There is a bug in pyp_utils/renumber() such that the
offspring stored in myped[i].sons, myped[i].daus, and
myped[i].unks are not updated to reflect changes in
animal IDs when a pedigree is renumbered.
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This can be fixed using the idmap and backmap dictionaries
in the NewPedigree object. It will be fixed in 2.0.0a20.
Given a pedigree object named 'example':
example.kw['renumber'] = 1
Will produce a renumbered pedigree with correctly renumbered
This bug is fairly complicated and needs some explanation.
If you load a pedigree and renumber it out-of-the-date, i.e.
using the renumber option, there is no problem. When a
pedigree is loaded, pyp_utils/assign_offspring is always
called by the preprocessor, and this call is made after any
calls to pyp_utils/renumber(). In this case, the offspring
lists contain renumbered IDs. However, if you do not
renumber a pedigree when you initially load it, and you call
pyp_utils/renumber() later, the offspring lists are NOT
updated. However, a call to pedobj.renumber() will always
correctly renumber both the pedigree and the offspring lists.
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