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Second, this may be an opportunity to improve the relationship between AnyVar and vrs-python. The AnyVar VcfRegistrar extends VCFAnnotator and overrides the internal _get_vrs_object() method. The only reason for doing so is to integrate with the AnyVar object store. But then AnyVar does not actually re-implement all the vrs-python functionality, which means there will be continual drift between the two implementations. It seems like whether you annotate a VCF with VRS IDs directly in vrs-python or via AnyVar that the behavior and result should be the same. That would make the tools easier to adopt and use. So perhaps a re-design of the vrs-python VCFAnnotator to provide a listener or callback. For example:
classVCFAnnotator:
# ...existing implementation...defon_vrs_object(self, vcf_coords: str, vrs_object: VrsObject) ->bool:
"""Called for each calculated VRS object prior to it being added to the VCF file. :param vcf_coords: The VCF coordinates of the VRS object :param vrs_object: The computed VRS object :return: True if the VRS object should be added to the output VCF, False otherwise """returnTrue# And in AnyVarclassVcfRegistrar(VCFAnnotator):
defon_vrs_object(self, vcf_coords: str, vrs_object: VrsObject) ->bool:
self.av.put_object(vrs_object)
returnTrue
originally posted by @ehclark in #470 (comment)
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