public VariantCollapser(List <CandidateAllele> knownCollapsableVariants, ICoverageCalculator coverageCalculator = null, float freqThreshold = 0f, float freqRatioThreshold = 0f)
{
_knownVariants = knownCollapsableVariants;
_coverageCalculator = coverageCalculator ?? new CoverageCalculator();
_freqThreshold = freqThreshold;
_freqRatioThreshold = freqRatioThreshold;
}
protected virtual IVariantCollapser CreateVariantCollapser(string chrName, ICoverageCalculator coverageCalculator)
{
return(_options.Collapse ?
new VariantCollapser(_knownVariants.ContainsKey(chrName) ? _knownVariants[chrName] : null, _options.ExcludeMNVsFromCollapsing, coverageCalculator, _options.CollapseFreqThreshold,
_options.CollapseFreqRatioThreshold)
: null);
}
public AlleleCaller(VariantCallerConfig config, ChrIntervalSet intervalSet = null,
IVariantCollapser variantCollapser = null, ICoverageCalculator coverageCalculator = null)
{
_config = config;
_intervalSet = intervalSet;
_collapser = variantCollapser;
_coverageCalculator = coverageCalculator ?? new CoverageCalculator();
_genotypeCalculator = config.GenotypeCalculator;
}
public IndelTargetCaller(float frequencyCutoff, ICoverageCalculator coverageCalculator = null)
{
_frequencyCutoff = frequencyCutoff;
_coverageCalculator = coverageCalculator ?? new CoverageCalculator();
}
