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MDU-PHL / pango-collapse

app to collapse Pango lineages for reporting
https://mdu-phl.github.io/pango-collapse/
GNU General Public License v3.0
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Should aliases be collapsed? #6

Closed ammaraziz closed 11 months ago

ammaraziz commented 1 year ago

Hi Wytamma,

I've been seeing weird results in our reporting output. After scratching my head, it turns out pango-collapse is collapsing aliases into non-aliased lineages. For example: EG.1 is an alias of XBB.1.9.2 which is on in collapse.txt.

The simple solution is to add the alias of XBB.1.9.2 to collapsed.txt but this will require constant monitoring of aliases. Another solution is to check the alias key to see if any lineage on the collapsed list has an alias and if it does, return the alias.

This is probably super low on your priority list because of budget changes. If I have time I will try to submit a pull request (but this will be in August!).

Thanks,

Ammar

ammaraziz commented 1 year ago

Another example: GA.1 collapsed into XBB. This one is especially confusing:

GA ->  XBB.1.17.1 -> XBB
Wytamma commented 1 year ago

Hey @ammaraziz, I think it’s the intended behaviour? EG.1 is XBB.1.9.2.1. So, if XBB.1.9.2 is in the collapse file all the sub-lineages should be collapsed up to XBB.1.9.2.

Same with GA.1... GA.1 is XBB.1.17.1.1. Because XBB is in the collapse file GA.1 is collapsed up to XBB. If any of the other lineages along the path from GA.1 to XBB were in the collapse file then GA.1 would only be collapsed up to that lineage.