Include fasta adjudicated mutations in json

oxfordmmm / gnomonicus

Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants

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Include fasta adjudicated mutations in json #45

Closed JeremyWesthead closed 11 months ago

JeremyWesthead commented 11 months ago

In cases of FASTA adjudication, currently only the effects block of the JSON is populated. This PR moves to report these within the mutations block where appropriate. This does not affect the mutations CSV. This should allow GPAS to pull out the ref/alt values in the usual manner for display. This only affects amino acid null calls (as nucleotide calls are already picked up)

JeremyWesthead commented 11 months ago

I wasn't sure if that would be desired as these come from the FASTA file rather than the VCF. Wouldn't be difficult to add though