griffithlab / civicpy

A python interface for the CIViC db application
MIT License
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Update the VCFWriter to handle indels #44

Closed susannasiebert closed 5 years ago

susannasiebert commented 5 years ago

This PR also removes the validation of variants on the sequence ontology and instead simply validates the coordinates. A convenience function is_valid_for_vcf on added that can be called on a variant object to determine whether or not it can be represented in a VCF. This method also gets called when adding a variant to a VCFWriter object.