rust-bio / rust-bio / 1155
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johanneskoester 
Myers matching for long patterns (block-based implementation) (#229)

* Fix for #117

* Make generic for different integer sizes and support any ambiguities

* Implement a traceback algorithm for obtaining a hit alignment

* Add cfg switch to handle the u128 type

* myers: Correct typing error

* Simplify bit vector type handling by removing the separate trait

Since type aliases consisting of multiple traits are not possible, there is still a trait named 'BitVec', which has no methods and is implemented for any type that meets the conditions.

* Switch to builder patttern for handling of ambiguities

* Fix distance() to return the smallest dist., not the one of the last hit

* Fix Alignment::yend

* Fix Alignment::pretty()

* Fix benchmark

* More consistent variable naming

* Correct a comment

* Temporary constructor func. for Alignment

* fmt

* fmt

* Change MyersBuilder functions to be non-consuming

* Apply clippy hint and improve documentation

* Fix another clippy warning

* Remove unnecessary associated type from BitVec trait

* Go back to require ExactSizeIterator in patterns

Patterns too long for BitVec caused overflow with left shift instead fo 
being caught by assertion

* Handle patterns of maximum length in State constructor

For example, patterns of lenght 64 caused a left shift overflow with 
BitVec = u64

* Rename variable and remove misleading description

* myers: use another way of constructing bit mask in move_up_many!()

* myers: fix another panic occurring with patterns of maximum length

* myers: Ensure that empty text does not cause panic

* Add infrastructure for fuzzing & fuzz target for myers module

* myers: make rustfmt happy

* myers: Change distances back to be stored in u8

Results in roughly 30% performance gain.

* myers: rename 'find_all_pos' to 'find_all'

* myers: Change traceback again; prefer substitutions over insertions

If there are mu... (continued)

7460 of 8131 relevant lines covered (91.75%)

0.92 hits per line

Jobs
ID Job ID Ran Files Coverage
1 1155.1 0
91.75
 Travis Job 1155.1
Source Files on build 1155
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