public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddDoubleValue("pLi", _pLI, "0.00e0");
jsonObject.AddDoubleValue("pRec", _pRec, "0.00e0");
jsonObject.AddDoubleValue("pNull", _pNull, "0.00e0");
jsonObject.AddDoubleValue("synZ", _synZ, "0.00e0");
jsonObject.AddDoubleValue("misZ", _misZ, "0.00e0");
jsonObject.AddDoubleValue("loeuf", _loeuf, "0.00e0");
sb.Append(JsonObject.CloseBrace);
return(StringBuilderCache.GetStringAndRelease(sb));
}
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.AddIntValue("sampleSize", SampleSize);
if (ObservedGains != 0)
{
jsonObject.AddIntValue("observedGains", ObservedGains);
}
if (ObservedLosses != 0)
{
jsonObject.AddIntValue("observedLosses", ObservedLosses);
}
jsonObject.AddDoubleValue("variantFreqAll", VariantFreqAll, "0.#####");
return(StringBuilderCache.GetStringAndRelease(sb));
}
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.AddIntValue("allAn", _allAlleleNumber);
jsonObject.AddIntValue("allAc", _allAlleleCount);
jsonObject.AddDoubleValue("allAf", _allAlleleFrequency, "0.######");
jsonObject.AddDoubleValue("afrAf", _afrAlleleFrequency, "0.######");
jsonObject.AddDoubleValue("amrAf", _amrAlleleFrequency, "0.######");
jsonObject.AddDoubleValue("eurAf", _eurAlleleFrequency, "0.######");
jsonObject.AddDoubleValue("easAf", _easAlleleFrequency, "0.######");
jsonObject.AddDoubleValue("sasAf", _sasAlleleFrequency, "0.######");
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("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.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();
if (CompleteOverlap.HasValue && !CompleteOverlap.Value)
{
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 (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 (PluginData != null)
{
foreach (var pluginData in PluginData)
{
jsonObject.AddStringValue(pluginData.Name, pluginData.GetJsonString(), false);
}
}
if (CompleteOverlap.HasValue)
{
jsonObject.AddBoolValue("completeOverlap", CompleteOverlap.Value);
}
sb.Append(JsonObject.CloseBrace);
}
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 string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
jsonObject.AddStringValue("hgnc", Hgnc);
if (IsSpliceAdjacent)
{
jsonObject.AddDoubleValue("acceptorGainScore", AcceptorGainScore, "0.#");
jsonObject.AddDoubleValue("acceptorGainDistance", AcceptorGainPosition);
jsonObject.AddDoubleValue("acceptorLossScore", AcceptorLossScore, "0.#");
jsonObject.AddDoubleValue("acceptorLossDistance", AcceptorLossPosition);
jsonObject.AddDoubleValue("donorGainScore", DonorGainScore, "0.#");
jsonObject.AddDoubleValue("donorGainDistance", DonorGainPosition);
jsonObject.AddDoubleValue("donorLossScore", DonorLossScore, "0.#");
jsonObject.AddDoubleValue("donorLossDistance", DonorLossPosition);
}
else
{
if (AcceptorGainScore >= MinSpliceAiScore)
{
jsonObject.AddDoubleValue("acceptorGainScore", AcceptorGainScore, "0.#");
jsonObject.AddDoubleValue("acceptorGainDistance", AcceptorGainPosition);
}
if (AcceptorLossScore >= MinSpliceAiScore)
{
jsonObject.AddDoubleValue("acceptorLossScore", AcceptorLossScore, "0.#");
jsonObject.AddDoubleValue("acceptorLossDistance", AcceptorLossPosition);
}
if (DonorGainScore >= MinSpliceAiScore)
{
jsonObject.AddDoubleValue("donorGainScore", DonorGainScore, "0.#");
jsonObject.AddDoubleValue("donorGainDistance", DonorGainPosition);
}
if (DonorLossScore >= MinSpliceAiScore)
{
jsonObject.AddDoubleValue("donorLossScore", DonorLossScore, "0.#");
jsonObject.AddDoubleValue("donorLossDistance", DonorLossPosition);
}
}
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);
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.AddStringValue("breakendEventId", Position.InfoData?.BreakendEventId);
jsonObject.AddDoubleValue("strandBias", Position.InfoData?.StrandBias, JsonCommon.FrequencyRoundingFormat);
jsonObject.AddDoubleValue("fisherStrandBias", Position.InfoData?.FisherStrandBias, "0.###");
jsonObject.AddDoubleValue("mappingQuality", Position.InfoData?.MappingQuality, "0.##");
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));
}
