/// <summary>
/// returns a string representation of our variant
/// </summary>
public override string ToString()
{
var sb = new StringBuilder();
var jsonObject = new JsonObject(sb);
// data section
sb.Append(JsonObject.OpenBrace);
// ==========
// positional
// ==========
jsonObject.AddStringValue(AncestralAlleleTag, AncestralAllele);
if (!IsReferenceMinor)
{
jsonObject.AddStringValue(AltAlleleTag, string.IsNullOrEmpty(AltAllele) ? "-" : AltAllele);
jsonObject.AddStringValue(RefAlleleTag, string.IsNullOrEmpty(RefAllele) ? "-" : RefAllele);
}
else
{
jsonObject.AddStringValue(RefAlleleTag, string.IsNullOrEmpty(RefAllele) ? "-" : RefAllele);
}
jsonObject.AddIntValue(BeginTag, ReferenceBegin);
jsonObject.AddStringValue(ChromosomeTag, ReferenceName);
jsonObject.AddStringValue(PhylopScoreTag, PhylopScore, false);
jsonObject.AddStringValues(DbsnpTag, DbSnpIds);
jsonObject.AddIntValue(EndTag, ReferenceEnd);
jsonObject.AddStringValue(GlobalMinorAlleleTag, GlobalMinorAllele);
jsonObject.AddStringValue(GmafTag, GlobalMinorAlleleFrequency, false);
jsonObject.AddBoolValue(IsReferenceMinorAlleleTag, true, IsReferenceMinor, "true");
jsonObject.AddStringValue(VariantTypeTag, VariantType);
jsonObject.AddStringValue(VidTag, VariantId);
// regulatory regions
if (RegulatoryRegions.Count > 0)
{
jsonObject.AddObjectValues(RegulatoryRegionsTag, RegulatoryRegions);
}
// ClinVar & COSMIC
if (ClinVarEntries.Count > 0)
{
jsonObject.AddObjectValues(ClinVarTag, ClinVarEntries);
}
if (CosmicEntries.Count > 0)
{
jsonObject.AddObjectValues(CosmicTag, CosmicEntries);
}
// Custom annotations
if (CustomItems.Count > 0)
{
AddCustomeItems(jsonObject);
}
// Custom Intervals
// if (CustomIntervals.Count > 0) jsonObject.AddObjectValues(CustomIntervals[0].Type, CustomIntervals);
if (CustomIntervals.Count > 0)
{
AddCustomeIntervals(jsonObject);
}
// =================
// Overlapping Genes
// =================
if (OverlappingGenes.Count > 0)
{
jsonObject.AddStringValues(OverlappingGenesTag, OverlappingGenes.ToArray());
}
// =================
// Overlapping Transcripts
// =================
if (SvOverlappingTranscripts.Any())
{
jsonObject.AddObjectValues(OverlappingTranscriptsTag, SvOverlappingTranscripts);
}
// ==========
// transcript
// ==========
var hasRefSeq = RefSeqTranscripts.Any();
var hasEnsembl = EnsemblTranscripts.Any();
if (hasRefSeq || hasEnsembl)
{
jsonObject.OpenObject(TranscriptsTag);
jsonObject.Reset();
if (hasRefSeq)
{
jsonObject.AddStringValues(RefseqTag, RefSeqTranscripts.Select(t => t.ToString()), false);
}
if (hasEnsembl)
{
jsonObject.AddStringValues(EnsemblTag, EnsemblTranscripts.Select(t => t.ToString()), false);
}
jsonObject.CloseObject();
}
// =======
// allelic
// =======
jsonObject.Reset(true);
jsonObject.AddStringValue(OneKgAllTag, AlleleFrequencyAll, false);
jsonObject.AddStringValue(OneKgAfrTag, AlleleFrequencyAfrican, false);
jsonObject.AddStringValue(OneKgAmrTag, AlleleFrequencyAdMixedAmerican, false);
jsonObject.AddStringValue(OneKgEasTag, AlleleFrequencyEastAsian, false);
jsonObject.AddStringValue(OneKgEurTag, AlleleFrequencyEuropean, false);
jsonObject.AddStringValue(OneKgSasTag, AlleleFrequencySouthAsian, false);
jsonObject.AddStringValue(OneKgAllAnTag, OneKgAlleleNumberAll, false);
jsonObject.AddStringValue(OneKgAfrAnTag, OneKgAlleleNumberAfrican, false);
jsonObject.AddStringValue(OneKgAmrAnTag, OneKgAlleleNumberAmerican, false);
jsonObject.AddStringValue(OneKgEasAnTag, OneKgAlleleNumberEastAsian, false);
jsonObject.AddStringValue(OneKgEurAnTag, OneKgAlleleNumberEuropean, false);
jsonObject.AddStringValue(OneKgSasAnTag, OneKgAlleleNumberSouthAsian, false);
jsonObject.AddStringValue(OneKgAllAcTag, OneKgAlleleCountAll, false);
jsonObject.AddStringValue(OneKgAfrAcTag, OneKgAlleleCountAfrican, false);
jsonObject.AddStringValue(OneKgAmrAcTag, OneKgAlleleCountAmerican, false);
jsonObject.AddStringValue(OneKgEasAcTag, OneKgAlleleCountEastAsian, false);
jsonObject.AddStringValue(OneKgEurAcTag, OneKgAlleleCountEuropean, false);
jsonObject.AddStringValue(OneKgSasAcTag, OneKgAlleleCountSouthAsian, false);
jsonObject.AddStringValue(EvsCoverageTag, EvsCoverage, false);
jsonObject.AddStringValue(EvsSamplesTag, EvsSamples, false);
jsonObject.AddStringValue(EvsAllTag, EvsAlleleFrequencyAll, false);
jsonObject.AddStringValue(EvsAfrTag, EvsAlleleFrequencyAfricanAmerican, false);
jsonObject.AddStringValue(EvsEurTag, EvsAlleleFrequencyEuropeanAmerican, false);
jsonObject.AddStringValue(ExacCoverageTag, ExacCoverage, false);
jsonObject.AddStringValue(ExacAllTag, ExacAlleleFrequencyAll, false);
jsonObject.AddStringValue(ExacAfrTag, ExacAlleleFrequencyAfrican, false);
jsonObject.AddStringValue(ExacAmrTag, ExacAlleleFrequencyAmerican, false);
jsonObject.AddStringValue(ExacEasTag, ExacAlleleFrequencyEastAsian, false);
jsonObject.AddStringValue(ExacFinTag, ExacAlleleFrequencyFinish, false);
jsonObject.AddStringValue(ExacNfeTag, ExacAlleleFrequencyNonFinish, false);
jsonObject.AddStringValue(ExacOthTag, ExacAlleleFrequencyOther, false);
jsonObject.AddStringValue(ExacSasTag, ExacAlleleFrequencySouthAsian, false);
jsonObject.AddStringValue(ExacAllAnTag, ExacAlleleNumberAll, false);
jsonObject.AddStringValue(ExacAfrAnTag, ExacAlleleNumberAfrican, false);
jsonObject.AddStringValue(ExacAmrAnTag, ExacAlleleNumberAmerican, false);
jsonObject.AddStringValue(ExacEasAnTag, ExacAlleleNumberEastAsian, false);
jsonObject.AddStringValue(ExacFinAnTag, ExacAlleleNumberFinish, false);
jsonObject.AddStringValue(ExacNfeAnTag, ExacAlleleNumberNonFinish, false);
jsonObject.AddStringValue(ExacOthAnTag, ExacAlleleNumberOther, false);
jsonObject.AddStringValue(ExacSasAnTag, ExacAlleleNumberSouthAsian, false);
jsonObject.AddStringValue(ExacAllAcTag, ExacAlleleCountAll, false);
jsonObject.AddStringValue(ExacAfrAcTag, ExacAlleleCountAfrican, false);
jsonObject.AddStringValue(ExacAmrAcTag, ExacAlleleCountAmerican, false);
jsonObject.AddStringValue(ExacEasAcTag, ExacAlleleCountEastAsian, false);
jsonObject.AddStringValue(ExacFinAcTag, ExacAlleleCountFinish, false);
jsonObject.AddStringValue(ExacNfeAcTag, ExacAlleleCountNonFinish, false);
jsonObject.AddStringValue(ExacOthAcTag, ExacAlleleCountOther, false);
jsonObject.AddStringValue(ExacSasAcTag, ExacAlleleCountSouthAsian, false);
sb.Append(JsonObject.CloseBrace);
return(sb.ToString());
}
/// <summary>
/// clears the data structure
/// </summary>
public void Clear()
{
AncestralAllele = null;
AltAllele = null;
ReferenceBegin = null;
ReferenceName = null;
DbSnpIds = null;
ReferenceEnd = null;
EvsCoverage = null;
EvsSamples = null;
ExacCoverage = null;
GlobalMinorAllele = null;
RefAllele = null;
IsReferenceMinor = false;
IsIntergenic = false;
IsReference = false;
IsReferenceNoCall = false;
GlobalMinorAlleleFrequency = null;
VariantId = null;
VariantType = null;
PhylopScore = null;
AlleleFrequencyAdMixedAmerican = null;
AlleleFrequencyAfrican = null;
AlleleFrequencyAll = null;
AlleleFrequencyEastAsian = null;
AlleleFrequencyEuropean = null;
AlleleFrequencySouthAsian = null;
EvsAlleleFrequencyAfricanAmerican = null;
EvsAlleleFrequencyEuropeanAmerican = null;
EvsAlleleFrequencyAll = null;
ExacAlleleFrequencyAll = null;
ExacAlleleFrequencyAfrican = null;
ExacAlleleFrequencyAmerican = null;
ExacAlleleFrequencyEastAsian = null;
ExacAlleleFrequencyFinish = null;
ExacAlleleFrequencyNonFinish = null;
ExacAlleleFrequencyOther = null;
ExacAlleleFrequencySouthAsian = null;
ExacAlleleNumberAfrican = null;
ExacAlleleNumberAmerican = null;
ExacAlleleNumberAll = null;
ExacAlleleNumberEastAsian = null;
ExacAlleleNumberFinish = null;
ExacAlleleNumberNonFinish = null;
ExacAlleleNumberOther = null;
ExacAlleleNumberSouthAsian = null;
ExacAlleleCountAfrican = null;
ExacAlleleCountAmerican = null;
ExacAlleleCountAll = null;
ExacAlleleCountEastAsian = null;
ExacAlleleCountFinish = null;
ExacAlleleCountNonFinish = null;
ExacAlleleCountOther = null;
ExacAlleleCountSouthAsian = null;
OneKgAlleleNumberAfrican = null;
OneKgAlleleNumberAmerican = null;
OneKgAlleleNumberAll = null;
OneKgAlleleNumberEastAsian = null;
OneKgAlleleNumberEuropean = null;
OneKgAlleleNumberSouthAsian = null;
OneKgAlleleCountAfrican = null;
OneKgAlleleCountAmerican = null;
OneKgAlleleCountAll = null;
OneKgAlleleCountEastAsian = null;
OneKgAlleleCountEuropean = null;
OneKgAlleleCountSouthAsian = null;
RefSeqTranscripts.Clear();
EnsemblTranscripts.Clear();
CosmicEntries.Clear();
ClinVarEntries.Clear();
RegulatoryRegions.Clear();
CustomItems.Clear();
CustomIntervals.Clear();
OverlappingGenes.Clear();
SvOverlappingTranscripts.Clear();
}
