Add create_vds function that only supports creating from gvcfs #716
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klaricch
requested changes
Jul 17, 2024
gnomad/utils/file_utils.py
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| """ | ||
| Combine gVCFs into a single VDS. | ||
| :param gvcfs: Path to file containing gVCF paths with no header. |
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can drop the types after params since they are already defined above
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Ah copilot you silly AI
gnomad/utils/file_utils.py
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| def create_vds( | ||
| gvcfs: str, | ||
| output_path: str, | ||
| temp_path: Optional[str] = None, |
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looks like temp path is required?
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Ah good catch
klaricch
requested changes
Jul 17, 2024
gnomad/utils/file_utils.py
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| save_path = temp_path + "combiner_plan.json" | ||
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| gvcfs = read_list_data(gvcfs) | ||
| intervals = read_list_data(intervals) if intervals else None |
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can replace to use hl.import_locus_intervals and then collect the intervals here
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Adds a function to create a VDS from GVCFs only. This is mainly a wrapper around hails function with limited utility. We can expand this function's utility to ingest VDS when the time comes and that is needed.