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bug in haplotypes_from_align

What happens

  • An exception is raised when using haplotypes_from_align with option impute_threshold.

How does it happen

  • This line causes the error
haps2 = egglib.stats.haplotypes_from_align(aln2, max_missing=0.5, impute_threshold=3)

What is the result

  • In case of a Python exception, provide the full traceback. Show us whatever is displayed and might be informative.
  File "/home/stephane/data/projects/methodo/egglib/training/2025-montpellier/egglib-training/pres/examples/stats1.py", line 25, in <module>
    haps2 = egglib.stats.haplotypes_from_align(aln2, max_missing=0.5, impute_threshold=3)
  File "/home/stephane/.local/lib/python3.13/site-packages/egglib/stats/_haplotypes.py", line 87, in haplotypes_from_align
    return _haplotypes(aln, max_missing, impute_threshold, struct, dest, multiple)
  File "/home/stephane/.local/lib/python3.13/site-packages/egglib/stats/_haplotypes.py", line 176, in _haplotypes
    site.reset(pl)
    ~~~~~~~~~~^^^^
TypeError: SiteHolder.reset() takes no arguments (1 given)
Edited Dec 09, 2025 by Stéphane De Mita
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