In dev branch these statistics are being calculated in make_beadplots but they are not being written to the JSON file:
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val['lineages'][lineage] = { |
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'nsamples': len(samples), |
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'lastcoldate': max(x['covv_collection_date'] for x in samples), |
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'residual': residuals[lineage] if lineage in residuals else 0, |
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'max_ndiffs': max(ndiffs), |
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'mean_ndiffs': sum(ndiffs) / len(ndiffs), |
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'mutations': mutations[lineage], |
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'infections': infection_prediction[lineage]['infections'], |
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'hunepi': infection_prediction[lineage]['hunepi'] if 'hunepi' in infection_prediction[lineage] else None, |
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'raw_lineage': lname |
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} |
In
devbranch these statistics are being calculated inmake_beadplotsbut they are not being written to the JSON file:covizu/batch.py
Lines 529 to 539 in 06848b3