public static List <BiasTestResult> GetStrandResultsFromFile(string biasFile)
{
var results = new List <BiasTestResult>();
if (File.Exists(biasFile))
{
using (StreamReader sr = new StreamReader(biasFile))
{
while (true)
{
string line = sr.ReadLine();
if (string.IsNullOrEmpty(line))
{
break;
}
var result = BiasTestResult.ResultFromLine(line);
if (result != null)
{
results.Add(result);
}
}
}
}
return(results);
}
public static BiasTestResult ResultFromLine(string line)
{
var result = new BiasTestResult();
string[] splat = line.Split('\t');
//header line
if (splat[0] == _headerString[0])
{
return(null);
}
if (splat.Length < _headerString.Length)
{
throw new System.Exception("Check strand bias file format matches the unit test.");
}
for (int i = 0; i < _headerString.Length; i++)
{
string value = splat[i];
string colHeader = _headerString[i];
switch (colHeader)
{
case "Position":
result.Position = int.Parse(value);
break;
case "Reference":
result.ReferenceAllele = value;
break;
case "Alternate":
result.AlternateAllele = value;
break;
case "Overall_Support":
result.OverallSupport = int.Parse(value);
break;
case "Overall_Coverage":
result.OverallCoverage = int.Parse(value);
break;
case "Forward_Support":
result.FinalFRSupport[0] = int.Parse(value);
break;
case "Reverse_Support":
result.FinalFRSupport[1] = int.Parse(value);
break;
case "Forward_Coverage":
result.FinalFRCoverage[0] = int.Parse(value);
break;
case "Reverse_Coverage":
result.FinalFRCoverage[1] = int.Parse(value);
break;
case "RawSupportCountByReadType_0":
result.RawFRSSupport[0] = int.Parse(value);
break;
case "RawSupportCountByReadType_1":
result.RawFRSSupport[1] = int.Parse(value);
break;
case "RawSupportCountByReadType_2":
result.RawFRSSupport[2] = int.Parse(value);
break;
case "RawCoverageCountByReadType_0":
result.RawFRSCoverage[0] = int.Parse(value);
break;
case "RawCoverageCountByReadType_1":
result.RawFRSCoverage[1] = int.Parse(value);
break;
case "RawCoverageCountByReadType_2":
result.RawFRSCoverage[2] = int.Parse(value);
break;
case "BiasAcceptable?":
result.HasStrandBias = !(bool.Parse(value));
break;
default:
break;
}
}
return(result);
}
