static void OldMain(string[] args)
{
StreamWriter SW = new StreamWriter(HOME + "CountsByDate.csv");
StreamReader SR = new StreamReader("FileLocations.csv");
string[] lines = SR.ReadToEnd().Split('\n');
lines = lines.Skip(1).ToArray();
// Parallel.ForEach(lines, line =>
Console.WriteLine("Starting");
foreach (string line in lines)
{
Console.WriteLine(line);
try
{
string[] split = line.Split(',');
string fname = split[0];
string patientid = split[1];
string date = split[2];
var mtReads = MitoDataGrabber.OutputMitoReadsFromBamFile(fname);
FastAFormatter fao = new FastAFormatter(HOME + patientid + ".fa");
long count = 0;
foreach (var seq in mtReads)
{
count++;
fao.Write(seq);
}
fao.Close();
FileInfo FI = new FileInfo(fname);
string size = FI.Length.ToString();
lock (SW)
{
SW.WriteLine(String.Join(",", patientid, count.ToString(), size, date));
Console.WriteLine(patientid + " has " + count.ToString() + " reads");
}
if (args.Length > 2)
{
break;
}
}
catch (Exception thrown)
{ Console.WriteLine(thrown.Message); }
}
//);
SW.Close();
}
public void OutputMTReads()
{
if (String.IsNullOrEmpty(Filename))
{
throw new ArgumentNullException("No input file specified");
}
if (!Filename.EndsWith(BAM_FILE_SUFFIX))
{
throw new ArgumentNullException("Input file must be a .BAM file");
}
if (string.IsNullOrEmpty(OutputFile))
{
OutputFile = Filename.Remove(Filename.Length - BAM_FILE_SUFFIX.Length) + DEFAULT_EXPORT_SUFFIX;
}
IEnumerable <ISequence> mtReads;
if (CRSAlignedOnly)
{
mtReads = MitoDataGrabber.OutputMitoReadsFromBamFileAlignedToCRSOnly(Filename, pfractionToOutput);
}
else
{
mtReads = MitoDataGrabber.OutputMitoReadsFromBamFile(Filename);
}
FastAFormatter fao = new FastAFormatter(OutputFile);
long count = 0;
foreach (var seq in mtReads)
{
count++;
fao.Write(seq);
}
fao.Close();
FileInfo FI = new FileInfo(OutputFile);
Console.WriteLine("Wrote " + count.ToString() + " reads to output file.");
Console.WriteLine("Of Size: " + GetMTDataFromBAM.Program.FormatMemorySize(FI.Length));
}