ts read and write (double cross over breakpoints included)

[LynxJinyangii]

ts read, sampling SNPs, and write out after simulation (mainly in R)
double cross over breakpoints included (mainly in Cpp)

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[gregorgorjanc]

@LynxJinyangii I had a quick look, but there are a lot of changes so it will take me time. Very quickly.

In R function documentation goes above the function when using Roxygen; no inside docstrings like in Python;) Please ensure all functions have at least some rudimentary docs so we know what the args are supposed to be (type, description, etc.). You will see in AlphaSimR that user facing functions have substantial docs, but also internal functions have some basic docs, so let's strive for that.

You don't need to mark code changes by "Jinyang edited/added/changed" - we have diff tool to track this.

It would be helpful if you communicate why we need another recHist (named recHistGen) instead of just modifying the existing one. We probably don't want to double the memory usage with effectively the same? information?

It would also be easier to review if you clearly set the intent behind the changes when you open a PR. Here is a good example gaynorr#276. Alternatively, a PR can just refer to an issue where the idea/implementation plan is laid out gaynorr#280.

Can you please briefly describe your changes here so we can understand the high-level approach before we get lost in the weeds of the code review?

[LynxJinyangii]

@gregorgorjanc Thanks for the feedback. I'm currently adding ts things to runMacsTs, things at the R level (e.g. makeFoundersFromTs.R) might still change. I'll come back to documentation and comments once the core structure is more defined.

Why use RecHistGen?

• Because I'm not sure how much of the downstream requires recHist, while recHist and recHistGen store slightly different information. Col 1: for both, original Hap (recHistGen: double xover between 2 markers included); Col2: start from where (recHist: index of SNP; recHistGen: positions in Morgan, which are for ts edges); (some examples in https://github.com/LynxJinyangii/AlphaSimR/blob/master/dev/notesRealBreakpoints.md, including a workflow from reading .tree file(s) to output extended one(s)).

Main changes:

• All the changes in .cpp (and related scripts, e.g. Class-SimParam.R, crossing.R...) are basically for recHistGen
• AlphaSimR2TsGen/AlphaSimR2Ts: get information from offspringPop and SP object (recHistGen included) to extend ts tables
• makeFoundersFromTs (functions inside are changing as mentioned above): read genotypes (sampling and filtering included) and calculate genMap

[LynxJinyangii]

To make the variants() -related functions work, I temporaily linked it to RcppTskit version on https://github.com/LynxJinyangii/RcppTskit/tree/add-multiple-functions-on-pr-131

[LynxJinyangii]

Recent commits are about runMacTS (or a staged way for advanced users: 1. ancestry simulation; 2. mutation simulation; 3. inbred leaf expansion (optional); 4. convert TS to MapPop (optional; sampling/filtering + map construction). For the introduction of the structure, I think it would be good to start from dev/testMaCSTS4.Rmd; then testMaCSTS1.Rmd, testMaCSTS2.Rmd and testMaCSTS3.Rmd.