popsim-consortium / popsim-consortium/stdpopsim
Allow more flexible sampling (e.g., from past times)
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- Dominant language
- Python
- Stars
- 144
- Forks
- 100
- Avg merge
- 2h 44m
- Merged PRs (30d)
- 2
Description
We're using sampling_time=None currently to denote populations that are never sampled from. In reality we should be able to sample from any population, it's mainly just a case of what time thoses samples should be at. This gets complicated though, since someone may want to sample at multiple times from the same population. Then, we can just use the standard msprime API for creating samples.
So, perhaps the current approach is a good compromise, covering the majority of cases people will want?
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Research direction
The issue names no files or tests. Start by reviewing the current handling of sampling_time=None and the standard msprime API for creating samples. Before implementation, clarify how multiple sampling times and past times should be represented; done would require an agreed sampling interface and corresponding tests.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100