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Add hail, polars, duckdb, pandas, pydantic, and tqdm as Python dependencies in divref/pyproject.toml. Add mypy ignore_missing_imports overrides for hail and tqdm (no type stubs). Add openjdk>=11 as a conda dependency in a new pixi 'hail' feature and include it in the default environment. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Replaces the template setup placeholder with actual project guidance: environment setup (uv + pixi), common commands, architecture overview, CLI registration pattern, and tool pipeline execution order. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add HailPath type alias and shared helper functions used across multiple Hail-based pipeline tools: to_hashable_items, get_haplo_sequence, variant_distance, and split_haplotypes. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Port rewrite_fasta.py from human-diversity-reference/scripts as a defopt-compatible toolkit tool. Filters a FASTA file to keep only canonical chromosomes (chr1-22, X, Y, MT). Fixes a potential UnboundLocalError by initialising keep=False before the loop and removes the unused header_line variable from the original. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Port create_gnomad_sites_vcf.py from human-diversity-reference/scripts as a defopt-compatible toolkit tool. Exports gnomAD variant sites above a given population frequency threshold as a VCF file with per-population frequency fields in the INFO column. Renames positional args path/vcf_path to sites_table_path/output_vcf_path for clarity. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
create_gnomad_sites_vcf.pyfromhuman-diversity-reference/scriptsas a defopt-compatible toolkit toolpath/vcf_pathtosites_table_path/output_vcf_pathfor clarityTest plan
uv run --directory divref poe check-allpasses🤖 Generated with Claude Code