warning: writing `&Vec` instead of `&[_]` involves a new object where a slice will do
   --> src/map.rs:175:10
    |
175 |     aln: &Vec<char>,
    |          ^^^^^^^^^^ help: change this to: `&[char]`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg

warning: unneeded `return` statement
   --> src/map.rs:197:5
    |
197 |     return encodings;
    |     ^^^^^^^^^^^^^^^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
help: remove `return`
    |
197 -     return encodings;
197 +     encodings
    |

warning: this expression creates a reference which is immediately dereferenced by the compiler
   --> src/map.rs:168:13
    |
168 |     run_to_aln(&runs, ms[i], params.threshold, params.k, &mut aln, &mut i);
    |                ^^^^^ help: change this to: `runs`
    |
    = 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: the loop variable `i` is used to index `ms`
   --> src/map.rs:167:18
    |
167 |     for mut i in 3..(len - 1) {
    |                  ^^^^^^^^^^^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_range_loop
    = note: `#[warn(clippy::needless_range_loop)]` on by default
help: consider using an iterator and enumerate()
    |
167 |     for (i, <item>) in ms.iter().enumerate().take((len - 1)).skip(3) {
    |         ~~~~~~~~~~~    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

warning: writing `&Vec` instead of `&[_]` involves a new object where a slice will do
   --> src/map.rs:158:9
    |
158 |     ms: &Vec<usize>,
    |         ^^^^^^^^^^^ help: change this to: `&[usize]`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg

warning: unneeded `return` statement
   --> src/map.rs:171:5
    |
171 |     return aln;
    |     ^^^^^^^^^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
help: remove `return`
    |
171 -     return aln;
171 +     aln
    |

warning: writing `&Vec` instead of `&[_]` involves a new object where a slice will do
   --> src/map.rs:139:9
    |
139 |     ms: &Vec<usize>,
    |         ^^^^^^^^^^^ help: change this to: `&[usize]`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg

warning: unneeded `return` statement
   --> src/map.rs:153:5
    |
153 |     return runs;
    |     ^^^^^^^^^^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
help: remove `return`
    |
153 -     return runs;
153 +     runs
    |

warning: using `clone` on type `usize` which implements the `Copy` trait
   --> src/map.rs:122:28
    |
122 |     let mut next_gap: usize = pos.clone();
    |                               ^^^^^^^^^^^ help: try dereferencing it: `*pos`
    |
    = 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 `if` has identical blocks
   --> src/map.rs:114:39
    |
114 |       } else if curr > threshold as i64 {
    |  _______________________________________^
115 | |     res[*pos] = 'M';
116 | |     } else if curr == next - 1 && curr > 0 {
    | |_____^
    |
note: same as this
   --> src/map.rs:116:44
    |
116 |       } else if curr == next - 1 && curr > 0 {
    |  ____________________________________________^
117 | |     res[*pos] = 'M';
118 | |     } else if curr == 0 && next == 1 && prev > 0 {
    | |_____^
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#if_same_then_else

warning: this `if` has identical blocks
   --> src/map.rs:112:51
    |
112 |       } else if next == 1 && curr == curr_ms as i64 {
    |  ___________________________________________________^
113 | |     res[*pos] = 'M';
114 | |     } else if curr > threshold as i64 {
    | |_____^
    |
note: same as this
   --> src/map.rs:114:39
    |
114 |       } else if curr > threshold as i64 {
    |  _______________________________________^
115 | |     res[*pos] = 'M';
116 | |     } else if curr == next - 1 && curr > 0 {
    | |_____^
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#if_same_then_else

warning: writing `&mut Vec` instead of `&mut [_]` involves a new object where a slice will do
   --> src/map.rs:100:10
    |
100 |     res: &mut Vec<char>,
    |          ^^^^^^^^^^^^^^ help: change this to: `&mut [char]`
    |
    = 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/map.rs:96:11
   |
96 |     runs: &Vec<i64>,
   |           ^^^^^^^^^ help: change this to: `&[i64]`
   |
   = 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 `if` has identical blocks
  --> src/map.rs:84:49
   |
84 |       } else if curr > threshold && next_run == 1 {
   |  _________________________________________________^
85 | |     curr as i64
86 | |     } else if curr > threshold && next_run < curr as i64 {
   | |_____^
   |
note: same as this
  --> src/map.rs:86:58
   |
86 |       } else if curr > threshold && next_run < curr as i64 {
   |  __________________________________________________________^
87 | |     curr as i64
88 | |     } else {
   | |_____^
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#if_same_then_else

warning: this `if` has identical blocks
  --> src/map.rs:82:49
   |
82 |       } else if curr > threshold && next_run <= 0 {
   |  _________________________________________________^
83 | |     curr as i64
84 | |     } else if curr > threshold && next_run == 1 {
   | |_____^
   |
note: same as this
  --> src/map.rs:84:49
   |
84 |       } else if curr > threshold && next_run == 1 {
   |  _________________________________________________^
85 | |     curr as i64
86 | |     } else if curr > threshold && next_run < curr as i64 {
   | |_____^
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#if_same_then_else

warning: this `if` has identical blocks
  --> src/map.rs:76:42
   |
76 |       } else if curr == k && next_run == 1 {
   |  __________________________________________^
77 | |     k as i64
78 | |     } else if curr == k && next_run < 0 {
   | |_____^
   |
note: same as this
  --> src/map.rs:78:41
   |
78 |       } else if curr == k && next_run < 0 {
   |  _________________________________________^
79 | |     k as i64
80 | |     } else if curr < threshold {
   | |_____^
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#if_same_then_else

warning: this `if` has identical blocks
  --> src/map.rs:74:46
   |
74 |       let run: i64 = if curr == k && next == k {
   |  ______________________________________________^
75 | |     k as i64
76 | |     } else if curr == k && next_run == 1 {
   | |_____^
   |
note: same as this
  --> src/map.rs:76:42
   |
76 |       } else if curr == k && next_run == 1 {
   |  __________________________________________^
77 | |     k as i64
78 | |     } else if curr == k && next_run < 0 {
   | |_____^
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#if_same_then_else
   = note: `#[warn(clippy::if_same_then_else)]` on by default

warning: unneeded `return` statement
  --> src/map.rs:92:5
   |
92 |     return run;
   |     ^^^^^^^^^^
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
help: remove `return`
   |
92 -     return run;
92 +     run
   |

warning: unneeded `return` statement
  --> src/map.rs:62:6
   |
62 |         return ms;
   |         ^^^^^^^^^
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
help: remove `return`
   |
62 ~         ms
63 |     },
64 ~     }
   |

warning: unneeded `return` statement
  --> src/map.rs:45:5
   |
45 |     return (sbwt, lcs);
   |     ^^^^^^^^^^^^^^^^^^
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
help: remove `return`
   |
45 -     return (sbwt, lcs);
45 +     (sbwt, lcs)
   |

warning: use of `unwrap_or` to construct default value
  --> src/build.rs:85:36
   |
85 |     let params = params_in.clone().unwrap_or(SBWTParams::default());
   |                                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `unwrap_or_default()`
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unwrap_or_default

warning: use of `unwrap_or` to construct default value
  --> src/build.rs:58:36
   |
58 |     let params = params_in.clone().unwrap_or(SBWTParams::default());
   |                                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `unwrap_or_default()`
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unwrap_or_default
   = note: `#[warn(clippy::unwrap_or_default)]` on by default

warning: unneeded `return` statement
  --> src/build.rs:77:5
   |
77 |     return (sbwt, lcs);
   |     ^^^^^^^^^^^^^^^^^^
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
   = note: `#[warn(clippy::needless_return)]` on by default
help: remove `return`
   |
77 -     return (sbwt, lcs);
77 +     (sbwt, lcs)
   |

warning: struct `Logger` is never constructed
  --> src/main.rs:28:8
   |
28 | struct Logger;
   |        ^^^^^^
   |
   = note: `#[warn(dead_code)]` on by default

warning: unused variable: `input_list`
  --> src/main.rs:89:6
   |
89 |         input_list,
   |         ^^^^^^^^^^ help: try ignoring the field: `input_list: _`