chore: add lower, lift, intersect, dna, expand_coord DIS methods

[SophiaPerzan-DG]

also:

• chore: remove index direction toggle in DIS

[Copilot]

Pull request overview

This PR extends DisjointIntervalSequence (DIS) with additional coordinate/interval manipulation and mapping utilities (including genomic ↔ DIS coordinate conversion and DNA extraction), updates documentation accordingly, and adds tests for the new behaviors. It also removes the prior DIS “index direction” toggle and introduces a Genome.dna(...) convenience path intended to accept a DIS directly.

Changes:

• Added DIS methods: expand_coord, _lower_coord, lower, genomic_span, _lift_position, lift_interval, intersect, and dna; removed the global index-direction toggle.
• Updated Genome.dna behavior to dispatch when passed a DisjointIntervalSequence.
• Added/expanded unit tests and documentation for the new DIS coordinate mapping and DNA behaviors.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/test_genome.py	Adds coverage for Genome.dna() when called with an Interval vs a DIS.
tests/test_diseq.py	Adds extensive tests for DIS coordinate expansion, lowering/lifting, intersection, span, and DNA.
genome_kit/genome.py	Changes Genome.dna implementation to dispatch for DIS inputs.
genome_kit/diseq.py	Implements new DIS methods (expand/lower/lift/intersect/dna) and removes index-direction configuration.
genome_kit/init.py	Exposes DisjointIntervalSequence in __all__.
docs-src/diseq.rst	Documents expand_coord, coordinate mapping (lower/lift_interval), and DIS DNA behavior (including Genome.dna(dis) convenience).

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[Copilot]

Pull request overview

Copilot reviewed 4 out of 4 changed files in this pull request and generated 3 comments.

Comments suppressed due to low confidence (1)

docs-src/diseq.rst:819

• The docs claim Genome.dna accepts a DIS directly (genome.dna(dis)), but GenomeDNA.__call__ only accepts Interval-typed arguments via PyAsInterval (see src/py_interval.h). Unless there’s an unshown overload, this example will raise TypeError. Either remove this claim/example or implement DIS dispatch in the DNA API.

For convenience, :py:meth:`Genome.dna <genome_kit.Genome.dna>` accepts a
DIS directly and dispatches to ``DisjointIntervalSequence.dna``, so
either of the following is equivalent::

    >>> dis.dna()
    >>> genome.dna(dis)