public void MatePairMapper1()
{
IList <ISequence> sequences = new List <ISequence>();
IList <MatePair> pairedreads = new List <MatePair>();
Sequence seq = new Sequence(Alphabets.DNA, "GGGAAAAATCAGATT");
seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor"
+ "substrate 1 (IRS1) on chromosome 2.X1:2K";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "ACGTGTGTGTCCCCC");
seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor"
+ "on chromosome 2.X1:10K";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "ACGTGTGKAAAAAAA");
seq.ID = ">gi|263191773|ref | H**o sapiens ........insulin receptor"
+ "on chromosome 2.X1:50K";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "GGGAAAAATCAGATT");
seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor"
+ "substrate 1 (IRS1) on chromosome 2.Y1:2K";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "ACGTGTGTGTCCCCC");
seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor"
+ "on chromosome 2.Y1:10K";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "ACGTGTGKAAAAAAA");
seq.ID = ">gi|263191773|ref | H**o sapiens ........insulin receptor"
+ "on chromosome 2.Y1:50K";
sequences.Add(seq);
MatePairMapper pair = new MatePairMapper();
pairedreads = Sort(pair.Map(sequences), sequences);
Assert.AreEqual(pairedreads.Count, 3);
ISequence expectedForward = new Sequence(Alphabets.DNA, "ACGTGTGKAAAAAAA");
ISequence expectedReverse = new Sequence(Alphabets.DNA, "ACGTGTGKAAAAAAA");
string lib = "50K";
Assert.AreEqual(pairedreads[0].GetForwardRead(sequences).ToString(), expectedForward.ToString());
Assert.AreEqual(pairedreads[0].GetReverseRead(sequences).ToString(), expectedReverse.ToString());
Assert.AreEqual(pairedreads[0].Library, lib);
Assert.AreEqual(pairedreads[0].MeanLengthOfLibrary, 65000);
Assert.AreEqual(pairedreads[0].StandardDeviationOfLibrary, 13334);
expectedForward = new Sequence(Alphabets.DNA, "ACGTGTGTGTCCCCC");
expectedReverse = new Sequence(Alphabets.DNA, "ACGTGTGTGTCCCCC");
lib = "10K";
Assert.AreEqual(pairedreads[1].GetForwardRead(sequences).ToString(), expectedForward.ToString());
Assert.AreEqual(pairedreads[1].GetReverseRead(sequences).ToString(), expectedReverse.ToString());
Assert.AreEqual(pairedreads[1].Library, lib);
Assert.AreEqual(pairedreads[1].MeanLengthOfLibrary, 10000);
Assert.AreEqual(pairedreads[1].StandardDeviationOfLibrary, 1000);
expectedForward = new Sequence(Alphabets.DNA, "GGGAAAAATCAGATT");
expectedReverse = new Sequence(Alphabets.DNA, "GGGAAAAATCAGATT");
lib = "2K";
Assert.AreEqual(pairedreads[2].GetForwardRead(sequences).ToString(), expectedForward.ToString());
Assert.AreEqual(pairedreads[2].GetReverseRead(sequences).ToString(), expectedReverse.ToString());
Assert.AreEqual(pairedreads[2].Library, lib);
Assert.AreEqual(pairedreads[2].MeanLengthOfLibrary, 2000);
Assert.AreEqual(pairedreads[2].StandardDeviationOfLibrary, 100);
}
