test: cover chrX haploid-male counting and MNV overlap branches

[ameynert]

Summary

Test coverage and observability for the haplotype core, plus a small readability fix. No behavior change (the _haploid_adjusted_call extraction and the haplo_coordinates sort-key unification are both behavior-preserving).

Changes

#78 — chrX haploid-male test. Extracted the inline chrX non-PAR haploid adjustment into _haploid_adjusted_call(locus, gt, sex_karyotype) (the subtlest correctness logic in compute_haplotypes, previously only guarded by opaque end-to-end counts). Added a focused test on a 2×2 synthetic MatrixTable: a chrX non-PAR male alt-carrier contributes one allele to call_stats (AN 3 = male haploid + female diploid), while the autosome locus stays diploid (AN 4).

#77 — observability. _compute_locus_groups now logs the number of variants it collects to the driver, so a memory spike at that (currently un-mitigated) collect + hl.literal broadcast is attributable — matching the existing attach_component_info / containment_dedup collect-site logs.

#83 — nits.

• Added the two untested MNV classify_pair branches (same_position_other, other_overlap) to the parametrized table.
• Unified haplo_coordinates's sort key with get_haplo_sequence's (position, len(ref)) (only the minimum position is read, and _max_reference_end is order-independent, so this is behavior-preserving) and added a comment noting the two must stay in lockstep.

Verification

• uv run --directory divref poe fix-and-check-all — 184 passed; ruff (check + format) and mypy clean.

Closes #77
Closes #78
Closes #83

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

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Run ID: 6d7b3ba4-47b8-4d72-bfe5-493bafcd155d

📥 Commits

Reviewing files that changed from the base of the PR and between 1736c06 and 12c7d19.

📒 Files selected for processing (4)

• divref/divref/haplotype.py
• divref/divref/tools/compute_haplotypes.py
• divref/tests/test_haplotype_compat.py
• divref/tests/tools/test_compute_haplotypes.py

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