public void ReadM(string m, MultipleIntersections expectedValue)
{
// Arrange & Act
var options = new CommandLineOptions();
var po = options.Parse(GenerateShortNameArguments(m: m).Split(' '), out bool _);
// Assert
Assert.True(po.MultipleIntersections == expectedValue);
}
/// <summary>
/// The configuration of MSPC process.
/// </summary>
/// <param name="replicateType">Sets the replicate type of the input samples.</param>
/// <param name="tauW">Sets weak p-value threshold.</param>
/// <param name="tauS">Sets stringent p-value threshold.</param>
/// <param name="gamma">Sets combined stringency threshold.</param>
/// <param name="c">Sets the minimum number of samples having overlapping peaks with a given peak.</param>
/// <param name="alpha">Sets Benjamini-Hochberg multiple testing correction threshold.</param>
/// <param name="multipleIntersections">Sets if the peak with lowest or highest p-value
/// should be used when multiple peaks from a sample overlap with a given peak.</param>
public Config(ReplicateType replicateType, double tauW, double tauS, double gamma, int c, float alpha, MultipleIntersections multipleIntersections)
{
ReplicateType = replicateType;
TauW = tauW;
TauS = tauS;
Gamma = gamma;
C = c;
Alpha = alpha;
MultipleIntersections = multipleIntersections;
}
private ReadOnlyDictionary <uint, Result <Peak> > InitializeAndRun(MultipleIntersections miChoice)
{
// 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();
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 void AssertGivenValuesAreValid()
{
switch (_cReplicate.Value().ToLower())
{
case "bio":
case "biological":
_vreplicate = ReplicateType.Biological;
break;
case "tec":
case "technical":
_vreplicate = ReplicateType.Technical;
break;
default:
throw new ArgumentException("Invalid value given for the `" + _cReplicate.LongName + "` argument.");
}
if (!double.TryParse(_cTauS.Value(), out _vtauS))
{
throw new ArgumentException("Invalid value given for the `" + _cTauS.LongName + "` argument.");
}
if (!double.TryParse(_cTauW.Value(), out _vtauW))
{
throw new ArgumentException("Invalid value given for the `" + _cTauW.LongName + "` argument.");
}
if (_vtauW <= _vtauS)
{
throw new ArgumentException("Stringency threshold (TauS) should be lower than weak threshold (TauW).");
}
if (_cGamma.HasValue() && !double.TryParse(_cGamma.Value(), out _vgamma))
{
throw new ArgumentException("Invalid value given for the `" + _cGamma.LongName + "` argument.");
}
_vgamma = _vgamma == -1 ? _vtauS : _vgamma;
if (_cAlpha.HasValue() && !float.TryParse(_cAlpha.Value(), out _valpha))
{
throw new ArgumentException("Invalid value given for the `" + _cAlpha.LongName + "` argument.");
}
if (_cC.HasValue())
{
if (_cC.Value().Contains("%"))
{
if (int.TryParse(_cC.Value().Replace("%", ""), out int percentage))
{
_vc = (_inputFiles.Count * percentage) / 100;
}
else
{
throw new ArgumentException("Invalid value given for the `" + _cC.ShortName + "` argument.");
}
}
else if (!int.TryParse(_cC.Value(), out _vc))
{
throw new ArgumentException("Invalid value given for the `" + _cC.ShortName + "` argument.");
}
if (_vc < 1)
{
_vc = 1;
}
}
if (_cM.HasValue())
{
switch (_cM.Value().ToLower())
{
case "lowest":
_vm = MultipleIntersections.UseLowestPValue;
break;
case "highest":
_vm = MultipleIntersections.UseHighestPValue;
break;
default:
throw new ArgumentException("Invalid value given for the `" + _cM.LongName + "` argument.");
}
}
if (_cOutput.HasValue())
{
OutputPath = _cOutput.Value();
}
if (_cDP.HasValue())
{
if (int.TryParse(_cDP.Value(), out int dp))
{
DegreeOfParallelism = dp;
}
else
{
throw new ArgumentException("Invalid value given for the `" + _cDP.LongName + "` argument.");
}
}
}
