Jerome Kelleher
Jerome Kelleher
It would be handy to have a top-level function that does simple simulations of ancestry and mutations. How about we do something like ```python def sim( samples, *, sequence_length=None, recombination_rate=None,...
#1371 added some type annotations for data classes. We should also annotate the top-level functions, as much as we can (some will be a little convoluted). Also add some documentation...
sim_ancestry supports providing an arbitrary rate map as input, but the underlying infrastructure currently assumes a single rate and will trip some assertions. Waiting on #1196 first.
Run a performance analysis on the DTWF for a large simulation and see where the time is being spent. Since it seems like we're not using the Fenwick tree at...
For some applications it will be useful to condition on a specific ancestral sequence. This should basically be the same as the MatrixMutationModel, except it takes as first parameter the...
A fundamental part of the work in coalescent simulation is to keep track of the amount of ancestral material remaining for each interval along the genome. In msprime we currently...
Originally discussed in PR #1953: > I think the solution to this (for the next msprime?) is to include a `generation_time` argument that scales all the times, and would make...
Our analysis of the running time of Hudson's algorithm in the msprime 1.0 paper predicts that a lot of the time spent for long genomes will be in events that...
It would be very useful to be able to support pedigrees that have either no time associated, or partial time values. We avoided doing this in the initial implementation as...
In #1858 we added the sim_pedigree function, which is a forwards-time WF simulator. It would be useful to be able to simulate pedigrees under different demographies, etc but implementing all...