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 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 TestContigBuilder1()
{
const int KmerLength = 11;
const int DangleThreshold = 3;
const int RedundantThreshold = 10;
List <ISequence> readSeqs = TestInputs.GetDanglingReads();
this.SequenceReads.Clear();
this.SetSequenceReads(readSeqs);
this.KmerLength = KmerLength;
DanglingLinksThreshold = DangleThreshold;
DanglingLinksPurger = new DanglingLinksPurger(DangleThreshold);
RedundantPathLengthThreshold = RedundantThreshold;
RedundantPathsPurger = new RedundantPathsPurger(RedundantThreshold);
ContigBuilder = new SimplePathContigBuilder();
CreateGraph();
UnDangleGraph();
RemoveRedundancy();
long graphCount = Graph.NodeCount;
long graphEdges = Graph.GetNodes().Select(n => n.ExtensionsCount).Sum();
IEnumerable <ISequence> contigs = BuildContigs();
long contigsBuiltGraphCount = this.Graph.NodeCount;
long contigsBuilt = Graph.GetNodes().Select(n => n.ExtensionsCount).Sum();
// Compare the two graphs
Assert.AreEqual(1, contigs.Count());
HashSet <string> expectedContigs = new HashSet <string>()
{
"ATCGCTAGCATCGAACGATCATT"
};
foreach (ISequence contig in contigs)
{
string s = new string(contig.Select(a => (char)a).ToArray());
Assert.IsTrue(expectedContigs.Contains(s));
}
Assert.AreEqual(graphCount, contigsBuiltGraphCount);
Assert.AreEqual(graphEdges, contigsBuilt);
}
