public static TruthVariant FromLine(string s)
{
TruthVariant truth = new TruthVariant();
string[] splat = s.Split();
truth.Chr = splat[0];
truth.Pos = splat[1];
truth.Ref = splat[2];
truth.Alt = splat[3];
truth.VariantExist = splat[4].Equals("1");
truth.VariantStatus = splat[5];
truth.VariantSource = splat[6];
truth.VariantConfirmed = splat[7];
truth.VariantId = string.Concat(truth.Chr, "_", truth.Pos, "_", truth.Ref, "_", truth.Alt);
return(truth);
}
public TruthItem(string sampleTruthFile, string sampleId)
{
SampleId = sampleId;
VariantsInfo = new Dictionary <string, TruthVariant>();
using (StreamReader sr = new StreamReader(sampleTruthFile))
{
while (true)
{
string line = sr.ReadLine();
if (string.IsNullOrEmpty(line))
{
break;
}
TruthVariant t = TruthVariant.FromLine(line);
string variantPositionId = t.Chr + "_" + t.Pos;
//Logger.WriteToLog($"\n read variant truth: {variantPositionId}\n");
if (!t.VariantStatus.Equals("FAIL"))
{
if (!ValidPositions.ContainsKey(variantPositionId))
{
ValidPositions[variantPositionId] = new HashSet <string>()
{
t.Ref
};
}
else
{
ValidPositions[variantPositionId].Add(t.Ref);
}
if (t.VariantStatus.Equals("PASS"))
{
if (!PassPositions.ContainsKey(variantPositionId))
{
PassPositions[variantPositionId] = true;
}
if (t.VariantExist)
{
if (!VariantExistPositions.ContainsKey(variantPositionId))
{
VariantExistPositions[variantPositionId] = t.VariantSource;
}
VariantsInfo.Add(t.VariantId, t);
}
}
}
}
}
NumberOfExistedVariant = VariantExistPositions.Count;
NumberOfPassPositions = PassPositions.Count;
NumberOfValidPositions = ValidPositions.Count;
//note: this is a modification based on our current data and cannot generalized to other cases
//when more than one variant exist check if they are caused by the same source
if (NumberOfExistedVariant > 1)
{
HashSet <string> variantSourceHashSet = new HashSet <string>();
foreach (KeyValuePair <string, string> kvp in VariantExistPositions)
{
variantSourceHashSet.Add(kvp.Value);
}
NumberOfExistedVariant = variantSourceHashSet.Count;
}
}
