/// <summary>
/// Step 1: Building k-mers from sequence reads
/// Step 2: Build de bruijn graph for input set of k-mers.
/// Sets the _assemblerGraph field.
/// </summary>
protected virtual void CreateGraph()
{
Graph = new DeBruijnGraph(this.kmerLength);
Graph.Build(this.sequenceReads);
}
/// <summary>
/// Validate graph generated using DeBruijnGraph.CreateGraph() with kmers
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void ValidateDeBruijnGraphBuild(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.KmerLengthNode);
// Get the input reads and build kmers
IEnumerable<ISequence> sequenceReads = null;
using (FastAParser parser = new FastAParser(filePath))
{
sequenceReads = parser.Parse();
this.KmerLength = int.Parse(kmerLength, (IFormatProvider)null);
this.SequenceReads.Clear();
this.SetSequenceReads(sequenceReads.ToList());
DeBruijnGraph graph = new DeBruijnGraph(this.KmerLength);
graph.Build(this.SequenceReads);
ValidateGraph(graph, nodeName);
}
ApplicationLog.WriteLine(@"Padena BVT : DeBruijnGraph Build() validation for Padena step2 completed successfully");
}