test: add happy-path test for compute_haplotype_statistics

[ameynert]

Summary

• Uses pre-committed chr1_100001_200000_haplotypes.ht and chr1_100001_200000.gnomad_afs.ht test data
• Patches hl.init() (Spark context already running from session fixture)
• Asserts both .hgdp.tsv and .gnomad.tsv output files are written with correct headers, row counts (1 freq × 1 window), and exact counts (24 unique haplotypes, 473 gnomAD variants at freq ≥ 0.005, window=5000)

Closes #24

Test plan

• uv run --directory divref poe check-all passes (format/lint failures are pre-existing in untracked extract_gnomad_single_afs.py)
• compute_haplotype_statistics reaches 100% test coverage

🤖 Generated with Claude Code

Summary by CodeRabbit

• Tests
  • Added comprehensive test coverage for haplotype statistics computation to validate output file generation, data format integrity, and result accuracy.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: e8dc81a1-9a97-42a6-8ad6-8e96840f9958

📥 Commits

Reviewing files that changed from the base of the PR and between 316c402 and 71510c7.

📒 Files selected for processing (1)

• divref/tests/tools/test_compute_haplotype_statistics.py

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📝 Walkthrough

Walkthrough

A new test module is added to verify the compute_haplotype_statistics tool. The test constructs input paths, invokes the tool with mocked Hail initialization, and validates that expected TSV output files are created with correct headers and data rows containing specific expected values.

Changes

Cohort / File(s)	Summary
Test Module Addition divref/tests/tools/test_compute_haplotype_statistics.py	New test file exercising the compute_haplotype_statistics tool. Verifies output TSV files (HGDP and gnomAD) are created with expected column headers and validates row counts and parsed values for frequency cutoffs and window sizes.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

Possibly related PRs

• feat: add compute_haplotype_statistics tool #9: Implements the compute_haplotype_statistics tool that is directly exercised and validated by this test module.

Poem

🐰 A test hops in with care so keen,
Checking haplotypes, frequencies seen,
TSV files, headers bright,
Data rows counted just right! ✨

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately describes the main change: adding a happy-path test for the compute_haplotype_statistics tool, which matches the changeset.
Linked Issues check	✅ Passed	The pull request directly addresses issue #24 by implementing a comprehensive test for compute_haplotype_statistics that validates headers, row counts, and expected haplotype/variant counts.
Out of Scope Changes check	✅ Passed	All changes are focused on adding test coverage for compute_haplotype_statistics; no unrelated modifications to production code or other features are present.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch am_test_compute_haplotype_statistics

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