The following actions uses node12 which is deprecated and will be forced to run on node16: amannn/[email protected]. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

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: 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_borrow

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_borrow

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: 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_borrow

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_borrow

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

warning: casting to the same type is unnecessary (`i64` -> `i64`) --> src/bcf/report/table_report/alignment_reader.rs:308:40 | 308 | 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 (`f64` -> `f64`) --> src/bcf/report/table_report/alignment_reader.rs:286:39 | 286 | end_position: p as f64 + 1.3, | ^^^^^^^^ help: try: `p` | = 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 (`f64` -> `f64`) --> src/bcf/report/table_report/alignment_reader.rs:285:41 | 285 | start_position: p as f64 + 0.7, | ^^^^^^^^ help: try: `p` | = 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:217:51 | 217 | ... 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

warning: use of `char::is_digit` with literal radix of 10 --> src/bcf/report/oncoprint.rs:291:60 | 291 | ... ex_var.chars().filter(|c| !c.is_digit(10)).collect(); | ^^^^^^^^^^^^^^ help: try: `c.is_ascii_digit()` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#is_digit_ascii_radix = note: `#[warn(clippy::is_digit_ascii_radix)]` on by default

warning: called `unwrap` on `info` after checking its variant with `is_none` --> src/bcf/report/oncoprint.rs:261:48 | 245 | ... if info.is_none() { | ----------------- help: try: `if let Some(..) = info` ... 261 | ... for val in info.unwrap() { | ^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_unwrap = note: `#[warn(clippy::unnecessary_unwrap)]` on by default

warning: casting the result of `i32::abs()` to u32 --> src/bcf/match_variants.rs:247:24 | 247 | if (l1 as i32 - l2 as i32).abs() as u32 <= max_len_diff && dist <= max_dist { | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace with: `(l1 as i32 - l2 as i32).unsigned_abs()` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_abs_to_unsigned

warning: casting the result of `i32::abs()` to u32 --> src/bcf/match_variants.rs:238:24 | 238 | let dist = (self.centerpoint(allele) as i32 - other.centerpoint(b) as i32).abs() as u32; | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace with: `(self.centerpoint(allele) as i32 - other.centerpoint(b) as i32).unsigned_abs()` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_abs_to_unsigned

warning: casting the result of `i32::abs()` to u32 --> src/bcf/match_variants.rs:131:40 | 131 | Some(svlens.iter().map(|l| l.abs() as u32).collect_vec()) | ^^^^^^^^^^^^^^ help: replace with: `l.unsigned_abs()` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_abs_to_unsigned = note: `#[warn(clippy::cast_abs_to_unsigned)]` on by default

warning: the borrowed expression implements the required traits --> src/bcf/match_variants.rs:73:45 | 73 | let mut outbcf = bcf::Writer::from_path(&"-", &header, false, Format::Bcf)?; | ^^^^ help: change this to: `"-"` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow

warning: the borrowed expression implements the required traits --> src/bcf/fix_iupac_alleles.rs:26:55 | 26 | ... if valid_alphabet.is_word(&[*base]) { | ^^^^^^^^ help: change this to: `[*base]` | = 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

warning: casting to the same type is unnecessary (`i64` -> `i64`) --> src/bam/depth.rs:79:13 | 79 | start as i64 + (max_read_length * 2) as i64, | ^^^^^^^^^^^^ help: try: `start` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast