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WGS-TB / PathOGiST

This repository contains the pipeline for the multi-criterion genomic analysis of bacterial pathogens
GNU General Public License v3.0
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Spoligotype Distance Matrix Generation #6

Closed jwcodee closed 5 years ago

jwcodee commented 5 years ago

Spotyping does not generate distance matrix. Need to add the capability to generate distance matrix to both the distance and all subcommand in PATHOGIST

jwcodee commented 5 years ago

On a similar note, since spoligotyping is limited to TB, whats the plan for the user if they are running pathogist on non TB. Do they remove the spoligotyping from the config.yaml or what?

jwcodee commented 5 years ago

The spotyping functions are fixed and are hooked up to distance subcommand. The all subcommand hook up is currently being tested