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());
}
public void SerializeJson(StringBuilder sb)
{
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddIntValue("exon", Exon);
jsonObject.AddIntValue("intron", Intron);
jsonObject.AddObjectValues("fusions", GeneFusions);
sb.Append(JsonObject.CloseBrace);
}
public void AddObjectValues_NullArray()
{
var sb = StringBuilderCache.Acquire();
var json = new JsonObject(sb);
json.AddObjectValues("test1", null as Point[]);
var observedResult = StringBuilderCache.GetStringAndRelease(sb);
Assert.Equal(string.Empty, observedResult);
}
public override string ToString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddIntValue("exon", Exon);
jsonObject.AddIntValue("intron", Intron);
jsonObject.AddObjectValues("fusions", GeneFusions);
sb.Append(JsonObject.CloseBrace);
return StringBuilderCache.GetStringAndRelease(sb);
}
private static void WriteGeneAnnotations(ICollection <IAnnotatedGene> annotatedGenes, JsonWriter writer)
{
if (annotatedGenes.Count == 0)
{
return;
}
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
jsonObject.AddObjectValues("genes", annotatedGenes, true);
writer.WriteAnnotatedGenes(StringBuilderCache.GetStringAndRelease(sb));
}
public void AddObjectValues_TwoTimes()
{
var sb = StringBuilderCache.Acquire();
var json = new JsonObject(sb);
var points = new Point[2];
points[0] = new Point(1, 2);
points[1] = new Point(3, 4);
var points2 = new Point[1];
points2[0] = new Point(5, 6);
json.AddObjectValues("test1", points);
json.AddObjectValues("test2", points2);
const string expectedResult = "\"test1\":[{\"X\":1,\"Y\":2},{\"X\":3,\"Y\":4}],\"test2\":[{\"X\":5,\"Y\":6}]";
var observedResult = StringBuilderCache.GetStringAndRelease(sb);
Assert.Equal(expectedResult, observedResult);
}
private static string GetHeader(IProvider geneAnnotationProvider)
{
var sb = new StringBuilder();
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("annotator", "Nirvana " + CommandLineUtilities.Version);
jsonObject.AddStringValue("creationTime", Date.CurrentTimeStamp);
jsonObject.AddIntValue("schemaVersion", SaCommon.SchemaVersion);
jsonObject.AddObjectValues("dataSources", geneAnnotationProvider.DataSourceVersions);
sb.Append(JsonObject.CloseBrace);
return(sb.ToString());
}
public void SerializeJson(StringBuilder sb)
{
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("id", ID);
jsonObject.AddStringValue("isAlleleSpecific", IsAlleleSpecific, false);
jsonObject.AddStringValue("refAllele", RefAllele);
jsonObject.AddStringValue("altAllele", AltAllele);
jsonObject.AddStringValue("gene", Gene);
jsonObject.AddIntValue("sampleCount", SampleCount);
jsonObject.AddObjectValues("studies", Studies);
sb.Append(JsonObject.CloseBrace);
}
public void SerializeJson(StringBuilder sb)
{
var jsonObject = new JsonObject(sb);
// data section
sb.Append(JsonObject.OpenBrace);
jsonObject.AddIntValue("intron", _intron);
jsonObject.AddIntValue("exon", _exon);
if (_fusions.Count > 0)
{
jsonObject.AddObjectValues("fusions", _fusions);
}
sb.Append(JsonObject.CloseBrace);
}
public override string ToString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddIntValue("mimNumber", MimNumber);
jsonObject.AddStringValue("description", _description?.Replace(@"\'", @"'"));
if (_phenotypes.Count > 0)
{
jsonObject.AddObjectValues("phenotypes", _phenotypes);
}
sb.Append(JsonObject.CloseBrace.ToString());
return(StringBuilderCache.GetStringAndRelease(sb));
}
public override string ToString()
{
var sb = new StringBuilder();
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("mimNumber", _mimNumber.ToString());
jsonObject.AddStringValue("hgnc", Hgnc);
jsonObject.AddStringValue("description", _description);
if (_phenotypes.Count > 0)
{
jsonObject.AddObjectValues("phenotypes", _phenotypes);
}
sb.Append(JsonObject.CloseBrace.ToString());
return(sb.ToString());
}
public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
JsonSchema.TotalItems++;
JsonSchema.CountKeyIfAdded(jsonObject.AddIntValue("mimNumber", _mimNumber), "mimNumber");
JsonSchema.CountKeyIfAdded(jsonObject.AddStringValue("geneName", string.IsNullOrEmpty(_geneName) ? null : JsonConvert.SerializeObject(_geneName), false), "geneName");
//Serialized string has the double quote at the beginning and the end
JsonSchema.CountKeyIfAdded(jsonObject.AddStringValue("description", string.IsNullOrEmpty(_description) ? null : JsonConvert.SerializeObject(_description), false), "description");
if (_phenotypes.Count > 0)
{
JsonSchema.CountKeyIfAdded(jsonObject.AddObjectValues("phenotypes", _phenotypes), "phenotypes");
}
sb.Append(JsonObject.CloseBrace);
return(StringBuilderCache.GetStringAndRelease(sb));
}
private void AddCustomeIntervals(JsonObject jsonObject)
{
var intervalGroups = new Dictionary <string, List <ICustomInterval> >();
foreach (var customInterval in CustomIntervals)
{
var type = customInterval.Type;
if (intervalGroups.ContainsKey(type))
{
intervalGroups[type].Add(customInterval);
}
else
{
intervalGroups[type] = new List <ICustomInterval> {
customInterval
};
}
}
foreach (var intervalGroup in intervalGroups)
{
jsonObject.AddObjectValues(intervalGroup.Key, intervalGroup.Value);
}
}
private void AddCustomeItems(JsonObject jsonObject)
{
var customGroups = new Dictionary <string, IList <ICustomAnnotation> >();
foreach (var customItem in CustomItems)
{
var type = customItem.AnnotationType;
if (customGroups.ContainsKey(type))
{
customGroups[type].Add(customItem);
}
else
{
customGroups[type] = new List <ICustomAnnotation> {
customItem
};
}
}
foreach (var customGroup in customGroups)
{
jsonObject.AddObjectValues(customGroup.Key, customGroup.Value);
}
}
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));
}
/// <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());
}
