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);
}
}
private static void AddCustomIntervals(VariantAlternateAllele altAllele, JsonVariant jsonVariant)
{
// adding the custom intervals
if (altAllele.CustomIntervals == null)
{
return;
}
jsonVariant.CustomIntervals.Clear();
foreach (var custInterval in altAllele.CustomIntervals)
{
jsonVariant.CustomIntervals.Add(custInterval);
}
}
private void FindCorrespondingJsonVariant(VariantAlternateAllele altAllele)
{
_currJsonVariant = null;
foreach (var annotatedAllele in AnnotatedAlternateAlleles)
{
var jsonVariant = annotatedAllele as JsonVariant;
if (jsonVariant?.ReferenceBegin != altAllele.Start)
{
continue;
}
if (jsonVariant.SaAltAllele != altAllele.SuppAltAllele)
{
continue;
}
_currJsonVariant = jsonVariant;
}
}
