warning: using `clone` on type `MapOpts` which implements the `Copy` trait
   --> src/cli/main.rs:259:56
    |
259 |                     res.append(&mut kbo::map(ref_contig, &sbwt, &lcs, map_opts.clone()));
    |                                                                       ^^^^^^^^^^^^^^^^ help: try removing the `clone` call: `map_opts`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy

warning: using `clone` on type `FindOpts` which implements the `Copy` trait
   --> src/cli/main.rs:196:73
    |
196 |                         res.append(&mut kbo::find(&seq.reverse_complement(), &sbwt, &lcs, find_opts.clone())
    |                                                                                           ^^^^^^^^^^^^^^^^^ help: try removing the `clone` call: `find_opts`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy

warning: this expression creates a reference which is immediately dereferenced by the compiler
   --> src/cli/main.rs:196:67
    |
196 |                         res.append(&mut kbo::find(&seq.reverse_complement(), &sbwt, &lcs, find_opts.clone())
    |                                                                                     ^^^^ help: change this to: `lcs`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow

warning: this expression creates a reference which is immediately dereferenced by the compiler
   --> src/cli/main.rs:196:60
    |
196 |                         res.append(&mut kbo::find(&seq.reverse_complement(), &sbwt, &lcs, find_opts.clone())
    |                                                                              ^^^^^ help: change this to: `sbwt`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow

warning: using `clone` on type `FindOpts` which implements the `Copy` trait
   --> src/cli/main.rs:190:42
    |
190 |                         res = kbo::find(&seq, &sbwt, &lcs, find_opts.clone())
    |                                                            ^^^^^^^^^^^^^^^^^ help: try removing the `clone` call: `find_opts`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
    = note: `#[warn(clippy::clone_on_copy)]` on by default

warning: this expression creates a reference which is immediately dereferenced by the compiler
   --> src/cli/main.rs:190:36
    |
190 |                         res = kbo::find(&seq, &sbwt, &lcs, find_opts.clone())
    |                                                      ^^^^ help: change this to: `lcs`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow

warning: this expression creates a reference which is immediately dereferenced by the compiler
   --> src/cli/main.rs:190:29
    |
190 |                         res = kbo::find(&seq, &sbwt, &lcs, find_opts.clone())
    |                                               ^^^^^ help: change this to: `sbwt`
    |
    = 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: using `clone` on type `f64` which implements the `Copy` trait
   --> src/lib.rs:370:33
    |
370 |     match_opts.max_error_prob = find_opts.max_error_prob.clone();
    |                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try removing the `clone` call: `find_opts.max_error_prob`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy
    = note: `#[warn(clippy::clone_on_copy)]` on by default

warning: field assignment outside of initializer for an instance created with Default::default()
   --> src/lib.rs:370:5
    |
370 |     match_opts.max_error_prob = find_opts.max_error_prob.clone();
    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    |
note: consider initializing the variable with `MatchOpts { max_error_prob: find_opts.max_error_prob.clone() }` and removing relevant reassignments
   --> src/lib.rs:369:5
    |
369 |     let mut match_opts = MatchOpts::default();
    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#field_reassign_with_default
    = note: `#[warn(clippy::field_reassign_with_default)]` on by default

warning: doc list item without indentation
  --> src/lib.rs:29:5
   |
29 | //! map](https://docs.rs/ska/latest/ska/#ska-map).
   |     ^
   |
   = help: if this is supposed to be its own paragraph, add a blank line
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation
help: indent this line
   |
29 | //!   map](https://docs.rs/ska/latest/ska/#ska-map).
   |     ++

warning: doc list item without indentation
  --> src/lib.rs:28:5
   |
28 | //! [snippy](https://github.com/tseemann/snippy) and [ska
   |     ^
   |
   = help: if this is supposed to be its own paragraph, add a blank line
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation
help: indent this line
   |
28 | //!   [snippy](https://github.com/tseemann/snippy) and [ska
   |     ++

warning: doc list item without indentation
  --> src/lib.rs:27:5
   |
27 | //! the reference. Map solves the same problem as
   |     ^
   |
   = help: if this is supposed to be its own paragraph, add a blank line
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation
help: indent this line
   |
27 | //!   the reference. Map solves the same problem as
   |     ++

warning: doc list item without indentation
  --> src/lib.rs:26:5
   |
26 | //! sequence, and reports the nucleotide sequence of the alignment relative to
   |     ^
   |
   = help: if this is supposed to be its own paragraph, add a blank line
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation
help: indent this line
   |
26 | //!   sequence, and reports the nucleotide sequence of the alignment relative to
   |     ++

warning: doc list item without indentation
  --> src/lib.rs:24:5
   |
24 | //! [blast](https://blast.ncbi.nlm.nih.gov/Blast.cgi).
   |     ^
   |
   = help: if this is supposed to be its own paragraph, add a blank line
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation
help: indent this line
   |
24 | //!   [blast](https://blast.ncbi.nlm.nih.gov/Blast.cgi).
   |     ++

warning: doc list item without indentation
  --> src/lib.rs:23:5
   |
23 | //! reference. Find is useful for problems that can be solved with
   |     ^
   |
   = help: if this is supposed to be its own paragraph, add a blank line
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation
help: indent this line
   |
23 | //!   reference. Find is useful for problems that can be solved with
   |     ++

warning: doc list item without indentation
  --> src/lib.rs:22:5
   |
22 | //! reference and reports the local alignment segments found within the
   |     ^
   |
   = help: if this is supposed to be its own paragraph, add a blank line
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation
   = note: `#[warn(clippy::doc_lazy_continuation)]` on by default
help: indent this line
   |
22 | //!   reference and reports the local alignment segments found within the
   |     ++