MRG: avoid clones by using new Signature::try_into() -> KmerMinHash
#471
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…water into ctb_misc_cleanup
…water into ctb_misc2
…water into ctb_misc2
…water into ctb_misc_cleanup
#434) * preliminary victory * compiles and mostly runs * cleanup, split to new module * cleanup and comment * more cleanup of diff * cargo fmt * fix fmt * restore n_failed * comment failing test * cleanup and de-vec * create module/submodule structure * comment for later * get rid of vec * beg for help * cleanup and doc
…water into ctb_misc2
ctb
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Signature::try_into() -> KmerMinHashSignature::try_into() -> KmerMinHash
This was referenced Oct 13, 2024
luizirber
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Oct 15, 2024
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Oct 15, 2024
…ing (#3352) This PR builds on the refactoring in #3342 to do less downsampling and also avoids doing intersections twice (per #3196). Benchmarks in sourmash-bio/sourmash_plugin_branchwater#471 are pretty astonishing... Fixes #3196 --------- Co-authored-by: Luiz Irber <[email protected]>
…water into avoid_clones
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NOTE: PR into #430. Includes #467.
gather comparison
Comparing latest MultiCollection benchmarks from #430 to this PR, for SRR1976948, we see:
manysearch comparison
Comparing to
manysearchbenchmarking results in #463, we see:* this run used sig.zip files and manifest CSVs in the benchmarking.
So this is a major improvement in both time and memory over, really, everything since v0.8.6!
The last line shows that there is now a major benefit to using lists of .sig.zip files and/or manifest CSVs that point at zip files: basically, only the relevant sketch (k=21/31/51 or whatever) is being loaded, and there's no double-loading to generate the manifest (as introduced in 0.9.0). This was supposed to be one of the major benefits of #430 so I'm very happy about these results showing that's the case!! The extra memory usage is presumably because so much more of the time is being spent in calculations vs loading.