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feat: add compute_haplotype_statistics tool#9

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ameynert wants to merge 1 commit intoam_07_compute_haplotypesfrom
am_08_compute_haplotype_statistics
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feat: add compute_haplotype_statistics tool#9
ameynert wants to merge 1 commit intoam_07_compute_haplotypesfrom
am_08_compute_haplotype_statistics

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Summary

  • Ports compute_haplotype_statistics.py from human-diversity-reference/scripts as a defopt-compatible toolkit tool
  • Evaluates unique haplotype counts and gnomAD variant counts across all combinations of provided frequency cutoffs and window sizes
  • Writes results to two TSV files (haplotype counts and variant counts)
  • window_sizes and frequency_cutoffs are now list parameters (--window-sizes 100 500 1000) rather than comma-delimited strings

Test plan

  • uv run --directory divref poe check-all passes

🤖 Generated with Claude Code

@ameynert ameynert had a problem deploying to github-actions-snakemake-linting April 10, 2026 22:59 — with GitHub Actions Failure
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@ameynert ameynert force-pushed the am_07_compute_haplotypes branch from 250c6ca to b8eef18 Compare April 10, 2026 23:17
Port compute_haplotype_statistics.py from human-diversity-reference/scripts
as a defopt-compatible toolkit tool. Evaluates unique haplotype counts and
gnomAD variant counts across all combinations of provided frequency cutoffs
and window sizes, writing results to two TSV files. window_sizes and
frequency_cutoffs are now list parameters (--window-sizes 100 500 1000)
rather than comma-delimited strings.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@ameynert ameynert force-pushed the am_08_compute_haplotype_statistics branch from 746189f to 7012193 Compare April 10, 2026 23:17
@ameynert ameynert temporarily deployed to github-actions-snakemake-linting April 10, 2026 23:17 — with GitHub Actions Inactive
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