Add a "recipes" page for the documentation, which provide tested examples of
how to use BioSeque...

In BioJulia discussion 11, and BioJulia/Contributing, we've decided to make the
template less ve...

We accidentally didn't run CI on Julia 1.5 before.

This was not needed previously as the version of Random was tied to the version
of Julia, but in...

This also fixes an issue in the translation code, and adds another constructor
to LongSubSeq tha...

Relax the requirement of `Alphabet`, such that it is no longer necessary to
check for a valid en...

This has been consistently broken ever since it was introduced. Also, the tests
take like 20 min...

Use a more principled approach, such that we now guarantee that ambiguous DNA
and RNA is transla...

* Remove the erroneous method Base.:*() with empty Varargs, and make sure
that there is at lea...

Mitigate breaking Julia change for Julia 1.11

Turns out Julia is allowed to change the types ...

DNA_Gap cannot be meaningfully translated, as it does not correspond to any
nucleotides, not ev...

Update URLs from biojulia.net to biojulia.dev

Even though passing your own state to iterate is undefined behaviour, we can use a trick from `B...

This only applies to LongDNA encoded from byte-like inputs, since this uses a
fast path in BioS...

This object is undocumented internals, and is replaced by default_rng().

When materializing a seqview, a slice of the underlying buffer is copied
directly, for efficien...

BioSequences pirated BioSymbols by overloading `gap`, `isambigous`, `isgap` and
`iscertain`. Re...

* Add iterate method for Alphabets

* fixup

* fixup

Add the SnoopPrecompile dependency to improve precompilation. While BioSequences
is already eff...

Documentation for `findall` method.

- Add doctests to unit tests.
- Include minor doctest corrections.
- Enable checkdocs for buil...

* Add rand!([::AbstractRNG], ::LongSequence, [::Sampler]) methods

I had apparently forgotten ...

Commit 3c8f501 changed Julia compat to from 1.5 to 1.6, since the join method
used sum with ini...

Current hashing behaviour hashes equal biosequences with different encodings to
different value...

Small fixes and simplifications

Fix ambiguity errors

Julia 1.8 introduces LazyString, which is useful in error throwing code....

Previously, it was only possible to join BioSequences. Now, one can call
join(LongRNA{2}, (RNA_...

* Sequence hashing: Bugfix and slight simplification

Slightly simplify hashing code and fix a...

Fixes #225

Add tests for edge case

Fixup

Fiixup

🐛 in iscanonical / canonical
Fixes #225

🐛 in...

Add `findall` method

BioSequences recently rewrote the entire set of `Base.find*` functions f...

Co-authored-by: Ciarán O’Mara <[email protected]>

* Bugfix: Fix unbound function call `count_zero_nibbles` to `count_0000_nibbles`
* Bugfix: Fix ...

* CHANGELOG: Point users to MinHash.jl / Kmers.jl for removed functionality in v3
* CHANGELOG: ...

Co-authored-by: Ciarán O'Mara <[email protected]>

Add more tests and fix various small bugs

Add `BioSequences.has_interface` function

* Rename the un-released method `stringbyte(::Alphabet, ::UInt8)` to `ascii_encode`
* Remove th...

* Remove sequence conversion to/from String and Vector

* Fix REPL blocks in docs
* Fix ambiguities in doctests

Remove StableRNGs from dependencies.
Methods for LongSequence generation now default to using R...

Fix documenter warnings about broken links

Fix doctests after type alias renaming

Approximate search now returns nothing when no match is found

Remove undefined exports

Add findfirst method for BioSymbol

Export RE.Regex and RE.RegexMatch as BioRegex and BioRegexMatch

Add fast equality for BioSequence