search

tskit-dev / msprime

Simulate genealogical trees and genomic sequence data using population genetic models
GNU General Public License v3.0
170 stars 84 forks source link

Recording recombination events #2186

Closed GertjanBisschop closed 1 year ago

GertjanBisschop commented 1 year ago

We currently record recombination events with two nodes, one for each lineage that contributed ancestral material to the child of those nodes. Forwards in time one would say that this child node is the recombinant. This can clearly be confusing: see this tskit issue.

Digging into previous issues, the 2 RE-node encoding seems to have been discussed earlier (see #1942, #1979). I am struggling to see though how our more flexible additional_nodes API would change anything about the issues raised previously. I might be wrong, will read through what was discussed previously.

jeromekelleher commented 1 year ago

Yes, I think this isn't something we can change. My bad.