public int GetClusterReferenceSupport(IEnumerable <ICluster> clusters)
{
var clusterVead = new Vead("test", GetConsensusSites());
var numRef = 0;
foreach (VariantSite vs in clusterVead.SiteResults)
{
// Nima: If cluster contains reference or X>X at this site, this site won't be included in the MNV.
// So veads that support reference for this cluster can hold any variant at these sites (hence using N>N).
// In the following example, cluster reference support for Cluster3 includes both Cluster1 and Cluster4
//---------------------------------------
// Sites S1 S2 S3
// Cluster1 R R R
// Cluster2 R R X
// Cluster3 R X X
// Cluster4 X R R
//----------------------------------------
//Cluster3's refVead N>N R>R R>R
//
// However, if the cluster is all ref we should avoid all N>N, and instead have the original R>R
// In example above:
//Cluster1's refVead R>R R>R R>R
if (vs.IsReference || vs.VcfAlternateAllele == vs.VcfReferenceAllele)
{
vs.VcfReferenceAllele = "N";
vs.VcfAlternateAllele = "N";
if (vs.IsReference)
{
numRef++;
}
}
else // If cluster contains a variant at this site, ref veads need to contain ref>ref at this site.
{
vs.VcfReferenceAllele = vs.VcfReferenceAllele[0].ToString();
vs.VcfAlternateAllele = vs.VcfReferenceAllele;
}
}
var refVead = clusterVead;
// Check if all variants were reference, assign original consensus to refVead
if (numRef == clusterVead.SiteResults.Count())
{
refVead = new Vead("test", GetConsensusSites());
}
var clusterRefVeadGroup = new VeadGroup(refVead);
var numVariants = clusterRefVeadGroup.NumSitesPerVead;
var cluterRefSupport = 0;
foreach (var cls in clusters)
{
List <VeadGroup> vgs = cls.GetVeadGroups();
foreach (var vg in vgs)
{
var agreement = new Agreement(vg, clusterRefVeadGroup);
if (agreement.NumDisagreement == 0 &&
agreement.NumAgreement >= numVariants)
{
cluterRefSupport += vg.NumVeads;
}
}
}
return(cluterRefSupport);
}