public void GetRelativeWeights()
{
var setOfClusters = CreateDefaultSetOfClusters();
var weights = setOfClusters.GetRelativeWeights();
Assert.Equal(0, weights.Count);
var veadgroups = ClusterTestHelpers.GetSampleVeadGroups();
var cluster = new Cluster("test", veadgroups);
setOfClusters.AddCluster(cluster);
weights = setOfClusters.GetRelativeWeights();
Assert.Equal(1, weights.Count);
Assert.Equal(1, weights["test"]);
var veadgroups2 = ClusterTestHelpers.GetSampleVeadGroups();
var cluster2 = new Cluster("test2", veadgroups2);
setOfClusters.AddCluster(cluster2);
weights = setOfClusters.GetRelativeWeights();
Assert.Equal(2, weights.Count);
Assert.Equal(.5, weights["test"]);
Assert.Equal(.5, weights["test2"]);
}
public void ReAssignWorstFit()
{
var setOfClusters = CreateDefaultSetOfClusters();
var veadgroups = ClusterTestHelpers.GetSampleVeadGroups(3, 1, prefix: _random.Next().ToString());
var cluster = new Cluster("test", veadgroups);
setOfClusters.AddCluster(cluster);
Assert.Equal(1, setOfClusters.NumClusters);
Assert.Equal(3, setOfClusters.Clusters.First().NumVeads);
// Only one cluster: shouldn't do anything.
setOfClusters.ReAssignWorstFit();
Assert.Equal(1, setOfClusters.NumClusters);
Assert.Equal(3, setOfClusters.Clusters.First().NumVeads);
//TODO this does not yield expected results. See the TODO in SetOfClusters.ReassignWorstFit
//// If reassigning worst leaves cluster empty, remove that cluster
//var veadgroups2 = ClusterTestHelpers.GetSampleVeadGroups(1,1, prefix: _random.Next().ToString());
//var cluster2 = new Cluster("test2", veadgroups2);
//setOfClusters.AddCluster(cluster2);
//Assert.Equal(2, setOfClusters.NumClusters);
//setOfClusters.ReAssignWorstFit();
//Assert.Equal(1, setOfClusters.NumClusters);
//Assert.Equal(4, setOfClusters.Clusters.First().NumVeads);
}
public void Cluster()
{
var veadgroups = ClusterTestHelpers.GetSampleVeadGroups();
var cluster = new Cluster("test", veadgroups);
Assert.Equal("test", cluster.Name);
}
public void GetVeadGroups()
{
var veadGroups = ClusterTestHelpers.GetSampleVeadGroups();
var cluster = new Cluster("test", veadGroups);
Assert.Equal(1, cluster.GetVeadGroups().Count);
}
public void AddFromList()
{
var initialVeadGroups = ClusterTestHelpers.GetSampleVeadGroups();
var cluster = new Cluster("test", initialVeadGroups);
cluster.Add(ClusterTestHelpers.GetSampleVeadGroups(3, 2));
Assert.Equal(3, cluster.GetVeadGroups().Count);
}
public void Remove()
{
var initialVeadGroups = ClusterTestHelpers.GetSampleVeadGroups(3, 3);
var cluster = new Cluster("test", initialVeadGroups);
Assert.Equal(3, cluster.GetVeadGroups().Count);
cluster.Remove(initialVeadGroups.First());
Assert.Equal(2, cluster.GetVeadGroups().Count);
}
public void CreateAndAddCluster()
{
var setOfClusters = CreateDefaultSetOfClusters();
var veadgroups = ClusterTestHelpers.GetSampleVeadGroups();
setOfClusters.CreateAndAddCluster(veadgroups.First());
Assert.Equal(1, setOfClusters.Clusters.Count());
Assert.Equal("#1", setOfClusters.Clusters.First().Name);
}
public void AddCluster()
{
var setOfClusters = CreateDefaultSetOfClusters();
var veadgroups = ClusterTestHelpers.GetSampleVeadGroups();
var cluster = new Cluster("test", veadgroups);
setOfClusters.AddCluster(cluster);
Assert.Equal(1, setOfClusters.Clusters.Count());
}
public void SetCountsAtConsensusSites()
{
var initialVeadGroups = ClusterTestHelpers.GetSampleVeadGroups();
var cluster = new Cluster("test", initialVeadGroups);
Assert.Equal(1, cluster.GetVeadGroups().Count);
Assert.Equal(2, cluster.GetConsensusSites().Count());
// CountsAtSites should be same length as GetConsensusSites
Assert.Equal(2, cluster.CountsAtSites.Length);
Assert.Equal(new List <int>()
{
4, 4
}, cluster.CountsAtSites);
}
public void ResetConsensus()
{
var initialVeadGroups = ClusterTestHelpers.GetSampleVeadGroups(3, 3);
var cluster = new Cluster("test", initialVeadGroups);
Assert.Equal(3, cluster.NumVeadGroups);
Assert.Equal(9, cluster.NumVeads);
Assert.Equal(2, cluster.GetConsensusSites().Count());
foreach (var initialVeadGroup in initialVeadGroups.ToList())
{
cluster.Remove(initialVeadGroup);
}
Assert.Equal(0, cluster.NumVeadGroups);
Assert.Equal(0, cluster.NumVeads);
Assert.Equal(0, cluster.GetConsensusSites().Count());
}
public void GetVeadCountsInCluster()
{
var initialVeadGroups = ClusterTestHelpers.GetSampleVeadGroups(3, 3);
var cluster = new Cluster("test", initialVeadGroups);
var variantSite = new VariantSite(0)
{
VcfReferenceAllele = "A", VcfAlternateAllele = "T"
};
var variantSite2 = new VariantSite(0)
{
VcfReferenceAllele = "A", VcfAlternateAllele = "C"
};
var sites = new List <VariantSite>()
{
variantSite, variantSite2
};
Assert.Equal(9, cluster.GetVeadCountsInCluster(sites)[variantSite]);
Assert.Equal(0, cluster.GetVeadCountsInCluster(sites)[variantSite2]);
}
public void FindBestClusterFits()
{
var setOfClusters = CreateDefaultSetOfClusters();
var veadgroups = ClusterTestHelpers.GetSampleVeadGroups(prefix: _random.Next().ToString());
var cluster = new Cluster("test", veadgroups);
setOfClusters.AddCluster(cluster);
var veadgroups2 = ClusterTestHelpers.GetSampleVeadGroups(prefix: _random.Next().ToString());
var cluster2 = new Cluster("test2", veadgroups2);
setOfClusters.AddCluster(cluster2);
var matchingVeadGroup = ClusterTestHelpers.GetSampleVeadGroups(useAlternateVariantSites: false,
prefix: _random.Next().ToString());
var misMatchingVeadGroup = ClusterTestHelpers.GetSampleVeadGroups(useAlternateVariantSites: true,
prefix: _random.Next().ToString());
var bestFits = setOfClusters.GetClusterFits(matchingVeadGroup.First());
Assert.Equal(1, bestFits.Count);
Assert.Equal(2, bestFits.Keys.First());
Assert.Equal(2, bestFits[2].Count);
//TODO
var mismatchCluster = new Cluster("mismatch", misMatchingVeadGroup);
setOfClusters.AddCluster(mismatchCluster);
bestFits = setOfClusters.GetClusterFits(matchingVeadGroup.First());
foreach (var fit in bestFits)
{
Console.WriteLine("{0}: {1}", fit.Key, fit.Value.Count);
}
//Assert.Equal(2, bestFits.Count);
}
public void GetBestAgreement()
{
var initialVeadGroups = ClusterTestHelpers.GetSampleVeadGroups(3, 1);
var matchVeadGroups = ClusterTestHelpers.GetSampleVeadGroups(3, 1, false, _random.Next().ToString());
var nonMatchVeadGroups = ClusterTestHelpers.GetSampleVeadGroups(3, 1, true, _random.Next().ToString());
var cluster = new Cluster("test", initialVeadGroups);
var bestAgreement = cluster.GetBestAgreementWithVeadGroup(matchVeadGroups.First(), 0);
Assert.Equal(0, bestAgreement.NumDisagreement);
Assert.Equal(2, bestAgreement.NumAgreement);
// Since we're starting with default Agreement (0,0), will never get a bestAgreement worse than that...
bestAgreement = cluster.GetBestAgreementWithVeadGroup(nonMatchVeadGroups.First(), 5);
//Assert.Equal(2, bestAgreement.NumDisagreement);
Assert.Equal(0, bestAgreement.NumDisagreement);
Assert.Equal(0, bestAgreement.NumAgreement);
// If we're over the max num disagreements, return null
bestAgreement = cluster.GetBestAgreementWithVeadGroup(nonMatchVeadGroups.First(), 1);
Assert.True(bestAgreement == null);
}
public void RemoveCluster()
{
var setOfClusters = CreateDefaultSetOfClusters();
var veadgroups = ClusterTestHelpers.GetSampleVeadGroups();
var cluster = new Cluster("test", veadgroups);
setOfClusters.AddCluster(cluster);
var veadgroups2 = ClusterTestHelpers.GetSampleVeadGroups();
var cluster2 = new Cluster("test2", veadgroups2);
setOfClusters.AddCluster(cluster2);
Assert.Equal(2, setOfClusters.Clusters.Count());
setOfClusters.RemoveCluster("test");
var clustersRemaining = setOfClusters.Clusters;
Assert.Equal(1, clustersRemaining.Count());
Assert.Equal("test2", clustersRemaining.First().Name);
}
public void GetWorstAgreement()
{
var initialVeadGroups = ClusterTestHelpers.GetSampleVeadGroups(3, 1);
var matchVeadGroups = ClusterTestHelpers.GetSampleVeadGroups(3, 1);
var nonMatchVeadGroups = ClusterTestHelpers.GetSampleVeadGroups(3, 1, true);
var cluster = new Cluster("test", initialVeadGroups);
// If there's only one veadgroup, that will by default be the "worst"
var worst = cluster.GetWorstAgreement();
Assert.Equal(initialVeadGroups.First(), worst);
// This is a tie, they're both the same, first will go
cluster.Add(matchVeadGroups);
worst = cluster.GetWorstAgreement();
Assert.Equal(initialVeadGroups.First(), worst);
// The non-matching group should be the worst agreement
cluster.Add(nonMatchVeadGroups);
worst = cluster.GetWorstAgreement();
Assert.Equal(nonMatchVeadGroups.First(), worst);
}
public void RemoveWorstClusters()
{
//check it works with zero clusters.
var setOfClusters = CreateDefaultSetOfClusters();
Assert.Equal(0, setOfClusters.NumClusters);
int result = setOfClusters.RemoveWorstClusters(0);
Assert.Equal(0, setOfClusters.NumClusters);
Assert.Equal(0, result);
result = setOfClusters.RemoveWorstClusters(2);
Assert.Equal(0, setOfClusters.NumClusters);
Assert.Equal(0, result);
//check it works with one cluster
var veadgroups = ClusterTestHelpers.GetSampleVeadGroups();
var cluster = new Cluster("test", veadgroups);
setOfClusters.AddCluster(cluster);
result = setOfClusters.RemoveWorstClusters(0);
Assert.Equal(1, setOfClusters.NumClusters);
Assert.Equal(1, result);
result = setOfClusters.RemoveWorstClusters(1);
Assert.Equal(0, setOfClusters.NumClusters);
Assert.Equal(1, result);
setOfClusters.AddCluster(cluster);
Assert.Equal(1, setOfClusters.NumClusters);
result = setOfClusters.RemoveWorstClusters(2);
Assert.Equal(0, setOfClusters.NumClusters);
Assert.Equal(1, result);
//check it works with two clusters (equal clusters)
setOfClusters.AddCluster(cluster);
var clusterSame = new Cluster("same", veadgroups);
setOfClusters.AddCluster(clusterSame);
Assert.Equal(2, setOfClusters.NumClusters);
result = setOfClusters.RemoveWorstClusters(0);
Assert.Equal(2, setOfClusters.NumClusters);
Assert.Equal(2, result);
result = setOfClusters.RemoveWorstClusters(1);
Assert.Equal(2, setOfClusters.NumClusters);
Assert.Equal(2, result);
result = setOfClusters.RemoveWorstClusters(2);
Assert.Equal(0, setOfClusters.NumClusters);
Assert.Equal(2, result);
//check it works with two clusters (unequal clusters)
//So there is one distinct worst cluster (ie, result==1).
var smallnum_veadgroups = ClusterTestHelpers.GetSampleVeadGroups(numVeads: 2, numVeadGroups: 1);
setOfClusters.AddCluster(cluster);
var clusterSmall = new Cluster("small", smallnum_veadgroups);
setOfClusters.AddCluster(clusterSmall);
Assert.Equal(2, setOfClusters.NumClusters);
result = setOfClusters.RemoveWorstClusters(0);
Assert.Equal(2, setOfClusters.NumClusters);
Assert.Equal(1, result);
result = setOfClusters.RemoveWorstClusters(1);
Assert.Equal(1, setOfClusters.NumClusters);
Assert.Equal(1, result);
setOfClusters.AddCluster(clusterSmall);
Assert.Equal(2, setOfClusters.NumClusters);
result = setOfClusters.RemoveWorstClusters(2);
Assert.Equal(1, setOfClusters.NumClusters);
Assert.Equal(1, result);
//three clusters (one low, two high weighted):
setOfClusters.AddCluster(clusterSmall);
setOfClusters.AddCluster(clusterSame);
Assert.Equal(3, setOfClusters.NumClusters);
result = setOfClusters.RemoveWorstClusters(0);
Assert.Equal(3, setOfClusters.NumClusters);
Assert.Equal(1, result);
result = setOfClusters.RemoveWorstClusters(1);
Assert.Equal(2, setOfClusters.NumClusters);
Assert.Equal(1, result);
Assert.NotEqual("small", setOfClusters.Clusters[0].Name);
Assert.NotEqual("small", setOfClusters.Clusters[1].Name);
//four clusters (two low, two high weighted):
setOfClusters.AddCluster(clusterSmall);
var smallnum2_veadgroups = ClusterTestHelpers.GetSampleVeadGroups(numVeads: 1, numVeadGroups: 2);
var clusterSmall2 = new Cluster("small2", smallnum_veadgroups);
setOfClusters.AddCluster(clusterSmall2);
Assert.Equal(4, setOfClusters.NumClusters);
result = setOfClusters.RemoveWorstClusters(0);
Assert.Equal(4, setOfClusters.NumClusters);
Assert.Equal(2, result);
result = setOfClusters.RemoveWorstClusters(1);
Assert.Equal(4, setOfClusters.NumClusters);
Assert.Equal(2, result);
result = setOfClusters.RemoveWorstClusters(3);
Assert.Equal(2, setOfClusters.NumClusters);
Assert.Equal(2, result);
result = setOfClusters.RemoveWorstClusters(1);
Assert.Equal(2, setOfClusters.NumClusters);
Assert.Equal(2, result);
Assert.NotEqual("small", setOfClusters.Clusters[0].Name);
Assert.NotEqual("small", setOfClusters.Clusters[1].Name);
Assert.NotEqual("small2", setOfClusters.Clusters[0].Name);
Assert.NotEqual("small2", setOfClusters.Clusters[1].Name);
result = setOfClusters.RemoveWorstClusters(56);
Assert.Equal(0, setOfClusters.NumClusters);
Assert.Equal(2, result);
}