warning: useless use of `vec!`
  --> src/bcf/report/mod.rs:94:28
   |
94 |     let csv_report_files = vec![("csv_report.css", include_str!("../../csv/csv_report.css"))];
   |                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: you can use an array directly: `[("csv_report.css", include_str!("../../csv/csv_report.css"))]`
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_vec

warning: useless use of `vec!`
  --> src/bcf/report/mod.rs:93:28
   |
93 |     let vcf_report_files = vec![("oncoprint.css", include_str!("css/oncoprint.css"))];
   |                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: you can use an array directly: `[("oncoprint.css", include_str!("css/oncoprint.css"))]`
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_vec

warning: useless use of `vec!`
  --> src/bcf/report/mod.rs:38:28
   |
38 |       let vcf_report_files = vec![
   |  ____________________________^
39 | |         ("jsonm.min.js", include_str!("js/jsonm.min.js")),
40 | |         ("table-report.js", include_str!("js/table-report.js")),
41 | |         ("report.js", include_str!("js/report.js")),
42 | |         ("gene-report.js", include_str!("js/gene-report.js")),
43 | |     ];
   | |_____^
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_vec
   = note: `#[warn(clippy::useless_vec)]` on by default
help: you can use an array directly
   |
38 ~     let vcf_report_files = [("jsonm.min.js", include_str!("js/jsonm.min.js")),
39 +         ("table-report.js", include_str!("js/table-report.js")),
40 +         ("report.js", include_str!("js/report.js")),
41 ~         ("gene-report.js", include_str!("js/gene-report.js"))];
   |

warning: `filter_map()` will run forever if the iterator repeatedly produces an `Err`
  --> src/fastq/filter.rs:44:48
   |
44 |         HashSet::<String>::from_iter(f.lines().filter_map(Result::ok).collect::<Vec<String>>());
   |                                                ^^^^^^^^^^^^^^^^^^^^^^ help: replace with: `map_while(Result::ok)`
   |
note: this expression returning a `std::io::Lines` may produce an infinite number of `Err` in case of a read error
  --> src/fastq/filter.rs:44:38
   |
44 |         HashSet::<String>::from_iter(f.lines().filter_map(Result::ok).collect::<Vec<String>>());
   |                                      ^^^^^^^^^
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#lines_filter_map_ok
   = note: `#[warn(clippy::lines_filter_map_ok)]` on by default

warning: this looks like a failed attempt at checking for the file extension
   --> src/fastq/collapse_reads_to_fragments/mod.rs:177:152
    |
177 | ...with(".gz"), fq3_path.as_ref().ends_with(".gz")) {
    |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `fq3_path.as_ref().extension().is_some_and(|ext| ext == "gz")`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#path_ends_with_ext

warning: this looks like a failed attempt at checking for the file extension
   --> src/fastq/collapse_reads_to_fragments/mod.rs:177:117
    |
177 | ..._with(".gz"), fq2_out.as_ref().ends_with(".gz"), fq3_path.as_ref().ends_with(".gz")) {
    |                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `fq2_out.as_ref().extension().is_some_and(|ext| ext == "gz")`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#path_ends_with_ext

warning: this looks like a failed attempt at checking for the file extension
   --> src/fastq/collapse_reads_to_fragments/mod.rs:177:82
    |
177 | ..._with(".gz"), fq1_out.as_ref().ends_with(".gz"), fq2_out.as_ref().ends_with(".gz"), fq3_path.as_ref().ends_with(".gz")) {
    |                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `fq1_out.as_ref().extension().is_some_and(|ext| ext == "gz")`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#path_ends_with_ext

warning: this looks like a failed attempt at checking for the file extension
   --> src/fastq/collapse_reads_to_fragments/mod.rs:177:51
    |
177 | ...ends_with(".gz"), fq2.as_ref().ends_with(".gz"), fq1_out.as_ref().ends_with(".gz"), fq2_out.as_ref().ends_with(".gz"), fq3_path.as_ref...
    |                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `fq2.as_ref().extension().is_some_and(|ext| ext == "gz")`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#path_ends_with_ext

warning: this looks like a failed attempt at checking for the file extension
   --> src/fastq/collapse_reads_to_fragments/mod.rs:177:20
    |
177 | ...   match (fq1.as_ref().ends_with(".gz"), fq2.as_ref().ends_with(".gz"), fq1_out.as_ref().ends_with(".gz"), fq2_out.as_ref().ends_with(...
    |              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `fq1.as_ref().extension().is_some_and(|ext| ext == "gz")`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#path_ends_with_ext

warning: this looks like a failed attempt at checking for the file extension
   --> src/fastq/collapse_reads_to_fragments/mod.rs:140:44
    |
140 |                 let w: Box<dyn Write> = if path.as_ref().ends_with(".gz") {
    |                                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `path.as_ref().extension().is_some_and(|ext| ext == "gz")`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#path_ends_with_ext

warning: this looks like a failed attempt at checking for the file extension
   --> src/fastq/collapse_reads_to_fragments/mod.rs:127:43
    |
127 |                 let r: Box<dyn Read> = if path.as_ref().ends_with(".gz") {
    |                                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `path.as_ref().extension().is_some_and(|ext| ext == "gz")`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#path_ends_with_ext
    = note: `#[warn(clippy::path_ends_with_ext)]` on by default

warning: the borrowed expression implements the required traits
  --> src/fastq/collapse_reads_to_fragments/pipeline.rs:96:41
   |
96 |             str::from_utf8(&self.db.get(&Self::as_key(i as u64))?.unwrap()).unwrap(),
   |                                         ^^^^^^^^^^^^^^^^^^^^^^^ help: change this to: `Self::as_key(i as u64)`
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrows_for_generic_args

warning: the borrowed expression implements the required traits
  --> src/fastq/collapse_reads_to_fragments/pipeline.rs:88:13
   |
88 |             &Self::as_key(i as u64),
   |             ^^^^^^^^^^^^^^^^^^^^^^^ help: change this to: `Self::as_key(i as u64)`
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrows_for_generic_args

warning: transmute from a `u64` to a `[u8; 8]`
  --> src/fastq/collapse_reads_to_fragments/pipeline.rs:82:18
   |
82 |         unsafe { mem::transmute::<u64, [u8; 8]>(i) }
   |                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider using `to_ne_bytes()`: `i.to_ne_bytes()`
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#transmute_num_to_bytes
   = note: `#[warn(clippy::transmute_num_to_bytes)]` on by default

warning: iterating on a map's values
   --> src/csv/report.rs:488:41
    |
488 |         let unique_values: HashSet<_> = count_values.iter().map(|(_, v)| v).collect();
    |                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `count_values.values()`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#iter_kv_map
    = note: `#[warn(clippy::iter_kv_map)]` on by default

warning: this expression can be written more simply using `.retain()`
   --> src/bcf/report/table_report/static_reader.rs:136:9
    |
136 | /         matches_wr = matches_wr
137 | |             .into_iter()
138 | |             .filter(|b| random_rows.contains(&(b.row as u32)))
139 | |             .collect();
    | |______________________^ help: consider calling `.retain()` instead: `matches_wr.retain(|b| random_rows.contains(&(b.row as u32)))`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_retain

warning: this expression can be written more simply using `.retain()`
   --> src/bcf/report/table_report/static_reader.rs:132:9
    |
132 | /         reads_wr = reads_wr
133 | |             .into_iter()
134 | |             .filter(|b| random_rows.contains(&(b.row as u32)))
135 | |             .collect();
    | |______________________^ help: consider calling `.retain()` instead: `reads_wr.retain(|b| random_rows.contains(&(b.row as u32)))`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_retain
    = note: `#[warn(clippy::manual_retain)]` on by default

warning: use of `or_insert_with` to construct default value
   --> src/bcf/report/table_report/create_report_table.rs:515:64
    |
515 |                     let entry = info_map.entry(tag.to_owned()).or_insert_with(Vec::new);
    |                                                                ^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `or_default()`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unwrap_or_default

warning: use of `or_insert_with` to construct default value
   --> src/bcf/report/table_report/create_report_table.rs:507:64
    |
507 |                     let entry = info_map.entry(tag.to_owned()).or_insert_with(Vec::new);
    |                                                                ^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `or_default()`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unwrap_or_default

warning: use of `or_insert_with` to construct default value
   --> src/bcf/report/table_report/create_report_table.rs:499:64
    |
499 |                     let entry = info_map.entry(tag.to_owned()).or_insert_with(Vec::new);
    |                                                                ^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `or_default()`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unwrap_or_default

warning: the borrowed expression implements the required traits
   --> src/bcf/report/table_report/create_report_table.rs:472:25
    |
472 |                         &"\"Consequence annotations from Ensembl VEP. Format: ",
    |                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: change this to: `"\"Consequence annotations from Ensembl VEP. Format: "`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrows_for_generic_args

warning: used consecutive `str::replace` call
   --> src/bcf/report/table_report/create_report_table.rs:456:11
    |
456 |     hgvsg.replace('.', "_").replace('>', "_").replace(':', "_")
    |           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace with: `replace(['.', '>', ':'], "_")`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#collapsible_str_replace
    = note: `#[warn(clippy::collapsible_str_replace)]` on by default

warning: the borrowed expression implements the required traits
  --> src/bcf/report/table_report/create_report_table.rs:64:55
   |
64 |     let mut vcf = rust_htslib::bcf::Reader::from_path(&vcf_path).unwrap();
   |                                                       ^^^^^^^^^ help: change this to: `vcf_path`
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrows_for_generic_args

warning: casting to the same type is unnecessary (`i64` -> `i64`)
   --> src/bcf/report/table_report/alignment_reader.rs:431:20
    |
431 |     let position = snip.pos as i64 + read_offset;
    |                    ^^^^^^^^^^^^^^^ help: try: `snip.pos`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

warning: casting to the same type is unnecessary (`i64` -> `i64`)
   --> src/bcf/report/table_report/alignment_reader.rs:367:51
    |
367 | ...                   match_start = snip.pos as i64 + read_offset;
    |                                     ^^^^^^^^^^^^^^^ help: try: `snip.pos`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast