Read new sample metadata fields from MGS repo
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dp-rice commented
Jeff has been adding some new sample metadata to the MGS pipeline, including county and is_enriched. Our code should read this data and use it where appropriate. @jeffkaufman, when you think the metadata fields are reasonably stable could you please list them here?
It would also be good to be able to read incomplete entries (including ones that are missing the reads field) and handle the missing data without crashing.
dp-rice commented
From @jeffkaufman in #56:
When you update this to pull the latest data you'll want to either limit to ones with enrichment=viral or calculate separate estimates for viral and panel enrichment.