Vcf import#38
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Agent-Logs-Url: https://github.com/wassermanlab/variome/sessions/f02ede57-a542-4d6c-af7f-fdf2921a5a89 Co-authored-by: bradwbradw <4715252+bradwbradw@users.noreply.github.com>
Agent-Logs-Url: https://github.com/wassermanlab/variome/sessions/b3671cac-0f12-4ffb-b817-3e7a3339a23a Co-authored-by: bradwbradw <4715252+bradwbradw@users.noreply.github.com>
…ult to 10 lines Agent-Logs-Url: https://github.com/wassermanlab/variome/sessions/da34cf9d-d625-4f28-8824-8bdfbbd1fdc6 Co-authored-by: bradwbradw <4715252+bradwbradw@users.noreply.github.com>
…nlab/variome into copilot/refactor-import-bvl-vcf
…age dataclass Agent-Logs-Url: https://github.com/wassermanlab/variome/sessions/3e2dee96-ef8d-4aea-87c6-75ae70792689 Co-authored-by: bradwbradw <4715252+bradwbradw@users.noreply.github.com>
Agent-Logs-Url: https://github.com/wassermanlab/variome/sessions/3e2dee96-ef8d-4aea-87c6-75ae70792689 Co-authored-by: bradwbradw <4715252+bradwbradw@users.noreply.github.com>
…nlab/variome into copilot/refactor-import-bvl-vcf
Co-authored-by: Copilot <copilot@github.com>
…_tests.sh, update README Agent-Logs-Url: https://github.com/wassermanlab/variome/sessions/1e116eff-26a6-468a-a64d-a14e0a21dea7 Co-authored-by: bradwbradw <4715252+bradwbradw@users.noreply.github.com>
…ring Agent-Logs-Url: https://github.com/wassermanlab/variome/sessions/1e116eff-26a6-468a-a64d-a14e0a21dea7 Co-authored-by: bradwbradw <4715252+bradwbradw@users.noreply.github.com>
Co-authored-by: Copilot <copilot@github.com>
…UT_TSV_PATH Agent-Logs-Url: https://github.com/wassermanlab/variome/sessions/a434cd54-6084-40b1-b231-4fa51141dbd5 Co-authored-by: bradwbradw <4715252+bradwbradw@users.noreply.github.com>
…l to test script Agent-Logs-Url: https://github.com/wassermanlab/variome/sessions/a434cd54-6084-40b1-b231-4fa51141dbd5 Co-authored-by: bradwbradw <4715252+bradwbradw@users.noreply.github.com>
…vcf.py Agent-Logs-Url: https://github.com/wassermanlab/variome/sessions/e5223a97-0c88-46ff-ba05-c415580a076a Co-authored-by: bradwbradw <4715252+bradwbradw@users.noreply.github.com>
… prevent hang Agent-Logs-Url: https://github.com/wassermanlab/variome/sessions/a4ed6ccc-e518-4203-9b12-72414525d6a3 Co-authored-by: bradwbradw <4715252+bradwbradw@users.noreply.github.com>
Agent-Logs-Url: https://github.com/wassermanlab/variome/sessions/d26c26b9-8342-4f99-b347-afa5e28b38f4 Co-authored-by: bradwbradw <4715252+bradwbradw@users.noreply.github.com>
Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Copilot <copilot@github.com>
Agent-Logs-Url: https://github.com/wassermanlab/variome/sessions/03ffe5fe-5fdf-4bc6-ade7-c38c95099b92 Co-authored-by: bradwbradw <4715252+bradwbradw@users.noreply.github.com>
Refactor VCF import: move filters to management package, add `import_bvl_vcf` management command
Co-authored-by: Copilot <copilot@github.com>
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This is a new import script that converts a joint VCF file (Variant Call Format, with frequency data) into streams, one for each table in the bvl models. It can be adapted to work with the existing import script by replacing the TSV-reading step with code that reads the stream outputs from there. But at this point, the main runtime for the new scripts (
vcf_import/VCF_publish) just outputs TSVs, as a way to ensure accuracy by comparing with existing TSV file examples.