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_borrows_for_generic_args

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_borrows_for_generic_args

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_borrows_for_generic_args

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_borrows_for_generic_args = note: `#[warn(clippy::needless_borrows_for_generic_args)]` 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: use of `or_insert_with` to construct default value --> src/data_structures/annot_map.rs:176:14 | 176 | .or_insert_with(IntervalTree::new); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `or_default()` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unwrap_or_default

warning: use of `or_insert_with` to construct default value --> src/data_structures/annot_map.rs:112:14 | 112 | .or_insert_with(IntervalTree::new); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `or_default()` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unwrap_or_default

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: use of `or_insert_with` to construct default value --> src/alignment/sparse.rs:347:14 | 347 | .or_insert_with(Vec::new) | ^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `or_default()` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unwrap_or_default = note: `#[warn(clippy::unwrap_or_default)]` on by default

warning: using `clone` on type `TracebackCell` which implements the `Copy` trait --> src/alignment/poa.rs:704:13 | 704 | traceback.get(traceback.last.index() + 1, n).clone(), | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try dereferencing it: `*traceback.get(traceback.last.index() + 1, n)` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy

warning: using `clone` on type `TracebackCell` which implements the `Copy` trait --> src/alignment/poa.rs:690:17 | 690 | traceback.get(traceback.last.index() + 1, j).clone(), | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try dereferencing it: `*traceback.get(traceback.last.index() + 1, j)` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy

warning: the loop variable `j` is used to index `max_in_column` --> src/alignment/poa.rs:684:18 | 684 | for j in 0..n + 1 { | ^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_range_loop help: consider using an iterator and enumerate() | 684 | for (j, <item>) in max_in_column.iter().enumerate().take(n + 1) { | ~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

warning: using `clone` on type `i32` which implements the `Copy` trait --> src/alignment/poa.rs:531:31 | 531 | 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

warning: this loop could be written as a `for` loop --> src/alignment/poa.rs:530:17 | 530 | 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:525:13 | 525 | 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: using `clone` on type `AlignmentOperation` which implements the `Copy` trait --> src/alignment/poa.rs:338:22 | 338 | ops.push(self.get(i, j).op.clone()); | ^^^^^^^^^^^^^^^^^^^^^^^^^ help: try removing the `clone` call: `self.get(i, j).op` | = 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: length comparison to zero --> src/alignment/poa.rs:300:65 | 300 | if !(self.matrix[i].1 > j || self.matrix[i].2 <= j) && (self.matrix[i].0.len() > 0) { | ^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `!is_empty` is clearer and more explicit: `!self.matrix[i].0.is_empty()` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero = note: `#[warn(clippy::len_zero)]` on by default

warning: unneeded `return` statement --> src/alignment/poa.rs:302:13 | 302 | return &self.matrix[i].0[real_position]; | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = 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` | 302 - return &self.matrix[i].0[real_position]; 302 + &self.matrix[i].0[real_position] |

warning: the loop variable `current_seq` is only used to index `seq_pretty` --> src/alignment/poa.rs:135:36 | 135 | for current_seq in 0..sequences.len() { | ^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_range_loop = note: `#[warn(clippy::needless_range_loop)]` on by default help: consider using an iterator | 135 | for <item> in seq_pretty.iter_mut().take(sequences.len()) { | ~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

warning: casting a character literal to `u8` truncates --> src/alignment/poa.rs:132:33 | 132 | con_pretty.push('-' as u8); | ^^^^^^^^^ help: use a byte literal instead: `b'-'` | = note: `char` is four bytes wide, but `u8` is a single byte = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#char_lit_as_u8

warning: casting a character literal to `u8` truncates --> src/alignment/poa.rs:126:33 | 126 | con_pretty.push('-' as u8); | ^^^^^^^^^ help: use a byte literal instead: `b'-'` | = note: `char` is four bytes wide, but `u8` is a single byte = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#char_lit_as_u8

warning: casting a character literal to `u8` truncates --> src/alignment/poa.rs:121:50 | 121 | seq_pretty[current_seq].push('-' as u8); | ^^^^^^^^^ help: use a byte literal instead: `b'-'` | = note: `char` is four bytes wide, but `u8` is a single byte = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#char_lit_as_u8

warning: casting a character literal to `u8` truncates --> src/alignment/poa.rs:115:50 | 115 | seq_pretty[current_seq].push('-' as u8); | ^^^^^^^^^ help: use a byte literal instead: `b'-'` | = note: `char` is four bytes wide, but `u8` is a single byte = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#char_lit_as_u8 = note: `#[warn(clippy::char_lit_as_u8)]` 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

warning: manual implementation of `Option::map` --> src/alignment/distance.rs:166:9 | 166 | / if let Some(x) = editdistancek::edit_distance_bounded( 167 | | alpha, 168 | | beta, 169 | | min(k as usize, max(alpha.len(), beta.len())), ... | 173 | | None 174 | | } | |_________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_map = note: `#[warn(clippy::manual_map)]` on by default help: try | 166 ~ editdistancek::edit_distance_bounded( 167 + alpha, 168 + beta, 169 + min(k as usize, max(alpha.len(), beta.len())), 170 + ).map(|x| x as u32) |

warning: unused import: `XYEmission` --> src/stats/pairhmm/pairhmm.rs:20:63 | 20 | EmissionParameters, GapParameters, StartEndGapParameters, XYEmission, | ^^^^^^^^^^ | = note: `#[warn(unused_imports)]` on by default

warning: 'test' may be misspelled as 'tests' --> src/data_structures/smallints.rs:198:7 | 198 | #[cfg(tests)] | ^^^^^ help: did you mean: `test` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#maybe_misused_cfg = note: `#[warn(clippy::maybe_misused_cfg)]` on by default