Implement tree sequence

[gregorgorjanc]

This is a big one and a project on its own, but here are some initial ideas

• use tskit C library to store tree sequence?
• import tree sequence, split some sites as QTL and SNP array, the rest as tree sequence sites ...
• licencing issues? AlphaSimR is MIT, tskitC is GPL

[gregorgorjanc]

Peter Ralph directed me to this implementation doc for SLiM https://github.com/MesserLab/SLiM/blob/master/treerec/implementation.md

[gaynorr]

Need to change recombination tracking in AlphaSimR to keep track of all recombinations and not just observed recombinations. This can be accomplished by not processing recombination output from findBivalent and only processing the output within bivalent for the purposes of copying data.

The full history can then be fowarded along to recombination tracking. Processing will be needed in the current recombination history list, because it depends on this data being processed. Perhaps we need to recombination histories, or some adjustments to the current IBD tracking to process as needed.

[gaynorr]

Mutations need to be tracked for tree sequences. This can be added to SimParam.

[gaynorr]

https://www.slendr.net/articles/vignette-05-tree-sequences.html

Look at this article for an example implementation in R.