public ValidationParser(PileupProcessorOptions options, MpileupResult result)
{
_options = options;
_parser = options.GetPileupItemParser(false);
_rdFilter = new PileupItemReadDepthFilter(options.MinimumReadDepth, options.MinimumBaseQuality);
_normalTest = new PileupItemNormalTest(options.MaximumPercentageOfMinorAlleleInNormal);
_tumorTest = new PileupItemTumorTest(options.MinimumReadsOfMinorAlleleInTumor, options.MinimumPercentageOfMinorAlleleInTumor);
_result = result;
}
public ValidationParser(PileupProcessorOptions options, MpileupResult result)
{
_options = options;
_parser = options.GetPileupItemParser(false);
_rdFilter = new PileupItemReadDepthFilter(options.MinimumReadDepth, options.MinimumBaseQuality);
_normalTest = new PileupItemNormalTest(options.MaximumPercentageOfMinorAlleleInNormal);
_tumorTest = new PileupItemTumorTest(options.MinimumReadsOfMinorAlleleInTumor, options.MinimumPercentageOfMinorAlleleInTumor);
_result = result;
}
public MpileupParser(PileupProcessorOptions options, MpileupResult result)
{
_options = options;
_normalTest = new PileupItemNormalTest(options.MaximumPercentageOfMinorAlleleInNormal);
_tumorTest = new PileupItemTumorTest(options.MinimumReadsOfMinorAlleleInTumor, options.MinimumPercentageOfMinorAlleleInTumor);
_parser = options.GetPileupItemParser();
_result = result;
if (File.Exists(_options.ExcludeBedFile))
{
bedMap = new BedItemFile <BedItem>().ReadFromFile(_options.ExcludeBedFile).ToGroupDictionary(m => m.Seqname);
}
}
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
{
}
}
}
