delete old reference data code 😝 (#990)

* first pass update vat * merge feature * fix the diff for now * include_queries * interval ht * tests * exclude * nicer * fix inteval test * split fn * eigen test * clinvar wip * hgmd * clinvar * gnomad genomes and exomes * delete * 38 snv_indel done * mito tests * done with tests? * custom_select * fields test * disable write new samples tests for now * working on tests * update update vat with new samples tests * extra file * other skipped test * make select and filter similar * tweak * rename path and locus/interval filtering * make select and filter similar (#988) * make select and filter similar * tweak * Cleanest set diff * Finish off * Tests passing! * ruff * ruff * Change the params * Fix params * params * More clinvar mocking * hardcode these * delete a bunch of stuff * ruff * remove rdc and crdq * delete v02 * remove comment references to deleted file * last test --------- Co-authored-by: Benjamin Blankenmeister <[email protected]> Co-authored-by: Benjamin Blankenmeister <[email protected]>
broadinstitute · Nov 25, 2024 · a3baf5a · a3baf5a
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diff --git a/download_and_create_reference_datasets/v02/create_ht__cadd.py b/download_and_create_reference_datasets/v02/create_ht__cadd.py
diff --git a/download_and_create_reference_datasets/v02/create_ht__clinvar.py b/download_and_create_reference_datasets/v02/create_ht__clinvar.py
diff --git a/download_and_create_reference_datasets/v02/create_ht__combined_reference_data.py b/download_and_create_reference_datasets/v02/create_ht__combined_reference_data.py
diff --git a/download_and_create_reference_datasets/v02/create_ht__eigen.py b/download_and_create_reference_datasets/v02/create_ht__eigen.py
diff --git a/download_and_create_reference_datasets/v02/create_ht__mpc.py b/download_and_create_reference_datasets/v02/create_ht__mpc.py
diff --git a/download_and_create_reference_datasets/v02/create_ht__primate_ai.py b/download_and_create_reference_datasets/v02/create_ht__primate_ai.py
diff --git a/download_and_create_reference_datasets/v02/create_ht__topmed.py b/download_and_create_reference_datasets/v02/create_ht__topmed.py
diff --git a/download_and_create_reference_datasets/v02/hail_scripts/write_1kg_ht.py b/download_and_create_reference_datasets/v02/hail_scripts/write_1kg_ht.py
diff --git a/download_and_create_reference_datasets/v02/hail_scripts/write_cadd_ht.py b/download_and_create_reference_datasets/v02/hail_scripts/write_cadd_ht.py
diff --git a/download_and_create_reference_datasets/v02/hail_scripts/write_ccREs_ht.py b/download_and_create_reference_datasets/v02/hail_scripts/write_ccREs_ht.py
diff --git a/download_and_create_reference_datasets/v02/hail_scripts/write_clinvar_ht.py b/download_and_create_reference_datasets/v02/hail_scripts/write_clinvar_ht.py
diff --git a/download_and_create_reference_datasets/v02/hail_scripts/write_combined_interval_ref_data.py b/download_and_create_reference_datasets/v02/hail_scripts/write_combined_interval_ref_data.py
diff --git a/download_and_create_reference_datasets/v02/hail_scripts/write_combined_reference_data_ht.py b/download_and_create_reference_datasets/v02/hail_scripts/write_combined_reference_data_ht.py