feat: add DisjointIntervalSequence API

[SophiaPerzan-DG]

Feature is WIP and subject to change in future PRs

• Base class and properties set up

In short, the DisjointIntervalSequence API allows users to more easily work with intervals meant to span multiple disjoint intervals (use-case: working with transcripts in spliced RNA space)

To release, I'm thinking we can create a separate diseq-preprelease branch where we manually update the version in setup.py to be suffixed with a1 (e.g. 7.3.1a1) to denote an alpha version, and manually trigger release by creating a tag off that branch.

I didn't addDisjointIntervalSequence to __all__ under __init__.py so people need to manually import the class in order to use the feature (since it's still WIP).

[SophiaPerzan-DG]

This whole index toggle thing will be removed in a future PR. This was a workaround while this requirement was still uncertain.

[Copilot]

Pull request overview

Adds an initial (WIP) DisjointIntervalSequence API for working with flattened coordinates over disjoint genomic intervals, along with tests and Sphinx documentation.

Changes:

• Introduces genome_kit.diseq with DisjointIntervalSequence and IndexDirection.
• Adds a comprehensive unittest suite for DIS construction, properties, and dunder methods.
• Wires DIS into docs (diseq page + API docs) and exposes it via genome_kit/__init__.py.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
genome_kit/diseq.py	New core implementation of DIS and index-direction conventions.
tests/test_diseq.py	New unit tests validating initialization, construction helpers, properties, and dunders.
genome_kit/__init__.py	Imports DisjointIntervalSequence at the package top level.
docs-src/index.rst	Adds diseq to the docs TOC.
docs-src/diseq.rst	New conceptual/usage documentation for DIS.
docs-src/api.rst	Adds API reference entries for IndexDirection and DisjointIntervalSequence.

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[ovesh]

I'm thinking we can create a separate diseq-preprelease branch where we manually update the version in setup.py to be suffixed with a1 (e.g. 7.3.1a1) to denote an alpha version, and manually trigger release by creating a tag off that branch.

I've found a few different ways this can be approached (e.g seperate alpha branch, directory filters, etc). Decide on one and add it to this PR or a separate PR (or explain in more detail). Lowest effort should be prioritized.

I didn't addDisjointIntervalSequence to all under init.py so people need to manually import the class in order to use the feature

This might actually be sufficient.

[ovesh]

I've never touched this file, and now I realize that the Utr class I added (way back) isn't in the api docs 😳

and who knows what else

[ovesh]

I don't really get this. Does "On Coordinate Strand" map to a field on the DSI? Or are you just trying to explain the diagram?

[SophiaPerzan-DG]

It does map to a field on the DIS. I'll rework that section to include code as well, which should hopefully clear things up a bit.

[ovesh]

Was this a requested feature?

[SophiaPerzan-DG]

I wouldn't say it was an explicitly requested feature, but users mentioned wanting to create DIS from exons, cds, etc. FWIW this feature was implemented in the first 'rough draft' PR you created, and I just continued from there. I don't have a preference as to whether this part of the code is included or not (I can see an argument for either side), so if you think it's worth removing lmk.

[ovesh]

let's remove to keep the api space a bit smaller, can add later if needed. sorry I missed it in my original branch.

[s22chan]

I feel this should be a bitflag if so, wouldn't users wants exons/cds + utrs?

[ovesh]

preemptively approving with one minor doc comment

[ovesh]

not blocking, but a code example that demonstrates the behavioral differences between a vanilla interval and a simple dji interval would be helpful.