[maps.data] PGG Data is missing from some countries

farhat-lab / gentb-site

The genTB project, the Django site, variant calling and prediciton pipeline, and mapping pipeline with hooks to two ravens

https://gentb.hms.harvard.edu

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[maps.data] PGG Data is missing from some countries #109

Closed mahafarhat closed 5 years ago

mahafarhat commented 7 years ago

PGG data should be available for all strains yet it only shows for some countries- we need to investigate why and repair this

mahafarhat commented 6 years ago

All PGG should be replaced by with a spoligotype generated with the C++ code or coll-et-al lineage generated with Luca's code. Definitely a task for our interns.

mahafarhat commented 6 years ago

We have new lineage labels generated by @ejfresch we should use these instead of PGG/spoligo/MIRU families etc, we should have one lineage call per isolate, and remove others/unnecessary redundancies.

Mohib with @ejfresch 's help

mahafarhat commented 5 years ago

done!