ts: Design a way to import or initiate ts in SP

[gregorgorjanc]

In #4 we discuss on how to generate or import tree sequence into R and to generate haplotypes for standard AlphaSimR simulation.

We also want to take the imported tree sequence and grow if further in AlphaSimR.

Assuming we have founderTs with multiple chromosomes (this functionality does not yet exist atm!) and converter asMapPop() from #4 then we could do:

# founderTs is obtained in an appropriate way
founderGenomes = asMapPop(founderTs, segSites = 3)
# asMapPop should recognise how many chromosomes (how many separate tree sequences we have in founderTs)
SP = SimParam$new(founderGenomes)
# Continue with AlphaSimR as usually with the "box of haplotype" approach and
# ignoring tree sequence entirely from this point onwards
# (it was used only to get base population haplotypes stored in founderGenomes)

But we could also create a new class MapPopTs which extends MapPop by also holding tree sequence, so that when we do:

founderGenomesTs = asMapPopTs(founderTs, segSites = 3)
SP = SimParam$new(founderGenomesTs)
SP$ts # place where ts will live in R/AlphaSimR
# Continue with AlphaSimR

we would have base population haplotypes and tree sequence in founderGenomesTs and by passing founderGenomesTs to SimParam$new(founderGenomesTs) we would also automatically set SP$setTrackTs(TRUE).

Alternative to using founderGenomesTs would be to do:

founderGenomes = asMapPop(founderTs, segSites = 3)
SP = SimParam$new(founderGenomes)
SP$setTrackTs(TRUE)
# this would initiate empty tree sequence (ignoring the past!) and we would grow it from this point onwards
SP$ts # place where ts will live in R/AlphaSimR
# Continue with AlphaSimR

or

founderGenomes = asMapPop(founderTs, segSites = 3)
SP = SimParam$new(founderGenomes)
SP$importTs(founderTs) # import the tree sequence
SP$setTrackTs(TRUE) # grow it from this point onwards
SP$ts # place where ts will live in R/AlphaSimR
# Continue with AlphaSimR

@LynxJinyangii @hannesbecher

[gregorgorjanc]

This page lists a minimal C code on how to initiate ts and add edge table rows https://tskit.dev/tskit/docs/stable/c-api.html

[gregorgorjanc]

I have opened issue regarding saving the original rec position #6, but I am thinking that this is a low level thing, which we could punt further down the road (since it's a tricky change and it won't be obvious where we save it) and at the moment rather focus on initialising the tree sequence in SP object using the C API and growing it with "changed" recombination positions ("changed" to the nearest tracked marker) - then we switch to actual recombination position.