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add calclib #3

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nebfield wants to merge 60 commits intomainPGScatalog/pygscatalog:mainfrom devPGScatalog/pygscatalog:devCopy head branch name to clipboard

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Commits on Jan 16, 2024

• add exceptions

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• add QueryError

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• add InvalidAccessionErrors

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Commits on Jan 18, 2024

• refactor to include normalise() and private modules

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• add functions for normalise

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• add combine CLI

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Commits on Jan 19, 2024

• add test combineapp

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• Update README.md

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• use threadpoolexecutor

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Commits on Jan 22, 2024

• migrate to relative imports, add liftover

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• export genomebuild

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• update lockfile

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• update lockfile

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• fix import

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• add liftover to combine cli

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• fix test

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Commits on Jan 23, 2024

• improve dunder methods

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• fix test

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• add coverage

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• move read_header

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• Revert "add coverage"

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Commits on Jan 26, 2024

• add progress bar

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• add autoapi and docs

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• ignore autoapi

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• add targetvariants class

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Commits on Jan 29, 2024

• simplfy reading zstd/gz with xopen and add ID to TargetVariant

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• set up pyarrow support for TargetVariants

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Commits on Jan 30, 2024

• add tqdm

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• add pyarrow and exports

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• fix test

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• export NormalisedScoringFile

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• add dataframe classes

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• improve context managers

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Commits on Jan 31, 2024

• update matchlib

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Commits on Feb 1, 2024

• add tests

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Commits on Feb 2, 2024

• write out scorefiles

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• refactor writing out scorefiles

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• make plinkframes internal

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Commits on Feb 5, 2024

• add PlinkScoreFiles

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• fix labelling

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• use labelled df to write scoring files

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Commits on Feb 6, 2024

• fix tests

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• extract plinkscorefiles

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• fix tests

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Commits on Feb 7, 2024

• check log counts

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• fix test

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• add matchlib to docs

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• update exports

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• add matchlib pytest

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• install all extras for tests

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Commits on Feb 8, 2024

• add match cli

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• add matchapp tests

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• update pytest action

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• sort test output to get consistent results

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• bump dependency for node 20

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Commits on Feb 9, 2024

• add merge cli

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• fix test

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• add support for writing --split and --combined

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• update docs and tests

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• add polygenicscore to calclib

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