private static string ExtractDbId(IAnnotatedVariant annotatedVariant, string idField)
{
var dbSnp = new VcfField();
var nonDbsnpIds = GetNonDbsnpIds(idField);
if (nonDbsnpIds != null)
{
foreach (var nonDbsnpId in nonDbsnpIds)
{
dbSnp.Add(nonDbsnpId);
}
}
foreach (var altAllele in annotatedVariant.AnnotatedAlternateAlleles)
{
if (altAllele.DbSnpIds == null)
{
continue;
}
foreach (var id in altAllele.DbSnpIds)
{
dbSnp.Add(id);
}
}
return(dbSnp.GetString(""));
}
public void EmptyDbSnp()
{
var dbSnpField = new VcfField();
var expected = ".";
var observed = dbSnpField.GetString("");
Assert.Equal(expected, observed);
}
private void AddInfoField(string infoField, IAnnotatedVariant annotatedVariant, StringBuilder sb)
{
var infoEntries = new VcfField();
if (!string.IsNullOrEmpty(infoField))
{
infoEntries.Add(infoField);
}
ExtractInfo(annotatedVariant as UnifiedJson, infoEntries);
infoField = infoEntries.GetString("");
// remove .
if (infoField == ".")
{
infoField = "";
}
sb.Append(infoField);
var csqs = new List <CsqEntry>();
ExtractCsqs(annotatedVariant as UnifiedJson, 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(".");
}
}