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(".");
}
}
private static void ExtractInfo(IAnnotatedPosition annotatedPosition, VcfField infoEntries)
{
var alleleFreq1000G = new VcfInfoKeyValue("AF1000G");
var ancestralAllele = new VcfPositionalInfo("AA");
var phyloP = new VcfInfoKeyValue("phyloP");
var suppAnnotationSources = new Dictionary <string, VcfInfoKeyValue>();
var isSaArrayInfo = new Dictionary <string, bool>();
var numInputAltAlleles = annotatedPosition.Position.AltAlleles.Length;
foreach (var alternateAllele in annotatedPosition.AnnotatedVariants)
{
foreach (var sa in alternateAllele.SupplementaryAnnotations)
{
if (!suppAnnotationSources.ContainsKey(sa.SaDataSource.KeyName))
{
suppAnnotationSources[sa.SaDataSource.KeyName] = new VcfInfoKeyValue(sa.SaDataSource.VcfkeyName);
isSaArrayInfo[sa.SaDataSource.KeyName] = sa.SaDataSource.IsArray;
}
}
}
foreach (var kvp in suppAnnotationSources)
{
if (isSaArrayInfo[kvp.Key])
{
continue;
}
for (var i = 0; i < numInputAltAlleles; i++)
{
kvp.Value.Add(null);
}
}
for (var i = 0; i < numInputAltAlleles; i++)
{
alleleFreq1000G.Add(null);
}
var inputGenotypeIndex = GetInputGenotypeIndex(annotatedPosition.Position.AltAlleles, annotatedPosition.AnnotatedVariants);
// understand the number of annotation contains in the whole vcf line
for (int i = 0; i < annotatedPosition.AnnotatedVariants.Length; i++)
{
var annotatedVariant = annotatedPosition.AnnotatedVariants[i];
var genotypeIndex = inputGenotypeIndex[i] + 1;
if (annotatedVariant.Variant.IsRefMinor)
{
infoEntries.Add("RefMinor");
}
phyloP.Add(annotatedVariant.PhylopScore?.ToString(CultureInfo.InvariantCulture));
foreach (var sa in annotatedVariant.SupplementaryAnnotations)
{
if (!sa.SaDataSource.MatchByAllele && !sa.IsAlleleSpecific && sa.SaDataSource.KeyName != GlobalAlleleKeyName)
{
continue;
}
if (sa.SaDataSource.KeyName == DbSnpKeyName)
{
continue;
}
if (sa.SaDataSource.KeyName == RefMinorKeyName)
{
continue;
}
foreach (var vcfAnnotation in sa.GetVcfStrings())
{
if (string.IsNullOrEmpty(vcfAnnotation))
{
continue;
}
if (sa.SaDataSource.KeyName == OneKgKeyName)
{
var contents = vcfAnnotation.Split(';');
var freq = contents[0];
var ancestryAllele = string.IsNullOrEmpty(contents[1]) ? null : contents[1];
alleleFreq1000G.Add(freq, genotypeIndex);
ancestralAllele.AddValue(ancestryAllele);
continue;
}
if (sa.SaDataSource.IsArray && sa.IsAlleleSpecific)
{
suppAnnotationSources[sa.SaDataSource.KeyName].Add(
genotypeIndex.ToString(CultureInfo.InvariantCulture) + '|' + vcfAnnotation);
}
else if (!sa.SaDataSource.IsArray)
{
suppAnnotationSources[sa.SaDataSource.KeyName].Add(vcfAnnotation, genotypeIndex);
}
}
}
}
foreach (var value in suppAnnotationSources.Values)
{
infoEntries.Add(value.GetString());
}
infoEntries.Add(ancestralAllele.GetString());
infoEntries.Add(alleleFreq1000G.GetString());
infoEntries.Add(phyloP.GetString());
}
