 if address[qgram as usize + 1] - a != 0 {
   |                            ^^^^^^^^^^^^^^ help: try: `qgram`
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

warning: casting to the same type is unnecessary (`usize` -> `usize`)
  --> src/data_structures/qgram_index.rs:96:33
   |
96 |                 let a = address[qgram as usize];
   |                                 ^^^^^^^^^^^^^^ help: try: `qgram`
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

warning: casting to the same type is unnecessary (`u32` -> `u32`)
  --> src/data_structures/qgram_index.rs:74:46
   |
74 |         let qgram_count = alphabet.len().pow(q as u32);
   |                                              ^^^^^^^^ help: try: `q`
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

warning: casting to the same type is unnecessary (`usize` -> `usize`)
   --> src/data_structures/interval_tree/array_backed_interval_tree.rs:202:17
    |
202 |         let n = self.entries.len() as usize;
    |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `self.entries.len()`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

warning: unsafe function's docs miss `# Safety` section
   --> src/data_structures/fmindex.rs:561:5
    |
561 | /     pub unsafe fn from_fmindex_unchecked(
562 | |         fmindex: FMIndex<DBWT, DLess, DOcc>,
563 | |     ) -> FMDIndex<DBWT, DLess, DOcc> {
    | |____________________________________^
    |
    = 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 to the same type is unnecessary (`usize` -> `usize`)
   --> src/data_structures/bwt.rs:181:9
    |
181 |         bytecount::count(&bwt[lo_idx + 1..=r], a) as usize + lo_occ
    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `bytecount::count(&bwt[lo_idx + 1..=r], a)`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

warning: casting to the same type is unnecessary (`usize` -> `usize`)
   --> src/data_structures/bwt.rs:174:37
    |
174 |                     return hi_occ - bytecount::count(&bwt[r + 1..=hi_idx], a) as usize;
    |                                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `bytecount::count(&bwt[r + 1..=hi_idx], a)`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

warning: casting to the same type is unnecessary (`u32` -> `u32`)
   --> src/alignment/sparse.rs:455:23
    |
455 |           let max_inc = (min(
    |  _______________________^
456 | |             seq1.len() as u32 - this_match.0,
457 | |             seq2.len() as u32 - this_match.1,
458 | |         ) as u32)
    | |_________________^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast
help: try
    |
455 ~         let max_inc = min(
456 +             seq1.len() as u32 - this_match.0,
457 +             seq2.len() as u32 - this_match.1,
458 +         )
    |

warning: using `clone` on type `i32` which implements the `Copy` trait
   --> src/alignment/poa.rs:320:31
    |
320 |                     weight += edge.weight().clone();
    |                               ^^^^^^^^^^^^^^^^^^^^^ help: try dereferencing it: `*edge.weight()`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
    = note: `#[warn(clippy::clone_on_copy)]` on by default

warning: this loop could be written as a `for` loop
   --> src/alignment/poa.rs:319:17
    |
319 |                 while let Some(edge) = edges.next() {
    |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `for edge in edges`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#while_let_on_iterator

warning: this loop could be written as a `for` loop
   --> src/alignment/poa.rs:314:13
    |
314 |             while let Some(neighbour_node) = neighbour_nodes.next() {
    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `for neighbour_node in neighbour_nodes`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#while_let_on_iterator
    = note: `#[warn(clippy::while_let_on_iterator)]` on by default

warning: casting to the same type is unnecessary (`u32` -> `u32`)
    --> src/alignment/pairwise/banded.rs:1265:70
     |
1265 |                     self.add_gap((r as u32, c as u32), (rows as u32, cols as u32), w);
     |                                                                      ^^^^^^^^^^^ help: try: `cols`
     |
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

warning: casting to the same type is unnecessary (`u32` -> `u32`)
    --> src/alignment/pairwise/banded.rs:1265:57
     |
1265 |                     self.add_gap((r as u32, c as u32), (rows as u32, cols as u32), w);
     |                                                         ^^^^^^^^^^^ help: try: `rows`
     |
     = 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