Add utilites to update Echo filters and reference genotypes #8867
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mcovarr
approved these changes
Jun 14, 2024
| site_filtering_data : list[str] | ||
| Paths to site filtering files. | ||
| vets_filtering_data : list[str] | ||
| Paths to VETS/VQSR filtering files. |
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ploidy_data is missing from these docs
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| hl.vds.VariantDataset( | ||
| reference_data=reference_data, variant_data=variant_data | ||
| ).write(output_path, overwrite=True) |
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- The
overwrite=Truemakes me nervous, though my teammates may overrule me on that 😅. This could also be a (defaulted) function parameter. - It might be useful to return the
VariantDatasetobject so that callers can introspect after these transformations.
Suggested change
| hl.vds.VariantDataset( | |
| reference_data=reference_data, variant_data=variant_data | |
| ).write(output_path, overwrite=True) | |
| vds = hl.vds.VariantDataset(reference_data=reference_data, variant_data=variant_data) | |
| vds.write(output_path) | |
| return vds |
| avros : Sequence[str] | ||
| List of paths for raw site filtering data | ||
| site_path : str | ||
| Path to site filters table where, if a hail table exists, it will be read, unless ``force`` is true |
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This update is backwards. The force parameter will always recreate the table.
chrisvittal
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chrisvittal
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Jun 15, 2024
| avros : Sequence[str] | ||
| List of paths for raw site filtering data | ||
| site_path : str | ||
| Path to site filters table where, if a hail table exists, it will be read, unless ``force`` is true |
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This update is backwards. The force parameter will always recreate the table.
This should prevent us from needing to localize the data to run the pipeline.
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