* cleaner version of scores

* refactor: remove lazy_static + clean up scores

* clean

* use std lazylock

* Update MSRV to 1.80

* Update README.md with updated MSRV

---------

Co-authored-by: Felix Wiegand <[email protected]>

* fixed clippy warnings caused by legacy numeric constants

* correct formatting

… LazyMatches::dist_at() (#640)

This PR includes some changes to the `bio::pattern_matching::myers`
code. The initial motivation was to improve the [pattern matching
feature](https://markschl.github.io/seqtool-docs/find/#approximate-matching)
in [this](https://github.com/markschl/seqtool) sequence handling tool,
but I ended up also including some code from refactoring efforts that I
actually started some years ago already.

Summary:

* Added a `LazyMatches::dist_at()` method complementing the already
existing `hit_at`, `path_at`, etc.
(e318e4c)
* Refactoring of code that computes the alignment path (traceback) with
the aim to make it more understandable
(f8d1f89,
53d177b,
be1e35c). The methods of the
`TracebackHandler` trait were changed (code re-grouped), but the
behaviour should not have changed (alignment paths found to be correct
with fuzzing). In addition, there are many additional doc comments, and
some more references to the Myers paper. A small deviation from the
paper in `long.rs` (no padding with wildcards) is more clearly
documented. I looked at this again, but I can't find any issues with my
approach. The fact that the simple and block-based implementation yield
the same results (with fuzzing, comparing single u64 or u128 with
multi-u8 block version) further suggests there are no issues with this
code.
* The fuzzing code was extended to also test ambiguities and wildcards
and include a comparison to Edlib (commented out to avoid introducing
another dependency) (f8d1f89,
97104c2)
* Fixed two small bugs:
1. Fix panic in `LazyMatches::...at()` methods if called with an end
position for a match with distance > k
(e318e4c)
2. fixed panics with very large `max_dist`
(`...::long::Myers::distance()` did always panic)
(5445989)
* Updated the documentation, also improving the module descriptions,
which were partly outdated (not adapted to the block-based
implementation) (1d39dec). A small
change to the `ukkonen` docs was also made
(1a7432d)
* Some performance evaluations (thereby simplifying the benchmark code,
47f8fe6), added some `#[inline]`
(b383561), although I had to remove one
again due to some performance regression I don't fully understand
(694f573). Bottom line:
`Myers::find_all()` appears faster now, everything else is equally fast.
* Fixed some small warnings in other `pattern_matching` modules
(298b1f9). I checked that it compiles
under Rust 1.65.0, although I had to downgrade to multimap 0.10.0 for
this.
* Updated the copyright notice in mod.rs with my name
(1d39dec) (hopefully fine like this,
otherwise I can adjust)
* Slightly changed the behaviour of `MyersMatcher::ambig()`, allowing it
to be called multiple times on the same symbol
(3be7543)

Possible remaining issues.
* The inlining of `fn next...()` is now a little inconsistent,
unfortunately (due to 694f573)
* I'm not entirely sure if the term *linear-time* in
`pattern_matching/mod.rs` still applies for the block-based algorithm,
which is O(nk). If k is kept constant, then time scales linearly with
text length (which would also qualify the Ukkonen algorithm as being
linear-time).

Thanks for considering this PR!

---------

Co-authored-by: markschl <[email protected]>
Co-authored-by: Johannes Köster <[email protected]>

Added
[BEDPE](https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format)
files reader and writer.

The code was copied from `src/io/bed.rs` and slightly modified, as such
the tests are nearly the same and `cargo test` passed.

---------

Co-authored-by: Johannes Köster <[email protected]>
Co-authored-by: Johannes Koester <[email protected]>

🤖 I have created a release *beep* *boop*
---


## [3.0.0](v2.3.0...v3.0.0)
(2025-09-19)


### ⚠ BREAKING CHANGES

* improved API and internals for pattern_matching::myers and add
LazyMatches::dist_at()
([#640](#640))

### Features

* Added BEDPE file support
([#631](#631))
([61adf2a](61adf2a))
* improved API and internals for pattern_matching::myers and add
LazyMatches::dist_at()
([#640](#640))
([122a44d](122a44d))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>