private VariantCall[] LoadIlluminaFinalReportVariant(string line)
{
if (line[0] != 'r')
{
return null;
}
if (line[1] != 's')
{
return null;
}
if (_splitter == null)
{
var testSplit = line.Split('\t');
_splitter = new StringSplitter(testSplit.Length);
}
_splitter.Split(line, '\t');
var lineSplit = _splitter.Results;
var newVar = new VariantCall();
newVar.Id = lineSplit[0];
newVar.AlleleA = lineSplit[16];
newVar.AlleleB = lineSplit[17];
return new[] { newVar };
}
private VariantCall[] LoadIlluminaMatrixReportVariant(string line)
{
if (line[0] != 'r')
{
return null;
}
if (line[1] != 's')
{
return null;
}
if (_splitter == null)
{
var testSplit = line.Split('\t');
_splitter = new StringSplitter(testSplit.Length);
}
_splitter.Split(line, '\t');
var lineSplit = _splitter.Results;
var variants = new VariantCall[lineSplit.Length - 1];
for (var i = 1; i < lineSplit.Length; i++)
{
var variant = new VariantCall();
variant.Id = lineSplit[0];
variant.AlleleA = lineSplit[i][0].ToString();
variant.AlleleB = lineSplit[i][1].ToString();
variants[i - 1] = variant;
}
return variants;
}
private VariantCall[] LoadVcfVariant(string line)
{
//Check for comment headers
if (line.Length < 2)
{
return null;
}
if (line.Substring(0, 2) == "##")
{
return null;
}
if (line[0] == '#')
{
return null;
}
if (_splitter == null)
{
var testSplit = line.Split('\t');
_splitter = new StringSplitter(testSplit.Length);
}
_splitter.Split(line, '\t');
var lineSplit = _splitter.Results;
//Check if we passed QC
if (lineSplit[6] != "PASS")
{
return null;
}
//Check if id starts with rs
if (lineSplit[2][0] != 'r')
{
return null;
}
if (lineSplit[2][1] != 's')
{
return null;
}
//Create variant
var newVar = new VariantCall();
newVar.Id = lineSplit[2];
newVar.VcfRef = lineSplit[3];
newVar.VcfAlt = lineSplit[4];
return new[] {newVar};
}
