protected override void Process(BamWorkRequest workRequest, ChrReference chrReference)
{
var writerKey = GetChrOutputPath(workRequest, chrReference.Name);
var caller = _factory.CreateSomaticVariantCaller(chrReference, workRequest.BamFilePath,
_writerByChrLookup[writerKey], _biasWriterByChrLookup[writerKey], null, Genome.ChromosomesToProcess);
caller.Execute();
}
protected override void Process(BamWorkRequest workRequest, ChrReference chrReference)
{
var bamWriter = _writerLookup[workRequest];
if (!string.IsNullOrEmpty(_chrFilter) && _chrFilter != chrReference.Name)
{
// just write out that chromosome's info as is
WriteChromosomeReads(workRequest.BamFilePath, chrReference.Name, bamWriter);
}
else
{
// do realignment
var caller = _factory.CreateRealigner(chrReference, workRequest.BamFilePath,
bamWriter);
caller.Execute();
bamWriter.FlushAllBufferedRecords();
}
}
protected override void Process(BamWorkRequest workRequest, ChrReference chrReference)
{
// do nothing
}
private string GetChrOutputPath(BamWorkRequest workRequest, string chrName)
{
return(workRequest.OutputFilePath + "_" + chrName);
}