Multi letter alleles (e.g. indels) in haplotypes()

[hyanwong]

There was discussion of this in the following PR: #426. @jeromekelleher is keen not to open the multi-letter-allele can of worms, unless there is demand from users. @hyanwong thinks that (in the case of haplotype output) the semantics are reasonably clear, and being able to output haplotype strings containing indels will be needed by users quite soon.

Some of this is probably only relevant once finite site tree sequences have been implemented. But (IMO) if we think it is reasonable to concatenate widely spaced SNPs into a string of letters, it is also reasonable to concatenate multi-letter haplotypes from an infinite-sites TS, as long as each allele takes the same number of characters. This is what this PR does.

Also from that PR, a quick summary - do we think it useful to be able to output small indels as aligned haplotypes, e.g.

Sample1: .A.T.---.G.T
Sample2: .A.C.---.G.A
Sample3: .A.T.ATT.G.A

Note that the current code does not output the . between sites (an optional convention to represents non-variable regions between variants) - I put them there for clarity, and also because I think it might be a useful addition to address #353 (comment)

[hyanwong]

p.s. I'm also opening this as a PR because I don't want to lose the work I've done on this, especially the fast function coded herein (sitewise_allele_max_bytes()) which speedily calculates the maximum byte length of all the alleles at a site, for all sites. I think this might be generally useful however we chose to deal with multi-letter alleles.

[codecov]

Codecov Report

Merging #427 into master will increase coverage by 0.02%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #427      +/-   ##
==========================================
+ Coverage   86.73%   86.75%   +0.02%     
==========================================
  Files          20       20              
  Lines       14115    14137      +22     
  Branches     2745     2747       +2     
==========================================
+ Hits        12242    12264      +22     
  Misses        963      963              
  Partials      910      910

Flag	Coverage Δ
#c_tests	87.87% <100%> (+0.02%)	⬆️
#python_c_tests	90.59% <100%> (+0.03%)	⬆️
#python_tests	99.24% <100%> (ø)	⬆️

Impacted Files	Coverage Δ
python/tskit/trees.py	98.76% <100%> (+0.02%)	⬆️

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[hyanwong]

Temporarily closing due to lack of bandwidth for dealing with finite sites / multiletter alleles. May be worth revisiting later