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);
}
}
public AbstractPileupProcessor(PileupProcessorOptions options)
{
_options = options;
}
public MpileupResultCountFormat(PileupProcessorOptions options, bool outputNotCovered)
{
this.options = options;
this.outputNotCovered = outputNotCovered;
}
public PileupProcessorSingleThread(PileupProcessorOptions options)
: base(options)
{ }
public PileupProcessorParallelChromosome(PileupProcessorOptions options)
: base(options)
{
}
public MpileupResultProcessor(PileupProcessorOptions options)
: base(options)
{
_options = options;
}
public PileupProcessorParallelChromosome(PileupProcessorOptions options)
: base(options)
{ }
public PileupProcessorSingleThread(PileupProcessorOptions options)
: base(options)
{
}
public AbstractPileupProcessor(PileupProcessorOptions options)
{
_options = options;
}
public MpileupResultProcessor(PileupProcessorOptions options)
: base(options)
{
_options = options;
}
