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popsim-consortium / analysis2

Analysis for the second consortium paper.
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Patch sp plot #73

Closed andrewkern closed 2 years ago

andrewkern commented 2 years ago

here is a patch for the bug that @lntran26 found and reported in #71, which appeared to be an issue with ploting stairwayplot results.

In examining things, what was happening was that a helper function being used to expand the list of file names with stairwayplot results to plot was expanding over too many wildcards, and so inappropriate reps (e.g. between demographies) were being plotting together.

this PR provides a fix for this bug that will close #71

andrewkern commented 2 years ago

thanks @lntran26 -- some of these edits didn't work for me. i've pushed further changes, fixes some other bugs that i saw, but am still trying to figure out whats going on with the SP output

andrewkern commented 2 years ago

okay, i can now confirm that this patch is working. here are representative plots from a run of the config.yaml settings. Both of these are Chr21, Gamma DFE on exons:

Constant demography, all_estimated_Ne.pdf

OOA: all_estimated_Ne (1).pdf

andrewkern commented 2 years ago

i have rebased and squashed this PR so will merge.