feat: add create_fasta_and_index tool#11
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ameynert wants to merge 2 commits intoam_09_compute_variation_ratiosfrom
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feat: add create_fasta_and_index tool#11ameynert wants to merge 2 commits intoam_09_compute_variation_ratiosfrom
ameynert wants to merge 2 commits intoam_09_compute_variation_ratiosfrom
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✨ Finishing Touches🧪 Generate unit tests (beta)
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Port create_fasta_and_index.py from human-diversity-reference/scripts as a defopt-compatible toolkit tool. Generates DivRef FASTA sequences with flanking reference context and a DuckDB index for use by remap_divref. Reuses get_haplo_sequence and split_haplotypes from divref.haplotype. Renames the chr loop variable to chrom to avoid shadowing the built-in, fixes a loop-variable closure bug (B023), and replaces print/typer.echo with logging. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds tests/tools/__init__.py to create the package and test_create_fasta_and_index.py with happy-path tests for get_haplo_sequence and split_haplotypes. The Hail JVM test is marked skip; the remaining tests pass. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
create_fasta_and_index.pyfromhuman-diversity-reference/scriptsas a defopt-compatible toolkit toolremap_divrefget_haplo_sequenceandsplit_haplotypesfromdivref.haplotypechrloop variable tochromto avoid shadowing the built-in, and replacesprint/typer.echowith loggingtests/tools/test_create_fasta_and_index.pywith happy-path tests forget_haplo_sequenceandsplit_haplotypes(Hail JVM test marked skip)Test plan
uv run --directory divref poe check-allpassesuv run --directory divref pytest tests/tools/test_create_fasta_and_index.py— all non-skip tests pass🤖 Generated with Claude Code