Jerome Kelleher
Jerome Kelleher
Is support for [jupyter-cache](https://jupyter-cache.readthedocs.io/en/latest/) something that is planned/feasible in jupyter-sphinx? It is very useful to be able to avoid reexecuting code blocks over and over when working on a page.
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...
Added as a TODO in #2443
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...
The current VCF spec version is [4.3](http://samtools.github.io/hts-specs/VCFv4.3.pdf). The VCF we're outputting is marked as 4.2. Check if there's anything new in the spec that contradicts current usage, and update the...
Follow up to #2445. The default sample names in our VCF mapping are always ``tsk_0``, ``tsk_1`` etc, and these may not have anything to do with the IDs of the...
We are currently using the ``tree_sequence`` attribute of a way of determining whether a variant is a frozen copy or not. We also use the ``variant->site.position`` attribute as a way...
In #2439 we added the MetadataTable as the superclass of tables that have a metadata column. However, much of the functionality around dealing with things that do/don't have metadata is...
See #2127. See also #1190 for when keep_unary_in_individuals was added. This is a quick prototype to show how it can be done. Essentially we just need to make a second...