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Dev#61

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jermp merged 35 commits intomasterfrom
dev
Jun 5, 2025
Merged

Dev#61
jermp merged 35 commits intomasterfrom
dev

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@jermp jermp commented Jun 5, 2025

This PR includes several changes and build performance improvements:

  • added flag to CMakeLists.txt to gate option arch=native (CC @rob-p);
  • user can now specify a RAM limit to build the index;
  • the build_index step is now done in parallel;
  • blocks of minimizer tuples are sorted in parallel using a custom parallel_sort function, coded in parallel_sort.hpp (which might also have independent interest);
  • streaming of minimizers during file parsing;
  • minimizers are now computed in streaming way using the "re-scan" method which is faster (and simpler) than the "monotone-queue" method used before;
  • the next() method of minimizer_enumerator is templated as it used to be before.

@jermp jermp merged commit d21959b into master Jun 5, 2025
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