Allow duplicate nodes in variant decoding

[benjeffery]

Fixes #3323

[benjeffery]

@jeromekelleher Annoyingly we have to do some extra book-keeping here for duplicate nodes. Would appreciate some thoughts on the approach.

[codecov]

Codecov Report

❌ Patch coverage is 63.63636% with 8 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.78%. Comparing base (488b02b) to head (9b82ae7).
⚠️ Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
c/tskit/genotypes.c	60.00%	5 Missing and 3 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3325      +/-   ##
==========================================
- Coverage   89.80%   89.78%   -0.02%     
==========================================
  Files          29       29              
  Lines       31062    31075      +13     
  Branches     5687     5690       +3     
==========================================
+ Hits        27894    27902       +8     
- Misses       1779     1783       +4     
- Partials     1389     1390       +1     

Flag	Coverage Δ
c-tests	86.82% <60.00%> (-0.03%)	⬇️
lwt-tests	80.38% <ø> (ø)
python-c-tests	87.05% <ø> (ø)
python-tests	98.84% <100.00%> (+<0.01%)	⬆️
python-tests-no-jit	33.54% <0.00%> (-0.01%)	⬇️
python-tests-numpy1	50.09% <0.00%> (-0.02%)	⬇️

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Files with missing lines	Coverage Δ
python/tskit/trees.py	98.89% <100.00%> (+<0.01%)	⬆️
c/tskit/genotypes.c	83.56% <60.00%> (-0.92%)	⬇️

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[jeromekelleher]

I don't think it's worth doing, no. I tried before and it's too complicated with not that big a gain in flexibility. We've basically painted ourselves into a corner here I think and should just live with it.

[benjeffery]

One option is to allow duplicate nodes at the alignments level by just copying there after decoding.

[jeromekelleher]

I vote we drop it and live with slightly annoying workarounds. It's not a backwards compatible thing, can easily be changed post 1.0