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Merge pull request #1053 from broadinstitute/benb/remove_hardcoded_datasettype_allele_validation
bug fix: handle set of dataset types during allele type validation
2 parents bfde429 + fb0f6fe commit 49e90e3

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v03_pipeline/lib/reference_datasets/reference_dataset.py

Lines changed: 9 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -104,6 +104,12 @@ def version(self, reference_genome: ReferenceGenome) -> str:
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)
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return version
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def dataset_types(
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self,
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reference_genome: ReferenceGenome,
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) -> frozenset[DatasetType]:
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return CONFIG[self][reference_genome][DATASET_TYPES]
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@property
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def enums(self) -> dict | None:
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return CONFIG[self].get(ENUMS)
@@ -143,11 +149,9 @@ def get_ht(
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if enum_selects:
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ht = ht.transmute(**enum_selects)
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ht = filter_contigs(ht, reference_genome)
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# Reference Datasets are DatasetType agnostic, but these
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# methods (in theory) support SV/GCNV. SNV_INDEL
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# is passed as a proxy for non-SV/GCNV.
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validate_allele_type(ht, DatasetType.SNV_INDEL)
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validate_no_duplicate_variants(ht, reference_genome, DatasetType.SNV_INDEL)
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for dataset_type in self.dataset_types(reference_genome):
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validate_allele_type(ht, dataset_type)
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validate_no_duplicate_variants(ht, reference_genome, dataset_type)
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# NB: we do not filter with "filter" here
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# ReferenceDatasets are DatasetType agnostic and that
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# filter is only used at annotation time.

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