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Extra large kmers #17

Merged
merged 11 commits into from
Sep 27, 2024
Merged

Extra large kmers #17

merged 11 commits into from
Sep 27, 2024

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OndrejSladky
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@OndrejSladky OndrejSladky commented Mar 21, 2024

Support for k-mers up to 128.
Currently it is about 4 times slower for k-mers >64 than for k-mers up to 64.
My guess that the additional 2 times slowdown (2 times slower is required as software implementation of the type) comes from additional operations needed to compute hashes etc.

I.g. this could be optimized but i don't think it's a priority. Even the fact that those k are supported and they are not terribly slow should be an advantage.

Currently the only downside to this PR is rouhgly 2 times slowdown of compilation. I'll see what can be done with it.
EDIT: the compilation now takes about 3sec on my PC which i.g. should be okay.

@OndrejSladky OndrejSladky marked this pull request as draft March 21, 2024 13:33
@OndrejSladky OndrejSladky linked an issue Mar 21, 2024 that may be closed by this pull request
@OndrejSladky OndrejSladky marked this pull request as ready for review April 25, 2024 20:37
@karel-brinda karel-brinda merged commit 7718e3f into main Sep 27, 2024
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Support for k-mer sizes > 64
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