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Population-scale genomics
One of the most important comments I got in my thesis examination was regarding our definition of IBD. Our current implementation of `ibd_segments` treats segments as distinct if they have...
## Description This is a Python mockup of some functions that might help to keep the internal memory requirements of `ibd_segments` in check. Would work similarly for `link_ancestors` (and perhaps...
All three of these methods rely on an object called `ancestor_map` (C codebase) or `A` (Python mockups) to store segments that descend from each ancestral node in the tree sequence....
Fixes #2459 -- see the issue for discussion about why this is needed. Draft only at the moment. ### PR Checklist: - [ ] Tests that fully cover new/changed functionality....
This branch will be used by the new website demo deploy to show how the docs will look. We can merge this PR whenever we are happy with the new...
We added time benchmarks in #2454, it would also be useful to record the peak memory usage. This [page](https://www.baeldung.com/linux/process-peak-memory-usage) lists a few ways to do this which look interesting: -...
Initial proof of concept for making the TableCollection returned by ``ts.tables`` read-only. I've only done the plumbing for the NodeTable here, but the extension is pretty clear. The implementation is...
#2443 added a new file "export.md" with a section on VCF. The idea was to pull out most of the content that was previosly in the docstring and to give...
VCF [4.3](http://samtools.github.io/hts-specs/VCFv4.3.pdf) provides a mechanism to define pedigree information among samples. Since we have pedigree information in individual table we could in principle support this. Logging this issue as a...