private static string ExtractDbId(IAnnotatedPosition annotatedPosition)
{
var dbSnp = new VcfField();
var nonDbsnpIds = GetNonDbsnpIds(annotatedPosition.Position.VcfFields[VcfCommon.IdIndex]);
if (nonDbsnpIds != null)
{
foreach (var nonDbsnpId in nonDbsnpIds)
{
dbSnp.Add(nonDbsnpId);
}
}
foreach (var annotatedVariant in annotatedPosition.AnnotatedVariants)
{
foreach (var suppAnnotation in annotatedVariant.SupplementaryAnnotations)
{
if (suppAnnotation.SaDataSource.KeyName != DbSnpKeyName)
{
continue;
}
foreach (var s in suppAnnotation.GetVcfStrings())
{
dbSnp.Add(s);
}
}
}
return(dbSnp.GetString(""));
}
private void AddInfoField(IAnnotatedPosition annotatedPosition, StringBuilder sb)
{
var infoEntries = new VcfField();
var infoField = annotatedPosition.Position.InfoData.UpdatedInfoField;
if (!string.IsNullOrEmpty(infoField))
{
infoEntries.Add(infoField);
}
ExtractInfo(annotatedPosition, infoEntries);
infoField = infoEntries.GetString("");
// remove .
if (infoField == ".")
{
infoField = "";
}
sb.Append(infoField);
var csqs = new List <CsqEntry>();
ExtractCsqs(annotatedPosition, csqs);
if (csqs.Count != 0)
{
if (infoField.Length > 0)
{
sb.Append(";");
}
}
// append CSQ tags using delegate from annotator
sb.Append(GetCsqtAndCsqrVcfInfo(csqs));
if (csqs.Count == 0 && infoField.Length == 0)
{
sb.Append(".");
}
}
