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 void SerializeJson(StringBuilder sb)
{
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
_jsonSchema.TotalItems++;
if (_mimNumber >= 100000)
{
_jsonSchema.CountKeyIfAdded(jsonObject.AddIntValue("mimNumber", _mimNumber), "mimNumber");
}
_jsonSchema.CountKeyIfAdded(jsonObject.AddStringValue("phenotype", _phenotype), "phenotype");
if (_mapping != Mapping.unknown)
{
_jsonSchema.CountKeyIfAdded(jsonObject.AddStringValue("mapping", _mapping.ToString().Replace("_", " ")), "mapping");
}
if (_inheritance != null && _inheritance.Count > 0)
{
_jsonSchema.CountKeyIfAdded(jsonObject.AddStringValues("inheritances", _inheritance), "inheritances");
}
if (_comments.Length > 0)
{
_jsonSchema.CountKeyIfAdded(jsonObject.AddStringValues("comments", _comments.Select(x => x.ToString().Replace("_", " "))), "comments");
}
sb.Append(JsonObject.CloseBrace);
}
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()
{
if (AnnotatedVariants == null || AnnotatedVariants.Length == 0)
{
return(null);
}
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
string originalChromName = Position.VcfFields[0];
jsonObject.AddStringValue("chromosome", originalChromName);
jsonObject.AddIntValue("position", Position.Start);
if (Position.HasShortTandemRepeat)
{
jsonObject.AddStringValue("repeatUnit", Position.InfoData?.RepeatUnit);
jsonObject.AddIntValue("refRepeatCount", Position.InfoData?.RefRepeatCount);
}
if (Position.HasStructuralVariant)
{
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.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);
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);
if (_mimNumber >= 100000)
{
jsonObject.AddStringValue("mimNumber", _mimNumber.ToString());
}
jsonObject.AddStringValue("phenotype", _phenotype);
if (_mapping != Mapping.unknown)
{
jsonObject.AddStringValue("mapping", _mapping.ToString().Replace("_", " "));
}
if (_inheritance != null && _inheritance.Count > 0)
{
jsonObject.AddStringValues("inheritances", _inheritance);
}
if (_comments != Comments.unknown)
{
jsonObject.AddStringValue("comments", _comments.ToString().Replace("_", " "));
}
sb.Append(JsonObject.CloseBrace);
}
public void AddStringValues_TwoTimes()
{
var sb = StringBuilderCache.Acquire();
var json = new JsonObject(sb);
var strings = new[] { "A", "B", "C" };
var strings2 = new[] { "D", "E", "F" };
json.AddStringValues("test1", strings);
json.AddStringValues("test2", strings2, false);
const string expectedResult = "\"test1\":[\"A\",\"B\",\"C\"],\"test2\":[D,E,F]";
var observedResult = StringBuilderCache.GetStringAndRelease(sb);
Assert.Equal(expectedResult, observedResult);
}
public static string GetGeneAnnotation(GeneConfig input, string saManifestFilePath, string saPathPrefix)
{
var geneAnnotationProvider = new GeneAnnotationProvider(PersistentStreamUtils.GetStreams(
GetNgaFileList(saManifestFilePath, saPathPrefix, input.ngaUrls).ToList()));
var sb = new StringBuilder(1024 * 1024);
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue(JasixCommons.HeaderSectionTag, GetHeader(geneAnnotationProvider), false);
//not all gene symbols have annotations. So, we need to check and only output the ones that are not null
var geneAnnotations = input.geneSymbols.Select(geneSymbol => geneAnnotationProvider.Annotate(geneSymbol))
.Where(annotation => !string.IsNullOrEmpty(annotation))
.ToList();
jsonObject.AddStringValues("genes", geneAnnotations, false);
sb.Append(JsonObject.CloseBrace);
// AWS lambda response message can not be larger than 6MB
if (sb.Length > 6_000_000)
{
throw new UserErrorException("Too many genes provided in the request. Please decrease the number of genes and try again later.");
}
return(sb.ToString());
}
public static string GetHeader(string annotator, string creationTime, string genomeAssembly, int jsonSchemaVersion, string vepDataVersion, List <DataSourceVersion> dataSourceVersions, string[] sampleNames = null)
{
var sb = new StringBuilder();
var jsonObject = new JsonObject(sb);
sb.Append("{\"header\":{");
jsonObject.AddStringValue("annotator", annotator);
jsonObject.AddStringValue("creationTime", creationTime);
jsonObject.AddStringValue("genomeAssembly", genomeAssembly);
jsonObject.AddIntValue("schemaVersion", jsonSchemaVersion);
jsonObject.AddStringValue("dataVersion", vepDataVersion);
// print our data source versions
if (dataSourceVersions != null)
{
jsonObject.AddObjectValues("dataSources", dataSourceVersions);
}
if (sampleNames != null)
{
jsonObject.AddStringValues(SamplesTag, sampleNames);
}
sb.Append("},\"positions\":[\n");
return(sb.ToString());
}
private void AddSAstoJsonObject(JsonObject jsonObject)
{
var saDict = new Dictionary <string, (bool, List <string>)>();
foreach (var annotatedSa in SupplementaryAnnotations)
{
var sa = annotatedSa.SaDataSource;
if (!saDict.ContainsKey(sa.KeyName))
{
saDict[sa.KeyName] = (sa.IsArray, new List <string>());
}
var jsonStrings = annotatedSa.GetJsonStrings();
if (jsonStrings != null)
{
saDict[sa.KeyName].Item2.AddRange(jsonStrings);
}
}
foreach (var kvp in saDict)
{
if (kvp.Value.Item1)
{
jsonObject.AddStringValues(kvp.Key, kvp.Value.Item2.ToArray(), false);
}
else
{
jsonObject.AddStringValue(kvp.Key, kvp.Value.Item2[0], false);
}
}
}
private void OutputRequiredKeys(IReadOnlyCollection <string> requiredKeys)
{
if (requiredKeys.Count > 0)
{
_jsonObject.AddStringValues("required", requiredKeys);
}
}
private void AddConsequences(JsonObject jsonObject)
{
if (Consequences.Count == 0)
{
Consequences.Add(ConsequenceTag.transcript_variant);
}
jsonObject.AddStringValues("consequence", Consequences?.Select(ConsequenceUtil.GetConsequence));
}
public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
jsonObject.AddIntValue("id", CNVId);
jsonObject.AddStringValue("variantType", _cnvType.ToString());
if (_copyNumber != -1)
{
jsonObject.AddIntValue("copyNumber", _copyNumber);
}
jsonObject.AddStringValues("cancerTypes", GetJsonStrings(_cancerTypes), false);
jsonObject.AddStringValues("tissueTypes", GetJsonStrings(_tissueTypes), false);
return(sb.ToString());
}
public void AddStringValues_EmptyArray()
{
var sb = StringBuilderCache.Acquire();
var json = new JsonObject(sb);
json.AddStringValues("test1", new string[0]);
var observedResult = StringBuilderCache.GetStringAndRelease(sb);
Assert.Equal(string.Empty, observedResult);
}
public void SerializeJson(StringBuilder sb)
{
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("id", RegulatoryRegion.Id.WithoutVersion);
jsonObject.AddStringValue("type", RegulatoryRegion.Type.ToString());
jsonObject.AddStringValues("consequence", Consequences?.Select(ConsequenceUtil.GetConsequence));
sb.Append(JsonObject.CloseBrace);
}
/// <summary>
/// JSON string representation of our regulatory region
/// </summary>
public void SerializeJson(StringBuilder sb)
{
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("id", ID);
jsonObject.AddStringValue("type", Type);
jsonObject.AddStringValues("consequence", Consequence.ToArray());
sb.Append(JsonObject.CloseBrace);
}
public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
jsonObject.AddStringValue("id", Id);
jsonObject.AddStringValue("isAlleleSpecific", IsAlleleSpecific, false);
jsonObject.AddStringValue("refAllele", string.IsNullOrEmpty(ReferenceAllele) ? "-" : ReferenceAllele);
jsonObject.AddStringValue("altAllele",
SupplementaryAnnotationUtilities.ReverseSaReducedAllele(AlternateAllele));
jsonObject.AddStringValue("gene", Gene);
jsonObject.AddIntValue("sampleCount", SampleCount);
jsonObject.AddStringValues("cancerTypes", GetJsonStrings(GetCancerTypeCounts()), false);
jsonObject.AddStringValues("tissues", GetJsonStrings(GetTissueCounts()), 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 GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
jsonObject.AddStringValue("id", $"{Accession}.{Version}");
jsonObject.AddStringValue("reviewStatus", ClinVarCommon.ReviewStatusStrings[ReviewStatus]);
jsonObject.AddStringValue("lastUpdatedDate", LastUpdatedDate.ToString("yyyy-MM-dd"));
jsonObject.AddStringValues("significance", Significances);
return(StringBuilderCache.GetStringAndRelease(sb));
}
public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
//converting empty alleles to '-'
var refAllele = string.IsNullOrEmpty(ReferenceAllele) ? "-" : ReferenceAllele;
var altAllele = string.IsNullOrEmpty(AlternateAllele) ? "-" : AlternateAllele;
//the reduced alt allele should never be output
altAllele = SupplementaryAnnotationUtilities.ReverseSaReducedAllele(altAllele);
jsonObject.AddStringValue("id", Id);
jsonObject.AddStringValue("reviewStatus", ReviewStatusStrings[ReviewStatus]);
jsonObject.AddStringValue("isAlleleSpecific", IsAlleleSpecific, false);
jsonObject.AddStringValues("alleleOrigins", AlleleOrigins);
jsonObject.AddStringValue("refAllele", "N" == refAllele ? null : refAllele);
jsonObject.AddStringValue("altAllele", "N" == altAllele ? null : altAllele);
jsonObject.AddStringValues("phenotypes", Phenotypes);
jsonObject.AddStringValues("medGenIds", MedGenIDs);
jsonObject.AddStringValues("omimIds", OmimIDs);
jsonObject.AddStringValues("orphanetIds", OrphanetIDs);
jsonObject.AddStringValue("significance", Significance);
if (LastUpdatedDate != long.MinValue)
{
jsonObject.AddStringValue("lastUpdatedDate", new DateTime(LastUpdatedDate).ToString("yyyy-MM-dd"));
}
jsonObject.AddStringValues("pubMedIds", PubmedIds?.Select(id => id.ToString()));
return(StringBuilderCache.GetStringAndRelease(sb));
}
public void SerializeJson(StringBuilder sb)
{
var jsonObject = new JsonObject(sb);
//converting empty alleles to '-'
var refAllele = string.IsNullOrEmpty(ReferenceAllele)? "-":ReferenceAllele;
var altAllele = string.IsNullOrEmpty(AltAllele) ? "-" : AltAllele;
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("id", ID);
jsonObject.AddStringValue("reviewStatus", ReviewStatusStrings[ReviewStatus]);
jsonObject.AddStringValue("isAlleleSpecific", IsAlleleSpecific, false);
jsonObject.AddStringValues("alleleOrigins", _alleleOrigins);
jsonObject.AddStringValue("refAllele", "N" == refAllele ? null : refAllele);
jsonObject.AddStringValue("altAllele", "N" == altAllele ? null : altAllele);
jsonObject.AddStringValues("phenotypes", Phenotypes);
jsonObject.AddStringValues("medGenIDs", _medgenIds);
jsonObject.AddStringValues("omimIDs", OmimIDs);
jsonObject.AddStringValues("orphanetIDs", OrphanetIDs);
jsonObject.AddStringValue("significance", Significance);
if (LastUpdatedDate != long.MinValue)
{
jsonObject.AddStringValue("lastUpdatedDate", Date.GetDate(LastUpdatedDate));
}
jsonObject.AddStringValues("pubMedIds", PubmedIds?.Select(id => id.ToString()));
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);
jsonObject.AddStringValue("id", $"{_accession}.{_version}");
jsonObject.AddStringValue("reviewStatus", ClinVarCommon.ReviewStatusStrings[_reviewStatus]);
jsonObject.AddStringValues("significance", _significances);
jsonObject.AddStringValue("refAllele", ClinVarCommon.NormalizeAllele(RefAllele));
jsonObject.AddStringValue("altAllele", ClinVarCommon.NormalizeAllele(AltAllele));
jsonObject.AddStringValue("lastUpdatedDate", _lastUpdatedDate.ToString("yyyy-MM-dd"));
return(StringBuilderCache.GetStringAndRelease(sb));
}
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));
}
private void AddSuppIntervalToJsonObject(JsonObject jsonObject)
{
var saDict = new Dictionary <string, List <string> >();
foreach (var si in SupplementaryIntervals)
{
if (!saDict.ContainsKey(si.SupplementaryInterval.KeyName))
{
saDict[si.SupplementaryInterval.KeyName] = new List <string>();
}
saDict[si.SupplementaryInterval.KeyName].Add(si.ToString());
}
foreach (var kvp in saDict)
{
jsonObject.AddStringValues(kvp.Key, kvp.Value.ToArray(), false);
}
}
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("name", GeneName);
foreach (var geneAnnotation in Annotations)
{
if (geneAnnotation.IsArray)
{
jsonObject.AddStringValues(geneAnnotation.DataSource, geneAnnotation.JsonStrings, false);
}
else
{
jsonObject.AddStringValue(geneAnnotation.DataSource, geneAnnotation.JsonStrings[0], false);
}
}
sb.Append(JsonObject.CloseBrace);
}
public void SerializeJson(StringBuilder sb)
{
var jsonObject = new JsonObject(sb);
// data section
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("hgvsc", HgvsCodingName);
var consequence = new Consequences(Consequences, null);
if (Consequences.Count > 0)
{
jsonObject.AddStringValues("consequence", consequence.GetConsequenceStrings());
}
jsonObject.AddIntValue("intron", Intron);
jsonObject.AddIntValue("exon", Exon);
sb.Append(JsonObject.CloseBrace);
}
public override string ToString()
{
var sb = new StringBuilder();
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue(TranscriptTag, TranscriptID);
jsonObject.AddStringValue(BioTypeTag, BioType);
jsonObject.AddStringValue(AminoAcidsTag, AminoAcids);
jsonObject.AddStringValue(CdnaPosTag, ComplementaryDnaPosition);
jsonObject.AddStringValue(CodonsTag, Codons);
jsonObject.AddStringValue(CdsPosTag, CdsPosition);
jsonObject.AddStringValue(ExonsTag, Exons);
jsonObject.AddStringValue(IntronsTag, Introns);
jsonObject.AddStringValue(GeneIdTag, Gene);
jsonObject.AddStringValue(HgncTag, Hgnc);
jsonObject.AddStringValues(ConsequenceTag, Consequence?.ToArray());
jsonObject.AddStringValue(HgvscTag, HgvsCodingSequenceName);
jsonObject.AddStringValue(HgvspTag, HgvsProteinSequenceName);
jsonObject.AddStringValue(GeneFusionTag, GeneFusion, false);
jsonObject.AddStringValue(IsCanonicalTag, IsCanonical, false);
jsonObject.AddStringValue(PolyPhenScoreTag, PolyPhenScore, false);
jsonObject.AddStringValue(PolyPhenPredictionTag, PolyPhenPrediction);
jsonObject.AddStringValue(ProteinIdTag, ProteinID);
jsonObject.AddStringValue(ProteinPosTag, ProteinPosition);
jsonObject.AddStringValue(SiftScoreTag, SiftScore, false);
jsonObject.AddStringValue(SiftPredictionTag, SiftPrediction);
if (AdditionalInfo != null && AdditionalInfo.Count > 0)
{
foreach (var kvp in AdditionalInfo)
{
jsonObject.AddStringValue(kvp.Key, kvp.Value, false);
}
}
sb.Append(JsonObject.CloseBrace);
return(sb.ToString());
}
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());
}