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);
}
}
protected override MpileupResult GetMpileupResult()
{
Progress.SetMessage("Multiple thread mode, parallel by chromosome ...");
_threadCount = 0;
var chromosomes = new ConcurrentQueue <string>();
foreach (var chr in _options.ChromosomeNames)
{
chromosomes.Enqueue(chr);
}
var cts = new CancellationTokenSource();
var maxThreadCount = Math.Min(_options.ThreadCount, _options.ChromosomeNames.Count);
for (int i = 0; i < maxThreadCount; i++)
{
ThreadPool.QueueUserWorkItem(ParallelChromosome, new Tuple <CancellationTokenSource, ConcurrentQueue <string> >(cts, chromosomes));
}
Thread.Sleep(5000);
while (_threadCount > 0)
{
Thread.Sleep(100);
}
Progress.SetMessage("After thread finished ...");
var result = new MpileupResult(string.Empty, _options.CandidatesDirectory);
Progress.SetMessage("Merging summary information ...");
foreach (var chr in _options.ChromosomeNames)
{
var summaryFile = new MpileupResult(chr, _options.CandidatesDirectory).CandidateSummary;
var summary = new MpileupResultCountFormat(_options, false).ReadFromFile(summaryFile);
result.MergeWith(summary);
}
Progress.SetMessage("Loading candidates ...");
foreach (var file in Directory.GetFiles(_options.CandidatesDirectory, "*.wsm"))
{
var res = MpileupFisherResultFileFormat.ParseString(Path.GetFileNameWithoutExtension(file));
res.CandidateFile = file;
result.Results.Add(res);
}
return(result);
}
public void MergeWith(MpileupResult res)
{
this.TotalCount += res.TotalCount;
this.Ignored += res.Ignored;
this.NotCovered += res.NotCovered;
this.CandidateCount += res.CandidateCount;
this.GroupFisherFailed += res.GroupFisherFailed;
this.MinimumReadDepthFailed += res.MinimumReadDepthFailed;
this.OneEventFailed += res.OneEventFailed;
this.MinorAlleleDecreasedFailed += res.MinorAlleleDecreasedFailed;
this.MinorAlleleFailedInTumorSample += res.MinorAlleleFailedInTumorSample;
this.MinorAlleleFailedInNormalSample += res.MinorAlleleFailedInNormalSample;
this.Results.AddRange(res.Results);
}
public void MergeWith(MpileupResult res)
{
this.TotalCount += res.TotalCount;
this.Ignored += res.Ignored;
this.NotCovered += res.NotCovered;
this.CandidateCount += res.CandidateCount;
this.GroupFisherFailed += res.GroupFisherFailed;
this.MinimumReadDepthFailed += res.MinimumReadDepthFailed;
this.OneEventFailed += res.OneEventFailed;
this.MinorAlleleDecreasedFailed += res.MinorAlleleDecreasedFailed;
this.MinorAlleleFailedInTumorSample += res.MinorAlleleFailedInTumorSample;
this.MinorAlleleFailedInNormalSample += res.MinorAlleleFailedInNormalSample;
this.Results.AddRange(res.Results);
}
protected override MpileupResult GetMpileupResult()
{
Progress.SetMessage("Multiple thread mode, parallel by chromosome ...");
_threadCount = 0;
var chromosomes = new ConcurrentQueue<string>();
foreach (var chr in _options.ChromosomeNames)
{
chromosomes.Enqueue(chr);
}
var cts = new CancellationTokenSource();
var maxThreadCount = Math.Min(_options.ThreadCount, _options.ChromosomeNames.Count);
for (int i = 0; i < maxThreadCount; i++)
{
ThreadPool.QueueUserWorkItem(ParallelChromosome, new Tuple<CancellationTokenSource, ConcurrentQueue<string>>(cts, chromosomes));
}
Thread.Sleep(5000);
while (_threadCount > 0)
{
Thread.Sleep(100);
}
Progress.SetMessage("After thread finished ...");
var result = new MpileupResult(string.Empty, _options.CandidatesDirectory);
Progress.SetMessage("Merging summary information ...");
foreach (var chr in _options.ChromosomeNames)
{
var summaryFile = new MpileupResult(chr, _options.CandidatesDirectory).CandidateSummary;
var summary = new MpileupResultCountFormat(_options, false).ReadFromFile(summaryFile);
result.MergeWith(summary);
}
Progress.SetMessage("Loading candidates ...");
foreach (var file in Directory.GetFiles(_options.CandidatesDirectory, "*.wsm"))
{
var res = MpileupFisherResultFileFormat.ParseString(Path.GetFileNameWithoutExtension(file));
res.CandidateFile = file;
result.Results.Add(res);
}
return result;
}
public void TestParse()
{
var result = new MpileupResult("test", "c:/temp");
var parser = new MpileupParser(new PileupProcessorOptions(), result);
var line = File.ReadAllLines(@"../../../data/glmvc_mpileup.txt").First();
var fr = parser.Parse(line, false);
Assert.IsNotNull(fr);
Assert.AreEqual(354, fr.Item.Samples[0].Count);
Assert.AreEqual(406, fr.Item.Samples[1].Count);
Assert.AreEqual("G", fr.Group.SucceedName);
Assert.AreEqual("A", fr.Group.FailedName);
Assert.AreEqual(354, fr.Group.Sample1.Succeed);
Assert.AreEqual(0, fr.Group.Sample1.Failed);
Assert.AreEqual(262, fr.Group.Sample2.Succeed);
Assert.AreEqual(143, fr.Group.Sample2.Failed);
}
public void Test()
{
var result = new MpileupResult("test", "c:/temp");
var parser = new MpileupParser(new PileupProcessorOptions(), result);
var line = new Regex("\\s+").Replace("3 102196287 G 354 .$.$.$.$.$.$...,....,...,..,.....,,...........,....,,,.......,.,,..,......,..,.,,,.....,,.....,....,,,,...,...,,.,..........,.................,..................,,...,,.,..,,,,..,,....,,,.......,,..,,............,.........,....,,,.,,...,.....,.,,.,,,,..,.....,,.,........,,,,.,...,,.......,,,..,,,,,.,,.......,,.,.,.,,...,...,,...,,,,,..,.,,,,,,,.,.,,..,,,.,,^], BfBBBBIlpIGdqIIIIIII;Ih:IIqIIFHhIECFHIIIIHI<GIHIDIdFIIIGIIIHHIEIDIIIIFGIIIIIEIIIIIII9IIIIIIF<IIGIHhIIFIGIIIIDIIImHIIIHIIIBIHFIHIHGIG?IIDIHIBIIIIDIGIoIBIIIIIIIGIIIHIIGIIHIGIIIIDIIHIHIIHIIIIIIIHHIqHIIHII@IIIHBIGIII=HIIHIIIIIHHICHIGIGIIIGIHIHEIIBHIIIGIIIIIHGHIIIIIIIHIIIHHIBIII?H=IICEIIIHIGIHBIGGD=HGEIIIIIEGBBHBEDIFIIGHII?GIIGGDFEBIIHIGAHE@D>IEIEEIIGGHEEEE 100,100,100,100,100,100,99,99,98,98,98,97,97,97,97,96,96,96,96,96,96,96,95,94,94,93,93,93,93,92,92,92,91,91,91,90,90,90,90,89,89,88,88,88,88,88,88,88,87,87,87,86,86,86,86,86,85,85,85,84,84,84,83,82,82,82,82,82,82,81,81,81,80,80,79,79,78,78,77,77,76,76,76,75,75,75,74,74,73,72,72,71,69,69,69,69,69,68,68,68,68,67,65,65,65,65,64,64,63,62,61,61,61,61,61,61,61,61,61,60,60,60,60,60,60,60,59,59,59,59,59,59,59,59,59,59,59,58,58,58,58,58,58,58,58,58,57,57,57,56,55,55,55,55,54,54,54,53,53,52,52,52,51,51,50,50,50,50,50,49,48,48,63,48,47,47,47,46,46,46,46,46,45,45,45,45,45,44,44,44,44,43,43,43,43,42,42,42,42,42,42,41,41,41,41,41,41,41,40,40,40,40,40,38,39,39,39,39,39,38,38,37,37,37,37,37,36,44,36,35,34,34,34,33,33,32,32,32,32,32,31,31,31,30,30,29,28,28,27,27,27,26,26,26,26,26,26,29,26,25,28,25,24,24,24,24,23,23,23,23,23,23,23,23,22,22,21,21,21,21,21,20,20,20,20,20,20,20,20,20,20,19,19,19,19,19,19,19,18,47,18,17,17,17,17,16,16,16,16,16,15,15,15,14,14,13,13,13,13,12,12,12,11,10,10,10,10,10,9,9,9,9,9,9,9,9,9,8,8,7,7,7,7,6,6,6,6,6,6,6,6,6,5,5,4,4,4,4,3,3,3,3,3,2,2,2,1,1 406 .$......A.AAA...,a,AAa.,a.....aAA..a..A..A.A.A.A.A.A,aA,a,.,,..,,,.AAaaa.AA.,.A.A.,a,aA..AAa...,..,..Aa....A..AAA,..A,..A.a.....A..,......,a.A....AAA..A......,...,..AA..,,,,.....Aaa..A.AA,AAaAA.,a....A.,a,.....,,A.A..A..A..AA.a,...,..,a.A..AAaA.,,aa,,....,a,aa..A.AAaA.A,.a....A...aaA..A..,....A.A..,AA..,,a..A..AAA.a,AT.,.A.a,,,..A,...AA.,a,a.A.A.a,,,,a,.AA.,,a,.A.A..,a.A.AAAAA,,a,Aa,A,..A,,aA,a,,,a.,,,^].^]. BIGBEGI8I8EH:piI>IIEIIIIIHqHDIBBHFIIEIIIIo>pji@IIIHIIIIIIIIIIFIIIIpp:IIHHHDIFIIFHGHIGI>IIGIIFIIIIIGIGIGBDIIHIIIHIEIIIHIIIFGHIIIIIIIGIGIIIGIIHIEHIIHHmGIIIIGDIFIIIIHIDFIIIIIHIGHGInCIHIIG=GEFIIDIIIIIIIIIBIHIIIIIIIGIIGIIIGIIIbHIIIIIIIHHIIIIIIIIIHIIIAEIGIIBIIIIHGHDHHIHIHGHI@IHIIHIIIIIHHIGGIIIHIIIHIIIIIHGIIIHIHIIIIIIHIIHGI@I8IIIIEIFIIIHIIIIIIGH=GFGIIIHHBHGI8IDIIGGHBIGII:IBHIIIIIIGIED7EIH?GAGIGHEE<G9IGG>EEEEEE 100,100,99,99,99,99,99,99,99,98,98,98,98,98,97,97,96,96,96,96,96,96,95,95,95,94,94,94,93,93,93,93,93,93,92,92,92,92,92,91,91,90,90,90,89,89,89,89,87,87,87,87,87,86,85,85,85,84,84,84,84,82,82,82,81,81,80,80,80,79,79,79,79,79,79,78,78,78,78,78,77,77,76,76,76,76,76,76,76,75,75,75,75,75,75,74,74,74,73,71,71,71,71,70,69,69,68,68,67,67,67,66,65,65,65,65,65,64,64,64,64,63,63,63,63,63,62,62,61,61,61,60,60,60,60,59,59,59,59,59,59,59,59,58,58,58,58,58,58,58,58,57,57,57,56,56,56,56,56,56,56,56,55,55,54,54,53,53,53,53,53,53,52,52,52,52,51,51,51,51,51,51,51,51,50,49,49,49,49,49,49,48,47,47,46,46,46,46,46,45,45,45,44,44,44,44,44,44,44,43,43,43,43,43,43,43,42,42,42,42,41,41,41,41,41,41,41,40,40,40,40,40,39,39,39,39,38,38,38,38,38,37,37,36,36,36,36,36,36,35,35,35,35,35,35,35,34,34,34,34,34,34,34,34,34,33,33,33,33,33,32,32,31,31,31,31,31,30,30,29,29,29,29,28,28,28,28,28,28,27,27,27,27,27,27,27,27,26,26,26,26,25,25,24,24,24,24,24,23,23,23,23,23,23,23,23,22,22,22,21,21,21,21,21,21,21,21,20,20,47,27,19,19,19,19,19,19,19,18,18,18,18,17,16,16,16,16,16,16,16,16,16,15,15,15,15,15,15,15,15,15,29,15,15,15,15,14,14,14,14,14,13,13,13,13,13,12,12,12,12,12,12,12,12,11,11,11,10,10,9,9,9,8,8,8,8,7,7,7,6,6,6,6,5,5,4,4,4,4,4,4,3,3,3,3,3,3,3,2,2,2,2,2,1,1,1", "\t");
//File.WriteAllText(@"../../../data/glmvc_mpileup.txt", line);
var fr = parser.Parse(line, false);
Assert.IsNotNull(fr);
Assert.AreEqual(354, fr.Item.Samples[0].Count);
Assert.AreEqual(406, fr.Item.Samples[1].Count);
Assert.AreEqual("G", fr.Group.SucceedName);
Assert.AreEqual("A", fr.Group.FailedName);
Assert.AreEqual(354, fr.Group.Sample1.Succeed);
Assert.AreEqual(0, fr.Group.Sample1.Failed);
Assert.AreEqual(262, fr.Group.Sample2.Succeed);
Assert.AreEqual(143, fr.Group.Sample2.Failed);
}
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
{
}
}
}
protected virtual void WriteSummaryFile(MpileupResult summary)
{
new MpileupResultCountFormat(_options, outputNotCoveredSite).WriteToFile(_options.SummaryFilename, summary);
}
protected override MpileupResult GetMpileupResult()
{
var result = new MpileupResult(string.Empty, _options.CandidatesDirectory);
Progress.SetMessage("Single thread mode ...");
var parser = _options.GetPileupItemParser(false);
var pfile = new PileupFile(parser);
var mutationList = GetValidationList();
result.TotalCount = mutationList.Items.Length;
var map = mutationList.Items.ToDictionary(m => GenomeUtils.GetKey(m.Chr, m.Pos));
switch (_options.From)
{
case DataSourceType.Mpileup:
pfile.Open(_options.MpileupFile);
break;
case DataSourceType.BAM:
var posFile = Path.Combine(_options.CandidatesDirectory, "pos.bed");
mutationList.WriteToFile(posFile, 500);
var proc = new MpileupProcessor(_options).ExecuteSamtools(new[] { _options.NormalBam, _options.TumorBam }, "", posFile);
if (proc == null)
{
throw new Exception("Cannot execute mpileup.");
}
pfile.Open(proc.StandardOutput);
pfile.Samtools = proc;
break;
case DataSourceType.Console:
pfile.Open(Console.In);
break;
}
Progress.SetMessage("Total {0} entries in validation list", mutationList.Items.Length);
foreach (var m in map)
{
Console.WriteLine(m.Key);
}
using (pfile)
{
try
{
IMpileupParser proc = new ValidationParser(_options, result);
string line;
while ((line = pfile.ReadLine()) != null)
{
try
{
var locus = parser.GetSequenceIdentifierAndPosition(line);
var locusKey = GenomeUtils.GetKey(locus.SequenceIdentifier, locus.Position);
//Console.WriteLine(locusKey);
ValidationItem vitem = null;
if (!map.TryGetValue(locusKey, out vitem))
{
continue;
}
//Console.WriteLine("Parsing " + line);
var parres = proc.Parse(line, true);
if (!string.IsNullOrEmpty(parres.FailedReason))
{
Progress.SetMessage("{0}\t{1}\t{2} ~ {3}\t{4}", parres.Item.SequenceIdentifier, parres.Item.Position, parres.Group.Sample1, parres.Group.Sample2, parres.FailedReason);
}
result.Results.Add(parres);
}
catch (Exception ex)
{
var error = string.Format("parsing error {0}\n{1}", ex.Message, line);
Progress.SetMessage(error);
Console.Error.WriteLine(ex.StackTrace);
throw new Exception(error);
}
}
}
finally
{
if (pfile.Samtools != null)
{
try
{
pfile.Samtools.Kill();
}
// ReSharper disable once EmptyGeneralCatchClause
catch (Exception)
{
}
}
}
}
result.NotCovered = result.TotalCount - result.Results.Count;
return(result);
}
protected override MpileupResult GetMpileupResult()
{
var result = new MpileupResult(string.Empty, _options.CandidatesDirectory);
Progress.SetMessage("Single thread mode ...");
var parser = _options.GetPileupItemParser(false);
var pfile = new PileupFile(parser);
var mutationList = GetValidationList();
result.TotalCount = mutationList.Items.Length;
var map = mutationList.Items.ToDictionary(m => GenomeUtils.GetKey(m.Chr, m.Pos));
switch (_options.From)
{
case DataSourceType.Mpileup:
pfile.Open(_options.MpileupFile);
break;
case DataSourceType.BAM:
var posFile = Path.Combine(_options.CandidatesDirectory, "pos.bed");
mutationList.WriteToFile(posFile, 500);
var proc = new MpileupProcessor(_options).ExecuteSamtools(new[] { _options.NormalBam, _options.TumorBam }, "", posFile);
if (proc == null)
{
throw new Exception("Cannot execute mpileup.");
}
pfile.Open(proc.StandardOutput);
pfile.Samtools = proc;
break;
case DataSourceType.Console:
pfile.Open(Console.In);
break;
}
Progress.SetMessage("Total {0} entries in validation list", mutationList.Items.Length);
foreach (var m in map)
{
Console.WriteLine(m.Key);
}
using (pfile)
{
try
{
IMpileupParser proc = new ValidationParser(_options, result);
string line;
while ((line = pfile.ReadLine()) != null)
{
try
{
var locus = parser.GetSequenceIdentifierAndPosition(line);
var locusKey = GenomeUtils.GetKey(locus.SequenceIdentifier, locus.Position);
//Console.WriteLine(locusKey);
ValidationItem vitem = null;
if (!map.TryGetValue(locusKey, out vitem))
{
continue;
}
//Console.WriteLine("Parsing " + line);
var parres = proc.Parse(line, true);
if (!string.IsNullOrEmpty(parres.FailedReason))
{
Progress.SetMessage("{0}\t{1}\t{2} ~ {3}\t{4}", parres.Item.SequenceIdentifier, parres.Item.Position, parres.Group.Sample1, parres.Group.Sample2, parres.FailedReason);
}
result.Results.Add(parres);
}
catch (Exception ex)
{
var error = string.Format("parsing error {0}\n{1}", ex.Message, line);
Progress.SetMessage(error);
Console.Error.WriteLine(ex.StackTrace);
throw new Exception(error);
}
}
}
finally
{
if (pfile.Samtools != null)
{
try
{
pfile.Samtools.Kill();
}
// ReSharper disable once EmptyGeneralCatchClause
catch (Exception)
{
}
}
}
}
result.NotCovered = result.TotalCount - result.Results.Count;
return result;
}
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);
}
protected virtual void WriteSummaryFile(MpileupResult summary)
{
new MpileupResultCountFormat(_options, outputNotCoveredSite).WriteToFile(_options.SummaryFilename, summary);
}
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
{
}
}
}
