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HaploStats doesn't report correct low frequency haplotypes #38
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see fuller description of issue here: #60 (comment) and proposed solution here: #60 (comment) |
@sjmack looking at this issue, it seems that the low frequency truncation applies to both emhaplofreq and haplostats and is actually separate to the lack of counts (which is haplostats-specific). I would open up another issue for the numbers of copies. quick review of the code suggests it was disabled in the XML output pending a check of the numbers, there's a FIXME: https://github.com/alexlancaster/pypop/blob/main/src/PyPop/Haplo.py#L1013 |
@sjmack When you open up a new issue, I'd remove the comment in the code and re-run, and check to see if the copies are calculated correctly. if so, we can probably uncomment and add it. We should also unit tests for haplo-stats, so a self-contained |
@sjmack I made a branch to test this fix. in your local git clone you can pull it and rebuild to test it on your data:
if it works for you an passes all the unit tests I'll merge it with main. |
splitting off the count issue as a new issue in #65 and retitling this issue |
@alexlancaster I will try to get to this later this week. Sorry for the delay. |
See my final comment in Issue #28.
<haplostats>
is reporting converged haplotype frequency estimates differently from<emhaplofreq>
, is not reporting haplotype counts, and is truncating frequencies that were returned in scientific E-notation to eliminate the exponent.The text was updated successfully, but these errors were encountered: