tskit

tskit copied to clipboard

add method to transform coordinates by a RateMap

2

For instance, if we'd like to transform coordinates to be in genetic map units; as discussed with @lkirk @apragsdale @jeromekelleher .

petrelharp

Create a new merge() function, and use that for concatenate

19

## Description It appears as if `union` wasn't really the right underlying function to use for `concatenate`, e.g. it doesn't deal as expected with sites above samples, so I had...

hyanwong

`concatenate` is buggy with internal samples

1

As discovered in #3168, `union` is a node-wise union (not edge-wise) and so is not functioning how we imagined it was in implementing `concatenate`. For instance, the following fails: ```...

petrelharp

span-wise union

4

As discussed in #3168, something we'd like to do is squash together tree sequences describing different bits of the genome. For instance: say I've got simulations of 3L and 3R...

petrelharp

Mention how we use the issue tracker moving forward on the front page.

benjeffery

Prevent iterating over a TopologyCounter

6

Fixes #1462

benjeffery

SVG output needs to be compatible with "dark mode", e.g. in docs

7

With the ability to switch from dark to light mode, we need the SVGs to work both ways too. The shaded background in a tree seq viz is easy: we...

hyanwong

assigning to `ts.tables.metadata` does not produce an error message - need read only tables

7

For instance: ``` >>> ts = msprime.simulate(10) >>> ts.tables.metadata = b'abc' >>> ts.tables.metadata b'' >>> ts.tables.metadata_schema >>> basic_schema = tskit.MetadataSchema({'codec': 'json'}) >>> ts.tables.metadata_schema = basic_schema >>> ts.tables.metadata_schema ``` These are...

petrelharp

Refactor tests to use example tree sequences and parametrize

6

We currently have a mishmash of different ways of running tests on a range of different topologies. I think a good pattern will be to use pytest.mark.parametrize with a selection...

jeromekelleher

Nasty gotcha in the AFS calculation - mutation parents

3

I get strange results when trying to calculate the AFS for the following dataset: ```cpp // Same as the example from the PLOS paper but with back and recurring mutations...

lukashuebner