Multiple chromosomes

@DomNelson and I were just discussing the possibility of adding support for multiple chromosomes to tskit. One possibility which seems like it might be a reasonably smooth path forward is the following:

1. Add a chromosome table with an ID, name, length and metadata.
2. Add a chromosome column to the edge table. Within a chromosome, coordinates must be from 0 to the chromosome’s length.
3. Either deprecate the sequence_length property (probably best), or make it equal to the sum of the length of all chromosomes.

For things like trees() we could add an optional chromosome argument. If the tree sequence contains multiple chromosomes which would raise an error if it’s not specified. For tree sequences with a single chromosome, things would continue to work as now.

Any thoughts @petrelharp, @hyanwong, @bhaller, @molpopgen?

[petrelharp]

In terms of simplification then, each chromosome would be simplified separately,

I think you all are thinking about this, but if you simplify each chromosome separately, we’ll have to do an extra “merge” step at the end to ensure that the node tables agree across chromosomes. It would be nice to be able to parallelize, though!

I also lean towards ‘no thanks’. An extra benefit of sticking all chromosomes end-to-end is that it makes plotting easier.

[jeromekelleher]

I’m with @bhaller here on the ‘not right now, thanks’ assessment. The idea came up during a discussion and I wanted to get some feedback on what would be involved and how much hassle it would be. This isn’t a small change, so we definitely wouldn’t make it lightly, without considering performance implications and taking the impact on downstream users into account.

Let’s keep the issue open for discussion anyway though.