warning: dereferencing a tuple pattern where every element takes a reference
   --> src/strand.rs:296:36
    |
296 |             (&Option::Some(ref x), &Option::Some(ref x1)) => x.same(x1),
    |                                    ^^^^^^^^^^^^^^^^^^^^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrowed_reference
help: try removing the `&` and `ref` parts
    |
296 -             (&Option::Some(ref x), &Option::Some(ref x1)) => x.same(x1),
296 +             (&Option::Some(ref x), Option::Some(x1)) => x.same(x1),
    |

warning: dereferencing a tuple pattern where every element takes a reference
   --> src/strand.rs:296:14
    |
296 |             (&Option::Some(ref x), &Option::Some(ref x1)) => x.same(x1),
    |              ^^^^^^^^^^^^^^^^^^^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrowed_reference
    = note: `#[warn(clippy::needless_borrowed_reference)]` on by default
help: try removing the `&` and `ref` parts
    |
296 -             (&Option::Some(ref x), &Option::Some(ref x1)) => x.same(x1),
296 +             (Option::Some(x), &Option::Some(ref x1)) => x.same(x1),
    |

warning: this `impl` can be derived
  --> src/sequence.rs:61:1
   |
61 | / impl Default for SequenceReadPairOrientation {
62 | |     fn default() -> Self {
63 | |         None
64 | |     }
65 | | }
   | |_^
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#derivable_impls
   = help: remove the manual implementation...
help: ...and instead derive it...
   |
49 + #[derive(Default)]
50 | pub enum SequenceReadPairOrientation {
   |
help: ...and mark the default variant
   |
58 ~     #[default]
59 ~     None,
   |

warning: non-canonical implementation of `partial_cmp` on an `Ord` type
  --> src/genome.rs:32:1
   |
32 | /  impl PartialOrd for Interval {
33 | |      fn partial_cmp(&self, other: &Self) -> Option<cmp::Ordering> {
   | | __________________________________________________________________-
34 | ||         Some(self.contig.cmp(&other.contig).then_with(|| {
35 | ||             self.range
36 | ||                 .start
...  ||
39 | ||         }))
40 | ||     }
   | ||_____- help: change this to: `{ Some(std::cmp::Ord::cmp(self, other)) }`
41 | |  }
   | |__^
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#non_canonical_partial_ord_impl
   = note: `#[warn(clippy::non_canonical_partial_ord_impl)]` on by default

warning: the following explicit lifetimes could be elided: 'a
   --> src/annot/spliced.rs:178:10
    |
178 |     impl<'a> Iterator for Ins<'a> {
    |          ^^                   ^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
    |
178 -     impl<'a> Iterator for Ins<'a> {
178 +     impl Iterator for Ins<'_> {
    |

warning: the following explicit lifetimes could be elided: 'a
   --> src/annot/spliced.rs:112:10
    |
112 |     impl<'a> Iterator for Exes<'a> {
    |          ^^                    ^^
    |
    = 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
    |
112 -     impl<'a> Iterator for Exes<'a> {
112 +     impl Iterator for Exes<'_> {
    |

warning: this pattern creates a reference to a reference
  --> src/annot/refids.rs:70:25
   |
70 |             if let Some(ref r) = self.refids.get(id) {
   |                         ^^^^^
   |
   = 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
help: try
   |
70 ~             if let Some(r) = self.refids.get(id) {
71 ~                 r.clone()
   |

warning: doc list item without indentation
   --> src/annot/pos.rs:125:9
    |
125 |     /// features.
    |         ^
    |
    = 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
    |
125 |     ///   features.
    |         ++

warning: doc list item without indentation
   --> src/annot/pos.rs:124:9
    |
124 |     /// forward-strand features and increase it for reverse-strand
    |         ^
    |
    = 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
    |
124 |     ///   forward-strand features and increase it for reverse-strand
    |         ++

warning: doc list item without indentation
   --> src/annot/pos.rs:123:9
    |
123 |     /// positive `dist` will numerically decrease the position for
    |         ^
    |
    = 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
    |
123 |     ///   positive `dist` will numerically decrease the position for
    |         ++

warning: doc list item without indentation
  --> src/annot/pos.rs:94:9
   |
94 |     /// features.
   |         ^
   |
   = 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
   |
94 |     ///   features.
   |         ++

warning: doc list item without indentation
  --> src/annot/pos.rs:93:9
   |
93 |     /// forward-strand features and decrease it for reverse-strand
   |         ^
   |
   = 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
   |
93 |     ///   forward-strand features and decrease it for reverse-strand
   |         ++

warning: doc list item without indentation
  --> src/annot/pos.rs:92:9
   |
92 |     /// positive `dist` will numerically increase the position for
   |         ^
   |
   = 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
   |
92 |     ///   positive `dist` will numerically increase the position for
   |         ++

warning: doc list item without indentation
   --> src/annot/contig.rs:175:9
    |
175 |     /// expand for reverse-strand annotations.
    |         ^
    |
    = 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
    |
175 |     ///   expand for reverse-strand annotations.
    |         ++

warning: doc list item without indentation
   --> src/annot/contig.rs:174:9
    |
174 |     /// forward-strand annotations and the left, 5'-most end will
    |         ^
    |
    = 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
    |
174 |     ///   forward-strand annotations and the left, 5'-most end will
    |         ++

warning: doc list item without indentation
   --> src/annot/contig.rs:173:9
    |
173 |     /// right, 3'-most end of the contig will expand for
    |         ^
    |
    = 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
    |
173 |     ///   right, 3'-most end of the contig will expand for
    |         ++

warning: doc list item without indentation
   --> src/annot/contig.rs:148:9
    |
148 |     /// reverse-strand annotations.
    |         ^
    |
    = 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
    |
148 |     ///   reverse-strand annotations.
    |         ++

warning: doc list item without indentation
   --> src/annot/contig.rs:147:9
    |
147 |     /// annotations and the right, 3'-most end will expand for
    |         ^
    |
    = 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
    |
147 |     ///   annotations and the right, 3'-most end will expand for
    |         ++

warning: doc list item without indentation
   --> src/annot/contig.rs:146:9
    |
146 |     /// left, 5'-most end of the contig will expand for forward-strand
    |         ^
    |
    = 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
    |
146 |     ///   left, 5'-most end of the contig will expand for forward-strand
    |         ++

warning: this `impl` can be derived
  --> src/alignment.rs:52:1
   |
52 | / impl Default for AlignmentMode {
53 | |     fn default() -> Self {
54 | |         AlignmentMode::Global
55 | |     }
56 | | }
   | |_^
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#derivable_impls
   = note: `#[warn(clippy::derivable_impls)]` on by default
   = help: remove the manual implementation...
help: ...and instead derive it...
   |
45 + #[derive(Default)]
46 | pub enum AlignmentMode {
   |
help: ...and mark the default variant
   |
48 ~     #[default]
49 ~     Global,
   |