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MRG: Add threaded multigather to pyo3_branchwater code; add fastmultigather
CLI plugin.
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… into multigather
… into multigather
ctb
changed the title
Add threaded multigather to pymagsearch code.
MRG: Add threaded multigather to pyo3_branchwater code; add Aug 12, 2023
fastmultigather
CLI plugin.
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Add
fastmultigather
to plugin.This PR refactors the code into more reusable chunks and adds
fastmultigather
, which will take in multiple queries and run gather upon them. The basic memory usage will increase fromfastgather
because the multigather code loads multiple metagenomes into memory, but in exchange we only load the database once (at the beginning) and then process multiple metagenomes with it. 🎉Specifically, the multigather code does the following: