Open hyanwong opened 2 years ago
I guess this is the record_full_arg=True
option for the FixedPedigree model?
I guess this is the
record_full_arg=True
option for the FixedPedigree model?
I'm not sure that's quite the same. For instance, imagine if there is no recombination. We might still want all the intermediate nodes on all lineages present.
Tthe pedigree simulation code seems not to produce "unary" nodes for the intermediate nodes in the tree sequence, so even if a lineage goes through a known node, this information is lost. For instance, consider the following simulation:
Giving
If all nodes on a lineage were retained, we should have unary nodes at the same timepoints as nodes 10 and 14 on each of the other lineages. Indeed, these unary nodes, which appear to have been simplified away, might even be a coalescent node somewhere else in the simulation: I suspect this would be useful extra information to be able to retain, in some circumstances.