public override string ToString()
{
var sb = new StringBuilder();
var jsonObject = new JsonObject(sb);
// data section
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("variantFreq", VariantFrequency, false);
jsonObject.AddStringValue("totalDepth", TotalDepth, false);
jsonObject.AddStringValue("genotypeQuality", GenotypeQuality, false);
jsonObject.AddStringValue("copyNumber", CopyNumber, false);
jsonObject.AddStringValues("alleleDepths", AlleleDepths, false);
jsonObject.AddStringValue("genotype", Genotype);
jsonObject.AddBoolValue("failedFilter", FailedFilter, true, "true");
jsonObject.AddStringValues("splitReadCounts", SplitReadCounts, false);
jsonObject.AddStringValues("pairedEndReadCounts", PairEndReadCounts, false);
jsonObject.AddBoolValue("isEmpty", IsEmpty, true, "true");
jsonObject.AddBoolValue("lossOfHeterozygosity", IsLossOfHeterozygosity, true, "true");
jsonObject.AddStringValue("deNovoQuality", DenovoQuality, false);
sb.Append(JsonObject.CloseBrace);
return(sb.ToString());
}
public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
if (string.IsNullOrEmpty(RefAllele))
{
RefAllele = "-";
}
if (string.IsNullOrEmpty(AltAllele))
{
AltAllele = "-";
}
jsonObject.AddStringValue("refAllele", RefAllele);
jsonObject.AddStringValue("altAllele", AltAllele);
jsonObject.AddStringValues("diseases", _diseases?.Distinct());
if (_homoplasmy.HasValue)
{
jsonObject.AddBoolValue("hasHomoplasmy", _homoplasmy.Value, true);
}
if (_heteroplasmy.HasValue)
{
jsonObject.AddBoolValue("hasHeteroplasmy", _heteroplasmy.Value, true);
}
jsonObject.AddStringValue("status", _status);
jsonObject.AddStringValue("clinicalSignificance", _clinicalSignificance);
jsonObject.AddStringValue("scorePercentile", _scorePercentile, false);
jsonObject.AddIntValue("numGenBankFullLengthSeqs", _numGenBankFullLengthSeqs);
jsonObject.AddStringValues("pubMedIds", _pubMedIds);
return(StringBuilderCache.GetStringAndRelease(sb));
}
public void SerializeJson(StringBuilder sb)
{
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("transcript", Id.WithVersion);
jsonObject.AddStringValue("hgnc", GeneName);
jsonObject.AddBoolValue("isCanonical", IsCanonical);
jsonObject.AddBoolValue("partialOverlap", IsPartionalOverlap);
sb.Append(JsonObject.CloseBrace);
}
public void AddBoolValue_True_TwoTimes()
{
var sb = StringBuilderCache.Acquire();
var json = new JsonObject(sb);
json.AddBoolValue("test1", true);
json.AddBoolValue("test2", true);
const string expectedResult = "\"test1\":true,\"test2\":true";
var observedResult = StringBuilderCache.GetStringAndRelease(sb);
Assert.Equal(expectedResult, observedResult);
}
public void SerializeJson(StringBuilder sb)
{
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("id", Id);
jsonObject.AddStringValue("altAllele", "N" == AltAllele ? null : AltAllele);
jsonObject.AddStringValue("isAlleleSpecific", IsAlleleSpecific, false);
if (StringFields != null)
{
foreach (var stringField in StringFields)
{
jsonObject.AddStringValue(stringField.Key, stringField.Value);
}
}
if (BooleanFields != null)
{
foreach (var booleanField in BooleanFields)
{
jsonObject.AddBoolValue(booleanField, true, true, "true");
}
}
sb.Append(JsonObject.CloseBrace);
}
public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
jsonObject.AddStringValue("id", Id);
jsonObject.AddStringValue("altAllele", "N" == AlternateAllele ? null : AlternateAllele);
jsonObject.AddStringValue("isAlleleSpecific", IsAlleleSpecific, false);
if (StringFields != null)
{
foreach (var stringField in StringFields)
{
jsonObject.AddStringValue(stringField.Key, stringField.Value);
}
}
if (NumberFields != null)
{
foreach (var numFields in NumberFields)
{
jsonObject.AddStringValue(numFields.Key, numFields.Value.ToString(CultureInfo.InvariantCulture), false);
}
}
if (BooleanFields != null)
{
foreach (var booleanField in BooleanFields)
{
jsonObject.AddBoolValue(booleanField, true);
}
}
return(StringBuilderCache.GetStringAndRelease(sb));
}
public void SerializeJson(StringBuilder sb)
{
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("id", Id);
jsonObject.AddStringValue("altAllele", "N" == AlternateAllele ? null : AlternateAllele);
jsonObject.AddStringValue("isAlleleSpecific", IsAlleleSpecific, false);
if (StringFields != null)
{
foreach (var stringField in StringFields)
{
jsonObject.AddStringValue(stringField.Key, stringField.Value);
}
}
if (NumberFields != null)
{
foreach (var numFields in NumberFields)
{
jsonObject.AddStringValue(numFields.Key, numFields.Value.ToString(CultureInfo.InvariantCulture), false);
}
}
if (BooleanFields != null)
{
foreach (var booleanField in BooleanFields)
{
jsonObject.AddBoolValue(booleanField, true);
}
}
sb.Append(JsonObject.CloseBrace);
}
public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
jsonObject.AddStringValue("chromosome", Chromosome.EnsemblName);
jsonObject.AddIntValue("begin", Start);
jsonObject.AddIntValue("end", End);
jsonObject.AddStringValue("variantType", VariantType.ToString());
jsonObject.AddStringValue("id", Id);
jsonObject.AddStringValue("clinicalInterpretation", GetClinicalDescription(ClinicalInterpretation));
jsonObject.AddStringValues("phenotypes", Phenotypes);
jsonObject.AddStringValues("phenotypeIds", PhenotypeIds);
if (ObservedGains > 0)
{
jsonObject.AddIntValue("observedGains", ObservedGains);
}
if (ObservedLosses > 0)
{
jsonObject.AddIntValue("observedLosses", ObservedLosses);
}
jsonObject.AddBoolValue("validated", Validated);
return(StringBuilderCache.GetStringAndRelease(sb));
}
public string GetJsonString()
{
if (AnnotatedVariants == null || AnnotatedVariants.Length == 0)
{
return(null);
}
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
var originalChromName = Position.VcfFields[0];
jsonObject.AddStringValue("chromosome", originalChromName);
jsonObject.AddIntValue("position", Position.Start);
if (IsShortTandemRepeat())
{
jsonObject.AddStringValue("repeatUnit", Position.InfoData.RepeatUnit);
jsonObject.AddIntValue("refRepeatCount", Position.InfoData.RefRepeatCount);
}
jsonObject.AddIntValue("svEnd", Position.InfoData.End);
jsonObject.AddStringValue("refAllele", Position.RefAllele);
jsonObject.AddStringValues("altAlleles", Position.AltAlleles);
jsonObject.AddDoubleValue("quality", Position.Quality);
jsonObject.AddStringValues("filters", Position.Filters);
jsonObject.AddIntValues("ciPos", Position.InfoData.CiPos);
jsonObject.AddIntValues("ciEnd", Position.InfoData.CiEnd);
jsonObject.AddIntValue("svLength", Position.InfoData.SvLength);
jsonObject.AddDoubleValue("strandBias", Position.InfoData.StrandBias, JsonCommon.FrequencyRoundingFormat);
jsonObject.AddIntValue("jointSomaticNormalQuality", Position.InfoData.JointSomaticNormalQuality);
jsonObject.AddDoubleValue("recalibratedQuality", Position.InfoData.RecalibratedQuality);
jsonObject.AddIntValue("copyNumber", Position.InfoData.CopyNumber);
jsonObject.AddBoolValue("colocalizedWithCnv", Position.InfoData.ColocalizedWithCnv);
jsonObject.AddStringValue("cytogeneticBand", CytogeneticBand);
if (Position.Samples != null && Position.Samples.Length > 0)
{
jsonObject.AddStringValues("samples", Position.Samples.Select(s => s.GetJsonString()), false);
}
if (SupplementaryIntervals != null && SupplementaryIntervals.Any())
{
AddSuppIntervalToJsonObject(jsonObject);
}
jsonObject.AddStringValues("variants", AnnotatedVariants.Select(v => v.GetJsonString(originalChromName)), false);
sb.Append(JsonObject.CloseBrace);
return(StringBuilderCache.GetStringAndRelease(sb));
}
public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
jsonObject.AddIntValue("coverage", Coverage);
if (HasFailedFilters)
{
jsonObject.AddBoolValue("failedFilter", true);
}
jsonObject.AddStringValue("allAf", ComputingUtilities.ComputeFrequency(AllAlleleNumber, AllAlleleCount), false);
jsonObject.AddIntValue("allAn", AllAlleleNumber);
jsonObject.AddIntValue("allAc", AllAlleleCount);
jsonObject.AddIntValue("allHc", AllHomCount);
jsonObject.AddStringValue("afrAf", ComputingUtilities.ComputeFrequency(AfrAlleleNumber, AfrAlleleCount), false);
jsonObject.AddIntValue("afrAn", AfrAlleleNumber);
jsonObject.AddIntValue("afrAc", AfrAlleleCount);
jsonObject.AddIntValue("afrHc", AfrHomCount);
jsonObject.AddStringValue("amrAf", ComputingUtilities.ComputeFrequency(AmrAlleleNumber, AmrAlleleCount), false);
jsonObject.AddIntValue("amrAn", AmrAlleleNumber);
jsonObject.AddIntValue("amrAc", AmrAlleleCount);
jsonObject.AddIntValue("amrHc", AmrHomCount);
jsonObject.AddStringValue("easAf", ComputingUtilities.ComputeFrequency(EasAlleleNumber, EasAlleleCount), false);
jsonObject.AddIntValue("easAn", EasAlleleNumber);
jsonObject.AddIntValue("easAc", EasAlleleCount);
jsonObject.AddIntValue("easHc", EasHomCount);
jsonObject.AddStringValue("finAf", ComputingUtilities.ComputeFrequency(FinAlleleNumber, FinAlleleCount), false);
jsonObject.AddIntValue("finAn", FinAlleleNumber);
jsonObject.AddIntValue("finAc", FinAlleleCount);
jsonObject.AddIntValue("finHc", FinHomCount);
jsonObject.AddStringValue("nfeAf", ComputingUtilities.ComputeFrequency(NfeAlleleNumber, NfeAlleleCount), false);
jsonObject.AddIntValue("nfeAn", NfeAlleleNumber);
jsonObject.AddIntValue("nfeAc", NfeAlleleCount);
jsonObject.AddIntValue("nfeHc", NfeHomCount);
jsonObject.AddStringValue("asjAf", ComputingUtilities.ComputeFrequency(AsjAlleleNumber, AsjAlleleCount), false);
jsonObject.AddIntValue("asjAn", AsjAlleleNumber);
jsonObject.AddIntValue("asjAc", AsjAlleleCount);
jsonObject.AddIntValue("asjHc", AsjHomCount);
jsonObject.AddStringValue("sasAf", ComputingUtilities.ComputeFrequency(SasAlleleNumber, SasAlleleCount), false);
jsonObject.AddIntValue("sasAn", SasAlleleNumber);
jsonObject.AddIntValue("sasAc", SasAlleleCount);
jsonObject.AddIntValue("sasHc", SasHomCount);
jsonObject.AddStringValue("othAf", ComputingUtilities.ComputeFrequency(OthAlleleNumber, OthAlleleCount), false);
jsonObject.AddIntValue("othAn", OthAlleleNumber);
jsonObject.AddIntValue("othAc", OthAlleleCount);
jsonObject.AddIntValue("othHc", OthHomCount);
return(StringBuilderCache.GetStringAndRelease(sb));
}
public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
jsonObject.AddBoolValue("isReferenceMinor", true);
return(StringBuilderCache.GetStringAndRelease(sb));
}
public string GetVariantJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
if (string.IsNullOrEmpty(ReferenceAllele))
{
ReferenceAllele = "-";
}
if (string.IsNullOrEmpty(AlternateAllele))
{
AlternateAllele = "-";
}
jsonObject.AddStringValue("refAllele", ReferenceAllele);
jsonObject.AddStringValue("altAllele", AlternateAllele);
if (_diseases != null && _diseases.Count > 0)
{
jsonObject.AddStringValues("diseases", _diseases.Distinct().ToList());
}
if (_homoplasmy.HasValue)
{
jsonObject.AddBoolValue("hasHomoplasmy", _homoplasmy.Value, true);
}
if (_heteroplasmy.HasValue)
{
jsonObject.AddBoolValue("hasHeteroplasmy", _heteroplasmy.Value, true);
}
if (!string.IsNullOrEmpty(_status))
{
jsonObject.AddStringValue("status", _status);
}
if (!string.IsNullOrEmpty(_clinicalSignificance))
{
jsonObject.AddStringValue("clinicalSignificance", _clinicalSignificance);
}
if (!string.IsNullOrEmpty(_scorePercentile))
{
jsonObject.AddStringValue("scorePercentile", _scorePercentile, false);
}
return(StringBuilderCache.GetStringAndRelease(sb));
}
public void SerializeJson(StringBuilder sb)
{
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("transcript", Transcript.Id.WithVersion);
jsonObject.AddStringValue("bioType", GetBioType(Transcript.BioType));
jsonObject.AddStringValue("codons", GetAlleleString(ReferenceCodons, AlternateCodons));
jsonObject.AddStringValue("aminoAcids", GetAlleleString(ReferenceAminoAcids, AlternateAminoAcids));
if (MappedPosition != null)
{
jsonObject.AddStringValue("cdnaPos", GetRangeString(MappedPosition.CdnaStart, MappedPosition.CdnaEnd));
jsonObject.AddStringValue("cdsPos", GetRangeString(MappedPosition.CdsStart, MappedPosition.CdsEnd));
jsonObject.AddStringValue("exons", GetFractionString(MappedPosition.ExonStart, MappedPosition.ExonEnd, Transcript.NumExons));
jsonObject.AddStringValue("introns", GetFractionString(MappedPosition.IntronStart, MappedPosition.IntronEnd, Transcript.NumExons - 1));
jsonObject.AddStringValue("proteinPos", GetRangeString(MappedPosition.ProteinStart, MappedPosition.ProteinEnd));
}
var geneId = Transcript.Source == Source.Ensembl
? Transcript.Gene.EnsemblId.ToString()
: Transcript.Gene.EntrezGeneId.ToString();
jsonObject.AddStringValue("geneId", geneId);
jsonObject.AddStringValue("hgnc", Transcript.Gene.Symbol);
jsonObject.AddStringValues("consequence", Consequences?.Select(ConsequenceUtil.GetConsequence));
jsonObject.AddStringValue("hgvsc", HgvsCoding);
jsonObject.AddStringValue("hgvsp", HgvsProtein);
jsonObject.AddStringValue("geneFusion", GeneFusionAnnotation?.ToString(), false);
jsonObject.AddBoolValue("isCanonical", Transcript.IsCanonical);
jsonObject.AddDoubleValue("polyPhenScore", PolyPhen?.Score);
jsonObject.AddStringValue("polyPhenPrediction", PolyPhen?.Prediction);
if (Transcript.Translation != null)
{
jsonObject.AddStringValue("proteinId", Transcript.Translation.ProteinId.WithVersion);
}
jsonObject.AddDoubleValue("siftScore", Sift?.Score);
jsonObject.AddStringValue("siftPrediction", Sift?.Prediction);
if (PluginData != null)
{
foreach (var pluginData in PluginData)
{
jsonObject.AddStringValue(pluginData.Name, pluginData.GetJsonString(), false);
}
}
sb.Append(JsonObject.CloseBrace);
}
public string GetJsonContent()
{
var sb = new StringBuilder();
var jsonObject = new JsonObject(sb);
// data section
jsonObject.AddStringValue("chromosome", ReferenceName);
jsonObject.AddIntValue("begin", Start);
jsonObject.AddIntValue("end", End);
jsonObject.AddStringValue("source", Source);
jsonObject.AddStringValue("variantType", VariantType.ToString());
foreach (var kvp in PopulationFrequencies)
{
if (kvp.Value > 0)
{
jsonObject.AddStringValue(kvp.Key, kvp.Value.ToString("0.#####"), false);
}
}
foreach (var kvp in StringValues)
{
jsonObject.AddStringValue(kvp.Key, kvp.Value);
}
foreach (var kvp in IntValues)
{
jsonObject.AddIntValue(kvp.Key, kvp.Value);
}
foreach (var kvp in DoubleValues)
{
if (kvp.Value > 0)
{
jsonObject.AddStringValue(kvp.Key, kvp.Value.ToString("0.#####"), false);
}
}
foreach (var kvp in BoolValues)
{
jsonObject.AddBoolValue(kvp, true, true, "true");
}
foreach (var kvp in StringLists)
{
jsonObject.AddStringValues(kvp.Key, kvp.Value);
}
return(sb.ToString());
}
public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
// data section
jsonObject.AddStringValue("chromosome", Chromosome.EnsemblName);
jsonObject.AddIntValue("begin", Start);
jsonObject.AddIntValue("end", End);
jsonObject.AddStringValue("variantType", VariantType.ToString());
foreach (var kvp in PopulationFrequencies)
{
if (kvp.Value > 0)
{
jsonObject.AddStringValue(kvp.Key, kvp.Value.ToString("0.#####"), false);
}
}
foreach (var kvp in StringValues)
{
jsonObject.AddStringValue(kvp.Key, kvp.Value);
}
foreach (var kvp in IntValues)
{
jsonObject.AddIntValue(kvp.Key, kvp.Value);
}
foreach (var kvp in DoubleValues)
{
if (kvp.Value > 0)
{
jsonObject.AddStringValue(kvp.Key, kvp.Value.ToString("0.#####"), false);
}
}
foreach (var kvp in BoolValues)
{
jsonObject.AddBoolValue(kvp, true);
}
foreach (var kvp in StringLists)
{
jsonObject.AddStringValues(kvp.Key, kvp.Value.ToArray());
}
return(StringBuilderCache.GetStringAndRelease(sb));
}
public string GetJsonString()
{
var sb = new StringBuilder();
var jsonObject = new JsonObject(sb);
jsonObject.AddStringValue("allAf", ComputingUtilities.ComputeFrequency(_alleleNum, _alleleCount), false);
jsonObject.AddIntValue("allAn", _alleleNum);
jsonObject.AddIntValue("allAc", _alleleCount);
jsonObject.AddIntValue("allHc", _homCount);
if (_failedFilter)
{
jsonObject.AddBoolValue("failedFilter", true);
}
return(sb.ToString());
}
public string GetJsonString(string originalChromName)
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
// data section
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("vid", Variant.VariantId);
jsonObject.AddStringValue("chromosome", originalChromName);
jsonObject.AddIntValue("begin", Variant.Start);
jsonObject.AddIntValue("end", Variant.End);
jsonObject.AddBoolValue("isReferenceMinorAllele", Variant.IsRefMinor);
if (!Variant.IsRefMinor)
{
jsonObject.AddStringValue("refAllele",
string.IsNullOrEmpty(Variant.RefAllele) ? "-" : Variant.RefAllele);
jsonObject.AddStringValue("altAllele",
string.IsNullOrEmpty(Variant.AltAllele) ? "-" : Variant.AltAllele);
}
else
{
jsonObject.AddStringValue("refAllele",
string.IsNullOrEmpty(Variant.AltAllele) ? "-" : Variant.AltAllele);
}
var variantType = GetVariantType(Variant.Type);
jsonObject.AddStringValue("variantType", variantType.ToString());
jsonObject.AddBoolValue("isDecomposedVariant", Variant.IsDecomposed);
if (variantType.ToString() != "SNV")
{
jsonObject.AddBoolValue("isRecomposedVariant", Variant.IsRecomposed);
}
jsonObject.AddStringValue("hgvsg", HgvsgNotation);
jsonObject.AddDoubleValue("phylopScore", PhylopScore);
if (RegulatoryRegions?.Count > 0)
{
jsonObject.AddObjectValues("regulatoryRegions", RegulatoryRegions);
}
if (SupplementaryAnnotations.Count > 0)
{
AddSAstoJsonObject(jsonObject);
}
foreach (var pluginData in PluginDataSet)
{
jsonObject.AddStringValue(pluginData.Name, pluginData.GetJsonString(), false);
}
if (OverlappingGenes.Count > 0)
{
jsonObject.AddStringValues("overlappingGenes", OverlappingGenes);
}
if (OverlappingTranscripts.Count > 0)
{
jsonObject.AddObjectValues("overlappingTranscripts", OverlappingTranscripts);
}
if (EnsemblTranscripts?.Count > 0 || RefSeqTranscripts?.Count > 0)
{
jsonObject.AddGroupedObjectValues("transcripts", TranscriptLabels, RefSeqTranscripts, EnsemblTranscripts);
}
sb.Append(JsonObject.CloseBrace);
return(StringBuilderCache.GetStringAndRelease(sb));
}
public override string ToString()
{
// return if this is a reference site
// ReSharper disable once AssignNullToNotNullAttribute
if (!AnnotatedAlternateAlleles.Any())
{
return(null);
}
var sb = new StringBuilder();
var jsonObject = new JsonObject(sb);
if (NeedsVariantComma)
{
sb.Append(JsonObject.Comma);
sb.Append('\n');
}
else
{
NeedsVariantComma = true;
}
// data section
sb.Append(JsonObject.OpenBrace);
// ==========
// positional
// ==========
jsonObject.AddStringValue(ChromosomeTag, ReferenceName);
jsonObject.AddStringValue(RefAlleleTag, ReferenceAllele);
jsonObject.AddIntValue(PositionTag, ReferenceBegin);
jsonObject.AddStringValues("ciPos", CiPos, false);
jsonObject.AddStringValues("ciEnd", CiEnd, false);
jsonObject.AddIntValue("svLength", SvLength);
jsonObject.AddStringValue("quality", Quality, false);
jsonObject.AddStringValues("filters", Filters);
jsonObject.AddStringValues("altAlleles", AlternateAlleles);
jsonObject.AddStringValue("strandBias", StrandBias, false);
jsonObject.AddStringValue("jointSomaticNormalQuality", JointSomaticNormalQuality, false);
jsonObject.AddStringValue("recalibratedQuality", RecalibratedQuality, false);
jsonObject.AddStringValue("copyNumber", CopyNumber, false);
jsonObject.AddStringValue("cytogeneticBand", CytogeneticBand);
jsonObject.AddBoolValue("colocalizedWithCnv", ColocalizedWithCnv, true, TrueTag);
if (AnnotatedSamples != null)
{
jsonObject.AddStringValues(SamplesTag, AnnotatedSamples.Select(s => s.ToString()).ToArray(), false);
}
if (SupplementaryIntervals != null && SupplementaryIntervals.Any())
{
jsonObject.AddStringValues(StructuralVariantsTag, SupplementaryIntervals.Select(s => s.ToString()).ToArray(), false);
}
jsonObject.AddStringValues(VariantsTag, AnnotatedAlternateAlleles.Select(v => v.ToString()).ToArray(), false);
sb.Append(JsonObject.CloseBrace.ToString());
return(sb.ToString());
}
public void SerializeJson(StringBuilder sb)
{
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("transcript", Transcript.Id.WithVersion);
jsonObject.AddStringValue("source", Transcript.Source.ToString());
if (CompleteOverlap.HasValue && !CompleteOverlap.Value)
{
jsonObject.AddStringValue("bioType", GetBioType(Transcript.BioType));
}
jsonObject.AddStringValue("codons", GetCodonString(ReferenceCodons, AlternateCodons));
jsonObject.AddStringValue("aminoAcids", GetAminoAcidString(ReferenceAminoAcids, AlternateAminoAcids));
if (MappedPosition != null)
{
jsonObject.AddStringValue("cdnaPos", GetRangeString(MappedPosition.CoveredCdnaStart, MappedPosition.CoveredCdnaEnd));
jsonObject.AddStringValue("cdsPos", GetRangeString(MappedPosition.CoveredCdsStart, MappedPosition.CoveredCdsEnd));
jsonObject.AddStringValue("exons", GetFractionString(MappedPosition.ExonStart, MappedPosition.ExonEnd, Transcript.NumExons));
jsonObject.AddStringValue("introns", GetFractionString(MappedPosition.IntronStart, MappedPosition.IntronEnd, Transcript.NumExons - 1));
jsonObject.AddStringValue("proteinPos", GetRangeString(MappedPosition.CoveredProteinStart, MappedPosition.CoveredProteinEnd));
}
string geneId = Transcript.Source == Source.Ensembl
? Transcript.Gene.EnsemblId.ToString()
: Transcript.Gene.EntrezGeneId.ToString();
if (CompleteOverlap.HasValue && !CompleteOverlap.Value)
{
jsonObject.AddStringValue("geneId", geneId);
}
jsonObject.AddStringValue("hgnc", Transcript.Gene.Symbol);
if (Consequences != null)
{
AddConsequences(jsonObject);
}
jsonObject.AddStringValue("hgvsc", HgvsCoding);
jsonObject.AddStringValue("hgvsp", HgvsProtein);
jsonObject.AddObjectValue("geneFusion", _geneFusion);
jsonObject.AddBoolValue("isCanonical", Transcript.IsCanonical);
jsonObject.AddDoubleValue("polyPhenScore", PolyPhen?.Score);
jsonObject.AddStringValue("polyPhenPrediction", PolyPhen?.Prediction);
if (CompleteOverlap.HasValue && !CompleteOverlap.Value && Transcript.Translation != null)
{
jsonObject.AddStringValue("proteinId", Transcript.Translation.ProteinId.WithVersion);
}
jsonObject.AddDoubleValue("siftScore", Sift?.Score);
jsonObject.AddStringValue("siftPrediction", Sift?.Prediction);
if (ConservationScores != null && ConservationScores.Count > 0)
{
jsonObject.AddObjectValue("aminoAcidConservation", new AnnotatedConservationScore(ConservationScores));
}
if (CompleteOverlap.HasValue)
{
jsonObject.AddBoolValue("completeOverlap", CompleteOverlap.Value);
}
sb.Append(JsonObject.CloseBrace);
}
/// <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());
}
