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artic-network / civet

Cluster Investigation & Virus Epidemiology Tool
https://cov-lineages.org/resources/civet.html
GNU General Public License v3.0
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`-bicol` option also overrides `-sicol` option #150

Open rambaut opened 2 years ago

rambaut commented 2 years ago

By default the -sicol option uses column name sequence_name to match metadata to sequence id. But if you specify a different -bicol column to match your query then -sicol also changes. I don't think this is intuitive behaviour.

rambaut commented 2 years ago

Further to this perhaps it would be best to have an option -idcol which specifies the column to use for matching for all the options and then -sicol and -bicol (and -icol?) are used to override this for specific cases.