Fixed parseMacPathogenicity() to handle variants with multiple submitters that received both benign and pathogenic classifications, but no conflict is reported (i.e. isPathogenic == 1 and isBenign == 1 and isConflicted == 0)
Fixed bug reported in pull request #19: var.splitHGVSc, which doesn't consider strand information. When override = True, the ref and alt for genomic variants would be wrongly changed for minus strand transcripts. Changed to override = False
Fixed bug reported in pull request #19: fixed corrdinates in getMacClinVarTSV() to match readVCF().
Bug fixes in parsing of ClinVar information
Changes include:
Fixed parseMacPathogenicity() to handle variants with multiple submitters that received both benign and pathogenic classifications, but no conflict is reported (i.e.
isPathogenic == 1 and isBenign == 1 and isConflicted == 0)Fixed bug reported in pull request #19: var.splitHGVSc, which doesn't consider strand information. When override = True, the ref and alt for genomic variants would be wrongly changed for minus strand transcripts. Changed to override = False
Fixed bug reported in pull request #19: fixed corrdinates in getMacClinVarTSV() to match readVCF().