[INFO] fetching crate isONclust3 0.3.0...
[INFO] checking isONclust3-0.3.0 against master#642c19bfc3a5c1de985bf5d0cc8207ac9d22708a for pr-148577
[INFO] extracting crate isONclust3 0.3.0 into /workspace/builds/worker-0-tc1/source
[INFO] started tweaking crates.io crate isONclust3 0.3.0
[INFO] finished tweaking crates.io crate isONclust3 0.3.0
[INFO] tweaked toml for crates.io crate isONclust3 0.3.0 written to /workspace/builds/worker-0-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate isONclust3 0.3.0 on toolchain 642c19bfc3a5c1de985bf5d0cc8207ac9d22708a
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+642c19bfc3a5c1de985bf5d0cc8207ac9d22708a" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate isONclust3 0.3.0 already has a lockfile, it will not be regenerated
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+642c19bfc3a5c1de985bf5d0cc8207ac9d22708a" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[INFO] [stdout] f3b35f77bbe1f0cb250ca481a1c7e107b19e321d7c837f47897343944b268fd7
[INFO] running `Command { std: "docker" "start" "-a" "f3b35f77bbe1f0cb250ca481a1c7e107b19e321d7c837f47897343944b268fd7", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "f3b35f77bbe1f0cb250ca481a1c7e107b19e321d7c837f47897343944b268fd7", kill_on_drop: false }`
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[INFO] [stdout] warning: unused import: `std::collections::HashSet`
[INFO] [stdout]  --> src/generate_sorted_fastq_for_cluster.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::collections::HashSet;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variant `read_ids` should have an upper camel case name
[INFO] [stdout]  --> src/structs.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 |     read_ids(HashSet<T>),
[INFO] [stdout]   |     ^^^^^^^^ help: convert the identifier to upper camel case: `ReadIds`
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(non_camel_case_types)]` (part of `#[warn(nonstandard_style)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variant `mini_seqs` should have an upper camel case name
[INFO] [stdout]  --> src/structs.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 |     mini_seqs(HashSet<U>),
[INFO] [stdout]   |     ^^^^^^^^^ help: convert the identifier to upper camel case: `MiniSeqs`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `Minimizer_hashed` should have an upper camel case name
[INFO] [stdout]   --> src/structs.rs:20:12
[INFO] [stdout]    |
[INFO] [stdout] 20 | pub struct Minimizer_hashed {
[INFO] [stdout]    |            ^^^^^^^^^^^^^^^^ help: convert the identifier to upper camel case: `MinimizerHashed`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `Coord_obj` should have an upper camel case name
[INFO] [stdout]   --> src/structs.rs:48:19
[INFO] [stdout]    |
[INFO] [stdout] 48 | pub(crate) struct Coord_obj{
[INFO] [stdout]    |                   ^^^^^^^^^ help: convert the identifier to upper camel case: `CoordObj`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `FastqRecord_isoncl_init` should have an upper camel case name
[INFO] [stdout]    --> src/structs.rs:103:19
[INFO] [stdout]     |
[INFO] [stdout] 103 | pub(crate) struct FastqRecord_isoncl_init {
[INFO] [stdout]     |                   ^^^^^^^^^^^^^^^^^^^^^^^ help: convert the identifier to upper camel case: `FastqRecordIsonclInit`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `internal_gff` should have an upper camel case name
[INFO] [stdout]    --> src/structs.rs:111:19
[INFO] [stdout]     |
[INFO] [stdout] 111 | pub(crate) struct internal_gff {
[INFO] [stdout]     |                   ^^^^^^^^^^^^ help: convert the identifier to upper camel case: `InternalGff`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::Read`
[INFO] [stdout]   --> src/main.rs:32:5
[INFO] [stdout]    |
[INFO] [stdout] 32 | use std::io::Read;
[INFO] [stdout]    |     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `Seed_Map` should have an upper camel case name
[INFO] [stdout]   --> src/main.rs:43:6
[INFO] [stdout]    |
[INFO] [stdout] 43 | type Seed_Map = FxHashMap<u64, Vec<i32>>; // Change here to any other hash table implementation, e.g.,  HashMap<u64, Vec<i32>, nohash_has...
[INFO] [stdout]    |      ^^^^^^^^ help: convert the identifier to upper camel case: `SeedMap`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `Cluster_ID_Map` should have an upper camel case name
[INFO] [stdout]   --> src/main.rs:44:6
[INFO] [stdout]    |
[INFO] [stdout] 44 | type Cluster_ID_Map = FxHashMap<i32, Vec<i32>>; //  Change here to any other hash table implementation, e.g., HashMap<i32, Vec<i32>,nohas...
[INFO] [stdout]    |      ^^^^^^^^^^^^^^ help: convert the identifier to upper camel case: `ClusterIdMap`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `super::*`
[INFO] [stdout]    --> src/seeding_and_filtering_seeds.rs:432:9
[INFO] [stdout]     |
[INFO] [stdout] 432 |     use super::*;
[INFO] [stdout]     |         ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::collections::HashSet`
[INFO] [stdout]  --> src/generate_sorted_fastq_for_cluster.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::collections::HashSet;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variant `read_ids` should have an upper camel case name
[INFO] [stdout]  --> src/structs.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 |     read_ids(HashSet<T>),
[INFO] [stdout]   |     ^^^^^^^^ help: convert the identifier to upper camel case: `ReadIds`
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(non_camel_case_types)]` (part of `#[warn(nonstandard_style)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variant `mini_seqs` should have an upper camel case name
[INFO] [stdout]  --> src/structs.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 |     mini_seqs(HashSet<U>),
[INFO] [stdout]   |     ^^^^^^^^^ help: convert the identifier to upper camel case: `MiniSeqs`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `Minimizer_hashed` should have an upper camel case name
[INFO] [stdout]   --> src/structs.rs:20:12
[INFO] [stdout]    |
[INFO] [stdout] 20 | pub struct Minimizer_hashed {
[INFO] [stdout]    |            ^^^^^^^^^^^^^^^^ help: convert the identifier to upper camel case: `MinimizerHashed`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `Coord_obj` should have an upper camel case name
[INFO] [stdout]   --> src/structs.rs:48:19
[INFO] [stdout]    |
[INFO] [stdout] 48 | pub(crate) struct Coord_obj{
[INFO] [stdout]    |                   ^^^^^^^^^ help: convert the identifier to upper camel case: `CoordObj`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `FastqRecord_isoncl_init` should have an upper camel case name
[INFO] [stdout]    --> src/structs.rs:103:19
[INFO] [stdout]     |
[INFO] [stdout] 103 | pub(crate) struct FastqRecord_isoncl_init {
[INFO] [stdout]     |                   ^^^^^^^^^^^^^^^^^^^^^^^ help: convert the identifier to upper camel case: `FastqRecordIsonclInit`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `internal_gff` should have an upper camel case name
[INFO] [stdout]    --> src/structs.rs:111:19
[INFO] [stdout]     |
[INFO] [stdout] 111 | pub(crate) struct internal_gff {
[INFO] [stdout]     |                   ^^^^^^^^^^^^ help: convert the identifier to upper camel case: `InternalGff`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::Read`
[INFO] [stdout]   --> src/main.rs:32:5
[INFO] [stdout]    |
[INFO] [stdout] 32 | use std::io::Read;
[INFO] [stdout]    |     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `Seed_Map` should have an upper camel case name
[INFO] [stdout]   --> src/main.rs:43:6
[INFO] [stdout]    |
[INFO] [stdout] 43 | type Seed_Map = FxHashMap<u64, Vec<i32>>; // Change here to any other hash table implementation, e.g.,  HashMap<u64, Vec<i32>, nohash_has...
[INFO] [stdout]    |      ^^^^^^^^ help: convert the identifier to upper camel case: `SeedMap`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `Cluster_ID_Map` should have an upper camel case name
[INFO] [stdout]   --> src/main.rs:44:6
[INFO] [stdout]    |
[INFO] [stdout] 44 | type Cluster_ID_Map = FxHashMap<i32, Vec<i32>>; //  Change here to any other hash table implementation, e.g., HashMap<i32, Vec<i32>,nohas...
[INFO] [stdout]    |      ^^^^^^^^^^^^^^ help: convert the identifier to upper camel case: `ClusterIdMap`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rayon::prelude`
[INFO] [stdout]  --> src/clustering.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use rayon::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rayon::prelude`
[INFO] [stdout]  --> src/seeding_and_filtering_seeds.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use rayon::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rayon::prelude`
[INFO] [stdout]  --> src/gff_handling.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 9 | use rayon::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `BufRead`
[INFO] [stdout]  --> src/gff_handling.rs:3:26
[INFO] [stdout]   |
[INFO] [stdout] 3 | use std::io::{BufReader, BufRead};
[INFO] [stdout]   |                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rayon::prelude`
[INFO] [stdout]  --> src/write_output.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 9 | use rayon::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/clustering.rs:97:17
[INFO] [stdout]    |
[INFO] [stdout] 97 |             let mut shared_perc: f64;
[INFO] [stdout]    |                 ----^^^^^^^^^^^
[INFO] [stdout]    |                 |
[INFO] [stdout]    |                 help: remove this `mut`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/clustering.rs:179:17
[INFO] [stdout]     |
[INFO] [stdout] 179 |             let mut cl_vec= clusters_map.get_mut(seed_hash).unwrap();
[INFO] [stdout]     |                 ----^^^^^^
[INFO] [stdout]     |                 |
[INFO] [stdout]     |                 help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `verbose`
[INFO] [stdout]    --> src/clustering.rs:192:209
[INFO] [stdout]     |
[INFO] [stdout] 192 | ...seed_infos_vec: &mut [i32], verbose:bool ){
[INFO] [stdout]     |                                ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_verbose`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `min_shared_minis`
[INFO] [stdout]    --> src/clustering.rs:268:90
[INFO] [stdout]     |
[INFO] [stdout] 268 | ...ap: &mut Seed_Map, min_shared_minis:f64, shared_seed_infos_vec: &mut Vec<i32>, verbose: bool){
[INFO] [stdout]     |                       ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_shared_minis`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `seq_len`
[INFO] [stdout]    --> src/seeding_and_filtering_seeds.rs:349:13
[INFO] [stdout]     |
[INFO] [stdout] 349 |         let seq_len= seq.len();
[INFO] [stdout]     |             ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_seq_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/generate_sorted_fastq_for_cluster.rs:116:9
[INFO] [stdout]     |
[INFO] [stdout] 116 |     let mut reader = fastq::Reader::from_file(Path::new(&in_file_path)).expect("We expect the file to exist");
[INFO] [stdout]     |         ----^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/gff_handling.rs:42:9
[INFO] [stdout]    |
[INFO] [stdout] 42 |     let mut reader = fasta::Reader::from_file(Path::new(path)).expect("We expect the file to exist");
[INFO] [stdout]    |         ----^^^^^^
[INFO] [stdout]    |         |
[INFO] [stdout]    |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `internal_id` is assigned to, but never used
[INFO] [stdout]   --> src/gff_handling.rs:46:13
[INFO] [stdout]    |
[INFO] [stdout] 46 |         let mut internal_id=0;
[INFO] [stdout]    |             ^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: consider using `_internal_id` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `internal_id` is never read
[INFO] [stdout]   --> src/gff_handling.rs:74:17
[INFO] [stdout]    |
[INFO] [stdout] 74 |                 internal_id += 1;
[INFO] [stdout]    |                 ^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout]    = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/gff_handling.rs:88:13
[INFO] [stdout]    |
[INFO] [stdout] 88 |         let mut rec = record.ok().expect("Error reading record.");
[INFO] [stdout]    |             ----^^^
[INFO] [stdout]    |             |
[INFO] [stdout]    |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `is_gene` is assigned to, but never used
[INFO] [stdout]    --> src/gff_handling.rs:168:13
[INFO] [stdout]     |
[INFO] [stdout] 168 |         let mut is_gene= false;
[INFO] [stdout]     |             ^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_is_gene` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `is_gene` is never read
[INFO] [stdout]    --> src/gff_handling.rs:224:21
[INFO] [stdout]     |
[INFO] [stdout] 224 |                     is_gene = true;
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `is_gene` is never read
[INFO] [stdout]    --> src/gff_handling.rs:214:21
[INFO] [stdout]     |
[INFO] [stdout] 214 |                     is_gene = false;
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `is_gene` is never read
[INFO] [stdout]    --> src/gff_handling.rs:178:21
[INFO] [stdout]     |
[INFO] [stdout] 178 |                     is_gene = true;
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/write_output.rs:70:21
[INFO] [stdout]    |
[INFO] [stdout] 70 |                 let mut id_vec: &mut Vec<FastqRecord_isoncl_init> = cluster_map.get_mut(cluster_id).unwrap();
[INFO] [stdout]    |                     ----^^^^^^
[INFO] [stdout]    |                     |
[INFO] [stdout]    |                     help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `cl_id`
[INFO] [stdout]   --> src/write_output.rs:88:10
[INFO] [stdout]    |
[INFO] [stdout] 88 |     for (cl_id, records) in cluster_map.into_iter(){
[INFO] [stdout]    |          ^^^^^ help: if this is intentional, prefix it with an underscore: `_cl_id`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `annotation_based` is assigned to, but never used
[INFO] [stdout]    --> src/main.rs:313:9
[INFO] [stdout]     |
[INFO] [stdout] 313 |     let mut annotation_based= false;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_annotation_based` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `now3`
[INFO] [stdout]    --> src/main.rs:372:17
[INFO] [stdout]     |
[INFO] [stdout] 372 |             let now3 = Instant::now();
[INFO] [stdout]     |                 ^^^^ help: if this is intentional, prefix it with an underscore: `_now3`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `annotation_based` is never read
[INFO] [stdout]    --> src/main.rs:326:13
[INFO] [stdout]     |
[INFO] [stdout] 326 |             annotation_based = true;
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `compute_d` is never used
[INFO] [stdout]   --> src/main.rs:46:4
[INFO] [stdout]    |
[INFO] [stdout] 46 | fn compute_d() -> [f64; 128] {
[INFO] [stdout]    |    ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `expected_number_errornous_kmers` is never used
[INFO] [stdout]   --> src/main.rs:59:4
[INFO] [stdout]    |
[INFO] [stdout] 59 | fn expected_number_errornous_kmers(quality_string: &str, k: usize, d:&[f64;128]) -> f64 {
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `calculate_error_rate` is never used
[INFO] [stdout]   --> src/main.rs:86:4
[INFO] [stdout]    |
[INFO] [stdout] 86 | fn calculate_error_rate(qual: &str, d_no_min: &[f64; 128]) -> f64 {
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_sorted_entries` is never used
[INFO] [stdout]    --> src/main.rs:102:4
[INFO] [stdout]     |
[INFO] [stdout] 102 | fn get_sorted_entries(mini_map_filtered: FxHashMap<i32, Vec<structs::Minimizer_hashed>>)->Vec<(i32, Vec<structs::Minimizer_hashed>)>{
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `filter_fastq_records` is never used
[INFO] [stdout]    --> src/main.rs:116:4
[INFO] [stdout]     |
[INFO] [stdout] 116 | fn filter_fastq_records(mut fastq_records:Vec<FastqRecord_isoncl_init>,d_no_min:[f64;128], q_threshold:f64,k:usize,d :[f64;128])->Vec<Fas...
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `convert_cl_id` is never used
[INFO] [stdout]    --> src/main.rs:134:4
[INFO] [stdout]     |
[INFO] [stdout] 134 | fn convert_cl_id(v: usize) -> Option<i32> {
[INFO] [stdout]     |    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `parse_fasta` is never used
[INFO] [stdout]  --> src/file_actions.rs:9:15
[INFO] [stdout]   |
[INFO] [stdout] 9 | pub(crate) fn parse_fasta(file_path: &str) -> Result<Vec<FastaRecord>, std::io::Error> {
[INFO] [stdout]   |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `new_Fx_hashset` is never used
[INFO] [stdout]   --> src/clustering.rs:28:4
[INFO] [stdout]    |
[INFO] [stdout] 28 | fn new_Fx_hashset()->FxHashSet<i32>{
[INFO] [stdout]    |    ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `detect_whether_shared` is never used
[INFO] [stdout]   --> src/clustering.rs:33:4
[INFO] [stdout]    |
[INFO] [stdout] 33 | fn detect_whether_shared(min_shared_minis:f64, shared_seed_infos: &FxHashMap<i32,i32>, minimizers: &[Minimizer_hashed]) -> (bool, i32) {
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `cow_to_string` is never used
[INFO] [stdout]   --> src/seeding_and_filtering_seeds.rs:34:4
[INFO] [stdout]    |
[INFO] [stdout] 34 | fn cow_to_string(cow: Cow<'_, [u8]>) -> String {
[INFO] [stdout]    |    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_canonical_kmer_minimizers_hashed` is never used
[INFO] [stdout]   --> src/seeding_and_filtering_seeds.rs:43:8
[INFO] [stdout]    |
[INFO] [stdout] 43 | pub fn get_canonical_kmer_minimizers_hashed(seq: &[u8], k_size: usize, w_size: usize, this_minimizers: &mut Vec<Minimizer_hashed>)  {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_kmer_minimizers_hashed` is never used
[INFO] [stdout]    --> src/seeding_and_filtering_seeds.rs:138:8
[INFO] [stdout]     |
[INFO] [stdout] 138 | pub fn get_kmer_minimizers_hashed(seq: &[u8], k_size: usize, w_size: usize, this_minimizers: &mut Vec<Minimizer_hashed>)  {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `average` is never used
[INFO] [stdout]    --> src/seeding_and_filtering_seeds.rs:277:4
[INFO] [stdout]     |
[INFO] [stdout] 277 | fn average(numbers: &[f64]) -> f64 {
[INFO] [stdout]     |    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `expected_number_errornous_kmers` is never used
[INFO] [stdout]   --> src/generate_sorted_fastq_for_cluster.rs:34:4
[INFO] [stdout]    |
[INFO] [stdout] 34 | fn expected_number_errornous_kmers(quality_string: &str, k: usize, d:&[f64;128]) -> f64 {
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `compute_d` is never used
[INFO] [stdout]   --> src/generate_sorted_fastq_for_cluster.rs:82:4
[INFO] [stdout]    |
[INFO] [stdout] 82 | fn compute_d() -> [f64; 128] {
[INFO] [stdout]    |    ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `print_statistics` is never used
[INFO] [stdout]    --> src/generate_sorted_fastq_for_cluster.rs:195:4
[INFO] [stdout]     |
[INFO] [stdout] 195 | fn print_statistics(fastq_records: &[FastqRecord_isoncl_init]){
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `detect_overlaps` is never used
[INFO] [stdout]   --> src/gff_handling.rs:23:4
[INFO] [stdout]    |
[INFO] [stdout] 23 | fn detect_overlaps(gene_map: &FxHashMap<i32,Vec<Coord_obj>>, this_gene_id:&i32, this_coords: &Vec<Coord_obj>, overlap_ctr: &mut i32){
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `parse_fasta_and_gen_clusters` is never used
[INFO] [stdout]   --> src/gff_handling.rs:39:4
[INFO] [stdout]    |
[INFO] [stdout] 39 | fn parse_fasta_and_gen_clusters(fasta_path: Option<&str>, coords: FxHashMap<String,FxHashMap<i32,Vec<Coord_obj>>>, clusters: &mut Cluster...
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `parse_gtf_and_collect_coords` is never used
[INFO] [stdout]   --> src/gff_handling.rs:82:4
[INFO] [stdout]    |
[INFO] [stdout] 82 | fn parse_gtf_and_collect_coords(gtf_path: Option<&str>, coords:&mut FxHashMap<String,FxHashMap<i32,Vec<Coord_obj>>>){
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `resolve_gff` is never used
[INFO] [stdout]    --> src/gff_handling.rs:134:15
[INFO] [stdout]     |
[INFO] [stdout] 134 | pub(crate) fn resolve_gff(gff_path: Option<&str>, fasta_path: Option<&str>,clusters: &mut Cluster_ID_Map, cluster_map: &mut Seed_Map,k:us...
[INFO] [stdout]     |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: enum `Cluster` is never used
[INFO] [stdout]  --> src/structs.rs:4:10
[INFO] [stdout]   |
[INFO] [stdout] 4 | pub enum Cluster<T, U> {
[INFO] [stdout]   |          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `Minimizer` is never constructed
[INFO] [stdout]   --> src/structs.rs:13:12
[INFO] [stdout]    |
[INFO] [stdout] 13 | pub struct Minimizer {
[INFO] [stdout]    |            ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `GtfEntry` is never constructed
[INFO] [stdout]   --> src/structs.rs:29:19
[INFO] [stdout]    |
[INFO] [stdout] 29 | pub(crate) struct GtfEntry {
[INFO] [stdout]    |                   ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `Coord_obj` is never constructed
[INFO] [stdout]   --> src/structs.rs:48:19
[INFO] [stdout]    |
[INFO] [stdout] 48 | pub(crate) struct Coord_obj{
[INFO] [stdout]    |                   ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `overlaps_with` is never used
[INFO] [stdout]   --> src/structs.rs:59:12
[INFO] [stdout]    |
[INFO] [stdout] 58 | impl Coord_obj{
[INFO] [stdout]    | -------------- method in this implementation
[INFO] [stdout] 59 |     pub fn overlaps_with(&self,other:&Coord_obj)-> bool{
[INFO] [stdout]    |            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `FastaRecord` is never constructed
[INFO] [stdout]   --> src/structs.rs:73:19
[INFO] [stdout]    |
[INFO] [stdout] 73 | pub(crate) struct FastaRecord {
[INFO] [stdout]    |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `FastqRecord` is never constructed
[INFO] [stdout]   --> src/structs.rs:88:19
[INFO] [stdout]    |
[INFO] [stdout] 88 | pub(crate) struct FastqRecord {
[INFO] [stdout]    |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `score` and `error_rate` are never read
[INFO] [stdout]    --> src/structs.rs:108:9
[INFO] [stdout]     |
[INFO] [stdout] 103 | pub(crate) struct FastqRecord_isoncl_init {
[INFO] [stdout]     |                   ----------------------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 108 |     pub score: f64,
[INFO] [stdout]     |         ^^^^^
[INFO] [stdout] 109 |     pub error_rate:f64,
[INFO] [stdout]     |         ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `internal_gff` is never constructed
[INFO] [stdout]    --> src/structs.rs:111:19
[INFO] [stdout]     |
[INFO] [stdout] 111 | pub(crate) struct internal_gff {
[INFO] [stdout]     |                   ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `get_err_rate`, `set_error_rate`, and `set_score` are never used
[INFO] [stdout]    --> src/structs.rs:132:12
[INFO] [stdout]     |
[INFO] [stdout] 118 | impl FastqRecord_isoncl_init{
[INFO] [stdout]     | ---------------------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 132 |     pub fn get_err_rate(&self)->&f64{&self.error_rate}
[INFO] [stdout]     |            ^^^^^^^^^^^^
[INFO] [stdout] 133 |     pub fn set_error_rate(&mut self, new_error_rate: f64){ self.error_rate = new_error_rate }
[INFO] [stdout]     |            ^^^^^^^^^^^^^^
[INFO] [stdout] 134 |     pub fn set_score(&mut self, new_score: f64) { self.score = new_score }
[INFO] [stdout]     |            ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: module `Parallelization_side` should have a snake case name
[INFO] [stdout]   --> src/main.rs:18:5
[INFO] [stdout]    |
[INFO] [stdout] 18 | mod Parallelization_side;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^ help: convert the identifier to snake case: `parallelization_side`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(non_snake_case)]` (part of `#[warn(nonstandard_style)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `new_Fx_hashset` should have a snake case name
[INFO] [stdout]   --> src/clustering.rs:28:4
[INFO] [stdout]    |
[INFO] [stdout] 28 | fn new_Fx_hashset()->FxHashSet<i32>{
[INFO] [stdout]    |    ^^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): `new_fx_hashset`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rayon::prelude`
[INFO] [stdout]  --> src/clustering.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use rayon::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rayon::prelude`
[INFO] [stdout]  --> src/seeding_and_filtering_seeds.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use rayon::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rayon::prelude`
[INFO] [stdout]  --> src/gff_handling.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 9 | use rayon::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `BufRead`
[INFO] [stdout]  --> src/gff_handling.rs:3:26
[INFO] [stdout]   |
[INFO] [stdout] 3 | use std::io::{BufReader, BufRead};
[INFO] [stdout]   |                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rayon::prelude`
[INFO] [stdout]  --> src/write_output.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 9 | use rayon::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/clustering.rs:97:17
[INFO] [stdout]    |
[INFO] [stdout] 97 |             let mut shared_perc: f64;
[INFO] [stdout]    |                 ----^^^^^^^^^^^
[INFO] [stdout]    |                 |
[INFO] [stdout]    |                 help: remove this `mut`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/clustering.rs:179:17
[INFO] [stdout]     |
[INFO] [stdout] 179 |             let mut cl_vec= clusters_map.get_mut(seed_hash).unwrap();
[INFO] [stdout]     |                 ----^^^^^^
[INFO] [stdout]     |                 |
[INFO] [stdout]     |                 help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `verbose`
[INFO] [stdout]    --> src/clustering.rs:192:209
[INFO] [stdout]     |
[INFO] [stdout] 192 | ...seed_infos_vec: &mut [i32], verbose:bool ){
[INFO] [stdout]     |                                ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_verbose`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `min_shared_minis`
[INFO] [stdout]    --> src/clustering.rs:268:90
[INFO] [stdout]     |
[INFO] [stdout] 268 | ...ap: &mut Seed_Map, min_shared_minis:f64, shared_seed_infos_vec: &mut Vec<i32>, verbose: bool){
[INFO] [stdout]     |                       ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_shared_minis`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `seq_len`
[INFO] [stdout]    --> src/seeding_and_filtering_seeds.rs:349:13
[INFO] [stdout]     |
[INFO] [stdout] 349 |         let seq_len= seq.len();
[INFO] [stdout]     |             ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_seq_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/generate_sorted_fastq_for_cluster.rs:116:9
[INFO] [stdout]     |
[INFO] [stdout] 116 |     let mut reader = fastq::Reader::from_file(Path::new(&in_file_path)).expect("We expect the file to exist");
[INFO] [stdout]     |         ----^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/gff_handling.rs:42:9
[INFO] [stdout]    |
[INFO] [stdout] 42 |     let mut reader = fasta::Reader::from_file(Path::new(path)).expect("We expect the file to exist");
[INFO] [stdout]    |         ----^^^^^^
[INFO] [stdout]    |         |
[INFO] [stdout]    |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `internal_id` is assigned to, but never used
[INFO] [stdout]   --> src/gff_handling.rs:46:13
[INFO] [stdout]    |
[INFO] [stdout] 46 |         let mut internal_id=0;
[INFO] [stdout]    |             ^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: consider using `_internal_id` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `internal_id` is never read
[INFO] [stdout]   --> src/gff_handling.rs:74:17
[INFO] [stdout]    |
[INFO] [stdout] 74 |                 internal_id += 1;
[INFO] [stdout]    |                 ^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout]    = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/gff_handling.rs:88:13
[INFO] [stdout]    |
[INFO] [stdout] 88 |         let mut rec = record.ok().expect("Error reading record.");
[INFO] [stdout]    |             ----^^^
[INFO] [stdout]    |             |
[INFO] [stdout]    |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `is_gene` is assigned to, but never used
[INFO] [stdout]    --> src/gff_handling.rs:168:13
[INFO] [stdout]     |
[INFO] [stdout] 168 |         let mut is_gene= false;
[INFO] [stdout]     |             ^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_is_gene` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `is_gene` is never read
[INFO] [stdout]    --> src/gff_handling.rs:224:21
[INFO] [stdout]     |
[INFO] [stdout] 224 |                     is_gene = true;
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `is_gene` is never read
[INFO] [stdout]    --> src/gff_handling.rs:214:21
[INFO] [stdout]     |
[INFO] [stdout] 214 |                     is_gene = false;
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `is_gene` is never read
[INFO] [stdout]    --> src/gff_handling.rs:178:21
[INFO] [stdout]     |
[INFO] [stdout] 178 |                     is_gene = true;
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/write_output.rs:70:21
[INFO] [stdout]    |
[INFO] [stdout] 70 |                 let mut id_vec: &mut Vec<FastqRecord_isoncl_init> = cluster_map.get_mut(cluster_id).unwrap();
[INFO] [stdout]    |                     ----^^^^^^
[INFO] [stdout]    |                     |
[INFO] [stdout]    |                     help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `cl_id`
[INFO] [stdout]   --> src/write_output.rs:88:10
[INFO] [stdout]    |
[INFO] [stdout] 88 |     for (cl_id, records) in cluster_map.into_iter(){
[INFO] [stdout]    |          ^^^^^ help: if this is intentional, prefix it with an underscore: `_cl_id`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `annotation_based` is assigned to, but never used
[INFO] [stdout]    --> src/main.rs:313:9
[INFO] [stdout]     |
[INFO] [stdout] 313 |     let mut annotation_based= false;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_annotation_based` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `now3`
[INFO] [stdout]    --> src/main.rs:372:17
[INFO] [stdout]     |
[INFO] [stdout] 372 |             let now3 = Instant::now();
[INFO] [stdout]     |                 ^^^^ help: if this is intentional, prefix it with an underscore: `_now3`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `annotation_based` is never read
[INFO] [stdout]    --> src/main.rs:326:13
[INFO] [stdout]     |
[INFO] [stdout] 326 |             annotation_based = true;
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `compute_d` is never used
[INFO] [stdout]   --> src/main.rs:46:4
[INFO] [stdout]    |
[INFO] [stdout] 46 | fn compute_d() -> [f64; 128] {
[INFO] [stdout]    |    ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `expected_number_errornous_kmers` is never used
[INFO] [stdout]   --> src/main.rs:59:4
[INFO] [stdout]    |
[INFO] [stdout] 59 | fn expected_number_errornous_kmers(quality_string: &str, k: usize, d:&[f64;128]) -> f64 {
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `calculate_error_rate` is never used
[INFO] [stdout]   --> src/main.rs:86:4
[INFO] [stdout]    |
[INFO] [stdout] 86 | fn calculate_error_rate(qual: &str, d_no_min: &[f64; 128]) -> f64 {
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_sorted_entries` is never used
[INFO] [stdout]    --> src/main.rs:102:4
[INFO] [stdout]     |
[INFO] [stdout] 102 | fn get_sorted_entries(mini_map_filtered: FxHashMap<i32, Vec<structs::Minimizer_hashed>>)->Vec<(i32, Vec<structs::Minimizer_hashed>)>{
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `filter_fastq_records` is never used
[INFO] [stdout]    --> src/main.rs:116:4
[INFO] [stdout]     |
[INFO] [stdout] 116 | fn filter_fastq_records(mut fastq_records:Vec<FastqRecord_isoncl_init>,d_no_min:[f64;128], q_threshold:f64,k:usize,d :[f64;128])->Vec<Fas...
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `convert_cl_id` is never used
[INFO] [stdout]    --> src/main.rs:134:4
[INFO] [stdout]     |
[INFO] [stdout] 134 | fn convert_cl_id(v: usize) -> Option<i32> {
[INFO] [stdout]     |    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `parse_fasta` is never used
[INFO] [stdout]  --> src/file_actions.rs:9:15
[INFO] [stdout]   |
[INFO] [stdout] 9 | pub(crate) fn parse_fasta(file_path: &str) -> Result<Vec<FastaRecord>, std::io::Error> {
[INFO] [stdout]   |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `new_Fx_hashset` is never used
[INFO] [stdout]   --> src/clustering.rs:28:4
[INFO] [stdout]    |
[INFO] [stdout] 28 | fn new_Fx_hashset()->FxHashSet<i32>{
[INFO] [stdout]    |    ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `detect_whether_shared` is never used
[INFO] [stdout]   --> src/clustering.rs:33:4
[INFO] [stdout]    |
[INFO] [stdout] 33 | fn detect_whether_shared(min_shared_minis:f64, shared_seed_infos: &FxHashMap<i32,i32>, minimizers: &[Minimizer_hashed]) -> (bool, i32) {
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `cow_to_string` is never used
[INFO] [stdout]   --> src/seeding_and_filtering_seeds.rs:34:4
[INFO] [stdout]    |
[INFO] [stdout] 34 | fn cow_to_string(cow: Cow<'_, [u8]>) -> String {
[INFO] [stdout]    |    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_canonical_kmer_minimizers_hashed` is never used
[INFO] [stdout]   --> src/seeding_and_filtering_seeds.rs:43:8
[INFO] [stdout]    |
[INFO] [stdout] 43 | pub fn get_canonical_kmer_minimizers_hashed(seq: &[u8], k_size: usize, w_size: usize, this_minimizers: &mut Vec<Minimizer_hashed>)  {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_kmer_minimizers_hashed` is never used
[INFO] [stdout]    --> src/seeding_and_filtering_seeds.rs:138:8
[INFO] [stdout]     |
[INFO] [stdout] 138 | pub fn get_kmer_minimizers_hashed(seq: &[u8], k_size: usize, w_size: usize, this_minimizers: &mut Vec<Minimizer_hashed>)  {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `average` is never used
[INFO] [stdout]    --> src/seeding_and_filtering_seeds.rs:277:4
[INFO] [stdout]     |
[INFO] [stdout] 277 | fn average(numbers: &[f64]) -> f64 {
[INFO] [stdout]     |    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `expected_number_errornous_kmers` is never used
[INFO] [stdout]   --> src/generate_sorted_fastq_for_cluster.rs:34:4
[INFO] [stdout]    |
[INFO] [stdout] 34 | fn expected_number_errornous_kmers(quality_string: &str, k: usize, d:&[f64;128]) -> f64 {
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `compute_d` is never used
[INFO] [stdout]   --> src/generate_sorted_fastq_for_cluster.rs:82:4
[INFO] [stdout]    |
[INFO] [stdout] 82 | fn compute_d() -> [f64; 128] {
[INFO] [stdout]    |    ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `print_statistics` is never used
[INFO] [stdout]    --> src/generate_sorted_fastq_for_cluster.rs:195:4
[INFO] [stdout]     |
[INFO] [stdout] 195 | fn print_statistics(fastq_records: &[FastqRecord_isoncl_init]){
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `detect_overlaps` is never used
[INFO] [stdout]   --> src/gff_handling.rs:23:4
[INFO] [stdout]    |
[INFO] [stdout] 23 | fn detect_overlaps(gene_map: &FxHashMap<i32,Vec<Coord_obj>>, this_gene_id:&i32, this_coords: &Vec<Coord_obj>, overlap_ctr: &mut i32){
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `parse_fasta_and_gen_clusters` is never used
[INFO] [stdout]   --> src/gff_handling.rs:39:4
[INFO] [stdout]    |
[INFO] [stdout] 39 | fn parse_fasta_and_gen_clusters(fasta_path: Option<&str>, coords: FxHashMap<String,FxHashMap<i32,Vec<Coord_obj>>>, clusters: &mut Cluster...
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `parse_gtf_and_collect_coords` is never used
[INFO] [stdout]   --> src/gff_handling.rs:82:4
[INFO] [stdout]    |
[INFO] [stdout] 82 | fn parse_gtf_and_collect_coords(gtf_path: Option<&str>, coords:&mut FxHashMap<String,FxHashMap<i32,Vec<Coord_obj>>>){
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `resolve_gff` is never used
[INFO] [stdout]    --> src/gff_handling.rs:134:15
[INFO] [stdout]     |
[INFO] [stdout] 134 | pub(crate) fn resolve_gff(gff_path: Option<&str>, fasta_path: Option<&str>,clusters: &mut Cluster_ID_Map, cluster_map: &mut Seed_Map,k:us...
[INFO] [stdout]     |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: enum `Cluster` is never used
[INFO] [stdout]  --> src/structs.rs:4:10
[INFO] [stdout]   |
[INFO] [stdout] 4 | pub enum Cluster<T, U> {
[INFO] [stdout]   |          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `Minimizer` is never constructed
[INFO] [stdout]   --> src/structs.rs:13:12
[INFO] [stdout]    |
[INFO] [stdout] 13 | pub struct Minimizer {
[INFO] [stdout]    |            ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `GtfEntry` is never constructed
[INFO] [stdout]   --> src/structs.rs:29:19
[INFO] [stdout]    |
[INFO] [stdout] 29 | pub(crate) struct GtfEntry {
[INFO] [stdout]    |                   ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `Coord_obj` is never constructed
[INFO] [stdout]   --> src/structs.rs:48:19
[INFO] [stdout]    |
[INFO] [stdout] 48 | pub(crate) struct Coord_obj{
[INFO] [stdout]    |                   ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `overlaps_with` is never used
[INFO] [stdout]   --> src/structs.rs:59:12
[INFO] [stdout]    |
[INFO] [stdout] 58 | impl Coord_obj{
[INFO] [stdout]    | -------------- method in this implementation
[INFO] [stdout] 59 |     pub fn overlaps_with(&self,other:&Coord_obj)-> bool{
[INFO] [stdout]    |            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `FastaRecord` is never constructed
[INFO] [stdout]   --> src/structs.rs:73:19
[INFO] [stdout]    |
[INFO] [stdout] 73 | pub(crate) struct FastaRecord {
[INFO] [stdout]    |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `FastqRecord` is never constructed
[INFO] [stdout]   --> src/structs.rs:88:19
[INFO] [stdout]    |
[INFO] [stdout] 88 | pub(crate) struct FastqRecord {
[INFO] [stdout]    |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `score` and `error_rate` are never read
[INFO] [stdout]    --> src/structs.rs:108:9
[INFO] [stdout]     |
[INFO] [stdout] 103 | pub(crate) struct FastqRecord_isoncl_init {
[INFO] [stdout]     |                   ----------------------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 108 |     pub score: f64,
[INFO] [stdout]     |         ^^^^^
[INFO] [stdout] 109 |     pub error_rate:f64,
[INFO] [stdout]     |         ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `internal_gff` is never constructed
[INFO] [stdout]    --> src/structs.rs:111:19
[INFO] [stdout]     |
[INFO] [stdout] 111 | pub(crate) struct internal_gff {
[INFO] [stdout]     |                   ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `get_err_rate`, `set_error_rate`, and `set_score` are never used
[INFO] [stdout]    --> src/structs.rs:132:12
[INFO] [stdout]     |
[INFO] [stdout] 118 | impl FastqRecord_isoncl_init{
[INFO] [stdout]     | ---------------------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 132 |     pub fn get_err_rate(&self)->&f64{&self.error_rate}
[INFO] [stdout]     |            ^^^^^^^^^^^^
[INFO] [stdout] 133 |     pub fn set_error_rate(&mut self, new_error_rate: f64){ self.error_rate = new_error_rate }
[INFO] [stdout]     |            ^^^^^^^^^^^^^^
[INFO] [stdout] 134 |     pub fn set_score(&mut self, new_score: f64) { self.score = new_score }
[INFO] [stdout]     |            ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: module `Parallelization_side` should have a snake case name
[INFO] [stdout]   --> src/main.rs:18:5
[INFO] [stdout]    |
[INFO] [stdout] 18 | mod Parallelization_side;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^ help: convert the identifier to snake case: `parallelization_side`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(non_snake_case)]` (part of `#[warn(nonstandard_style)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `new_Fx_hashset` should have a snake case name
[INFO] [stdout]   --> src/clustering.rs:28:4
[INFO] [stdout]    |
[INFO] [stdout] 28 | fn new_Fx_hashset()->FxHashSet<i32>{
[INFO] [stdout]    |    ^^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): `new_fx_hashset`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 07s
[INFO] running `Command { std: "docker" "inspect" "edadb024579ba317015bde3a902c424ba11ab79fe9ec2e2306615a79fa4c82b5", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "edadb024579ba317015bde3a902c424ba11ab79fe9ec2e2306615a79fa4c82b5", kill_on_drop: false }`
[INFO] [stdout] edadb024579ba317015bde3a902c424ba11ab79fe9ec2e2306615a79fa4c82b5
