Various AI agent-generated fixes - #348
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## master #348 +/- ##
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+ Coverage 90.87% 92.12% +1.24%
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Files 31 29 -2
Lines 2400 2857 +457
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+ Hits 2181 2632 +451
- Misses 219 225 +6
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Had an AI agent fix up grammar, typos and formatting.
GeneticCode is an AbstractDict{UInt64, AminoAcid}, and exposes a getindex
function which does not boundscheck, thereby exposing UB.
I think this issue is a smell of a deeper design issue with GeneticCode: If it
is an AbstractDict, why is the key an undocumented and internal encoding?
Why is GeneticDict private? How can users make their own?
Here, do a bandaid solution. We fix it properly in a breaking release.
When matching empty strings in sequence search, an edge case meant that the search could not advance, resulting in an infinite loop. Always advance the search even for zero-length results.
Fix issue where join! on unknown-sized iterators did not shrink the target sequence after joining. Also redesign it: Assume AbstractArray, AbstractSet and Tuple are stateless, and for all other iterables, collect the iterable first. Then, precompute the full length, copy in the content and verify the size matches.
E.g. `findnext(!=(DNA_A), rna"A")` should just return 1 without searching the RNA because DNA is unencodable in the RNA alphabet.
Previously, this would mutate the sequence and then throw when attempting to resize!. Now, add a method that throws up front. This does not solve the problem generally for non-resizable BioSequences, but I don't think there is a good way to address that. At least we can add this safety check even while not solving it generically.
GeneticCode subtypes AbstractDict, and so must yield Pairs.
This was documented but not actually implemented. Implementation is trivial.
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Had an AI agent review bugs in the codebase. I will fix them over a period of time, then merge.