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[EXP] some experiments in speeding up CounterGather #2113

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@ctb ctb commented Jul 9, 2022

Note: PR into #2123.

Digging into #1771 more.

Things to try -

  • screen out identical matches
  • try out an in-memory / on-disk SqliteIndex underneath counter?
  • apply threshold to entire counter class, rather than on a per-peek basis
  • try removing hashes in CounterGather

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codecov bot commented Jul 9, 2022

Codecov Report

Merging #2113 (a236e7a) into latest (526f785) will increase coverage by 0.07%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           latest    #2113      +/-   ##
==========================================
+ Coverage   91.61%   91.68%   +0.07%     
==========================================
  Files          99       99              
  Lines       11017    11022       +5     
  Branches     2167     2167              
==========================================
+ Hits        10093    10106      +13     
+ Misses        621      612       -9     
- Partials      303      304       +1     
Flag Coverage Δ
python 91.68% <100.00%> (+0.07%) ⬆️

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Impacted Files Coverage Δ
src/sourmash/index/__init__.py 96.36% <100.00%> (-0.36%) ⬇️
src/sourmash/sbt_storage.py 89.15% <0.00%> (+3.38%) ⬆️

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Base automatically changed from update/counter_gather to latest July 16, 2022 15:17
@ctb ctb changed the base branch from latest to avoid_remove_many July 18, 2022 13:19
Base automatically changed from avoid_remove_many to latest July 18, 2022 16:29
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ctb commented Jul 24, 2022

closing - see #2145.

@ctb ctb closed this Jul 24, 2022
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