iossifovlab / gpf

GPF: Genotypes and Phenotypes in Families
MIT License
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Fix impala2 import #632

Closed IvoTod closed 5 months ago

IvoTod commented 5 months ago

Background

Impala2 import had a bug when using has_variants helper method, due to the check being faulty in specific cases.

Implementation

Schema2 import is more dependent on the study layout being provided. Now there are 2 schema2 helpers for creating a study layout, one that uses the old behavior and creates all tables, and another intended for loading/reading, which checks for variants tables before adding them to the layout