private List <VeadGroup> AllocateReadsToClusters(List <VeadGroup> veadGroups, SetOfClusters clusters, int maxNumDisagreements)
{
var vgsRemaining = new List <VeadGroup>();
foreach (var vg in veadGroups)
{
var bestFits = clusters.GetClusterFits(vg);
if (bestFits.Count == 0)
{
vgsRemaining.Add(vg);
}
else
{
var bestCandidates = bestFits.Last().Value;
var bestcluster = bestCandidates[0];
if (_options.AllowClusterMerging)
{
bestcluster = ClusterMerger.MergeAllBestCandidates(clusters, maxNumDisagreements, bestCandidates, vg);
}
bestcluster.Add(vg);
}
}
return(vgsRemaining);
}
public void MergeAllBestCandidates()
{
var setOfClusters = new SetOfClusters(new ClusteringParameters());
var veadgroups = ClusterTestHelpers.GetSampleVeadGroups(prefix: "Original");
var cluster = new Cluster("test", veadgroups);
setOfClusters.AddCluster(cluster);
var veadgroups2 = ClusterTestHelpers.GetSampleVeadGroups(prefix: "Second");
var cluster2 = new Cluster("test2", veadgroups2);
setOfClusters.AddCluster(cluster2);
Assert.Equal(2, setOfClusters.NumClusters);
var veadgroups3 = ClusterTestHelpers.GetSampleVeadGroups(1, 1, prefix: "Tester");
// If can be merged, we should have 1 cluster.
var bestCluster = ClusterMerger.MergeAllBestCandidates(setOfClusters, 0, new List <Cluster> {
cluster, cluster2
}, veadgroups3.First());
Assert.Equal(1, setOfClusters.NumClusters);
}