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Made skalo command commensurable with the file input logic that runs …

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GitHub Actions / clippy succeeded Jan 15, 2025 in 1s

clippy

84 warnings

Details

Results

Message level Amount
Internal compiler error 0
Error 0
Warning 84
Note 0
Help 0

Versions

  • rustc 1.86.0-nightly (8361aef0d 2025-01-14)
  • cargo 1.86.0-nightly (088d49608 2025-01-10)
  • clippy 0.1.86 (8361aef0d7 2025-01-14)

Annotations

Check warning on line 286 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a function

warning: missing documentation for a function
   --> src/skalo_utils.rs:286:1
    |
286 | pub fn convert_combined(input: &str, k: usize) -> Result<String, String> {
    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Check warning on line 278 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a function

warning: missing documentation for a function
   --> src/skalo_utils.rs:278:1
    |
278 | pub fn count_occurrences(vec: &Vec<u32>) -> HashMap<u32, i32> {
    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Check warning on line 271 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a function

warning: missing documentation for a function
   --> src/skalo_utils.rs:271:1
    |
271 | pub fn jaccard_similarity(set1: &HashSet<&str>, set2: &HashSet<&str>) -> f32 {
    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Check warning on line 250 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a function

warning: missing documentation for a function
   --> src/skalo_utils.rs:250:1
    |
250 | pub fn check_homopolymer(limit_n: u32, first_kmer: String, l_middle_bases: Vec<String>) -> bool {
    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Check warning on line 230 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a function

warning: missing documentation for a function
   --> src/skalo_utils.rs:230:1
    |
230 | pub fn test_multiple_positions(l_middles: Vec<String>, last_kmer: String) -> bool {
    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Check warning on line 164 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a function

warning: missing documentation for a function
   --> src/skalo_utils.rs:160:1
    |
160 | / pub fn collect_middle_bases(
161 | |     vec_variants: Vec<VariantInfo>,
162 | |     len_k_graph: usize,
163 | |     use_rev_complement: bool,
164 | | ) -> (Vec<String>, String) {
    | |__________________________^

Check warning on line 140 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a function

warning: missing documentation for a function
   --> src/skalo_utils.rs:140:1
    |
140 | pub fn calculate_ratio_missing(nb_total: usize, vec_variants: Vec<VariantInfo>) -> f32 {
    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Check warning on line 131 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a function

warning: missing documentation for a function
   --> src/skalo_utils.rs:131:1
    |
131 | pub fn compare_samples(str_1: &str, str_2: &str) -> bool {
    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Check warning on line 118 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for an associated function

warning: missing documentation for an associated function
   --> src/skalo_utils.rs:110:5
    |
110 | /     pub fn new(
111 | |         //entry_kmer: u128,
112 | |         //exit_kmer: u128,
113 | |         sequence: String,
...   |
117 | |         maj_samples: HashSet<&'a str>,
118 | |     ) -> Self {
    | |_____________^

Check warning on line 106 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a struct field

warning: missing documentation for a struct field
   --> src/skalo_utils.rs:106:5
    |
106 |     pub maj_samples: HashSet<&'a str>,
    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Check warning on line 105 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a struct field

warning: missing documentation for a struct field
   --> src/skalo_utils.rs:105:5
    |
105 |     pub count_samples: HashMap<&'a str, i32>,
    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Check warning on line 104 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a struct field

warning: missing documentation for a struct field
   --> src/skalo_utils.rs:104:5
    |
104 |     pub visited_nodes: HashSet<u128>,
    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Check warning on line 103 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a struct field

warning: missing documentation for a struct field
   --> src/skalo_utils.rs:103:5
    |
103 |     pub is_snp: bool,
    |     ^^^^^^^^^^^^^^^^

Check warning on line 102 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a struct field

warning: missing documentation for a struct field
   --> src/skalo_utils.rs:102:5
    |
102 |     pub sequence: String,
    |     ^^^^^^^^^^^^^^^^^^^^

Check warning on line 83 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a function

warning: missing documentation for a function
  --> src/skalo_utils.rs:83:1
   |
83 | pub fn get_last_nucleotide(encoded_kmer: u128) -> char {
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Check warning on line 67 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a function

warning: missing documentation for a function
  --> src/skalo_utils.rs:67:1
   |
67 | pub fn decode_kmer_skalo(encoded: u128, k: usize) -> String {
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Check warning on line 44 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a function

warning: missing documentation for a function
  --> src/skalo_utils.rs:44:1
   |
44 | pub fn encode_kmer(kmer: &str) -> u128 {
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Check warning on line 17 in src/skalo_utils.rs

@github-actions github-actions / clippy

missing documentation for a function

warning: missing documentation for a function
  --> src/skalo_utils.rs:17:1
   |
17 | pub fn rev_compl_u128(kmer: u128, k: usize) -> u128 {
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Check warning on line 420 in src/skalo.rs

@github-actions github-actions / clippy

missing documentation for a function

warning: missing documentation for a function
   --> src/skalo.rs:412:1
    |
412 | / pub fn filter_output_sequences(
413 | |     variant_groups: HashMap<String, Vec<VariantInfo>>,
414 | |     len_kmer: usize,
415 | |     all_samples: Vec<String>,
...   |
419 | |     input_name: &str,
420 | | ) {
    | |_^

Check warning on line 193 in src/skalo.rs

@github-actions github-actions / clippy

missing documentation for a function

warning: missing documentation for a function
   --> src/skalo.rs:187:1
    |
187 | / pub fn build_sequences<'a>(
188 | |     len_kmer: usize,
189 | |     all_kmers: &HashMap<u128, HashMap<u128, u32>>,
190 | |     start_kmers: &HashSet<u128>,
191 | |     end_kmers: &HashSet<u128>,
192 | |     index_map: &'a HashMap<u32, String>,
193 | | ) -> HashMap<String, Vec<VariantInfo<'a>>> {
    | |__________________________________________^

Check warning on line 140 in src/skalo.rs

@github-actions github-actions / clippy

missing documentation for a function

warning: missing documentation for a function
   --> src/skalo.rs:136:1
    |
136 | / pub fn identify_good_kmers(
137 | |     len_kmer: usize,
138 | |     all_kmers: &HashMap<u128, HashMap<u128, u32>>,
139 | |     index_map: &HashMap<u32, String>,
140 | | ) -> (HashSet<u128>, HashSet<u128>) {
    | |___________________________________^

Check warning on line 435 in src/lib.rs

@github-actions github-actions / clippy

missing documentation for a module

warning: missing documentation for a module
   --> src/lib.rs:435:1
    |
435 | pub mod skalo_utils;
    | ^^^^^^^^^^^^^^^^^^^

Check warning on line 434 in src/lib.rs

@github-actions github-actions / clippy

missing documentation for a module

warning: missing documentation for a module
   --> src/lib.rs:434:1
    |
434 | pub mod skalo;
    | ^^^^^^^^^^^^^
    |
note: the lint level is defined here
   --> src/lib.rs:406:9
    |
406 | #![warn(missing_docs)]
    |         ^^^^^^^^^^^^

Check warning on line 274 in src/skalo_utils.rs

@github-actions github-actions / clippy

casting to the same type is unnecessary (`f32` -> `f32`)

warning: casting to the same type is unnecessary (`f32` -> `f32`)
   --> src/skalo_utils.rs:274:22
    |
274 |     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

Check warning on line 221 in src/skalo_utils.rs

@github-actions github-actions / clippy

comparison to empty slice

warning: comparison to empty slice
   --> src/skalo_utils.rs:221:12
    |
221 |         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