chore: release 0.42.2 #745
johanneskoesterrust.yml
on: push
Formatting
12s
Linting
7m 2s
Testing
7m 59s
Annotations
66 warnings
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Formatting
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2, actions-rs/toolchain@v1. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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Formatting
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/toolchain@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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Formatting
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/
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Formatting
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/
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Formatting
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/
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Formatting
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/
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useless use of `vec!`:
src/bcf/report/mod.rs#L94
warning: useless use of `vec!`
--> src/bcf/report/mod.rs:94:28
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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"))]`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_vec
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useless use of `vec!`:
src/bcf/report/mod.rs#L93
warning: useless use of `vec!`
--> src/bcf/report/mod.rs:93:28
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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"))]`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_vec
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useless use of `vec!`:
src/bcf/report/mod.rs#L38
warning: useless use of `vec!`
--> src/bcf/report/mod.rs:38:28
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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
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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"))];
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`filter_map()` will run forever if the iterator repeatedly produces an `Err`:
src/fastq/filter.rs#L44
warning: `filter_map()` will run forever if the iterator repeatedly produces an `Err`
--> src/fastq/filter.rs:44:48
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44 | HashSet::<String>::from_iter(f.lines().filter_map(Result::ok).collect::<Vec<String>>());
| ^^^^^^^^^^^^^^^^^^^^^^ help: replace with: `map_while(Result::ok)`
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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
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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
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this looks like a failed attempt at checking for the file extension:
src/fastq/collapse_reads_to_fragments/mod.rs#L177
warning: this looks like a failed attempt at checking for the file extension
--> src/fastq/collapse_reads_to_fragments/mod.rs:177:152
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177 | ...with(".gz"), fq3_path.as_ref().ends_with(".gz")) {
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `fq3_path.as_ref().extension().is_some_and(|ext| ext == "gz")`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#path_ends_with_ext
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this looks like a failed attempt at checking for the file extension:
src/fastq/collapse_reads_to_fragments/mod.rs#L177
warning: this looks like a failed attempt at checking for the file extension
--> src/fastq/collapse_reads_to_fragments/mod.rs:177:117
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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")`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#path_ends_with_ext
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this looks like a failed attempt at checking for the file extension:
src/fastq/collapse_reads_to_fragments/mod.rs#L177
warning: this looks like a failed attempt at checking for the file extension
--> src/fastq/collapse_reads_to_fragments/mod.rs:177:82
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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")`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#path_ends_with_ext
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this looks like a failed attempt at checking for the file extension:
src/fastq/collapse_reads_to_fragments/mod.rs#L177
warning: this looks like a failed attempt at checking for the file extension
--> src/fastq/collapse_reads_to_fragments/mod.rs:177:51
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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")`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#path_ends_with_ext
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this looks like a failed attempt at checking for the file extension:
src/fastq/collapse_reads_to_fragments/mod.rs#L177
warning: this looks like a failed attempt at checking for the file extension
--> src/fastq/collapse_reads_to_fragments/mod.rs:177:20
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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")`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#path_ends_with_ext
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this looks like a failed attempt at checking for the file extension:
src/fastq/collapse_reads_to_fragments/mod.rs#L140
warning: this looks like a failed attempt at checking for the file extension
--> src/fastq/collapse_reads_to_fragments/mod.rs:140:44
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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")`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#path_ends_with_ext
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this looks like a failed attempt at checking for the file extension:
src/fastq/collapse_reads_to_fragments/mod.rs#L127
warning: this looks like a failed attempt at checking for the file extension
--> src/fastq/collapse_reads_to_fragments/mod.rs:127:43
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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")`
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= 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
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the borrowed expression implements the required traits:
src/fastq/collapse_reads_to_fragments/pipeline.rs#L96
warning: the borrowed expression implements the required traits
--> src/fastq/collapse_reads_to_fragments/pipeline.rs:96:41
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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)`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrows_for_generic_args
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the borrowed expression implements the required traits:
src/fastq/collapse_reads_to_fragments/pipeline.rs#L88
warning: the borrowed expression implements the required traits
--> src/fastq/collapse_reads_to_fragments/pipeline.rs:88:13
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88 | &Self::as_key(i as u64),
| ^^^^^^^^^^^^^^^^^^^^^^^ help: change this to: `Self::as_key(i as u64)`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrows_for_generic_args
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transmute from a `u64` to a `[u8; 8]`:
src/fastq/collapse_reads_to_fragments/pipeline.rs#L82
warning: transmute from a `u64` to a `[u8; 8]`
--> src/fastq/collapse_reads_to_fragments/pipeline.rs:82:18
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82 | unsafe { mem::transmute::<u64, [u8; 8]>(i) }
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider using `to_ne_bytes()`: `i.to_ne_bytes()`
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= 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
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iterating on a map's values:
src/csv/report.rs#L488
warning: iterating on a map's values
--> src/csv/report.rs:488:41
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488 | let unique_values: HashSet<_> = count_values.iter().map(|(_, v)| v).collect();
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `count_values.values()`
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= 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
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this expression can be written more simply using `.retain()`:
src/bcf/report/table_report/static_reader.rs#L136
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
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this expression can be written more simply using `.retain()`:
src/bcf/report/table_report/static_reader.rs#L132
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
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use of `or_insert_with` to construct default value:
src/bcf/report/table_report/create_report_table.rs#L515
warning: use of `or_insert_with` to construct default value
--> src/bcf/report/table_report/create_report_table.rs:515:64
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515 | let entry = info_map.entry(tag.to_owned()).or_insert_with(Vec::new);
| ^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `or_default()`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unwrap_or_default
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use of `or_insert_with` to construct default value:
src/bcf/report/table_report/create_report_table.rs#L507
warning: use of `or_insert_with` to construct default value
--> src/bcf/report/table_report/create_report_table.rs:507:64
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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
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use of `or_insert_with` to construct default value:
src/bcf/report/table_report/create_report_table.rs#L499
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
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the borrowed expression implements the required traits:
src/bcf/report/table_report/create_report_table.rs#L472
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: "`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrows_for_generic_args
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used consecutive `str::replace` call:
src/bcf/report/table_report/create_report_table.rs#L456
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
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the borrowed expression implements the required traits:
src/bcf/report/table_report/create_report_table.rs#L64
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
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casting to the same type is unnecessary (`i64` -> `i64`):
src/bcf/report/table_report/alignment_reader.rs#L431
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
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casting to the same type is unnecessary (`i64` -> `i64`):
src/bcf/report/table_report/alignment_reader.rs#L367
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
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casting to the same type is unnecessary (`i64` -> `i64`):
src/bcf/report/table_report/alignment_reader.rs#L308
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
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casting to the same type is unnecessary (`f64` -> `f64`):
src/bcf/report/table_report/alignment_reader.rs#L286
warning: casting to the same type is unnecessary (`f64` -> `f64`)
--> src/bcf/report/table_report/alignment_reader.rs:286:39
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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
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casting to the same type is unnecessary (`f64` -> `f64`):
src/bcf/report/table_report/alignment_reader.rs#L285
warning: casting to the same type is unnecessary (`f64` -> `f64`)
--> src/bcf/report/table_report/alignment_reader.rs:285:41
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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
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casting to the same type is unnecessary (`i64` -> `i64`):
src/bcf/report/table_report/alignment_reader.rs#L217
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
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use of `char::is_digit` with literal radix of 10:
src/bcf/report/oncoprint.rs#L291
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
|
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casting the result of `i32::abs()` to u32:
src/bcf/match_variants.rs#L247
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
|
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casting the result of `i32::abs()` to u32:
src/bcf/match_variants.rs#L238
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
|
|
casting the result of `i32::abs()` to u32:
src/bcf/match_variants.rs#L131
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
|
|
the borrowed expression implements the required traits:
src/bcf/match_variants.rs#L73
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_borrows_for_generic_args
|
|
use of `or_insert_with` to construct default value:
src/bcf/match_variants.rs#L42
warning: use of `or_insert_with` to construct default value
--> src/bcf/match_variants.rs:42:22
|
42 | .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
|
|
use of `or_insert_with` to construct default value:
src/bcf/match_variants.rs#L40
warning: use of `or_insert_with` to construct default value
--> src/bcf/match_variants.rs:40:58
|
40 | let recs = inner.entry(chrom.to_owned()).or_insert_with(BTreeMap::new);
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `or_default()`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unwrap_or_default
|
|
the borrowed expression implements the required traits:
src/bcf/fix_iupac_alleles.rs#L26
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_borrows_for_generic_args
|
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casting to the same type is unnecessary (`i64` -> `i64`):
src/bam/depth.rs#L79
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
|
|
casting to the same type is unnecessary (`i64` -> `i64`):
src/bam/depth.rs#L78
warning: casting to the same type is unnecessary (`i64` -> `i64`)
--> src/bam/depth.rs:78:13
|
78 | start as i64,
| ^^^^^^^^^^^^ help: try: `start`
|
= 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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use of `or_insert_with` to construct default value:
src/bam/collapse_reads_to_fragments/pipeline.rs#L237
warning: use of `or_insert_with` to construct default value
--> src/bam/collapse_reads_to_fragments/pipeline.rs:237:42
|
237 | ... .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
|
|
use of `or_insert_with` to construct default value:
src/bam/collapse_reads_to_fragments/pipeline.rs#L205
warning: use of `or_insert_with` to construct default value
--> src/bam/collapse_reads_to_fragments/pipeline.rs:205:46
|
205 | ... .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
|
|
use of `or_insert_with` to construct default value:
src/bam/collapse_reads_to_fragments/pipeline.rs#L181
warning: use of `or_insert_with` to construct default value
--> src/bam/collapse_reads_to_fragments/pipeline.rs:181:46
|
181 | ... .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
|
|
use of `or_insert_with` to construct default value:
src/bam/collapse_reads_to_fragments/pipeline.rs#L70
warning: use of `or_insert_with` to construct default value
--> src/bam/collapse_reads_to_fragments/pipeline.rs:70:18
|
70 | .or_insert_with(HashSet::new)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `or_default()`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unwrap_or_default
= note: `#[warn(clippy::unwrap_or_default)]` on by default
|
|
the borrowed expression implements the required traits:
src/bam/anonymize_reads.rs#L46
warning: the borrowed expression implements the required traits
--> src/bam/anonymize_reads.rs:46:30
|
46 | .push_tag(b"LN", &(end - start)),
| ^^^^^^^^^^^^^^ help: change this to: `(end - start)`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrows_for_generic_args
= note: `#[warn(clippy::needless_borrows_for_generic_args)]` on by default
|
|
slow zero-filling initialization:
src/bam/anonymize_reads.rs#L26
warning: slow zero-filling initialization
--> src/bam/anonymize_reads.rs:26:5
|
25 | let mut reference = Vec::new();
| ---------- help: consider replacing this with: `vec![0; (end - start) as usize]`
26 | reference.resize((end - start) as usize, 0);
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#slow_vector_initialization
= note: `#[warn(clippy::slow_vector_initialization)]` on by default
|
|
Linting
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2, actions-rs/toolchain@v1, actions-rs/clippy-check@v1. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
|
|
Linting
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/toolchain@v1, actions-rs/clippy-check@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
Linting
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/
|
|
Linting
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/
|
|
Linting
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/
|
|
Linting
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/
|
|
Testing
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2, actions-rs/toolchain@v1, Swatinem/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
|
|
Testing
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/toolchain@v1, Swatinem/[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/
|
|
Testing
The `save-state` 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/
|
|
Testing
The `save-state` 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/
|
|
Testing
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/
|
|
Testing
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/
|
|
Testing
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/
|
|
Testing
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/
|
|
Testing
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/
|