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warning: empty line after doc comment --> src/verify/seqvars.rs:36:5 | 36 | / /// Path to output TSV file. 37 | | | |_^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#empty_line_after_doc_comments = help: if the empty line is unintentional remove it

warning: empty line after doc comment --> src/verify/seqvars.rs:32:5 | 32 | / /// Path to the reference FASTA file. 33 | | | |_^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#empty_line_after_doc_comments = note: `#[warn(clippy::empty_line_after_doc_comments)]` on by default = help: if the empty line is unintentional remove it

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.txs.serde.rs:1755:22 | 1755 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 1755 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 1755 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.txs.serde.rs:1637:14 | 1637 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 1637 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 1637 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.txs.serde.rs:1536:22 | 1536 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 1536 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 1536 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.txs.serde.rs:1442:14 | 1442 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 1442 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 1442 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.txs.serde.rs:1266:22 | 1266 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 1266 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 1266 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.txs.serde.rs:1089:14 | 1089 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 1089 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 1089 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.txs.serde.rs:964:22 | 964 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 964 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 964 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.txs.serde.rs:830:14 | 830 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 830 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 830 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.txs.serde.rs:729:22 | 729 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 729 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 729 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.txs.serde.rs:627:14 | 627 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 627 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 627 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.txs.serde.rs:498:22 | 498 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 498 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 498 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.txs.serde.rs:331:22 | 331 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 331 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 331 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.txs.serde.rs:158:22 | 158 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 158 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 158 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.txs.serde.rs:29:14 | 29 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 29 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 29 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.server.serde.rs:199:22 | 199 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes help: elide the lifetimes | 199 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 199 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: the following explicit lifetimes could be elided: 'de --> /home/runner/work/mehari/mehari/target/debug/build/mehari-bc7fb2165ed95fcc/out/mehari.server.serde.rs:70:22 | 70 | impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { | ^^^ ^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes = note: `#[warn(clippy::needless_lifetimes)]` on by default help: elide the lifetimes | 70 - impl<'de> serde::de::Visitor<'de> for GeneratedVisitor { 70 + impl serde::de::Visitor<'_> for GeneratedVisitor { |

warning: writing `&Vec` instead of `&[_]` involves a new object where a slice will do --> src/db/subset/mod.rs:241:19 | 241 | gene_symbols: &Vec<String>, | ^^^^^^^^^^^^ help: change this to: `&[String]` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg

warning: writing `&Vec` instead of `&[_]` involves a new object where a slice will do --> src/db/subset/mod.rs:228:21 | 228 | transcript_ids: &Vec<String>, | ^^^^^^^^^^^^ help: change this to: `&[String]` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg = note: `#[warn(clippy::ptr_arg)]` on by default

warning: this `map_or` is redundant --> src/db/create/mod.rs:1319:26 | 1319 | let seleno_tag = tx | __________________________^ 1320 | | .biotype 1321 | | .as_ref() 1322 | | .map_or(false, |bt| bt.contains(&BioType::Selenoprotein)) | |_____________________________________________________________________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_map_or help: use is_some_and instead | 1319 ~ let seleno_tag = tx 1320 + .biotype 1321 + .as_ref().is_some_and(|bt| bt.contains(&BioType::Selenoprotein)) |

warning: this `map_or` is redundant --> src/db/create/mod.rs:1305:15 | 1305 | | self | _______________^ 1306 | | .discards 1307 | | .get(&Identifier::Hgnc(*hgnc_id)) 1308 | | .map_or(false, |reason| !reason.is_empty()); | |___________________________________________________________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_map_or help: use is_some_and instead | 1305 ~ | self 1306 + .discards 1307 ~ .get(&Identifier::Hgnc(*hgnc_id)).is_some_and(|reason| !reason.is_empty()); |

warning: this `map_or` is redundant --> src/db/create/mod.rs:1303:24 | 1303 | let filtered = reason.map_or(false, |reason| !reason.is_empty()); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use is_some_and instead: `reason.is_some_and(|reason| !reason.is_empty())` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_map_or

warning: this `map_or` is redundant --> src/db/create/mod.rs:1256:32 | 1256 | let filtered = hgnc_reason.map_or(false, |reason| !reason.is_empty()); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use is_some_and instead: `hgnc_reason.is_some_and(|reason| !reason.is_empty())` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_map_or

warning: this `map_or` is redundant --> src/db/create/mod.rs:798:16 | 798 | if gene | ________________^ 799 | | .biotype 800 | | .as_ref() 801 | | .map_or(false, |bt| bt.contains(&BioType::Pseudogene)) | |______________________________________________________________________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_map_or help: use is_some_and instead | 798 ~ if gene 799 + .biotype 800 + .as_ref().is_some_and(|bt| bt.contains(&BioType::Pseudogene)) |

warning: this `map_or` is redundant --> src/db/create/mod.rs:732:58 | 732 | ...alid_cds_length || self.fixes.get(&Identifier::TxId(tx_id.clone())).map_or(false, |f| f.contains(Fix::Cds)) { | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use is_some_and instead: `self.fixes.get(&Identifier::TxId(tx_id.clone())).is_some_and(|f| f.contains(Fix::Cds))` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_map_or

warning: this `map_or` is redundant --> src/db/create/mod.rs:343:20 | 343 | if gene.biotype.as_ref().map_or(false, |bt| { | ____________________^ 344 | | bt.iter().any(|b| DISCARD_BIOTYPES_GENES.contains(b)) 345 | | }) { | |__________________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_map_or help: use is_some_and instead | 343 ~ if gene.biotype.as_ref().is_some_and(|bt| { 344 + bt.iter().any(|b| DISCARD_BIOTYPES_GENES.contains(b)) 345 ~ }) { |

warning: this `map_or` is redundant --> src/db/create/mod.rs:178:16 | 178 | || self | ________________^ 179 | | .biotype 180 | | .as_ref() 181 | | .map_or(false, |bt| bt.iter().any(|b| b.is_protein_coding())) | |_____________________________________________________________________________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_map_or help: use is_some_and instead | 178 ~ || self 179 + .biotype 180 + .as_ref().is_some_and(|bt| bt.iter().any(|b| b.is_protein_coding())) |

warning: this `map_or` is redundant --> src/db/check/mod.rs:535:31 | 535 | let has_transcripts = info.map_or(false, |info| { | _______________________________^ 536 | | info.iter() 537 | | .any(|a| matches!(a, Id::NcbiTranscript(_) | Id::EnsemblTranscript(_))) 538 | | }); | |__________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_map_or help: use is_some_and instead | 535 ~ let has_transcripts = info.is_some_and(|info| { 536 + info.iter() 537 + .any(|a| matches!(a, Id::NcbiTranscript(_) | Id::EnsemblTranscript(_))) 538 ~ }); |

warning: this `map_or` is redundant --> src/db/check/mod.rs:479:31 | 479 | let has_transcripts = info.map_or(false, |info| { | _______________________________^ 480 | | info.iter() 481 | | .any(|a| matches!(a, Id::NcbiTranscript(_) | Id::EnsemblTranscript(_))) 482 | | }); | |__________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_map_or = note: `#[warn(clippy::unnecessary_map_or)]` on by default help: use is_some_and instead | 479 ~ let has_transcripts = info.is_some_and(|info| { 480 + info.iter() 481 + .any(|a| matches!(a, Id::NcbiTranscript(_) | Id::EnsemblTranscript(_))) 482 ~ }); |

warning: elided lifetime has a name --> src/common/noodles.rs:79:24 | 76 | async fn records<'a>( | -- lifetime `'a` declared here ... 79 | ) -> LocalBoxStream<std::io::Result<RecordBuf>> { | ^ this elided lifetime gets resolved as `'a`

warning: elided lifetime has a name --> src/common/noodles.rs:63:24 | 60 | async fn records<'a>( | -- lifetime `'a` declared here ... 63 | ) -> LocalBoxStream<std::io::Result<RecordBuf>>; | ^ this elided lifetime gets resolved as `'a` | = note: `#[warn(elided_named_lifetimes)]` on by default

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