Test_pedigree.py with internal samples

[abureau]

I have modified TestSimulateThroughPedigree and the simulate_pedigree function to specify generations of subjects as internal samples. Setting internal_sample_gen=[True, False] on line 562 specifies that founders i.e. parents of a two-generation pedigree are samples, but not their children (probands). This results in Fatal Python error: Aborted with core dump in my setup.

[abureau]

I continue here the discussion of the closed pull request. I inserted the command tables.dump("test_shallow_internal.ts") at line 564 of test_pedigree.py. Then I called python3 algorithms.py --from-ts test_shallow_internal.ts 4 test.ts and got no error message. The tree object in the output test.ts seems fine, but I am not sure what to inspect.

No rush to reply, I just report now for later.

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 91.23%. Comparing base (af5bd81) to head (78255b6). Report is 3 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #2326   +/-   ##
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  Coverage   91.23%   91.23%           
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  Files          20       20           
  Lines       11816    11816           
  Branches     2293     2293           
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  Hits        10780    10780           
  Misses        568      568           
  Partials      468      468           

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C	91.23% <ø> (ø)
python	98.68% <ø> (ø)

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