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Improve GC counting code#332

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jakobnissen merged 1 commit intoBioJulia:masterfrom
jakobnissen:gccount
Jun 30, 2025
Merged

Improve GC counting code#332
jakobnissen merged 1 commit intoBioJulia:masterfrom
jakobnissen:gccount

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@jakobnissen
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When implementing BioJulia/Kmers.jl#48, I want to use BioSequences internals. Keep an open branch here for all optimisations I want to upstream.

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codecov bot commented Jun 4, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.86%. Comparing base (95d9218) to head (36b00f4).
Report is 21 commits behind head on master.

Additional details and impacted files
@@            Coverage Diff             @@
##           master     #332      +/-   ##
==========================================
+ Coverage   90.87%   91.86%   +0.99%     
==========================================
  Files          31       29       -2     
  Lines        2400     2804     +404     
==========================================
+ Hits         2181     2576     +395     
- Misses        219      228       +9     
Flag Coverage Δ
unittests 91.86% <100.00%> (+0.99%) ⬆️

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@jakobnissen jakobnissen marked this pull request as ready for review June 27, 2025 11:48
@kescobo
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kescobo commented Jun 27, 2025

Any of this that can be shunted off to BioGenerics.jl to avoid the need to duplicate? Or do you mean that BioSequences is a dependency of Kmers, and you want to make the change here instead of there?

@jakobnissen
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Yeah, I want to upstream some code from Kmers to BioSequences

@jakobnissen jakobnissen changed the title WIP: Improve bit-twiddling for kmer counting Improve GC counting code Jun 30, 2025
@jakobnissen jakobnissen merged commit d4b1426 into BioJulia:master Jun 30, 2025
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@jakobnissen jakobnissen deleted the gccount branch June 30, 2025 10:33
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2 participants