public void TestContigBuilder2()
{
const int KmerLength = 6;
const int RedundantThreshold = 10;
List<ISequence> readSeqs = TestInputs.GetRedundantPathReads();
SequenceReads.Clear();
this.SetSequenceReads(readSeqs);
this.KmerLength = KmerLength;
RedundantPathLengthThreshold = RedundantThreshold;
RedundantPathsPurger = new RedundantPathsPurger(RedundantThreshold);
ContigBuilder = new SimplePathContigBuilder();
CreateGraph();
RemoveRedundancy();
long graphCount = Graph.NodeCount;
long graphEdges = Graph.GetNodes().Select(n => n.ExtensionsCount).Sum();
IEnumerable<ISequence> contigs = BuildContigs();
long contigsBuiltGraphCount = Graph.NodeCount;
long contigsBuilt = Graph.GetNodes().Select(n => n.ExtensionsCount).Sum();
// Compare the two graphs
Assert.AreEqual(1, contigs.Count());
string s = new string(contigs.ElementAt(0).Select(a => (char)a).ToArray());
Assert.AreEqual("ATGCCTCCTATCTTAGCGATGCGGTGT", s);
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.SetSequenceReads(readSeqs);
this.KmerLength = KmerLength;
this.RedundantPathLengthThreshold = RedundantThreshold;
this.RedundantPathsPurger = new RedundantPathsPurger(RedundantThreshold);
this.CreateGraph();
long graphCount = this.Graph.NodeCount;
long graphEdges = this.Graph.GetNodes().Select(n => n.ExtensionsCount).Sum();
this.RemoveRedundancy();
long redundancyRemovedGraphCount = this.Graph.NodeCount;
long redundancyRemovedGraphEdge = this.Graph.GetNodes().Select(n => n.ExtensionsCount).Sum();
// Compare the two graphs
Assert.AreEqual(5, graphCount - redundancyRemovedGraphCount);
Assert.AreEqual(12, graphEdges - redundancyRemovedGraphEdge);
}
