Alignments using C API

[benjeffery]

Stacked on #3319

[codecov]

Codecov Report

❌ Patch coverage is 68.32298% with 51 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.68%. Comparing base (488b02b) to head (7d75d5a).

Files with missing lines	Patch %	Lines
c/tskit/genotypes.c	65.68%	17 Missing and 18 partials ⚠️
python/_tskitmodule.c	66.66%	9 Missing and 7 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3326      +/-   ##
==========================================
- Coverage   89.80%   89.68%   -0.13%     
==========================================
  Files          29       29              
  Lines       31062    31203     +141     
  Branches     5687     5724      +37     
==========================================
+ Hits        27894    27983      +89     
- Misses       1779     1805      +26     
- Partials     1389     1415      +26     

Flag	Coverage Δ
c-tests	86.70% <65.68%> (-0.15%)	⬇️
lwt-tests	80.38% <ø> (ø)
python-c-tests	86.88% <66.66%> (-0.18%)	⬇️
python-tests	98.84% <100.00%> (-0.01%)	⬇️
python-tests-no-jit	33.59% <0.00%> (+0.03%)	⬆️
python-tests-numpy1	50.16% <0.00%> (+0.05%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
c/tskit/trees.c	90.99% <ø> (ø)
python/tskit/trees.py	98.88% <100.00%> (-0.01%)	⬇️
python/_tskitmodule.c	86.88% <66.66%> (-0.18%)	⬇️
c/tskit/genotypes.c	80.22% <65.68%> (-4.27%)	⬇️

... and 1 file with indirect coverage changes

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