Adding variants iterator and other functions

[LynxJinyangii]

No description provided.

[codecov]

Codecov Report

❌ Patch coverage is 98.08307% with 6 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
RcppTskit/R/RcppTskit.R	94.91%	3 Missing ⚠️
RcppTskit/src/RcppTskit.cpp	98.18%	3 Missing ⚠️

📢 Thoughts on this report? Let us know!

[gregorgorjanc]

I have rebased this to the most recent main branch that contains previous PRs.

[gregorgorjanc]

There is quite a bit to review in this PR, so best to make a list of new things! @LynxJinyangii I would appreciate such communication so it's easier to follow your work and thoughts etc. Best to err on the slight "over communication" that "no communication";) Even just copying NEWS.md entries or linking to them in the PR message would be fab.

From what I gather, this is the list of additions we should review:

• rtsk_table_collection_sort and TableCollection$sort related to Do we have to add TableCollection$sort() method? #99
• rtsk_treeseq_get_samples and TreeSeqeunce$samples (do we need samples for TableCollection then too? - best to discuss; edit - there is no such method for TableCollection)
• rtsk_node_table_get_row and TableCollection$node_table_get_row (do we need node_table_get_row for TreeSequence too? - best to discuss)
• rtsk_const_tsk_no_check_integrity
• rtsk_variant_iterator_init, rtsk_variant_iterator_next, and TreeSequence$variants

[gregorgorjanc]

@LynxJinyangii I am comparing this R implementation against Python implementation at https://tskit.dev/tskit/docs/latest/python-api.html#tskit.TableCollection.sort and see that we have edge_start = 0L and no_check_integrity = FALSE, while Python version has edge_start=0, *, site_start=0, mutation_start=0. We must strive for parity of implementation, unless there is a strong need for deviation. Is there a reason you deviated from the Python version?

[gregorgorjanc]

@LynxJinyangii I have pushed changes to this branch/PR (rebased to main, which required sorting some merge conflicts; and come comments on sort), so best if you first pull before you start changes on your end.

[gregorgorjanc]

I have done some polishing of the code, docs, and terms in my recent commit&push. @LynxJinyangii make sure you git pull on your end so that you get these changes. I have reviewed all but variant/iteration stuff - that will take me more time - but you can work on the comments I provided above in the meantime and then we iterate.