/// <summary> /// Adds the ClinVar items in this object to the supplementary annotation object /// </summary> public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator saCreator, string refBases = null) { // check if the ref allele matches the refBases as a prefix if (!SupplementaryAnnotationUtilities.ValidateRefAllele(ReferenceAllele, refBases)) { return(null); //the ref allele for this entry did not match the reference bases. } // for insertions and deletions, the alternate allele has to be modified to conform with VEP convension var newAlleles = SupplementaryAnnotationUtilities.GetReducedAlleles(Start, ReferenceAllele, AltAllele); var newStart = newAlleles.Item1; var newRefAllele = newAlleles.Item2; var newAltAllele = newAlleles.Item3; if (newRefAllele != ReferenceAllele) { var additionalItem = new ClinVarItem(Chromosome, newStart, _alleleOrigins, newAltAllele, ID, ReviewStatusString, _medgenIds, _omimIds, _orphanetIds, _phenotypes, newRefAllele, Significance, _pubmedIds, LastUpdatedDate); return(additionalItem); } saCreator.SaPosition.ClinVarItems.Add(new ClinVarItem(Chromosome, newStart, _alleleOrigins, newAltAllele, ID, ReviewStatusString, _medgenIds, _omimIds, _orphanetIds, _phenotypes, newRefAllele, Significance, _pubmedIds, LastUpdatedDate)); return(null); }
public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator sa, string refBases = null) { // check if the ref allele matches the refBases as a prefix if (!SupplementaryAnnotationUtilities.ValidateRefAllele(ReferenceAllele, refBases)) { return(null); //the ref allele for this entry did not match the reference bases. } var newAlleles = SupplementaryAnnotationUtilities.GetReducedAlleles(Start, ReferenceAllele, AlternateAllele); var newStart = newAlleles.Item1; var newRefAllele = newAlleles.Item2; var newAltAllele = newAlleles.Item3; if (newRefAllele != ReferenceAllele) { return(new DbSnpItem(Chromosome, newStart, RsId, newRefAllele, RefAlleleFreq, newAltAllele, AltAlleleFreq, _infoField)); // we need to keep the vcfline for the sake of conflict resolution } // it's a SNV or MNV at this position SetSaFields(sa, newAltAllele); return(null); }
public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator sa, string refBases = null) { // check if the ref allele matches the refBases as a prefix if (!SupplementaryAnnotationUtilities.ValidateRefAllele(ReferenceAllele, refBases)) { return(null); //the ref allele for this entry did not match the reference bases. } // if this is a SV, if (IsInterval) { return(null); } var newAlleles = SupplementaryAnnotationUtilities.GetReducedAlleles(Start, ReferenceAllele, AlternateAllele); var newStart = newAlleles.Item1; var newRefAllele = newAlleles.Item2; var newAltAllele = newAlleles.Item3; if (newRefAllele != ReferenceAllele) { return(new OneKGenItem(Chromosome, newStart, Id, newRefAllele, newAltAllele, AncestralAllele, AllAlleleCount, AfrAlleleCount, AmrAlleleCount, EurAlleleCount, EasAlleleCount, SasAlleleCount, AllAlleleNumber, AfrAlleleNumber, AmrAlleleNumber, EurAlleleNumber, EasAlleleNumber, SasAlleleNumber, SvType, SvEnd, CiPos, CiEnd)); } SetSaFields(sa, newAltAllele); return(null); }
public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator saCreator, string refBases = null) { // check if the ref allele matches the refBases as a prefix if (!SupplementaryAnnotationUtilities.ValidateRefAllele(RefAllele, refBases)) { return(null); //the ref allele for this entry did not match the reference bases. } var newAlleles = SupplementaryAnnotationUtilities.GetReducedAlleles(Start, RefAllele, AltAllele); var newStart = newAlleles.Item1; var newRefAllele = newAlleles.Item2; var newAltAllele = newAlleles.Item3; if (newRefAllele != RefAllele) { return(new CosmicItem(Chromosome, newStart, ID, newRefAllele, newAltAllele, Gene, Studies, SampleCount)); } var newRefAlleleParsed = string.IsNullOrEmpty(newRefAllele) ? "-" : newRefAllele; var newItem = new CosmicItem(Chromosome, Start, ID, newRefAlleleParsed, newAltAllele, Gene, Studies, SampleCount); newItem.AddCosmicToSa(saCreator); return(null); }
public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator sa, string refBases = null) { // check if the ref allele matches the refBases as a prefix if (!SupplementaryAnnotationUtilities.ValidateRefAllele(ReferenceAllele, refBases)) { return(null); //the ref allele for this entry did not match the reference bases. } var newAlleles = SupplementaryAnnotationUtilities.GetReducedAlleles(Start, ReferenceAllele, AlternateAllele); var newStart = newAlleles.Item1; var newRefAllele = newAlleles.Item2; var newAltAllele = newAlleles.Item3; if (newRefAllele != ReferenceAllele) { return(new ExacItem(Chromosome, newStart, newRefAllele, newAltAllele, Coverage, AllAlleleNumber, AfrAlleleNumber, AmrAlleleNumber, EasAlleleNumber, FinAlleleNumber, NfeAlleleNumber, OthAlleleNumber, SasAlleleNumber, AllAlleleCount, AfrAlleleCount, AmrAlleleCount, EasAlleleCount, FinAlleleCount, NfeAlleleCount, OthAlleleCount, SasAlleleCount)); } SetSaFields(sa, newAltAllele); return(null); }
public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator saCreator, string refBases = null) { // check if the ref allele matches the refBases as a prefix if (!SupplementaryAnnotationUtilities.ValidateRefAllele(RefAllele, refBases)) { return(null); //the ref allele for this entry did not match the reference bases. } var newAlleles = SupplementaryAnnotationUtilities.GetReducedAlleles(Start, RefAllele, AltAllele); var newStart = newAlleles.Item1; var newRefAllele = newAlleles.Item2; var newAltAllele = newAlleles.Item3; if (newRefAllele != RefAllele) { return(new CustomItem(Chromosome, newStart, newRefAllele, newAltAllele, AnnotationType, Id, IsPositional, StringFields, BooleanFields)); } //for ins, del, indel without padding base, the altAllele will change even though the ref does not. saCreator.SaPosition.CustomItems.Add(new CustomItem(Chromosome, newStart, newRefAllele, newAltAllele, AnnotationType, Id, IsPositional, StringFields, BooleanFields)); return(null); }
public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator sa, string refBases = null) { // check if the ref allele matches the refBases as a prefix if (!SupplementaryAnnotationUtilities.ValidateRefAllele(ReferenceAllele, refBases)) { return(null); //the ref allele for this entry did not match the reference bases. } var newAlleles = SupplementaryAnnotationUtilities.GetReducedAlleles(Start, ReferenceAllele, AlternateAllele); var newStart = newAlleles.Item1; var newRefAllele = newAlleles.Item2; var newAltAllele = newAlleles.Item3; if (newRefAllele != ReferenceAllele) { return(new EvsItem(Chromosome, newStart, RsId, newRefAllele, newAltAllele, AllFreq, AfrFreq, EurFreq, Coverage, NumSamples)); } SetSaFields(sa, newAltAllele); return(null); }