edits related to production pipeline #114
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silastittes
commented
May 14, 2024
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| if wildcards.annots == "all_sites": | ||
| # Adding selection to the whole contig | ||
| contig.add_dfe(intervals=np.array([[0, int(contig.length)]]), DFE=dfe) | ||
| else: | ||
| ## Adding annotation only seletion on exon region | ||
| annot = species.get_annotations(wildcards.annots) | ||
| annot_intervals = annot.get_chromosome_annotations(wildcards.chrms) | ||
| contig.add_dfe(intervals=annot_intervals, DFE=dfe) |
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Can someone check this? I was getting a dfe is called before it's defined error. This logic resolves that, but I want to make sure it's correct otherwise.
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I think this PR is good to merge now. Still having some msmc2 hiccups with Vaquita, but I'll troubleshoot and submit some solution in a different PR (perhaps not running msmc2 on Vaquita if nothing else). |
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closes #115 |
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Silas is this ready to go? should I merge this? |
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Yeah I think so! I don't anticipate adding more changes. |
andrewkern
reviewed
Jul 23, 2024
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Needed to make some edits to get production pipeline going. Caught a bug or two in the process.
Let's leave this open for a little bit. May need to add more commits.