[chrisvittal]

SLocusValue no longer exposes the contig string's address (contigLong). Instead it provides contigIdx, the contig's index in the reference genome, and packed, the locus as (contig_index << 32) | position. The canonical locus computes both through the reference genome's contig-index lookup. SCanonicalLocusPointer's coercion, the only caller of contigLong, now matches on the canonical value directly.

contigType moves from PLocus to PCanonicalLocus, and locus prefix codes encode the packed integer instead of the global position. Prefix codes are unused, so the change is not observable.

Security Assessment

• This change cannot impact the Hail Batch instance as deployed by Broad Institute in GCP

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Reviewing files that changed from the base of the PR and between 11d5378 and 76d3613.

📒 Files selected for processing: 5

• hail/hail/src/is/hail/types/physical/PLocus.scala
• hail/hail/src/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointer.scala
• hail/hail/src/is/hail/types/physical/stypes/concrete/SUnreachable.scala
• hail/hail/src/is/hail/types/physical/stypes/interfaces/SLocus.scala
• hail/hail/test/src/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointerSuite.scala

💤 Files with no reviewable changes: 1

• hail/hail/src/is/hail/types/physical/PLocus.scala

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Walkthrough

Locus value implementations now provide a contig index and a packed value. Prefix codes encode the packed value. New property tests check these values against reference genomes and verify locus ordering.

Changes: Locus Encoding

Layer / File(s)	Summary
Locus values and prefix codes hail/hail/src/is/hail/types/physical/PLocus.scala, hail/hail/src/is/hail/types/physical/stypes/interfaces/SLocus.scala, hail/hail/src/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointer.scala, hail/hail/src/is/hail/types/physical/stypes/concrete/SUnreachable.scala, hail/hail/test/src/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointerSuite.scala	SLocusValue replaces contigLong with contigIdx and adds packed. Canonical locus values memoize the contig index and packed value. prefixCode encodes the packed value. Tests compare the values with reference genome representations and check locus ordering.

Priority: Low

Estimated code review effort: 3 (Moderate) | ~20 minutes

Change: Refactor

Suggested reviewers: ehigham

Merge Risk: Minimal · previous review 76d36

No confirmed issue prevents merging after normal build and test checks.

Security architecture risk: Low · up to 76d36

The inspected changes preserve copy ownership and include checks for locus ordering. No introduced security issue was identified. Risk remains limited but nonzero because encoded bytes change, and compatibility with external consumers has not been established.

Retained concerns
No architecture-level concerns identified.

Security review details

Security Blast Radius

• inferred — The demonstrated affected scope is locus encoding within query evaluation, including callers of the existing prefixCode IR function. The available evidence does not establish cross-tenant, credential, infrastructure, or data-store authority changes; deployment exposure and external byte consumers remain unresolved.

Trust Boundaries and Controls

• observed — The encoding path uses the reference genome attached to the locus value. Packing does not add explicit contig-membership or position validation. The former global-position path also relied on reference-genome lookup and did not explicitly validate position; no newly bypassed security control was established.

Pre-merge checks: 4

Check name	Status	Explanation
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.
Title check		The title clearly summarizes the main change: making the locus interface representation-agnostic.
Description check		The description explains the interface changes, implementation impact, and security assessment. It omits the explicit Change Description heading and issue reference, but the required information is ot…

Full details: Description check

Explanation

The description explains the interface changes, implementation impact, and security assessment. It omits the explicit Change Description heading and issue reference, but the required information is otherwise present.

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