WIP: skipmer improvements

[bluegenes]

Make skipmers robust, but keep #3395 functional in the meantime.

This PR:

• enables second skipmer types, so we have m1n3 in addition to m2n3
• switches to a reading frame approach for both translation + skipmers, which means we first build the reading frame, then kmerize, rather than building kmers + translating/skipping on the fly
• avoids "extended length" needed for skipping on the fly

Since this changes the SeqToHashes strategy a bit, there's one python test where we now see a different error.

Future thoughts:

• with the new structure, it would be straightforward to add validation to exclude protein k-mers with invalid amino acids (X). I guess I'm not entirely sure what happens to those atm...

[codspeed-hq]

CodSpeed Performance Report

Merging #3415 will not alter performance

_{Comparing parameterize-skips (28781bc) with try-skipmers (d7f59cf)}

Summary

✅ 21 untouched benchmarks

[codecov]

Codecov Report

Attention: Patch coverage is 78.30189% with 23 lines in your changes missing coverage. Please review.

Project coverage is 86.38%. Comparing base (d7f59cf) to head (28781bc).
Report is 18 commits behind head on try-skipmers.

Files with missing lines	Patch %	Lines
src/core/src/signature.rs	83.14%	15 Missing ⚠️
src/core/src/encodings.rs	0.00%	6 Missing ⚠️
src/core/src/sketch/minhash.rs	0.00%	2 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff                @@
##           try-skipmers    #3415      +/-   ##
================================================
- Coverage         86.45%   86.38%   -0.07%     
================================================
  Files               137      137              
  Lines             16141    16155      +14     
  Branches           2219     2219              
================================================
+ Hits              13955    13956       +1     
- Misses             1879     1892      +13     
  Partials            307      307              

Flag	Coverage Δ
hypothesis-py	25.43% <ø> (ø)
python	92.40% <ø> (ø)
rust	62.32% <78.30%> (-0.25%)	⬇️

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