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 void AddIntValues_TwoTimes()
{
var sb = StringBuilderCache.Acquire();
var json = new JsonObject(sb);
var ints = new[] { 1, 2, 3 };
var ints2 = new[] { 4, 5, 6 };
json.AddIntValues("test1", ints);
json.AddIntValues("test2", ints2);
const string expectedResult = "\"test1\":[1,2,3],\"test2\":[4,5,6]";
var observedResult = StringBuilderCache.GetStringAndRelease(sb);
Assert.Equal(expectedResult, observedResult);
}
public void AddIntValues_NullArray()
{
var sb = StringBuilderCache.Acquire();
var json = new JsonObject(sb);
json.AddIntValues("test1", null);
var observedResult = StringBuilderCache.GetStringAndRelease(sb);
Assert.Equal(string.Empty, observedResult);
}