public void AddVariantData(VariantFeature variant)
{
//add CytoGenetic band
CytogeneticBand = variant.CytogeneticBand;
// populating supplementary interval specific fields
PopulateSuppIntervalFields(variant.GetSupplementaryIntervals());
foreach (var altAllele in variant.AlternateAlleles)
{
var jsonVariant = new JsonVariant(altAllele, variant);
AnnotatedAlternateAlleles.Add(jsonVariant);
// custom intervals are not part of SA as they are a separate data structure
AddCustomIntervals(altAllele, jsonVariant);
if (altAllele.SupplementaryAnnotationPosition == null)
{
continue;
}
var sa = altAllele.SupplementaryAnnotationPosition;
sa.AddSaPositionToVariant(jsonVariant);
}
}
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());
}
