LocusGate: Operator-Neutral Graph Workspaces for Composable Pangenome Queries

Multi-stage pangenome analyses revisit one locus for sequence membership, path extraction, and neighborhood inspection, yet independently localized stages can expose different graph evidence. We make locality an explicit operator-neutral value with LocusGate, which materializes $\mathcal{W}(q)=⟨G^{\prime },\chi ⟩$ before dispatch from complete path-window anchors and deterministic budgeted expansion. The certificate $\chi$ binds visible graph content, construction settings, canonical ordering, and the answer domain of each consumer. This interface separates three guarantees: exact membership over declared embedded paths for $|q|\ge w+k-1$, deterministic extraction complete within $G^{\prime }$, and bounded neighborhood inspection over the certified traversal domain. We prove conditioned exactness for membership and show that certificate equality makes handoff and deterministic rematerialization produce identical normalized outputs for a fixed deterministic operator. By making region identity, guarantee scope, and immutable state travel together, LocusGate gives multi-stage pangenome queries one named body of graph evidence rather than operator-private locality choices.