public IFqFile ParseStandardFormat()
{
sw = new Stopwatch();
sw.Start();
int seqIndex = 0;
BufferedStream bs;
StreamReader reader;
try
{
bs = new BufferedStream(fileReader);
reader = new StreamReader(bs, System.Text.Encoding.ASCII);
if (IsFastqFile == true)
{
FastqController.getInstance().GetFqFileMap().FastqFileFormatType = FILE_FORMAT_TYPE;
FqNucleotideRead fqRead = new FqNucleotideRead(' ', ' ');
//fastqFile = FqFileSpecifier.getInstance().getFqFile(Preferences.getInstance().getMultiCoreProcessing());
fastqFile.setFastqFileName(fileName);
long nLine = -1L;
while ((fastqHeader = reader.ReadLine()) != null)
{
nLine++;
if (nLine % 4 != 0)
{
continue;
}
String seqlist = reader.ReadLine();
String infoHeader = reader.ReadLine();
String qscore = reader.ReadLine();
fqSeq = new FqSequence(seqIndex, fastqHeader, infoHeader, seqlist.Length);
seqIndex++;
for (int i = 0; i < (seqlist.Length); i++)
{
fqRead.resetFqNucleotideRead(seqlist[i], qscore[i]);
int hashcode = fqRead.getProxyCode();
fqSeq.addNucleotideRead(hashcode);
}
fastqFile.addFastqSequence(fqSeq);
nLine += 3;
}
sw.Stop();
Console.WriteLine("Time to Parse File: " + sw.Elapsed + "s");
}
}
finally
{
fileReader.Close();
}
return(fastqFile);
}
