public void TestContigBuilder2()
{
const int KmerLength = 6;
const int RedundantThreshold = 10;
List <ISequence> readSeqs = TestInputs.GetRedundantPathReads();
SequenceReads.Clear();
this.AddSequenceReads(readSeqs);
this.KmerLength = KmerLength;
RedundantPathLengthThreshold = RedundantThreshold;
RedundantPathsPurger = new RedundantPathsPurger(RedundantThreshold);
ContigBuilder = new SimplePathContigBuilder();
CreateGraph();
RemoveRedundancy();
int graphCount = Graph.Nodes.Count;
int graphEdges = Graph.Nodes.Select(n => n.ExtensionsCount).Sum();
IList <ISequence> contigs = BuildContigs();
int contigsBuiltGraphCount = Graph.Nodes.Count;
int contigsBuilt = Graph.Nodes.Select(n => n.ExtensionsCount).Sum();
// Compare the two graphs
Assert.AreEqual(1, contigs.Count);
Assert.AreEqual("ATGCCTCCTATCTTAGCGATGCGGTGT", contigs[0].ToString());
Assert.AreEqual(graphCount, contigsBuiltGraphCount);
Assert.AreEqual(graphEdges, contigsBuilt);
}
public void TestRedundantPathsPurger()
{
const int KmerLength = 5;
const int RedundantThreshold = 10;
List <ISequence> readSeqs = TestInputs.GetRedundantPathReads();
this.SequenceReads.Clear();
this.AddSequenceReads(readSeqs);
this.KmerLength = KmerLength;
this.RedundantPathLengthThreshold = RedundantThreshold;
this.RedundantPathsPurger = new RedundantPathsPurger(RedundantThreshold);
this.CreateGraph();
int graphCount = this.Graph.Nodes.Count;
int graphEdges = this.Graph.Nodes.Select(n => n.ExtensionsCount).Sum();
this.RemoveRedundancy();
int redundancyRemovedGraphCount = this.Graph.Nodes.Count;
int redundancyRemovedGraphEdge = this.Graph.Nodes.Select(n => n.ExtensionsCount).Sum();
// Compare the two graphs
Assert.AreEqual(5, graphCount - redundancyRemovedGraphCount);
Assert.AreEqual(12, graphEdges - redundancyRemovedGraphEdge);
}
public void TestContigGraphBuilder2()
{
const int KmerLength = 6;
const int RedundantThreshold = 10;
List <ISequence> readSeqs = TestInputs.GetRedundantPathReads();
this.SequenceReads.Clear();
this.AddSequenceReads(readSeqs);
this.KmerLength = KmerLength;
this.RedundantPathLengthThreshold = RedundantThreshold;
this.RedundantPathsPurger = new RedundantPathsPurger(RedundantThreshold);
this.ContigBuilder = new SimplePathContigBuilder();
this.CreateGraph();
this.RemoveRedundancy();
IList <ISequence> contigs = this.BuildContigs();
this.Graph.BuildContigGraph(contigs, KmerLength);
int contigGraphCount = this.Graph.Nodes.Count;
int contigGraphEdges = this.Graph.Nodes.Select(n => n.ExtensionsCount).Sum();
Assert.AreEqual(contigs.Count, contigGraphCount);
Assert.AreEqual(0, contigGraphEdges);
HashSet <string> contigSeqs = new HashSet <string>(contigs.Select(c => c.ToString()));
foreach (DeBruijnNode node in this.Graph.Nodes)
{
Assert.IsTrue(contigSeqs.Contains(this.Graph.GetNodeSequence(node).ToString()));
}
}