error: this `else { if .. }` block can be collapsed --> src/read_pair_iter.rs:329:16 | 329 | } else { | ________________^ 330 | | if let Some(p) = self.iters.paths[0].as_ref() { 331 | | let rdr = Self::open_fastq_confirm_fmt(p)?; 332 | | let parser = fastq::Parser::new(rdr); ... | 360 | | } 361 | | } | |_________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#collapsible_else_if note: the lint level is defined here --> src/lib.rs:12:9 | 12 | #![deny(warnings, unused)] | ^^^^^^^^ = note: `#[deny(clippy::collapsible_else_if)]` implied by `#[deny(warnings)]` help: collapse nested if block | 329 ~ } else if let Some(p) = self.iters.paths[0].as_ref() { 330 + let rdr = Self::open_fastq_confirm_fmt(p)?; 331 + let parser = fastq::Parser::new(rdr); 332 + let mut r1_iter = parser.ref_iter(); 333 + r1_iter 334 + .advance() 335 + .map_err(|e| FastqError::format(format!("Ran into trouble while getting first RA read to check if fastq was single ended.\n {:?}", e.to_string()), p, 0))?; 336 + let first_read_header = r1_iter 337 + .get() 338 + .map(|x| { 339 + x.head() 340 + .to_owned() 341 + .split(|x| *x == b' ' || *x == b'/') 342 + .next() 343 + .map(|x| x.to_owned()) 344 + }) 345 + .flatten(); 346 + r1_iter.advance().map_err(|e| FastqError::format(format!("Ran into trouble while getting second RA read to check if fastq was single ended.\n {:?}", e.to_string()), p, 4))?; 347 + let second_read_header = r1_iter 348 + .get() 349 + .map(|x| { 350 + x.head() 351 + .split(|x| *x == b' ' || *x == b'/') 352 + .next() 353 + .map(|x| x.to_owned()) 354 + }) 355 + .flatten(); 356 + Ok(first_read_header != second_read_header) 357 + } else { 358 + Ok(false) 359 + } |

error: this `else { if .. }` block can be collapsed --> src/read_pair_iter.rs:487:32 | 487 | } else { | ________________________________^ 488 | | if let Some(current_read_record) = current_read_record { 489 | | let read_length = read_lengths[WhichRead::R2 as usize]; 490 | | let fake_r2_read = OwnedRecord { ... | 498 | | } 499 | | } | |_________________________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#collapsible_else_if help: collapse nested if block | 487 ~ } else if let Some(current_read_record) = current_read_record { 488 + let read_length = read_lengths[WhichRead::R2 as usize]; 489 + let fake_r2_read = OwnedRecord { 490 + head: current_read_record.head().to_owned(), 491 + sep: Some(current_read_record.seq().to_owned()), 492 + seq: vec![], 493 + qual: vec![], 494 + }; 495 + let tr = TrimRecord::new(&fake_r2_read, read_length); 496 + rp.push_read(&tr, WhichRead::R2) 497 + } |

error: called `map(..).flatten()` on `Option` --> src/read_pair_iter.rs:339:22 | 339 | .map(|x| { | ______________________^ 340 | | x.head() 341 | | .to_owned() 342 | | .split(|x| *x == b' ' || *x == b'/') ... | 345 | | }) 346 | | .flatten(); | |______________________________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_flatten = note: `#[deny(clippy::map_flatten)]` implied by `#[deny(warnings)]` help: try replacing `map` with `and_then` and remove the `.flatten()` | 339 ~ .and_then(|x| { 340 + x.head() 341 + .to_owned() 342 + .split(|x| *x == b' ' || *x == b'/') 343 + .next() 344 + .map(|x| x.to_owned()) 345 ~ }); |

error: redundant closure --> src/read_pair_iter.rs:344:34 | 344 | ... .map(|x| x.to_owned()) | ^^^^^^^^^^^^^^^^ help: replace the closure with the method itself: `std::borrow::ToOwned::to_owned` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_closure_for_method_calls = note: `#[deny(clippy::redundant_closure_for_method_calls)]` implied by `#[deny(warnings)]`

error: called `map(..).flatten()` on `Option` --> src/read_pair_iter.rs:350:22 | 350 | .map(|x| { | ______________________^ 351 | | x.head() 352 | | .split(|x| *x == b' ' || *x == b'/') 353 | | .next() 354 | | .map(|x| x.to_owned()) 355 | | }) 356 | | .flatten(); | |______________________________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_flatten help: try replacing `map` with `and_then` and remove the `.flatten()` | 350 ~ .and_then(|x| { 351 + x.head() 352 + .split(|x| *x == b' ' || *x == b'/') 353 + .next() 354 + .map(|x| x.to_owned()) 355 ~ }); |

error: redundant closure --> src/read_pair_iter.rs:354:34 | 354 | ... .map(|x| x.to_owned()) | ^^^^^^^^^^^^^^^^ help: replace the closure with the method itself: `std::borrow::ToOwned::to_owned` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_closure_for_method_calls

error: used `assert_eq!` with a literal bool --> src/read_pair_iter.rs:641:9 | 641 | / assert_eq!( 642 | | false, 643 | | it.is_single_ended() 644 | | .expect("Ran into trouble checking if read was single ended") 645 | | ); | |_________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#bool_assert_comparison = note: `#[deny(clippy::bool_assert_comparison)]` implied by `#[deny(warnings)]` help: replace it with `assert!(..)` | 641 ~ assert!( 642 ~ !it.is_single_ended() 643 + .expect("Ran into trouble checking if read was single ended") |

error: used `assert_eq!` with a literal bool --> src/read_pair_iter.rs:663:9 | 663 | / assert_eq!( 664 | | true, 665 | | it.is_single_ended() 666 | | .expect("Ran into trouble checking if read was single ended") 667 | | ); | |_________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#bool_assert_comparison help: replace it with `assert!(..)` | 663 ~ assert!( 664 ~ it.is_single_ended() |

Clippy had exited with the 101 exit code