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Add ancestry normalisation to calclib #4

Merged
merged 24 commits into from
Mar 8, 2024
Merged

Add ancestry normalisation to calclib #4

merged 24 commits into from
Mar 8, 2024

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nebfield
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@nebfield nebfield commented Mar 1, 2024

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* add exceptions

* add QueryError

* add InvalidAccessionErrors

* refactor to include normalise() and private modules

* add functions for normalise

* add combine CLI

* add test combineapp

* Update README.md

* use threadpoolexecutor

* migrate to relative imports, add liftover

* export genomebuild

* update lockfile

* update lockfile

* fix import

* add liftover to combine cli

* fix test

* improve dunder methods

* fix test

* add coverage

* move read_header

* Revert "add coverage"

This reverts commit 0776f31.

* add progress bar

* add autoapi and docs

* ignore autoapi

* add targetvariants class

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

* set up pyarrow support for TargetVariants

* add tqdm

* add pyarrow and exports

* fix test

* export NormalisedScoringFile

* add dataframe classes

* improve context managers

* update matchlib

* add tests

* write out scorefiles

* refactor writing out scorefiles

* make plinkframes internal

* add PlinkScoreFiles

* fix labelling

* use labelled df to write scoring files

* fix tests

* extract plinkscorefiles

* fix tests

* check log counts

* fix test

* add matchlib to docs

* update exports

* add matchlib pytest

* install all extras for tests

* add match cli

* add matchapp tests

* update pytest action

* sort test output to get consistent results

* bump dependency for node 20

* add merge cli

* fix test

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

* update docs and tests
@nebfield nebfield marked this pull request as ready for review March 8, 2024 11:47
@nebfield nebfield merged commit ac15d59 into dev Mar 8, 2024
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@nebfield nebfield deleted the ancestry branch March 8, 2024 11:47
nebfield added a commit that referenced this pull request Mar 8, 2024
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