/// <summary>
/// Apply Distance constrains on given two nodes.
/// The distances between contigs are calculated using paired read information.
/// </summary>
/// <param name="childPath">Destination node.</param>
/// <param name="contigPairedReadMaps">Map of contigs and paired reads.</param>
/// <returns>Whether Distance between contig nodes lie in constraint or not.</returns>
private bool DistanceConstraint(
Paths childPath,
Dictionary<ISequence, IList<ValidMatePair>> contigPairedReadMaps)
{
IList<ValidMatePair> map;
if (contigPairedReadMaps.TryGetValue(this.graph.GetNodeSequence(childPath.CurrentNode.Key), out map))
{
float pathlength = this.GetPathLength(childPath);
if (childPath.CurrentNode.Value.IsSameOrientation)
{
if ((map[0].DistanceBetweenContigs[0] -
(3 * map[0].StandardDeviation[0]) <= pathlength) &&
(pathlength <= map[0].DistanceBetweenContigs[0] +
(3 * map[0].StandardDeviation[0])))
{
return true;
}
return false;
}
if ((map[0].DistanceBetweenContigs[1] -
(3 * map[0].StandardDeviation[1]) <= pathlength) &&
(pathlength <= map[0].DistanceBetweenContigs[1] +
(3 * map[0].StandardDeviation[1])))
{
return true;
}
return false;
}
return true;
}
/// <summary>
/// Get length of path traversed using BFS.
/// </summary>
/// <param name="childPath">Path travelled to reach destination node.</param>
/// <returns>Distance between first and last contig node.</returns>
private float GetPathLength(Paths childPath)
{
float distance = 0;
for (int index = 1; index < childPath.FamilyTree.Count; index++)
{
distance += this.graph.GetNodeSequence(childPath.FamilyTree[index].Key).Count - this.kmerLength;
}
distance -= this.kmerLength;
return distance;
}
/// <summary>
/// Add right extension of the nodes to queue.
/// </summary>
/// <param name="node">Current node.</param>
/// <param name="search">Queue for BFS.</param>
/// <param name="paths">List of paths.</param>
/// <param name="familyTree">Nodes visited for construction of paths.</param>
/// <param name="contigPairedReadMap">Contig and valid mate pair map.</param>
private void RightExtension(
KeyValuePair<Node, Edge> node,
Queue<Paths> search,
List<Paths> paths,
ScaffoldPath familyTree,
Dictionary<ISequence, IList<ValidMatePair>> contigPairedReadMap)
{
Paths childPath;
if (node.Key.RightExtensionNodes.Count > 0)
{
foreach (KeyValuePair<Node, Edge> child in node.Key.RightExtensionNodes)
{
childPath = new Paths();
childPath.CurrentNode = child;
if (familyTree == null)
{
childPath.FamilyTree.Add(node);
}
else
{
childPath.FamilyTree.AddRange(familyTree);
childPath.FamilyTree.Add(node);
}
childPath.NodeOrientation = true;
if (this.DistanceConstraint(childPath, contigPairedReadMap) &&
childPath.FamilyTree.Count < this.depth &&
!contigPairedReadMap.All(
t => childPath.FamilyTree.Any(k => t.Key == this.graph.GetNodeSequence(k.Key))))
{
search.Enqueue(childPath);
}
else
{
if (contigPairedReadMap.All(
t => childPath.FamilyTree.Any(k => t.Key == this.graph.GetNodeSequence(k.Key))))
{
paths.Add(childPath);
}
}
}
}
else
{
childPath = new Paths();
if (familyTree == null)
{
childPath.FamilyTree.Add(node);
}
else
{
childPath.FamilyTree.AddRange(familyTree);
childPath.FamilyTree.Add(node);
}
if (contigPairedReadMap.All(
t => childPath.FamilyTree.Any(k => t.Key == this.graph.GetNodeSequence(k.Key))))
{
paths.Add(childPath);
}
}
}
