/// <summary>
/// Update the attributes of the attributes map given the VariantContext to reflect the
/// proper chromosome-based VCF tags
/// </summary>
/// <param name="vc"> the VariantContext </param>
/// <param name="attributes"> the attributes map to populate; must not be null; may contain old values </param>
/// <param name="removeStaleValues"> should we remove stale values from the mapping? </param>
/// <param name="founderIds"> - Set of founders Ids to take into account. AF and FC will be calculated over the founders.
/// If empty or null, counts are generated for all samples as unrelated individuals </param>
/// <returns> the attributes map provided as input, returned for programming convenience </returns>
public static IDictionary<string, object> CalculateChromosomeCounts (VariantContext vc, IDictionary<string, object> attributes, bool removeStaleValues, ISet<string> founderIds)
{
int AN = vc.CalledChrCount;
// if everyone is a no-call, remove the old attributes if requested
if (AN == 0 && removeStaleValues) {
if (attributes.ContainsKey (VCFConstants.ALLELE_COUNT_KEY)) {
attributes.Remove (VCFConstants.ALLELE_COUNT_KEY);
}
if (attributes.ContainsKey (VCFConstants.ALLELE_FREQUENCY_KEY)) {
attributes.Remove (VCFConstants.ALLELE_FREQUENCY_KEY);
}
if (attributes.ContainsKey (VCFConstants.ALLELE_NUMBER_KEY)) {
attributes.Remove (VCFConstants.ALLELE_NUMBER_KEY);
}
return attributes;
}
if (vc.HasGenotypes) {
attributes [VCFConstants.ALLELE_NUMBER_KEY] = AN;
// if there are alternate alleles, record the relevant tags
if (vc.AlternateAlleles.Count > 0) {
List<double> alleleFreqs = new List<double> ();
List<int> alleleCounts = new List<int> ();
List<int> foundersAlleleCounts = new List<int> ();
double totalFoundersChromosomes = (double)vc.GetCalledChrCount (founderIds);
int foundersAltChromosomes;
foreach (Allele allele in vc.AlternateAlleles) {
foundersAltChromosomes = vc.GetCalledChrCount (allele, founderIds);
alleleCounts.Add (vc.GetCalledChrCount (allele));
foundersAlleleCounts.Add (foundersAltChromosomes);
if (AN == 0) {
alleleFreqs.Add (0.0);
} else {
double freq = (double)foundersAltChromosomes / totalFoundersChromosomes;
alleleFreqs.Add (freq);
}
}
if (alleleCounts.Count == 1) {
attributes [VCFConstants.ALLELE_COUNT_KEY] = alleleCounts [0];
} else {
attributes [VCFConstants.ALLELE_COUNT_KEY] = alleleCounts;
}
if (alleleFreqs.Count == 1) {
attributes [VCFConstants.ALLELE_FREQUENCY_KEY] = alleleFreqs [0];
} else {
attributes [VCFConstants.ALLELE_FREQUENCY_KEY] = alleleFreqs;
}
} else {
// if there's no alt AC and AF shouldn't be present
attributes.Remove (VCFConstants.ALLELE_COUNT_KEY);
attributes.Remove (VCFConstants.ALLELE_FREQUENCY_KEY);
}
}
return attributes;
}
/// <summary>
/// Update the attributes of the attributes map given the VariantContext to reflect the
/// proper chromosome-based VCF tags
/// </summary>
/// <param name="vc"> the VariantContext </param>
/// <param name="attributes"> the attributes map to populate; must not be null; may contain old values </param>
/// <param name="removeStaleValues"> should we remove stale values from the mapping? </param>
/// <param name="founderIds"> - Set of founders Ids to take into account. AF and FC will be calculated over the founders.
/// If empty or null, counts are generated for all samples as unrelated individuals </param>
/// <returns> the attributes map provided as input, returned for programming convenience </returns>
public static IDictionary <string, object> CalculateChromosomeCounts(VariantContext vc, IDictionary <string, object> attributes, bool removeStaleValues, ISet <string> founderIds)
{
int AN = vc.CalledChrCount;
// if everyone is a no-call, remove the old attributes if requested
if (AN == 0 && removeStaleValues)
{
if (attributes.ContainsKey(VCFConstants.ALLELE_COUNT_KEY))
{
attributes.Remove(VCFConstants.ALLELE_COUNT_KEY);
}
if (attributes.ContainsKey(VCFConstants.ALLELE_FREQUENCY_KEY))
{
attributes.Remove(VCFConstants.ALLELE_FREQUENCY_KEY);
}
if (attributes.ContainsKey(VCFConstants.ALLELE_NUMBER_KEY))
{
attributes.Remove(VCFConstants.ALLELE_NUMBER_KEY);
}
return(attributes);
}
if (vc.HasGenotypes)
{
attributes [VCFConstants.ALLELE_NUMBER_KEY] = AN;
// if there are alternate alleles, record the relevant tags
if (vc.AlternateAlleles.Count > 0)
{
List <double> alleleFreqs = new List <double> ();
List <int> alleleCounts = new List <int> ();
List <int> foundersAlleleCounts = new List <int> ();
double totalFoundersChromosomes = (double)vc.GetCalledChrCount(founderIds);
int foundersAltChromosomes;
foreach (Allele allele in vc.AlternateAlleles)
{
foundersAltChromosomes = vc.GetCalledChrCount(allele, founderIds);
alleleCounts.Add(vc.GetCalledChrCount(allele));
foundersAlleleCounts.Add(foundersAltChromosomes);
if (AN == 0)
{
alleleFreqs.Add(0.0);
}
else
{
double freq = (double)foundersAltChromosomes / totalFoundersChromosomes;
alleleFreqs.Add(freq);
}
}
if (alleleCounts.Count == 1)
{
attributes [VCFConstants.ALLELE_COUNT_KEY] = alleleCounts [0];
}
else
{
attributes [VCFConstants.ALLELE_COUNT_KEY] = alleleCounts;
}
if (alleleFreqs.Count == 1)
{
attributes [VCFConstants.ALLELE_FREQUENCY_KEY] = alleleFreqs [0];
}
else
{
attributes [VCFConstants.ALLELE_FREQUENCY_KEY] = alleleFreqs;
}
}
else
{
// if there's no alt AC and AF shouldn't be present
attributes.Remove(VCFConstants.ALLELE_COUNT_KEY);
attributes.Remove(VCFConstants.ALLELE_FREQUENCY_KEY);
}
}
return(attributes);
}
