public override IEnumerable <string> Process()
{
options.PrintParameter(Console.Out);
Progress.SetMessage("Single thread mode ...");
var parser = options.GetPileupItemParser();
var pfile = new PileupFile(parser);
var mutationList = new ValidationFile().ReadFromFile(options.BedFile);
var map = mutationList.Items.ToDictionary(m => GenomeUtils.GetKey(m.Chr, m.Pos));
var posFile = Path.Combine(options.OutputFile + ".pos.bed");
mutationList.WriteToFile(posFile, 500);
var proc = new MpileupProcessor(options).ExecuteSamtools(options.BamFiles, "", posFile);
if (proc == null)
{
return(null);
}
pfile.Open(proc.StandardOutput);
pfile.Samtools = proc;
Progress.SetMessage("Total {0} entries in extraction list", mutationList.Items.Length);
var result = new Dictionary <ValidationItem, PileupItem>();
using (pfile)
{
try
{
string line;
string lastChrom = string.Empty;
while ((line = pfile.ReadLine()) != null)
{
try
{
var locus = parser.GetSequenceIdentifierAndPosition(line);
var locusKey = GenomeUtils.GetKey(locus.SequenceIdentifier, locus.Position);
if (!locus.SequenceIdentifier.Equals(lastChrom))
{
Progress.SetMessage("Processing chromosome " + locus.SequenceIdentifier + " ...");
lastChrom = locus.SequenceIdentifier;
}
ValidationItem vitem = null;
if (!map.TryGetValue(locusKey, out vitem))
{
continue;
}
result[vitem] = parser.GetValue(line);
}
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)
{
}
}
}
}
if (result.Count == 0)
{
throw new Exception("Nothing found. Look at the log file for error please.");
}
using (var sw = new StreamWriter(options.OutputFile))
{
sw.WriteLine("{0}\t{1}", mutationList.Header, options.GetBamNames().Merge("\t"));
var emptyevents = new string('\t', options.BamFiles.Count);
foreach (var mu in mutationList.Items)
{
sw.Write("{0}", mu.Line);
PileupItem item;
if (result.TryGetValue(mu, out item))
{
foreach (var sample in item.Samples)
{
sample.InitEventCountList(false);
if (sample.EventCountList.Count > 0)
{
sw.Write("\t{0}", (from ecl in sample.EventCountList
let v = string.Format("{0}:{1}", ecl.Event, ecl.Count)
select v).Merge(","));
}
else
{
sw.Write("\t");
}
}
}
else
{
sw.Write(emptyevents);
}
sw.WriteLine();
}
}
return(new[] { options.OutputFile });
}
public override IEnumerable<string> Process()
{
options.PrintParameter(Console.Out);
Progress.SetMessage("Single thread mode ...");
var parser = options.GetPileupItemParser();
var pfile = new PileupFile(parser);
var mutationList = new ValidationFile().ReadFromFile(options.BedFile);
var map = mutationList.Items.ToDictionary(m => GenomeUtils.GetKey(m.Chr, m.Pos));
var posFile = Path.Combine(options.OutputFile + ".pos.bed");
mutationList.WriteToFile(posFile, 500);
var proc = new MpileupProcessor(options).ExecuteSamtools(options.BamFiles, "", posFile);
if (proc == null)
{
return null;
}
pfile.Open(proc.StandardOutput);
pfile.Samtools = proc;
Progress.SetMessage("Total {0} entries in extraction list", mutationList.Items.Length);
var result = new Dictionary<ValidationItem, PileupItem>();
using (pfile)
{
try
{
string line;
string lastChrom = string.Empty;
while ((line = pfile.ReadLine()) != null)
{
try
{
var locus = parser.GetSequenceIdentifierAndPosition(line);
var locusKey = GenomeUtils.GetKey(locus.SequenceIdentifier, locus.Position);
if (!locus.SequenceIdentifier.Equals(lastChrom))
{
Progress.SetMessage("Processing chromosome " + locus.SequenceIdentifier + " ...");
lastChrom = locus.SequenceIdentifier;
}
ValidationItem vitem = null;
if (!map.TryGetValue(locusKey, out vitem))
{
continue;
}
result[vitem] = parser.GetValue(line);
}
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)
{
}
}
}
}
if (result.Count == 0)
{
throw new Exception("Nothing found. Look at the log file for error please.");
}
using (var sw = new StreamWriter(options.OutputFile))
{
sw.WriteLine("{0}\t{1}", mutationList.Header, options.GetBamNames().Merge("\t"));
var emptyevents = new string('\t', options.BamFiles.Count);
foreach (var mu in mutationList.Items)
{
sw.Write("{0}", mu.Line);
PileupItem item;
if (result.TryGetValue(mu, out item))
{
foreach (var sample in item.Samples)
{
sample.InitEventCountList(false);
if (sample.EventCountList.Count > 0)
{
sw.Write("\t{0}", (from ecl in sample.EventCountList
let v = string.Format("{0}:{1}", ecl.Event, ecl.Count)
select v).Merge(","));
}
else
{
sw.Write("\t");
}
}
}
else
{
sw.Write(emptyevents);
}
sw.WriteLine();
}
}
return new[] { options.OutputFile };
}
