Moved rest of skalo code into ska, using Indel command runs the code … #239
jhellewell14Annotations
80 warnings
|
missing documentation for a function:
src/skalo_read_graph.rs#L6
warning: missing documentation for a function
--> src/skalo_read_graph.rs:6:1
|
6 | / pub fn build_sequences<'a>(
7 | | len_kmer: usize,
8 | | all_kmers: &HashMap<u128, HashMap<u128, u32>>,
9 | | start_kmers: &HashSet<u128>,
10 | | end_kmers: &HashSet<u128>,
11 | | index_map: &'a HashMap<u32, String>,
12 | | ) -> HashMap<String, Vec<VariantInfo<'a>>> {
| |__________________________________________^
|
|
missing documentation for a function:
src/skalo_utils.rs#L192
warning: missing documentation for a function
--> src/skalo_utils.rs:192:1
|
192 | / pub fn filter_output_sequences(
193 | | variant_groups: HashMap<String, Vec<VariantInfo>>,
194 | | len_kmer: usize,
195 | | all_samples: Vec<String>,
... |
199 | | input_name: &str,
200 | | ) {
| |_^
|
|
missing documentation for a function:
src/skalo_utils.rs#L132
warning: missing documentation for a function
--> src/skalo_utils.rs:132:1
|
132 | / pub fn identify_good_kmers(
133 | | len_kmer: usize,
134 | | all_kmers: &HashMap<u128, HashMap<u128, u32>>,
135 | | index_map: &HashMap<u32, String>,
136 | | ) -> (HashSet<u128>, HashSet<u128>) {
| |___________________________________^
|
|
missing documentation for an associated function:
src/skalo_utils.rs#L111
warning: missing documentation for an associated function
--> src/skalo_utils.rs:111:5
|
111 | / pub fn new(
112 | | //entry_kmer: u128,
113 | | //exit_kmer: u128,
114 | | sequence: String,
... |
118 | | maj_samples: HashSet<&'a str>,
119 | | ) -> Self {
| |_____________^
|
|
missing documentation for a struct field:
src/skalo_utils.rs#L107
warning: missing documentation for a struct field
--> src/skalo_utils.rs:107:5
|
107 | pub maj_samples: HashSet<&'a str>,
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
|
missing documentation for a struct field:
src/skalo_utils.rs#L106
warning: missing documentation for a struct field
--> src/skalo_utils.rs:106:5
|
106 | pub count_samples: HashMap<&'a str, i32>,
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
|
missing documentation for a struct field:
src/skalo_utils.rs#L105
warning: missing documentation for a struct field
--> src/skalo_utils.rs:105:5
|
105 | pub visited_nodes: HashSet<u128>,
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
|
missing documentation for a struct field:
src/skalo_utils.rs#L104
warning: missing documentation for a struct field
--> src/skalo_utils.rs:104:5
|
104 | pub is_snp: bool,
| ^^^^^^^^^^^^^^^^
|
|
missing documentation for a struct field:
src/skalo_utils.rs#L103
warning: missing documentation for a struct field
--> src/skalo_utils.rs:103:5
|
103 | pub sequence: String,
| ^^^^^^^^^^^^^^^^^^^^
|
|
missing documentation for a function:
src/skalo_utils.rs#L84
warning: missing documentation for a function
--> src/skalo_utils.rs:84:1
|
84 | pub fn get_last_nucleotide(encoded_kmer: u128) -> char {
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
|
missing documentation for a function:
src/skalo_utils.rs#L68
warning: missing documentation for a function
--> src/skalo_utils.rs:68:1
|
68 | pub fn decode_kmer(encoded: u128, k: usize) -> String {
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
|
missing documentation for a function:
src/skalo_utils.rs#L45
warning: missing documentation for a function
--> src/skalo_utils.rs:45:1
|
45 | pub fn encode_kmer(kmer: &str) -> u128 {
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
|
missing documentation for a function:
src/skalo_utils.rs#L18
warning: missing documentation for a function
--> src/skalo_utils.rs:18:1
|
18 | pub fn rev_compl_u128(kmer: u128, k: usize) -> u128 {
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
|
missing documentation for a function:
src/skalo_utils.rs#L5
warning: missing documentation for a function
--> src/skalo_utils.rs:5:1
|
5 | pub fn rev_compl(seq: &str) -> String {
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
|
missing documentation for a module:
src/lib.rs#L437
warning: missing documentation for a module
--> src/lib.rs:437:1
|
437 | pub mod skalo_read_graph;
| ^^^^^^^^^^^^^^^^^^^^^^^^
|
|
missing documentation for a module:
src/lib.rs#L434
warning: missing documentation for a module
--> src/lib.rs:434:1
|
434 | pub mod skalo_utils;
| ^^^^^^^^^^^^^^^^^^^
|
note: the lint level is defined here
--> src/lib.rs:406:9
|
406 | #![warn(missing_docs)]
| ^^^^^^^^^^^^
|
|
casting to the same type is unnecessary (`f32` -> `f32`):
src/skalo_read_graph.rs#L234
warning: casting to the same type is unnecessary (`f32` -> `f32`)
--> src/skalo_read_graph.rs:234:22
|
234 | let union_size = (set1.len() as f32 + set2.len() as f32 - intersection_size) as f32;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `(set1.len() as f32 + set2.len() as f32 - intersection_size)`
|
= 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
|
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this expression creates a reference which is immediately dereferenced by the compiler:
src/skalo_read_graph.rs#L132
warning: this expression creates a reference which is immediately dereferenced by the compiler
--> src/skalo_read_graph.rs:132:56
|
132 | ... majrule_samples.insert(&sample);
| ^^^^^^^ help: change this to: `sample`
|
= 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
|
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using `clone` on type `u128` which implements the `Copy` trait:
src/skalo_read_graph.rs#L109
warning: using `clone` on type `u128` which implements the `Copy` trait
--> src/skalo_read_graph.rs:109:37
|
109 | previous_kmer = good_next[0].clone();
| ^^^^^^^^^^^^^^^^^^^^ help: try removing the `clone` call: `good_next[0]`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
|
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using `clone` on type `u128` which implements the `Copy` trait:
src/skalo_read_graph.rs#L90
warning: using `clone` on type `u128` which implements the `Copy` trait
--> src/skalo_read_graph.rs:90:48
|
90 | ... good_next.push(kmer2.clone());
| ^^^^^^^^^^^^^ help: try removing the `clone` call: `kmer2`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
|
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using `clone` on type `u128` which implements the `Copy` trait:
src/skalo_read_graph.rs#L87
warning: using `clone` on type `u128` which implements the `Copy` trait
--> src/skalo_read_graph.rs:87:48
|
87 | ... good_next.push(kmer2.clone());
| ^^^^^^^^^^^^^ help: try removing the `clone` call: `kmer2`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
|
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using `clone` on type `u128` which implements the `Copy` trait:
src/skalo_read_graph.rs#L70
warning: using `clone` on type `u128` which implements the `Copy` trait
--> src/skalo_read_graph.rs:70:48
|
70 | ... kmer2_to_test.push(kmer2.clone());
| ^^^^^^^^^^^^^ help: try dereferencing it: `*kmer2`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
|
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using `clone` on type `u128` which implements the `Copy` trait:
src/skalo_read_graph.rs#L54
warning: using `clone` on type `u128` which implements the `Copy` trait
--> src/skalo_read_graph.rs:54:43
|
54 | let mut previous_kmer: u128 = next_kmer.clone();
| ^^^^^^^^^^^^^^^^^ help: try dereferencing it: `*next_kmer`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
|
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using `clone` on type `u128` which implements the `Copy` trait:
src/skalo_read_graph.rs#L52
warning: using `clone` on type `u128` which implements the `Copy` trait
--> src/skalo_read_graph.rs:52:28
|
52 | visited.insert(next_kmer.clone());
| ^^^^^^^^^^^^^^^^^ help: try dereferencing it: `*next_kmer`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
|
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using `clone` on type `u128` which implements the `Copy` trait:
src/skalo_read_graph.rs#L51
warning: using `clone` on type `u128` which implements the `Copy` trait
--> src/skalo_read_graph.rs:51:28
|
51 | visited.insert(kmer.clone());
| ^^^^^^^^^^^^ help: try dereferencing it: `*kmer`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
|
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using `clone` on type `u128` which implements the `Copy` trait:
src/skalo_read_graph.rs#L33
warning: using `clone` on type `u128` which implements the `Copy` trait
--> src/skalo_read_graph.rs:33:49
|
33 | let next_nucl = get_last_nucleotide(next_kmer.clone());
| ^^^^^^^^^^^^^^^^^ help: try dereferencing it: `*next_kmer`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
|
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using `clone` on type `u128` which implements the `Copy` trait:
src/skalo_read_graph.rs#L32
warning: using `clone` on type `u128` which implements the `Copy` trait
--> src/skalo_read_graph.rs:32:44
|
32 | let mut sequence = decode_kmer(kmer.clone(), len_kmer_graph);
| ^^^^^^^^^^^^ help: try dereferencing it: `*kmer`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
|
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comparison to empty slice:
src/skalo_utils.rs#L507
warning: comparison to empty slice
--> src/skalo_utils.rs:507:12
|
507 | if middle_bases == "" {
| ^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `middle_bases.is_empty()`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#comparison_to_empty
= note: `#[warn(clippy::comparison_to_empty)]` on by default
|
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returning the result of a `let` binding from a block:
src/skalo_utils.rs#L443
warning: returning the result of a `let` binding from a block
--> src/skalo_utils.rs:443:5
|
442 | let ratio_missing = missing_samples / nb_total as f32;
| ------------------------------------------------------ unnecessary `let` binding
443 | ratio_missing
| ^^^^^^^^^^^^^
|
= 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
|
442 ~
443 ~ missing_samples / nb_total as f32
|
|
|
the variable `state` is used as a loop counter:
src/skalo_utils.rs#L326
warning: the variable `state` is used as a loop counter
--> src/skalo_utils.rs:326:21
|
326 | for variant in vec_variants.iter().take(2) {
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider using: `for (state, variant) in vec_variants.iter().take(2).enumerate()`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_counter_loop
= note: `#[warn(clippy::explicit_counter_loop)]` on by default
|
|
using `clone` on type `u128` which implements the `Copy` trait:
src/skalo_utils.rs#L156
warning: using `clone` on type `u128` which implements the `Copy` trait
--> src/skalo_utils.rs:156:47
|
156 | let dna = decode_kmer(kmer.clone(), len_kmer_graph);
| ^^^^^^^^^^^^ help: try dereferencing it: `*kmer`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
|
|
using `clone` on type `u128` which implements the `Copy` trait:
src/skalo_utils.rs#L154
warning: using `clone` on type `u128` which implements the `Copy` trait
--> src/skalo_utils.rs:154:44
|
154 | start_kmers.insert(kmer.clone());
| ^^^^^^^^^^^^ help: try dereferencing it: `*kmer`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
|
|
unnecessary use of `to_string`:
src/io_utils.rs#L256
warning: unnecessary use of `to_string`
--> src/io_utils.rs:256:53
|
256 | let rc_encoded_kmer_2 = encode_kmer(&rc_kmer[1..].to_string());
| ^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `&rc_kmer[1..]`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_to_owned
|
|
unnecessary use of `to_string`:
src/io_utils.rs#L255
warning: unnecessary use of `to_string`
--> src/io_utils.rs:255:53
|
255 | let rc_encoded_kmer_1 = encode_kmer(&rc_kmer[..full_kmer.len() - 1].to_string());
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `&rc_kmer[..full_kmer.len() - 1]`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_to_owned
|
|
using `clone` on type `u32` which implements the `Copy` trait:
src/io_utils.rs#L252
warning: using `clone` on type `u32` which implements the `Copy` trait
--> src/io_utils.rs:252:45
|
252 | .insert(encoded_kmer_2, value_index.clone());
| ^^^^^^^^^^^^^^^^^^^ help: try removing the `clone` call: `value_index`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
|
|
unnecessary use of `to_string`:
src/io_utils.rs#L244
warning: unnecessary use of `to_string`
--> src/io_utils.rs:244:50
|
244 | let encoded_kmer_2 = encode_kmer(&full_kmer[1..].to_string());
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `&full_kmer[1..]`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_to_owned
|
|
unnecessary use of `to_string`:
src/io_utils.rs#L243
warning: unnecessary use of `to_string`
--> src/io_utils.rs:243:50
|
243 | let encoded_kmer_1 = encode_kmer(&full_kmer[..full_kmer.len() - 1].to_string());
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `&full_kmer[..full_kmer.len() - 1]`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_to_owned
= note: `#[warn(clippy::unnecessary_to_owned)]` on by default
|
|
using `clone` on type `u32` which implements the `Copy` trait:
src/io_utils.rs#L237
warning: using `clone` on type `u32` which implements the `Copy` trait
--> src/io_utils.rs:237:38
|
237 | index_map.insert(value_index.clone(), str_sample_id.to_string());
| ^^^^^^^^^^^^^^^^^^^ help: try removing the `clone` call: `value_index`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
|
|
using `clone` on type `u32` which implements the `Copy` trait:
src/io_utils.rs#L236
warning: using `clone` on type `u32` which implements the `Copy` trait
--> src/io_utils.rs:236:67
|
236 | all_indexes.insert(str_sample_id.to_string(), value_index.clone());
| ^^^^^^^^^^^^^^^^^^^ help: try removing the `clone` call: `value_index`
|
= 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
|
|
very complex type used. Consider factoring parts into `type` definitions:
src/io_utils.rs#L158
warning: very complex type used. Consider factoring parts into `type` definitions
--> src/io_utils.rs:158:6
|
158 | ) -> (
| ______^
159 | | usize,
160 | | Vec<String>,
161 | | HashMap<u128, HashMap<u128, u32>>,
162 | | HashMap<u32, String>,
163 | | ) {
| |_^
|
= 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
|
|
the following explicit lifetimes could be elided: 'a:
src/merge_ska_array.rs#L628
warning: the following explicit lifetimes could be elided: 'a
--> src/merge_ska_array.rs:628:6
|
628 | impl<'a, IntT> Iterator for KmerIter<'a, IntT>
| ^^ ^^
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
|
628 - impl<'a, IntT> Iterator for KmerIter<'a, IntT>
628 + impl<IntT> Iterator for KmerIter<'_, IntT>
|
|
|
empty line after doc comment:
src/ska_ref.rs#L110
warning: empty line after doc comment
--> src/ska_ref.rs:110:5
|
110 | / /// Mapping information
111 | |
| |_^
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#empty_line_after_doc_comments
= help: if the empty line is unintentional remove it
help: if the documentation should include the empty line include it in the comment
|
111 | ///
|
|
|
empty line after doc comment:
src/ska_ref.rs#L101
warning: empty line after doc comment
--> src/ska_ref.rs:101:5
|
101 | / /// Input sequence
102 | |
| |_^
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#empty_line_after_doc_comments
= note: `#[warn(clippy::empty_line_after_doc_comments)]` on by default
= help: if the empty line is unintentional remove it
help: if the documentation should include the empty line include it in the comment
|
102 | ///
|
|
|
the following explicit lifetimes could be elided: 'a:
src/ska_ref/idx_check.rs#L50
warning: the following explicit lifetimes could be elided: 'a
--> src/ska_ref/idx_check.rs:50:6
|
50 | impl<'a> Iterator for IdxCheckIter<'a> {
| ^^ ^^
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
|
50 - impl<'a> Iterator for IdxCheckIter<'a> {
50 + impl Iterator for IdxCheckIter<'_> {
|
|
|
the following explicit lifetimes could be elided: 'a:
src/ska_dict/bit_encoding.rs#L185
warning: the following explicit lifetimes could be elided: 'a
--> src/ska_dict/bit_encoding.rs:185:6
|
185 | impl<'a> UInt<'a> for u128 {
| ^^ ^^
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
|
185 - impl<'a> UInt<'a> for u128 {
185 + impl UInt<'_> for u128 {
|
|
|
the following explicit lifetimes could be elided: 'a:
src/ska_dict/bit_encoding.rs#L127
warning: the following explicit lifetimes could be elided: 'a
--> src/ska_dict/bit_encoding.rs:127:6
|
127 | impl<'a> UInt<'a> for u64 {
| ^^ ^^
|
= 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
|
127 - impl<'a> UInt<'a> for u64 {
127 + impl UInt<'_> for u64 {
|
|
|
operator precedence can trip the unwary:
src/ska_dict/bloom_filter.rs#L63
warning: operator precedence can trip the unwary
--> src/ska_dict/bloom_filter.rs:63:9
|
63 | / 1 << (key & 63)
64 | | | 1 << ((key >> 6) & 63)
| |____________________________________^ help: consider parenthesizing your expression: `(1 << (key & 63)) | (1 << ((key >> 6) & 63))`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bloom_filter.rs#L63
warning: operator precedence can trip the unwary
--> src/ska_dict/bloom_filter.rs:63:9
|
63 | / 1 << (key & 63)
64 | | | 1 << ((key >> 6) & 63)
65 | | | 1 << ((key >> 12) & 63)
| |_____________________________________^
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
help: consider parenthesizing your expression
|
63 ~ 1 << (key & 63)
64 + | 1 << ((key >> 6) & 63) | (1 << ((key >> 12) & 63))
|
|
|
operator precedence can trip the unwary:
src/ska_dict/bloom_filter.rs#L63
warning: operator precedence can trip the unwary
--> src/ska_dict/bloom_filter.rs:63:9
|
63 | / 1 << (key & 63)
64 | | | 1 << ((key >> 6) & 63)
65 | | | 1 << ((key >> 12) & 63)
66 | | | 1 << ((key >> 18) & 63)
| |_____________________________________^
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
help: consider parenthesizing your expression
|
63 ~ 1 << (key & 63)
64 + | 1 << ((key >> 6) & 63)
65 + | 1 << ((key >> 12) & 63) | (1 << ((key >> 18) & 63))
|
|
|
operator precedence can trip the unwary:
src/ska_dict/bloom_filter.rs#L63
warning: operator precedence can trip the unwary
--> src/ska_dict/bloom_filter.rs:63:9
|
63 | / 1 << (key & 63)
64 | | | 1 << ((key >> 6) & 63)
65 | | | 1 << ((key >> 12) & 63)
66 | | | 1 << ((key >> 18) & 63)
67 | | | 1 << ((key >> 24) & 63)
| |_____________________________________^
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
help: consider parenthesizing your expression
|
63 ~ 1 << (key & 63)
64 + | 1 << ((key >> 6) & 63)
65 + | 1 << ((key >> 12) & 63)
66 + | 1 << ((key >> 18) & 63) | (1 << ((key >> 24) & 63))
|
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L200
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:200:17
|
200 | self = (self >> 64 & 0x0000000000000000FFFFFFFFFFFFFFFF)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 64) & 0x0000000000000000FFFFFFFFFFFFFFFF`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L200
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:200:16
|
200 | self = (self >> 64 & 0x0000000000000000FFFFFFFFFFFFFFFF)
| ________________^
201 | | | (self & 0x0000000000000000FFFFFFFFFFFFFFFF) << 64;
| |_______________________________________________________________^ help: consider parenthesizing your expression: `(self >> 64 & 0x0000000000000000FFFFFFFFFFFFFFFF) | ((self & 0x0000000000000000FFFFFFFFFFFFFFFF) << 64)`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L198
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:198:17
|
198 | self = (self >> 32 & 0x00000000FFFFFFFF00000000FFFFFFFF)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 32) & 0x00000000FFFFFFFF00000000FFFFFFFF`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L198
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:198:16
|
198 | self = (self >> 32 & 0x00000000FFFFFFFF00000000FFFFFFFF)
| ________________^
199 | | | (self & 0x00000000FFFFFFFF00000000FFFFFFFF) << 32;
| |_______________________________________________________________^ help: consider parenthesizing your expression: `(self >> 32 & 0x00000000FFFFFFFF00000000FFFFFFFF) | ((self & 0x00000000FFFFFFFF00000000FFFFFFFF) << 32)`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L196
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:196:17
|
196 | self = (self >> 16 & 0x0000FFFF0000FFFF0000FFFF0000FFFF)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 16) & 0x0000FFFF0000FFFF0000FFFF0000FFFF`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L196
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:196:16
|
196 | self = (self >> 16 & 0x0000FFFF0000FFFF0000FFFF0000FFFF)
| ________________^
197 | | | (self & 0x0000FFFF0000FFFF0000FFFF0000FFFF) << 16;
| |_______________________________________________________________^ help: consider parenthesizing your expression: `(self >> 16 & 0x0000FFFF0000FFFF0000FFFF0000FFFF) | ((self & 0x0000FFFF0000FFFF0000FFFF0000FFFF) << 16)`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L194
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:194:17
|
194 | self = (self >> 8 & 0x00FF00FF00FF00FF00FF00FF00FF00FF)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 8) & 0x00FF00FF00FF00FF00FF00FF00FF00FF`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L194
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:194:16
|
194 | self = (self >> 8 & 0x00FF00FF00FF00FF00FF00FF00FF00FF)
| ________________^
195 | | | (self & 0x00FF00FF00FF00FF00FF00FF00FF00FF) << 8;
| |______________________________________________________________^ help: consider parenthesizing your expression: `(self >> 8 & 0x00FF00FF00FF00FF00FF00FF00FF00FF) | ((self & 0x00FF00FF00FF00FF00FF00FF00FF00FF) << 8)`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L192
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:192:17
|
192 | self = (self >> 4 & 0x0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 4) & 0x0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L192
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:192:16
|
192 | self = (self >> 4 & 0x0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F)
| ________________^
193 | | | (self & 0x0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F) << 4;
| |______________________________________________________________^ help: consider parenthesizing your expression: `(self >> 4 & 0x0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F) | ((self & 0x0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F) << 4)`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L190
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:190:17
|
190 | self = (self >> 2 & 0x33333333333333333333333333333333)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 2) & 0x33333333333333333333333333333333`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L190
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:190:16
|
190 | self = (self >> 2 & 0x33333333333333333333333333333333)
| ________________^
191 | | | (self & 0x33333333333333333333333333333333) << 2;
| |______________________________________________________________^ help: consider parenthesizing your expression: `(self >> 2 & 0x33333333333333333333333333333333) | ((self & 0x33333333333333333333333333333333) << 2)`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L136
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:136:17
|
136 | self = (self >> 32 & 0x00000000FFFFFFFF) | (self & 0x00000000FFFFFFFF) << 32;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 32) & 0x00000000FFFFFFFF`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L136
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:136:16
|
136 | self = (self >> 32 & 0x00000000FFFFFFFF) | (self & 0x00000000FFFFFFFF) << 32;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 32 & 0x00000000FFFFFFFF) | ((self & 0x00000000FFFFFFFF) << 32)`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L135
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:135:17
|
135 | self = (self >> 16 & 0x0000FFFF0000FFFF) | (self & 0x0000FFFF0000FFFF) << 16;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 16) & 0x0000FFFF0000FFFF`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L135
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:135:16
|
135 | self = (self >> 16 & 0x0000FFFF0000FFFF) | (self & 0x0000FFFF0000FFFF) << 16;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 16 & 0x0000FFFF0000FFFF) | ((self & 0x0000FFFF0000FFFF) << 16)`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L134
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:134:17
|
134 | self = (self >> 8 & 0x00FF00FF00FF00FF) | (self & 0x00FF00FF00FF00FF) << 8;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 8) & 0x00FF00FF00FF00FF`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L134
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:134:16
|
134 | self = (self >> 8 & 0x00FF00FF00FF00FF) | (self & 0x00FF00FF00FF00FF) << 8;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 8 & 0x00FF00FF00FF00FF) | ((self & 0x00FF00FF00FF00FF) << 8)`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L133
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:133:17
|
133 | self = (self >> 4 & 0x0F0F0F0F0F0F0F0F) | (self & 0x0F0F0F0F0F0F0F0F) << 4;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 4) & 0x0F0F0F0F0F0F0F0F`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L133
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:133:16
|
133 | self = (self >> 4 & 0x0F0F0F0F0F0F0F0F) | (self & 0x0F0F0F0F0F0F0F0F) << 4;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 4 & 0x0F0F0F0F0F0F0F0F) | ((self & 0x0F0F0F0F0F0F0F0F) << 4)`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L132
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:132:17
|
132 | self = (self >> 2 & 0x3333333333333333) | (self & 0x3333333333333333) << 2;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 2) & 0x3333333333333333`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L132
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:132:16
|
132 | self = (self >> 2 & 0x3333333333333333) | (self & 0x3333333333333333) << 2;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 2 & 0x3333333333333333) | ((self & 0x3333333333333333) << 2)`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/split_kmer.rs#L210
warning: operator precedence can trip the unwary
--> src/ska_dict/split_kmer.rs:210:34
|
210 | self.rc_upper = (self.rc_upper >> 2
| __________________________________^
211 | | | (IntT::from_encoded_base(rc_base(new_base))) << (2 * ((half_k * 2) - 1)))
| |______________________________________________________________________________________________^ help: consider parenthesizing your expression: `(self.rc_upper >> 2) | ((IntT::from_encoded_base(rc_base(new_base))) << (2 * ((half_k * 2) - 1)))`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/split_kmer.rs#L206
warning: operator precedence can trip the unwary
--> src/ska_dict/split_kmer.rs:206:34
|
206 | self.rc_lower = (self.rc_lower >> 2
| __________________________________^
207 | | | ((IntT::from_encoded_base(self.rc_middle_base)) << (2 * (half_k - 1))))
| |____________________________________________________________________________________________^ help: consider parenthesizing your expression: `(self.rc_lower >> 2) | ((IntT::from_encoded_base(self.rc_middle_base)) << (2 * (half_k - 1)))`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
|
|
operator precedence can trip the unwary:
src/ska_dict/split_kmer.rs#L199
warning: operator precedence can trip the unwary
--> src/ska_dict/split_kmer.rs:199:27
|
199 | self.upper = (self.upper << 2
| ___________________________^
200 | | | (IntT::from_encoded_base(self.middle_base) << (half_k * 2)))
| |_____________________________________________________________________________^ help: consider parenthesizing your expression: `(self.upper << 2) | (IntT::from_encoded_base(self.middle_base) << (half_k * 2))`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
= note: `#[warn(clippy::precedence)]` on by default
|
|
clippy_check
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
clippy_check
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/
|
|
clippy_check
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/
|
|
clippy_check
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/
|
|
clippy_check
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/
|