public void MergeTwoConsensusPeaks(int xLeft, int xRight, int yLeft, int yRight, int cLeft, int cRight)
{
// Arrange
var mspc = new Mspc();
var sA = new Bed <Peak>();
sA.Add(new Peak(left: xLeft, right: xRight, value: 0.01), _chr, _strand);
mspc.AddSample(0, sA);
var sB = new Bed <Peak>();
sB.Add(new Peak(left: yLeft, right: yRight, value: 0.01), _chr, _strand);
mspc.AddSample(1, sB);
// Act
mspc.Run(new Config(ReplicateType.Biological, 1, 1, 1, 1, 1F, MultipleIntersections.UseLowestPValue));
var cp = mspc.GetConsensusPeaks()[_chr].First();
// Assert
Assert.True(cp.Source.Left == cLeft && cp.Source.Right == cRight);
}
private ReadOnlyDictionary <uint, Result <Peak> > InitializeAndRun(MultipleIntersections miChoice, bool trackSupportingPeaks = false)
{
// Arrange
var sA = new Bed <Peak>();
sA.Add(r11, _chr, _strand);
var sB = new Bed <Peak>();
sB.Add(r21, _chr, _strand);
sB.Add(r22, _chr, _strand);
sB.Add(r23, _chr, _strand);
var mspc = new Mspc(trackSupportingPeaks);
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
// Act
return(mspc.Run(new Config(ReplicateType.Biological, 1e-4, 1e-8, 1e-8, 2, 1F, miChoice)));
}
private Bed <Peak> CreateSample(int offset, int chrCount, int iCount)
{
var rtv = new Bed <Peak>();
for (int c = 0; c < chrCount; c++)
{
for (int i = 0; i < iCount; i++)
{
rtv.Add(
new Peak(
left: (10 * i) + 1 + offset,
right: (10 * i) + 4 + offset,
value: 1E-6,
name: "r1" + i
),
"chr" + c,
'*');
}
}
return(rtv);
}
public void T2()
{
// Arrange
var sA = new Bed <Peak>();
var r11 = new Peak(left: 10, right: 26, value: 1e-4, name: "r11");
sA.Add(r11, _chr, _strand);
var sB = new Bed <Peak>();
var r21 = new Peak(left: 5, right: 12, value: 1e-4, name: "r21");
var r22 = new Peak(left: 16, right: 18, value: 1e-7, name: "r22");
var r23 = new Peak(left: 22, right: 28, value: 1e-4, name: "r23");
sB.Add(r21, _chr, _strand);
sB.Add(r22, _chr, _strand);
sB.Add(r23, _chr, _strand);
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
var config = new Config(ReplicateType.Biological, 1e-3, 1e-8, 1e-8, 2, 1F, MultipleIntersections.UseLowestPValue);
// Act
var res = mspc.Run(config);
// Assert
Assert.True(res[0].Chromosomes[_chr].Get(Attributes.Confirmed).Count() == 1);
Assert.False(res[0].Chromosomes[_chr].Get(Attributes.Discarded).Any());
Assert.True(res[0].Chromosomes[_chr].Get(Attributes.Confirmed).ToList()[0].Source.CompareTo(r11) == 0);
Assert.True(res[1].Chromosomes[_chr].Get(Attributes.Confirmed).Count() == 1);
Assert.True(res[1].Chromosomes[_chr].Get(Attributes.Discarded).Count() == 2);
Assert.True(res[1].Chromosomes[_chr].Get(Attributes.Confirmed).ToList()[0].Source.CompareTo(r22) == 0);
Assert.True(res[1].Chromosomes[_chr].Get(Attributes.Discarded).ToList()[0].Source.CompareTo(r21) == 0);
Assert.True(res[1].Chromosomes[_chr].Get(Attributes.Discarded).ToList()[1].Source.CompareTo(r23) == 0);
}
private string RunMSPCAndExportResultsWithMultiChr()
{
var s0 = new Bed <Peak>();
for (int i = 0; i < peaks.Count; i++)
{
s0.Add(peaks[i], chrs[i], _strand);
}
var s1 = new Bed <Peak>();
s1.Add(new Peak(800, 900, 1E-2), "chr5", _strand);
var mspc = new Mspc();
mspc.AddSample(0, s0);
mspc.AddSample(1, s1);
mspc.Run(new Config(ReplicateType.Biological, 1e-4, 1e-5, 1e-5, 1, 0.05F, MultipleIntersections.UseLowestPValue));
var path = Environment.CurrentDirectory + Path.DirectorySeparatorChar + "MSPCTests_" + new Random().NextDouble().ToString();
new Exporter <Peak>().Export(_sidfm, mspc.GetResults(), mspc.GetConsensusPeaks(), new Options(path, false, _attributes));
return(path);
}
private ReadOnlyDictionary <uint, Result <Peak> > RunThenCancelMSPC(int iCount, Status status)
{
var sA = new Bed <Peak>();
var sB = new Bed <Peak>();
for (int i = 0; i < iCount; i++)
{
sA.Add(new Peak(
left: (10 * i) + 1,
right: (10 * i) + 4,
value: 1E-4,
summit: 0,
name: "r1" + i),
_chr, _strand);
sB.Add(new Peak(
left: (10 * i) + 6,
right: (10 * i) + 9,
value: 1E-5,
summit: 0,
name: "r1" + i),
_chr, _strand);
}
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
var config = new Config(ReplicateType.Biological, 1e-1, 1e-2, 1e-2, 1, 0.05F, MultipleIntersections.UseLowestPValue);
switch (status)
{
case Status.Init:
_continueIni = new AutoResetEvent(false);
_continueIni.Reset();
mspc.StatusChanged += WaitingIni;
// MSPC is expected to confirm peaks using the following configuration.
mspc.RunAsync(config);
_continueIni.WaitOne();
break;
case Status.Process:
_continuePrc = new AutoResetEvent(false);
_continuePrc.Reset();
mspc.StatusChanged += WaitingPrc;
// MSPC is expected to confirm peaks using the following configuration.
mspc.RunAsync(config);
_continuePrc.WaitOne();
break;
case Status.MTC:
_continueMtc = new AutoResetEvent(false);
_continueMtc.Reset();
mspc.StatusChanged += WaitingMtc;
// MSPC is expected to confirm peaks using the following configuration.
mspc.RunAsync(config);
_continueMtc.WaitOne();
break;
case Status.Consensu:
_continueCon = new AutoResetEvent(false);
_continueCon.Reset();
mspc.StatusChanged += WaitingCon;
// MSPC is expected to confirm peaks using the following configuration.
mspc.RunAsync(config);
_continueCon.WaitOne();
break;
}
// With the following configuration, MSPC discards all the peaks.
// This can help asserting if the asynchronous process of
// the previous execution is canceled, and instead the following asynchronous
// execution is completed.
mspc.RunAsync(new Config(ReplicateType.Biological, 1e-10, 1e-20, 1e-200, 1, 0.05F, MultipleIntersections.UseLowestPValue));
mspc.Done.WaitOne();
return(mspc.GetResults());
}