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Ran 20 Apr 2026 02:36PM UTC

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Build # 24672294631

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push

github

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web-flow

Commit Message

Add unified Outcome type for multi-outcome effects (#299) (#330)

An ``Outcome`` is "one possible consequence of a variant" with
provenance attached:

* the :class:`MutationEffect` it represents
* a probability / confidence score (or ``None`` if unscored)
* a string naming the source that produced it
* an open-ended ``evidence`` dict

This is the interchange format between varcode's built-in
classifiers (which nominate candidates), external splice predictors
(SpliceAI, Pangolin — score candidates), RNA-seq evidence callers
(Isovar — upgrade / downgrade with read support), and long-read /
assembly-based tools (resolve breakpoint ambiguity). None of those
integrations are wired up yet; the type exists so they can plug in
without churning the core classes.

Harmonization: ``MultiOutcomeEffect`` now exposes
``outcomes -> tuple[Outcome, ...]``. Default implementation wraps
existing ``candidates`` under ``source="varcode"`` and no
probability. Existing ``candidates`` / ``alternate_effect``
accessors stay for back-compat; new code should read ``outcomes``.

``ExonicSpliceSite`` — the only existing ``MultiOutcomeEffect``
subclass with a real two-outcome shape — gets the new accessor
automatically via the default implementation.

Bump minor version to 4.2.0 for the new public type.

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