feat: adding 50bp filter for REF/ALT on clinvar-sv import (#293) #380
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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/
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this expression creates a reference which is immediately dereferenced by the compiler:
src/clinvar_sv/cli/query.rs#L342
warning: this expression creates a reference which is immediately dereferenced by the compiler
--> src/clinvar_sv/cli/query.rs:342:60
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342 | print_record(&mut out_writer, args.out_format, &record)?;
| ^^^^^^^ help: change this to: `record`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow
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this expression creates a reference which is immediately dereferenced by the compiler:
src/clinvar_sv/cli/query.rs#L339
warning: this expression creates a reference which is immediately dereferenced by the compiler
--> src/clinvar_sv/cli/query.rs:339:20
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339 | .query(&range)
| ^^^^^^ help: change this to: `range`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow
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this expression creates a reference which is immediately dereferenced by the compiler:
src/clinvar_sv/cli/query.rs#L279
warning: this expression creates a reference which is immediately dereferenced by the compiler
--> src/clinvar_sv/cli/query.rs:279:48
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279 | let contig = extract_chrom::from_range(&range, Some(&self.meta.genome_release))?;
| ^^^^^^ help: change this to: `range`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow
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the borrowed expression implements the required traits:
src/clinvar_sv/cli/import.rs#L53
warning: the borrowed expression implements the required traits
--> src/clinvar_sv/cli/import.rs:53:38
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53 | Box::new(std::fs::File::open(&path_in_jsonl)?)
| ^^^^^^^^^^^^^^ help: change this to: `path_in_jsonl`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow
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the borrowed expression implements the required traits:
src/clinvar_sv/cli/import.rs#L50
warning: the borrowed expression implements the required traits
--> src/clinvar_sv/cli/import.rs:50:13
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50 | &path_in_jsonl,
| ^^^^^^^^^^^^^^ help: change this to: `path_in_jsonl`
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= 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
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redundant field names in struct initialization:
src/clinvar_sv/cli/query.rs#L223
warning: redundant field names in struct initialization
--> src/clinvar_sv/cli/query.rs:223:13
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223 | meta: meta,
| ^^^^^^^^^^ help: replace it with: `meta`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
= note: `#[warn(clippy::redundant_field_names)]` on by default
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