Jerome Kelleher

We currently don't have any simple C example code for decoding variants. This is useful both for C API users and ourselves for timing/bug tracking purposes. This is roughly what...

Table collection returned by ts.tables not read-only.

1

> 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...

Provide TreeSequence array access to ragged columns

2

#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...

Add flags_array and time_array to Tree class?

9

#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...

In #2334 we simplified the semantics of the ``population`` argument in split_edges and decapitate to default to -1 rather than inherit from the child node. It will probably be useful...

Index required for efficient random access for trees

14

Current TreeSequence.at() and other methods to seek to a particular tree work by iterating along the trees. This isn't very efficient, if we want to get a tree in the...

Allow windows not bracketed by 0, L

5

Currently windows in the stats calculations insist on starting with 0 and ending with L. Relax this to allow windows within the sequence.

[Drawing] Add a TreeSequence.draw() method?

7

We're getting some very powerful tools with the new draw_svg() functions, but we're missing a simple way to annotate a tree sequence (like say, node colours) without having to be...

This would be useful for generating the last tree in the ordering, as discussed in #944. We'd like to be able to write ```python tree = tskit.Tree.unrank((-1, 0), 6) ```

Add TreeSequence.max_time, min_time attributes

9

There are many situations where it's handy to know what the max and min times are, and it would be nice if we could avoid having to do a full...