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Population-scale genomics
In #2384 , I added a test to check that the string representation of a `Variant` object is correctly formatted. The test involves doing regexp matching (using a predefined pattern)...
> One thing that has been bugging me is the description of mutability. If you have a tree sequence, calling the functions that change it do not raise an error...
#2424 added direct numpy access to the non-ragged table columns from the TreeSequence object. We should provide access also for the ragged columns (at some point). Some issues: 1. Should...
#1320 added arrays for the underlying tree vectors. I think it's probably a good idea to add the flags_array and time_array to the Tree class also, since these are things...
At the moment the `Variant` class is listed under the "simple container classes" heading, here: https://tskit.dev/tskit/docs/stable/python-api.html#the-variant-class but that doesn't seem like a sensible description any more. We could move it...
It would be handy for notebooks and jupyterbooks to be able to set a style for `tskit` generated SVG and HTML in a given session. A method such as `tskit.set_svg_style(css_string)`...
Somehow this one got missed. Sorry @szhan!
Currently this results in an error: ```python >>> tc = tskit.TableCollection(1) >>> tc.individuals=tskit.IndividualTable() Traceback (most recent call last): File "", line 1, in AttributeError: can't set attribute ``` Is there...
@castedo has suggested using information-theoretic metrics (e.g., mutual information) to assess imputation accuracy. One appealing feature of IT metrics is that they can handle multi-allelic sites easily (as I understand...
I would like to be able to reorder the individuals so that the IDs change but the structure is all the same. I would similarly like to be able to...