/// <summary>
/// Removes nodes that are part of dangling links.
/// </summary>
/// <param name="deBruijnGraph">Input graph.</param>
/// <param name="nodesList">List of dangling link nodes.</param>
public void RemoveErroneousNodes(DeBruijnGraph deBruijnGraph, DeBruijnPathList nodesList)
{
// Argument Validation
if (deBruijnGraph == null)
throw new ArgumentNullException("deBruijnGraph");
if (nodesList == null)
throw new ArgumentNullException("nodesList");
var lastNodes = new HashSet<DeBruijnNode>(nodesList.Paths.Select(nl => nl.PathNodes.Last()));
// Update extensions and Delete nodes from graph.
deBruijnGraph.RemoveNodes(
nodesList.Paths.AsParallel().SelectMany(nodes =>
{
RemoveLinkNodes(nodes, lastNodes);
return nodes.PathNodes;
}));
}
/// <summary>
/// Gets end node of redundant path cluster
/// All paths in input are part of a redundant path cluster
/// So all of them have the same start and the end node.
/// Return the last node of first path.
/// </summary>
/// <param name="paths">List of redundant paths.</param>
/// <returns>End node of redundant path cluster.</returns>
private static DeBruijnNode GetEndNode(DeBruijnPathList paths)
{
return paths.Paths.First().PathNodes.Last();
}
/// <summary>
/// Extract best path from list of paths. For the current cluster
/// of paths, return only those that should be removed.
/// </summary>
/// <param name="divergingPaths">List of redundant paths.</param>
/// <returns>List of paths nodes to be deleted.</returns>
private static DeBruijnPathList ExtractBestPath(DeBruijnPathList divergingPaths)
{
// Find "best" path. Except for best path, return rest for removal
int bestPathIndex = GetBestPath(divergingPaths);
DeBruijnPath bestPath = divergingPaths.Paths[bestPathIndex];
divergingPaths.Paths.RemoveAt(bestPathIndex);
// There can be overlap between redundant paths.
// Remove path nodes that occur in best path
foreach (var path in divergingPaths.Paths)
{
path.RemoveAll(n => bestPath.PathNodes.Contains(n));
}
return divergingPaths;
}
/// <summary>
/// Gets the best path from the list of diverging paths.
/// Path that has maximum sum of 'count' of belonging k-mers is best.
/// In case there are multiple 'best' paths, we arbitrarily return one of them.
/// </summary>
/// <param name="divergingPaths">List of diverging paths.</param>
/// <returns>Index of the best path.</returns>
private static int GetBestPath(DeBruijnPathList divergingPaths)
{
// We find the index of the 'best' path.
long max = -1;
int maxIndex = -1;
// Path that has the maximum sum of 'count' of belonging k-mers is the winner
for (int i = 0; i < divergingPaths.Paths.Count; i++)
{
long sum = divergingPaths.Paths[i].PathNodes.Sum(n => n.KmerCount);
if (sum > max)
{
max = sum;
maxIndex = i;
}
}
return maxIndex;
}
/// <summary>
/// Removes nodes that are part of redundant paths.
/// </summary>
/// <param name="deBruijnGraph">De Bruijn graph.</param>
/// <param name="nodesList">Path nodes to be deleted.</param>
public void RemoveErroneousNodes(DeBruijnGraph deBruijnGraph, DeBruijnPathList nodesList)
{
if (this.graph == null)
{
throw new ArgumentNullException("deBruijnGraph");
}
DeBruijnGraph.ValidateGraph(deBruijnGraph);
if (nodesList == null)
{
throw new ArgumentNullException("nodesList");
}
this.graph = deBruijnGraph;
// Neighbors of all nodes have to be updated.
HashSet<DeBruijnNode> deleteNodes = new HashSet<DeBruijnNode>(
nodesList.Paths.AsParallel().SelectMany(nl => nl.PathNodes));
// Update extensions for deletion
// No need for read-write lock as deleteNode's dictionary is being read,
// and only other graph node's dictionaries are updated.
Parallel.ForEach(
deleteNodes,
node =>
{
foreach (DeBruijnNode extension in node.GetExtensionNodes())
{
// If the neighbor is also to be deleted, there is no use of updation in that case
if (!deleteNodes.Contains(extension))
{
extension.RemoveExtensionThreadSafe(node);
}
}
});
// Delete nodes from graph
this.graph.RemoveNodes(deleteNodes);
}
