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.