public BaseAndQualityAndPosition(int position, int insertSizeRelativeToPosition, BaseAndQuality BandQ)
{
this.BaseWithQuality = BandQ;
this.Position = position;
this.InsertPositionPassedRefPosition = (ushort) insertSizeRelativeToPosition;
}
public BaseAndQualityAndPosition(int position, int insertSizeRelativeToPosition, BaseAndQuality BandQ)
{
this.BaseWithQuality = BandQ;
this.Position = position;
this.InsertPositionPassedRefPosition = (ushort)insertSizeRelativeToPosition;
}
/// <summary>
/// Calculates the conditional probability that a base comes from each of A, C, G, T
/// based on the observed read and quality and current parameter settings.
/// </summary>
/// <returns>The gonditional probabilities.</returns>
/// <param name="freqs">Freqs.</param>
/// <param name="data">Data.</param>
/// <param name="bp">Bp.</param>
private static double updateConditionalProbabilities(BasePairFrequencies freqs, double[] data, BaseAndQuality bp)
{
//Calculate conditional probability that the base comes from the observed base.
double probRight = BaseQualityUtils.GetCorrectProbability(bp.PhredScore);
double probWrong = .333333333 * BaseQualityUtils.GetErrorProbability(bp.PhredScore);
double totProb = 0.0;
for (int i = 0; i < data.Length; i++)
{
var freq = freqs.Frequencies[i];
if (freq != 0.0)
{
double prob = freq * (i == bp.Base ? probRight : probWrong);
totProb += prob;
data[i] = prob;
}
}
for (int i = 0; i < data.Length; i++)
{
data[i] /= totProb;
}
return(Math.Log(totProb));
}