private void ProcessNeighborhood(VcfNeighborhood neighborhood, NeighborhoodClusterer clusterer, IEnumerable <VeadGroup> collapsedReads)
{
Logger.WriteToLog("Processing Neighborhood {0}.", neighborhood.Id);
try
{
var clusters = clusterer.ClusterVeadGroups(collapsedReads.ToList());
if (clusters != null)
{
Logger.WriteToLog("Found " + clusters.Clusters.Length + " clusters in Nbhd " + neighborhood.Id);
//tjd+
//Commenting out for speed. We currently never use these results
//neighborhood.PhasingProbabiltiies =
// VariantPhaser.GetPhasingProbabilities(neighborhood.VcfVariantSites, clusters);
//tjd-
}
bool crushNbhdVariantsToSamePositon = !_factory.Options.VcfWritingParams.AllowMultipleVcfLinesPerLoci;
neighborhood.AddMnvsFromClusters(clusters.Clusters,
_factory.Options.BamFilterParams.MinimumBaseCallQuality, _factory.Options.VariantCallingParams.MaximumVariantQScore,
crushNbhdVariantsToSamePositon);
neighborhood.SetGenotypesAndPruneExcessAlleles();
}
catch (Exception ex)
{
Logger.WriteToLog("Error processing neighborhood {0}", neighborhood.Id);
Logger.WriteExceptionToLog(ex);
}
}
public void AddMnvsFromClusters()
{
//TODO even with mock cluster this takes too much setting up.
var nbhd = new VcfNeighborhood(new VariantCallingParameters(), "chr1", new VariantSite(120), new VariantSite(121), "T");
var vead = PhasedVariantTestUtilities.CreateVeadFromStringArray("r1", new[, ] {
{ "C", "A" }, { "G", "A" }, { "T", "A" }
});
var vead2 = PhasedVariantTestUtilities.CreateVeadFromStringArray("r2", new[, ] {
{ "C", "A" }, { "G", "A" }, { "T", "A" }
});
var vead3 = PhasedVariantTestUtilities.CreateVeadFromStringArray("r3", new[, ] {
{ "C", "A" }, { "G", "A" }, { "T", "A" }
});
var veads = new List <Vead> {
vead, vead2, vead3
};
nbhd.ReferenceSequence = "CGT";
var mockCluster = new Mock <ICluster>();
mockCluster.Setup(c => c.CountsAtSites).Returns(new[] { 10, 3, 5 });
var consensus = PhasedVariantTestUtilities.CreateVeadGroup(veads);
mockCluster.Setup(c => c.GetConsensusSites()).Returns(consensus.SiteResults);
mockCluster.Setup(c => c.GetVeadGroups()).Returns(new List <VeadGroup>()
{
consensus
});
nbhd.AddMnvsFromClusters(new List <ICluster>()
{
mockCluster.Object
}, 20, 100);
var allele = nbhd.CandidateVariants.First();
Assert.Equal(6, allele.TotalCoverage);
Assert.Equal(6, allele.AlleleSupport);
Assert.Equal("CGT", allele.Reference);
Assert.Equal("AAA", allele.Alternate);
var depths = nbhd.DepthAtSites(new List <ICluster>()
{
mockCluster.Object
});
Assert.Equal(3, depths.Length);
Assert.Equal(3, depths[0]);
Assert.Equal(3, depths[1]);
Assert.Equal(3, depths[2]);
}