protected virtual string GetReadNamesSection(int st, int ed)
{
if (Reads != null)
{
string retStr = "";
foreach (SeqRead sq in Reads)
{
NameRead nq = sq as NameRead;
if (nq == null)
{
throw new Exception("Sequences were not loaded with read names!");
}
if (HasOverLap(nq, st, ed))
{
if (retStr.Length > 1)
{
retStr += "\t" + nq.Name;
}
else
{
retStr = nq.Name;
}
}
}
return(retStr);
}
else
{
return("");
}
}
protected void LoadBAMNameFile(string fileName)
{
int count = 0;
using (StreamReader st = new StreamReader(fileName)) {
string line = "";
while ((int)'@' == st.Peek())
{
st.ReadLine();
}
while ((line = st.ReadLine()) != null)
{
string[] spstrs = line.Split('\t');
if (spstrs [2].Length > 2 && spstrs.Length >= 10)
{
int start = int.Parse(spstrs [3]);
NameRead sq = new NameRead(this, start, spstrs [9].Length + start, spstrs[0]);
AllBAMPairs.Add(new SeqScaffPair(spstrs [2], sq));
count++;
if (count % 1000000 == 0)
{
int tot = count / 1000000;
MainData.UpdateLog("Read " + tot + "M seqs from " + MainData.MainWindow.MaxLenString(fileName, 20), true);
}
}
}
}
//Parallel.ForEach(lines, x =>
// {
// ProcessLines(x);
// });
}