Bugfix/sap 11534 handle clnhgvs using measure set name#58
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kevin-dunnicliffe wants to merge 23 commits intomacarthur-lab:masterfrom
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Bugfix/sap 11534 handle clnhgvs using measure set name#58kevin-dunnicliffe wants to merge 23 commits intomacarthur-lab:masterfrom
kevin-dunnicliffe wants to merge 23 commits intomacarthur-lab:masterfrom
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…from XML file. SAP-4037
…equired for Sapientia. Stored in data-frame as clnsig. SAP-4037
…using in our ClinVar VCFs. Set ID column to dbSNP/rsID
…d_indels SAP-7990 : Modify XML parser to include variants with non-standard VC…
…thogenicity SAP-6265 : Show most severe pathogenicity for conflicted variants
…nt_numbers_in_vcf_header SAP-8224 : Output expected variant numbers in ClinVar VCF header
…ant_name SAP-8219 : Add "rs" the front of the rsID
…for_latest_clinvar SAP-8222 : compatibility for latest clinvar
…Assertion_clnsig SAP-8433 : Add pathogenicity mapping for old terms
…_descriptions SAP-8478 : Add human-readable descriptions for INFO fields in VCF header
…n_from_vcf_header SAP-8360 : Pass ClinVar version to VCF writer to add version and date…
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This branch is based on feature/congenica_headers, because this repo does not seem to have been merged anywhere for some time.