public void AddSampleVars(SampleVariant vr)
{
if (varTypes == null)
{
varTypes = new Dictionary <string, List <SampleVariant> > ();
}
if (!varTypes.ContainsKey(vr.BioS.ID))
{
varTypes.Add(vr.BioS.ID, new List <SampleVariant> ());
}
varTypes[vr.BioS.ID].Add(vr);
}
protected static void LoadVarFile(string fName, BioSample [] samps, bool genotyped)
{
char[] seps = { '/', '|' };
int count = 0;
using (StreamReader sr = new StreamReader(fName)) {
while ((int)'#' == sr.Peek())
{
sr.ReadLine();
}
string[] spstrs;
string line;
while ((line = sr.ReadLine()) != null)
{
spstrs = line.Split('\t');
if (spstrs [6] == "PASS")
{
Variant v;
string[] sps = spstrs [4].Split(',');
if (sps.Length == 1)
{
v = new Variant(int.Parse(spstrs [1]), spstrs [3], spstrs [4]);
}
else if (sps.Length == 2)
{
v = new Variant(int.Parse(spstrs [1]), spstrs [3], sps [0], sps [1]);
}
else
{
v = new Variant(int.Parse(spstrs [1]), spstrs [3], sps [0], sps [1], sps [2]);
}
if (genotyped)
{
int genLen = spstrs.Length;
int stInd = 9;
for (int i = stInd; i < genLen; i++)
{
bool parsed = true;
string[] sps2 = spstrs [i].Split(':');
string[] sps3 = sps2 [0].Split(seps);
int ma = 0;
int al = 0;
if (!int.TryParse(sps3 [0], out ma))
{
parsed = false;
}
if (sps3.Length > 1)
{
if (!int.TryParse(sps3 [1], out al))
{
parsed = false;
}
}
if (parsed)
{
SampleVariant s = new SampleVariant(ma, al, samps [i - stInd]);
v.AddSampleVars(s);
}
}
}
AllVarPairs.Add(new VarScaffPair(spstrs [0], v));
count++;
if (count % 100000 == 0)
{
int tot = count / 100000;
MainData.UpdateLog("Read " + tot + "00K variants from " + MainData.MainWindow.MaxLenString(fName, 20), true);
}
}
}
}
}
