Add densify_all_reference_sites to perform a densify at all sites in a reference HT
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…nstitute/gnomad_methods into jg/generalize_densify_at_all_ref_sites
…nstitute/gnomad_methods into jg/generalize_densify_at_all_ref_sites
… into jg/generalize_densify_at_all_ref_sites # Conflicts: # gnomad/utils/sparse_mt.py
mike-w-wilson
approved these changes
Jan 18, 2024
| mt = mtds.variant_data | ||
| else: | ||
| mt = mtds | ||
| entry_keep_fields.add("END") |
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I'm not sure I know the use keep for keeping END here? Is it if you passed the vds.reference_data to this function with adding "END" to the entry_keep_fields?
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This supports a sparse MT, the END is in the reference_data of the VDS which we handle differently below, but in the sparse MT it's all in one so we need to make sure we keep it when when we localize entries
Co-authored-by: Mike Wilson <[email protected]>
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I have been using this notebook for testing: http://localhost:8123/notebooks/gnomad-julia/gnomad_v4/test_v4_densify_all_reference_sites.ipynb