Redesigned preprocessing #215
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… optimizations do SILO using duckdb
… structs and logic Remove obsolete partitioning structs and logic Remove no longer necessary code in preprocessing_config Remove obsolete partitioning structs and logic Remove MetadataReader
…of preprocessing and shorter functions
fengelniederhammer
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fengelniederhammer
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Dec 18, 2023
Since GenSpectrum/LAPIS-SILO#215 is merged now
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Dec 19, 2023
Since GenSpectrum/LAPIS-SILO#215 is merged now
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Still very much WIP, but this is a redesign of the entire preprocessing to
(i) get rid of the CSVReader dependency
(ii) more easily allow generic input files
(iii) prepare internal storage of sequences for bulk download and then down the road: full SQL support via duckdb