protected void LoadBAMFile(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]);
SeqRead sq = new SeqRead(this, start, spstrs [9].Length + start);
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);
// });
}
protected void ProcessLines(string line)
{
string[] spstrs = line.Split('\t');
if (spstrs [2].Length > 2)
{
int start = int.Parse(spstrs [3]);
SeqRead sq = new SeqRead(this, start, spstrs [9].Length + start);
AllBAMPairs.Add(new SeqScaffPair(spstrs [2], sq));
}
}
public bool HasOverLap(SeqRead sq)
{
if ((sq.Start >= Start && sq.Start <= End) || (sq.End <= End && sq.End >= Start) || (sq.Start <= Start && sq.End >= End))
{
return(true);
}
else
{
return(false);
}
}
public void AddRead(SeqRead _read)
{
if (Reads == null)
{
Reads = new List <SeqRead> ();
}
MainData.LoadedSeqs++;
lock (Reads) {
Reads.Add(_read);
}
}
public bool HasOverLap(SeqRead sq, int st, int ed)
{
if ((sq.Start >= st && sq.Start <= ed) || (sq.End <= ed && sq.End >= st) || (sq.Start <= st && sq.End >= ed))
{
return(true);
}
else
{
return(false);
}
}
public override void SendRead(SeqRead seq)
{
foreach (KeyValuePair <string, List <GeneElement> > kvp in Elements)
{
foreach (GeneElement ge in kvp.Value)
{
if (ge.HasOverLap(seq))
{
ge.AddRead(seq);
}
}
}
base.SendRead(seq);
}
public void SendRead(SeqRead seq)
{
foreach (KeyValuePair <string, Gene> kvp in Genes)
{
if (kvp.Value.HasOverLap(seq))
{
kvp.Value.SendRead(seq);
}
}
foreach (KeyValuePair <string, Region> kvp in Regions)
{
if (kvp.Value.HasOverLap(seq))
{
kvp.Value.SendRead(seq);
}
}
}
public virtual void SendRead(SeqRead seq)
{
AddRead(seq);
if (RegElements != null)
{
foreach (KeyValuePair <string, List <MiscElement> > kvp in RegElements)
{
foreach (MiscElement ge in kvp.Value)
{
if (ge.HasOverLap(seq))
{
ge.AddRead(seq);
}
}
}
}
}
public SeqScaffPair(string scf, SeqRead sq)
{
Scaffold = scf;
Read = sq;
}