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ucsd-ccbb / VAPr

VAPr: A Python package for NoSQL variant data storage, annotation and prioritization
MIT License
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Optimize variant filtering/prioritization #15

Closed kmfisch closed 6 years ago

kmfisch commented 7 years ago

Write unit tests for queries, optimize performance

kmfisch commented 7 years ago

also double check query syntax (False vs false, etc)

AmandaBirmingham commented 6 years ago

tests/test_filtering.py contains unit tests for queries. Query performance has been improved by including sample id constraints only when we want to query a subset of sample ids rather than all of them (see https://github.com/ucsd-ccbb/VAPr/blob/8a232f170e2d087fb5c31b9b95c95e43b2e9ade3/VAPr/filtering.py#L98 )