Add PMID to finding notes #4209
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hanars
commented
Jul 1, 2024
| ], [ | ||
| 'Broad_HG00731_1_248367227', 'Broad_HG00731', 'Broad_exome_VCGS_FAM203_621_D2', 'SNV/INDEL', 'GRCh37', '1', | ||
| '248367227', 'TC', 'T', 'CA1501729', 'RP11', '', '', '', 'Homozygous', '', 'paternal', '', '', 'Known', '', | ||
| 'MONDO:0044970', '', 'Uncertain', '', 'Broad_HG00732', 'SR-ES', '', '', '', '', '', '', '', | ||
| ], [ | ||
| 'Broad_HG00731_19_1912634', 'Broad_HG00731', 'Broad_exome_VCGS_FAM203_621_D2', 'SNV/INDEL', 'GRCh38', '19', |
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this row was always in the table, we just were not explicitly testing it before
hanars
commented
Jul 1, 2024
| @@ -165,7 +165,7 @@ def parse_anvil_metadata( | |||
| airtable_fields: Iterable[str] = None, mme_value: Aggregate = None, include_svs: bool = True, | |||
| variant_json_fields: Iterable[str] = None, variant_attr_fields: Iterable[str] = None, post_process_variant: Callable[[dict, list[dict]], dict] = None, | |||
| include_no_individual_families: bool = False, omit_airtable: bool = False, include_family_name_display: bool = False, include_family_sample_metadata: bool = False, | |||
| include_discovery_sample_id: bool = False, include_mondo: bool = False, include_parent_mnvs: bool = False, | |||
| include_discovery_sample_id: bool = False, include_mondo: bool = False, omit_parent_mnvs: bool = False, | |||
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changes the default behavior of this function to include parent MNVs since that is the behavior we want almost everywhere, so the one place we don't want it sets that explicitly
hanars
commented
Jul 1, 2024
| 'sv_name': _get_sv_name(v), | ||
| 'notes': discovery_notes, | ||
| } | ||
| def _get_discovery_notes(variant, gene_variants, omit_parent_mnvs): |
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functionality did not change, only indenting
jklugherz
approved these changes
Jul 2, 2024
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