public override IEnumerable<string> Process()
{
var bamList = ReadBamList();
var process = ExecuteSamtools(bamList);
if (process == null)
{
throw new Exception("Fail to execute samtools.");
}
var vcfItems = new VcfItemListFormat().ReadFromFile(_options.InputFile);
vcfItems.Header = vcfItems.Header + "\t" + bamList.ConvertAll(m => m.Value).Merge("\t");
var vcfMap = vcfItems.Items.ToDictionary(m => GetKey(m.Seqname, m.Start));
var parser = _options.GetPileupItemParser();
var pfile = new PileupFile(parser);
pfile.Open(process.StandardOutput);
try
{
using (pfile)
{
string line;
while ((line = pfile.ReadLine()) != null)
{
var item = parser.GetSequenceIdentifierAndPosition(line);
var key = GetKey(item.SequenceIdentifier, item.Position);
VcfItem vcf;
if (!vcfMap.TryGetValue(key, out vcf))
{
continue;
}
item = parser.GetValue(line);
foreach (var sample in item.Samples)
{
var refCount = sample.Count(m => m.Event.Equals(vcf.RefAllele));
var altCount = sample.Count(m => m.Event.Equals(vcf.AltAllele));
vcf.Line = vcf.Line + string.Format("\t{0}:{1}", refCount, altCount);
}
}
}
}
finally
{
try
{
if (process != null) process.Kill();
}
catch
{ }
}
new VcfItemListFormat().WriteToFile(_options.OutputFile, vcfItems);
return new string[] { _options.OutputFile };
}
public override IEnumerable <string> Process()
{
var bamList = ReadBamList();
var process = ExecuteSamtools(bamList);
if (process == null)
{
throw new Exception("Fail to execute samtools.");
}
var vcfItems = new VcfItemListFormat().ReadFromFile(_options.InputFile);
vcfItems.Header = vcfItems.Header + "\t" + bamList.ConvertAll(m => m.Value).Merge("\t");
var vcfMap = vcfItems.Items.ToDictionary(m => GetKey(m.Seqname, m.Start));
var parser = _options.GetPileupItemParser();
var pfile = new PileupFile(parser);
pfile.Open(process.StandardOutput);
try
{
using (pfile)
{
string line;
while ((line = pfile.ReadLine()) != null)
{
var item = parser.GetSequenceIdentifierAndPosition(line);
var key = GetKey(item.SequenceIdentifier, item.Position);
VcfItem vcf;
if (!vcfMap.TryGetValue(key, out vcf))
{
continue;
}
item = parser.GetValue(line);
foreach (var sample in item.Samples)
{
var refCount = sample.Count(m => m.Event.Equals(vcf.RefAllele));
var altCount = sample.Count(m => m.Event.Equals(vcf.AltAllele));
vcf.Line = vcf.Line + string.Format("\t{0}:{1}", refCount, altCount);
}
}
}
}
finally
{
try
{
if (process != null)
{
process.Kill();
}
}
catch
{ }
}
new VcfItemListFormat().WriteToFile(_options.OutputFile, vcfItems);
return(new string[] { _options.OutputFile });
}