ga4gh / ga4gh/vrs-python

Create VcfReader class or standalone function which takes INFO key-value pairs and reconstructs VRS Alleles

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Dominant language
Python
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Description

We let people annotate VCFs with info we claim is enough to reconstruct the VRS Alleles for each record, but we don't provide the code to do that.

Providing this would be useful to users, would prove that the annotations do work, and would be useful in testing.

If we go the VcfReader route we should provide a generator interface over the records which returns the original pysam records, along with the list of VRS Allele objects constructed from the annotations.

If the input is not already annotated, it should fail.

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