/// <summary>
/// Get simple paths in the graph.
/// </summary>
/// <returns>List of simple paths.</returns>
private List <ISequence> GetSimplePaths(bool createContigSequences)
{
//set flag to false so we can find any nodes that are missed during the build
_graph.SetNodeVisitState(false);
List <ISequence> paths = new List <ISequence>();
Parallel.ForEach(_graph.GetNodes(), node =>
{
int validLeftExtensionsCount = node.LeftExtensionNodesCount;
int validRightExtensionsCount = node.RightExtensionNodesCount;
if (validLeftExtensionsCount + validRightExtensionsCount == 0)
{
node.IsVisited = true;
// Island. Check coverage
if (_coverageThreshold == -1)
{
if (createContigSequences)
{
lock (paths)
{
paths.Add(_graph.GetNodeSequence(node));
}
}
}
else
{
if (node.KmerCount < _coverageThreshold)
{
node.MarkNodeForDelete();
}
}
}
else if (validLeftExtensionsCount == 1 && validRightExtensionsCount == 0)
{
TraceSimplePath(paths, node, false, createContigSequences, true);
}
else if (validRightExtensionsCount == 1 && validLeftExtensionsCount == 0)
{
TraceSimplePath(paths, node, true, createContigSequences, true);
}
});
//All paths starting from ends have now been found, however graph nodes entirely enclosed in a
//circular loop have been skipped, since these are small plasmids, etc. fast enough to do not in parallel.
//Must also be done sequentially to avoid grabbing nodes from the same circle in the graph concurrently
foreach (var node in _graph.GetUnvisitedNodes())
{
TraceSimplePath(paths, node, true, createContigSequences, false);
}
// Reset flag state to false, likely unnecessary as any method using the visit state flag
// should set it to false independently
_graph.SetNodeVisitState(false);
return(paths);
}
