search

MDU-PHL / pango-collapse

app to collapse Pango lineages for reporting
https://mdu-phl.github.io/pango-collapse/
GNU General Public License v3.0
10 stars 1 forks source link

Split recombinants #8

Open Wytamma opened 11 months ago

Wytamma commented 11 months ago

Currently pango-collapse treats recombinants as separate lineages because there's not a clear way to collapse the multiple lineages.

For example if you have BA.2.10 and B.1.1.529 in the collapse file how should you collapse XBB? This gets more complicated for more diverse recombinants. 

           BM.1.1.1 -> B.1.1.529
         /
   XBB -
         \
           BJ.1 -> BA.2.10

We could potentially report both lineages? But that means you'd have to deal with multiple values in a single column in the output file.

Can we add this behaviour and make it configurable via a opt-in cli flag like --split-recombinants?

Related to (#7)