protected override MpileupResult GetMpileupResult()
{
var result = new MpileupResult(string.Empty, _options.CandidatesDirectory);
Progress.SetMessage("Single thread mode ...");
var parser = _options.GetPileupItemParser();
var pfile = new PileupFile(parser);
switch (_options.From)
{
case DataSourceType.Mpileup:
pfile.Open(_options.MpileupFile);
break;
case DataSourceType.BAM:
var proc = new MpileupProcessor(_options).ExecuteSamtools(new[] { _options.NormalBam, _options.TumorBam }.ToList(), _options.GetMpileupChromosomes());
if (proc == null)
{
return(null);
}
pfile.Open(proc.StandardOutput);
pfile.Samtools = proc;
break;
case DataSourceType.Console:
pfile.Open(Console.In);
break;
}
using (pfile)
{
try
{
IMpileupParser proc = new MpileupParser(_options, result);
string line;
while ((line = pfile.ReadLine()) != null)
//while ((item = pfile.Next("1", 48901870)) != null)
{
result.TotalCount++;
try
{
var item = proc.Parse(line, true);
if (item == null)
{
continue;
}
result.Results.Add(item);
}
catch (Exception ex)
{
throw new Exception(string.Format("parsing error {0}\n{1}", ex.Message, line));
}
}
}
finally
{
if (pfile.Samtools != null)
{
try
{
pfile.Samtools.Kill();
}
// ReSharper disable once EmptyGeneralCatchClause
catch (Exception)
{
}
}
}
}
return(result);
}
public void RunTask(string chr, CancellationTokenSource cts)
{
if (cts.IsCancellationRequested)
{
throw new UserTerminatedException();
}
var result = new MpileupResult(chr, _options.CandidatesDirectory);
Progress.SetMessage("Processing chromosome {0} in thread {1}", chr, Thread.CurrentThread.ManagedThreadId);
var process = ExecuteSamtools(new[] { _options.NormalBam, _options.TumorBam }, chr);
if (process == null)
{
throw new Exception(string.Format("Fail to execute samtools for chromosome {0}.", chr));
}
var parser = _options.GetPileupItemParser();
var pfile = new PileupFile(parser);
pfile.Open(process.StandardOutput);
var proc = new MpileupParser(_options, result)
{
Progress = this.Progress
};
try
{
using (pfile)
{
string line;
while ((line = pfile.ReadLine()) != null)
{
result.TotalCount++;
if (cts.IsCancellationRequested)
{
return;
}
try
{
proc.Parse(line);
}
catch (Exception ex)
{
throw new Exception(string.Format("Parsing mpileup entry failed : {0}\n{1}", ex.Message, line), ex);
}
}
new MpileupResultCountFormat(_options, true).WriteToFile(result.CandidateSummary, result);
Progress.SetMessage("Processing chromosome {0} in thread {1} finished.", chr, Thread.CurrentThread.ManagedThreadId);
}
}
catch (Exception ex)
{
cts.Cancel();
throw new Exception(string.Format("Processing chromosome {0} failed : {1}", result.Name, ex.Message), ex);
}
finally
{
try
{
if (process != null)
{
process.Kill();
}
}
catch
{
}
}
}
