/// <summary>
/// Calculates distance between contigs for each pair of Full Overlap.
/// </summary>
/// <param name="validPairedRead">Valid mate pairs which have full Overlap
/// and support a perticular orientation of contigs</param>
/// <param name="length">Length of forward contig.</param>
private static void CalculateDistance(ValidMatePair validPairedRead, int length)
{
//For reverse read sequence in forward direction.
validPairedRead.DistanceBetweenContigs.Add(
validPairedRead.PairedRead.MeanLengthOfLibrary - (length -
validPairedRead.ForwardReadStartPosition.First())
- (validPairedRead.ReverseReadStartPosition.First() + 1));
validPairedRead.StandardDeviation.Add(validPairedRead.PairedRead.StandardDeviationOfLibrary);
validPairedRead.Weight = 1;
//For reverse read sequence in reverse complementary direction.
validPairedRead.DistanceBetweenContigs.Add(
validPairedRead.PairedRead.MeanLengthOfLibrary - (length -
validPairedRead.ForwardReadStartPosition[0])
- (validPairedRead.ReverseReadReverseComplementStartPosition[0] + 1));
validPairedRead.StandardDeviation.Add(validPairedRead.PairedRead.StandardDeviationOfLibrary);
}
/// <summary>
/// Bundles all valid mate pairs in single edge but considering ±3σ limit.
/// </summary>
/// <param name="contigPairedRead">List of Valid Paired Reads</param>
private static void EdgeBundling(IList <ValidMatePair> contigPairedRead)
{
int index = 0;
List <ValidMatePair> estimatedDistances;
while (index < contigPairedRead.Count())
{
estimatedDistances = contigPairedRead.Where(distance =>
(contigPairedRead[index].DistanceBetweenContigs.First() - (3.0 *
contigPairedRead[index].StandardDeviation.First())
<= distance.DistanceBetweenContigs.First()) &&
distance.DistanceBetweenContigs[0] <=
(contigPairedRead[index].DistanceBetweenContigs.First() + (3.0 *
contigPairedRead[index].StandardDeviation.First()))).ToList();
if (estimatedDistances.Count > 1)
{
float p = (float)estimatedDistances.Sum(dist => dist.DistanceBetweenContigs[0]
/ Math.Pow(dist.StandardDeviation[0], 2));
float q = (float)estimatedDistances.Sum(sd => 1 / Math.Pow(sd.StandardDeviation[0], 2));
ValidMatePair distance = new ValidMatePair();
distance.DistanceBetweenContigs.Add(p / q);
distance.StandardDeviation.Add((float)(1 / Math.Sqrt(q)));
p = (float)estimatedDistances.Sum(dist => dist.DistanceBetweenContigs[1]
/ Math.Pow(dist.StandardDeviation[1], 2));
q = (float)estimatedDistances.Sum(sd => 1 / Math.Pow(sd.StandardDeviation[1], 2));
distance.DistanceBetweenContigs.Add(p / q);
distance.StandardDeviation.Add((float)(1 / Math.Sqrt(q)));
foreach (ValidMatePair est in estimatedDistances)
{
contigPairedRead.Remove(est);
}
distance.Weight = estimatedDistances.Count;
contigPairedRead.Add(distance);
index = 0;
}
else
{
index++;
}
}
}
/// <summary>
/// Further estimates distances using weighted mean
/// and standard deviation by merging valid mate pairs.
/// </summary>
/// <param name="distances">List of valid mate pairs.</param>
private static void CalculateWeigthedEdge(IList <ValidMatePair> distances)
{
ValidMatePair finalDistance = new ValidMatePair();
finalDistance.DistanceBetweenContigs.Add(
distances.Sum(distance => distance.DistanceBetweenContigs[0] * distance.Weight));
finalDistance.StandardDeviation.Add(
distances.Sum(distance => distance.StandardDeviation[0] * distance.Weight));
finalDistance.Weight = distances.Sum(distance => distance.Weight);
finalDistance.DistanceBetweenContigs[0] /= finalDistance.Weight;
finalDistance.StandardDeviation[0] /= finalDistance.Weight;
finalDistance.DistanceBetweenContigs.Add(
distances.Sum(distance => distance.DistanceBetweenContigs[1] * distance.Weight));
finalDistance.StandardDeviation.Add(
distances.Sum(distance => distance.StandardDeviation[0] * distance.Weight));
finalDistance.DistanceBetweenContigs[1] /= finalDistance.Weight;
finalDistance.StandardDeviation[1] /= finalDistance.Weight;
distances.Clear();
distances.Add(finalDistance);
}
