propagate purpose of sequencing to genbank and gisaid #201
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This PR includes two changes:
purpose_of_sequencing
field (or, failing that, thepurpose_of_sampling
field) into the Genbanknote
field and the GISAIDadditional_host_info
field, if either are available. If it is set to a PHA4GE-ontology-defined value for Variants of Concern screening, rewrite it to match a SPHERES-ontology-defined value for the same. The relevant python code is in theviral-phylo
repo.align_to_ref_merged_reads_aligned
andalign_to_ref_merged_bases_aligned
columns to theassembly_stats_tsv
output fromsarscov2_illumina_full
andsarscov2_sra_to_genbank