Added skalo/inputs.rs to src/ added an extra input command called Ind… #238
jhellewell14Annotations
2 errors and 38 warnings
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unresolved import `crate::skalo`:
src/lib.rs#L435
error[E0432]: unresolved import `crate::skalo`
--> src/lib.rs:435:12
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435 | use crate::skalo::read_input_file;
| ^^^^^ could not find `skalo` in the crate root
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clippy_check
Clippy had exited with the 101 exit code
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unused variable: `output_name`:
src/lib.rs#L790
warning: unused variable: `output_name`
--> src/lib.rs:790:13
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790 | output_name,
| ^^^^^^^^^^^ help: try ignoring the field: `output_name: _`
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unused variable: `max_missing`:
src/lib.rs#L789
warning: unused variable: `max_missing`
--> src/lib.rs:789:13
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789 | max_missing,
| ^^^^^^^^^^^ help: try ignoring the field: `max_missing: _`
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unused variable: `n_poly`:
src/lib.rs#L788
warning: unused variable: `n_poly`
--> src/lib.rs:788:13
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788 | n_poly,
| ^^^^^^ help: try ignoring the field: `n_poly: _`
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unused variable: `skf_file`:
src/lib.rs#L787
warning: unused variable: `skf_file`
--> src/lib.rs:787:13
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787 | skf_file,
| ^^^^^^^^ help: try ignoring the field: `skf_file: _`
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= note: `#[warn(unused_variables)]` on by default
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operator precedence can trip the unwary:
src/ska_dict/bloom_filter.rs#L63
warning: operator precedence can trip the unwary
--> src/ska_dict/bloom_filter.rs:63:9
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63 | / 1 << (key & 63)
64 | | | 1 << ((key >> 6) & 63)
| |____________________________________^ help: consider parenthesizing your expression: `(1 << (key & 63)) | (1 << ((key >> 6) & 63))`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bloom_filter.rs#L63
warning: operator precedence can trip the unwary
--> src/ska_dict/bloom_filter.rs:63:9
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63 | / 1 << (key & 63)
64 | | | 1 << ((key >> 6) & 63)
65 | | | 1 << ((key >> 12) & 63)
| |_____________________________________^
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
help: consider parenthesizing your expression
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63 ~ 1 << (key & 63)
64 + | 1 << ((key >> 6) & 63) | (1 << ((key >> 12) & 63))
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operator precedence can trip the unwary:
src/ska_dict/bloom_filter.rs#L63
warning: operator precedence can trip the unwary
--> src/ska_dict/bloom_filter.rs:63:9
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63 | / 1 << (key & 63)
64 | | | 1 << ((key >> 6) & 63)
65 | | | 1 << ((key >> 12) & 63)
66 | | | 1 << ((key >> 18) & 63)
| |_____________________________________^
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
help: consider parenthesizing your expression
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63 ~ 1 << (key & 63)
64 + | 1 << ((key >> 6) & 63)
65 + | 1 << ((key >> 12) & 63) | (1 << ((key >> 18) & 63))
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operator precedence can trip the unwary:
src/ska_dict/bloom_filter.rs#L63
warning: operator precedence can trip the unwary
--> src/ska_dict/bloom_filter.rs:63:9
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63 | / 1 << (key & 63)
64 | | | 1 << ((key >> 6) & 63)
65 | | | 1 << ((key >> 12) & 63)
66 | | | 1 << ((key >> 18) & 63)
67 | | | 1 << ((key >> 24) & 63)
| |_____________________________________^
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
help: consider parenthesizing your expression
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63 ~ 1 << (key & 63)
64 + | 1 << ((key >> 6) & 63)
65 + | 1 << ((key >> 12) & 63)
66 + | 1 << ((key >> 18) & 63) | (1 << ((key >> 24) & 63))
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L200
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:200:17
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200 | self = (self >> 64 & 0x0000000000000000FFFFFFFFFFFFFFFF)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 64) & 0x0000000000000000FFFFFFFFFFFFFFFF`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L200
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:200:16
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200 | self = (self >> 64 & 0x0000000000000000FFFFFFFFFFFFFFFF)
| ________________^
201 | | | (self & 0x0000000000000000FFFFFFFFFFFFFFFF) << 64;
| |_______________________________________________________________^ help: consider parenthesizing your expression: `(self >> 64 & 0x0000000000000000FFFFFFFFFFFFFFFF) | ((self & 0x0000000000000000FFFFFFFFFFFFFFFF) << 64)`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L198
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:198:17
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198 | self = (self >> 32 & 0x00000000FFFFFFFF00000000FFFFFFFF)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 32) & 0x00000000FFFFFFFF00000000FFFFFFFF`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L198
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:198:16
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198 | self = (self >> 32 & 0x00000000FFFFFFFF00000000FFFFFFFF)
| ________________^
199 | | | (self & 0x00000000FFFFFFFF00000000FFFFFFFF) << 32;
| |_______________________________________________________________^ help: consider parenthesizing your expression: `(self >> 32 & 0x00000000FFFFFFFF00000000FFFFFFFF) | ((self & 0x00000000FFFFFFFF00000000FFFFFFFF) << 32)`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L196
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:196:17
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196 | self = (self >> 16 & 0x0000FFFF0000FFFF0000FFFF0000FFFF)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 16) & 0x0000FFFF0000FFFF0000FFFF0000FFFF`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L196
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:196:16
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196 | self = (self >> 16 & 0x0000FFFF0000FFFF0000FFFF0000FFFF)
| ________________^
197 | | | (self & 0x0000FFFF0000FFFF0000FFFF0000FFFF) << 16;
| |_______________________________________________________________^ help: consider parenthesizing your expression: `(self >> 16 & 0x0000FFFF0000FFFF0000FFFF0000FFFF) | ((self & 0x0000FFFF0000FFFF0000FFFF0000FFFF) << 16)`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L194
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:194:17
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194 | self = (self >> 8 & 0x00FF00FF00FF00FF00FF00FF00FF00FF)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 8) & 0x00FF00FF00FF00FF00FF00FF00FF00FF`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L194
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:194:16
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194 | self = (self >> 8 & 0x00FF00FF00FF00FF00FF00FF00FF00FF)
| ________________^
195 | | | (self & 0x00FF00FF00FF00FF00FF00FF00FF00FF) << 8;
| |______________________________________________________________^ help: consider parenthesizing your expression: `(self >> 8 & 0x00FF00FF00FF00FF00FF00FF00FF00FF) | ((self & 0x00FF00FF00FF00FF00FF00FF00FF00FF) << 8)`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L192
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:192:17
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192 | self = (self >> 4 & 0x0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 4) & 0x0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L192
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:192:16
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192 | self = (self >> 4 & 0x0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F)
| ________________^
193 | | | (self & 0x0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F) << 4;
| |______________________________________________________________^ help: consider parenthesizing your expression: `(self >> 4 & 0x0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F) | ((self & 0x0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F0F) << 4)`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L190
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:190:17
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190 | self = (self >> 2 & 0x33333333333333333333333333333333)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 2) & 0x33333333333333333333333333333333`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L190
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:190:16
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190 | self = (self >> 2 & 0x33333333333333333333333333333333)
| ________________^
191 | | | (self & 0x33333333333333333333333333333333) << 2;
| |______________________________________________________________^ help: consider parenthesizing your expression: `(self >> 2 & 0x33333333333333333333333333333333) | ((self & 0x33333333333333333333333333333333) << 2)`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L136
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:136:17
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136 | self = (self >> 32 & 0x00000000FFFFFFFF) | (self & 0x00000000FFFFFFFF) << 32;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 32) & 0x00000000FFFFFFFF`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L136
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:136:16
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136 | self = (self >> 32 & 0x00000000FFFFFFFF) | (self & 0x00000000FFFFFFFF) << 32;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 32 & 0x00000000FFFFFFFF) | ((self & 0x00000000FFFFFFFF) << 32)`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L135
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:135:17
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135 | self = (self >> 16 & 0x0000FFFF0000FFFF) | (self & 0x0000FFFF0000FFFF) << 16;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 16) & 0x0000FFFF0000FFFF`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L135
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:135:16
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135 | self = (self >> 16 & 0x0000FFFF0000FFFF) | (self & 0x0000FFFF0000FFFF) << 16;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 16 & 0x0000FFFF0000FFFF) | ((self & 0x0000FFFF0000FFFF) << 16)`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L134
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:134:17
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134 | self = (self >> 8 & 0x00FF00FF00FF00FF) | (self & 0x00FF00FF00FF00FF) << 8;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 8) & 0x00FF00FF00FF00FF`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L134
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:134:16
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134 | self = (self >> 8 & 0x00FF00FF00FF00FF) | (self & 0x00FF00FF00FF00FF) << 8;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 8 & 0x00FF00FF00FF00FF) | ((self & 0x00FF00FF00FF00FF) << 8)`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L133
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:133:17
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133 | self = (self >> 4 & 0x0F0F0F0F0F0F0F0F) | (self & 0x0F0F0F0F0F0F0F0F) << 4;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 4) & 0x0F0F0F0F0F0F0F0F`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L133
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:133:16
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133 | self = (self >> 4 & 0x0F0F0F0F0F0F0F0F) | (self & 0x0F0F0F0F0F0F0F0F) << 4;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 4 & 0x0F0F0F0F0F0F0F0F) | ((self & 0x0F0F0F0F0F0F0F0F) << 4)`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L132
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:132:17
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132 | self = (self >> 2 & 0x3333333333333333) | (self & 0x3333333333333333) << 2;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 2) & 0x3333333333333333`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/bit_encoding.rs#L132
warning: operator precedence can trip the unwary
--> src/ska_dict/bit_encoding.rs:132:16
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132 | self = (self >> 2 & 0x3333333333333333) | (self & 0x3333333333333333) << 2;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider parenthesizing your expression: `(self >> 2 & 0x3333333333333333) | ((self & 0x3333333333333333) << 2)`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/split_kmer.rs#L210
warning: operator precedence can trip the unwary
--> src/ska_dict/split_kmer.rs:210:34
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210 | self.rc_upper = (self.rc_upper >> 2
| __________________________________^
211 | | | (IntT::from_encoded_base(rc_base(new_base))) << (2 * ((half_k * 2) - 1)))
| |______________________________________________________________________________________________^ help: consider parenthesizing your expression: `(self.rc_upper >> 2) | ((IntT::from_encoded_base(rc_base(new_base))) << (2 * ((half_k * 2) - 1)))`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/split_kmer.rs#L206
warning: operator precedence can trip the unwary
--> src/ska_dict/split_kmer.rs:206:34
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206 | self.rc_lower = (self.rc_lower >> 2
| __________________________________^
207 | | | ((IntT::from_encoded_base(self.rc_middle_base)) << (2 * (half_k - 1))))
| |____________________________________________________________________________________________^ help: consider parenthesizing your expression: `(self.rc_lower >> 2) | ((IntT::from_encoded_base(self.rc_middle_base)) << (2 * (half_k - 1)))`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
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operator precedence can trip the unwary:
src/ska_dict/split_kmer.rs#L199
warning: operator precedence can trip the unwary
--> src/ska_dict/split_kmer.rs:199:27
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199 | self.upper = (self.upper << 2
| ___________________________^
200 | | | (IntT::from_encoded_base(self.middle_base) << (half_k * 2)))
| |_____________________________________________________________________________^ help: consider parenthesizing your expression: `(self.upper << 2) | (IntT::from_encoded_base(self.middle_base) << (half_k * 2))`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#precedence
= note: `#[warn(clippy::precedence)]` on by default
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clippy_check
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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clippy_check
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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clippy_check
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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clippy_check
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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clippy_check
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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