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molpopgen / fwdpp

fwdpp is a C++ template library for implementing efficient forward-time population genetic simulations
http://fwdpp.readthedocs.io
GNU General Public License v3.0
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Add function to handle side effects of fixation removal #214

Open molpopgen opened 5 years ago

molpopgen commented 5 years ago

Adding site tables (#211) creates side-effects for simulations where fixations are "pruned". The required operations should be abstracted out into a function in fwdpp::ts.

molpopgen commented 4 years ago

Note for future self: we need a function to prune fixations from the tree sequences. There are two strategies one can envision:

  1. Remove mutations that lead to all alive nodes and zero preserved nodes. This method removes a subset of fixations.
  2. Remove all mutations that are on the root nodes of marginal trees with only 1 root. Without ancient samples, this accomplishes exactly what we want w/o the need for sample list updating.
molpopgen commented 4 years ago

I want to delay this until after #225 and #283 are dealt with. This one requires thinking.