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filter: Rewrite using SQLite3#1242

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victorlin wants to merge 15 commits intomasternextstrain/augur:masterfrom victorlin/filter-rewrite-using-sqlitenextstrain/augur:victorlin/filter-rewrite-using-sqliteCopy head branch name to clipboard

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Commits on Sep 6, 2024

• io: Add class interfaces for working with SQLite3

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• io: Split Metadata class into TabularFile and File

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• Allow custom delimiter, header, columns to TabularFile

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• io/sqlite3: Add methods to manage primary indexes

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• io/sqlite3: Add debugging function

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• dates: Allow ambiguity resolution method in get_numerical_date_from_value()

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• filter/run: Split into smaller functions by using shared variables in constants.py

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• (1/3) filter: Rewrite using SQLite3

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• 🚧 (2/3) filter: Rewrite using SQLite3

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• 🚧 (3/3) filter: Rewrite using SQLite3

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• dates: Remove unused is_date_ambiguous()

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• 🚧 filter: Add a --debug option

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• 🚧 Add timing output to --debug for long-running functions

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• 🚧 filter: Add --query-sqlite option

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• 🚧 support db file as metadata index

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