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;
}
