public VQRVcfWriter(string outputFilePath, VcfWriterConfig config, VcfWriterInputContext context, List <string> originalHeader, string phasingCommandLine, int bufferLimit = 2000) : base(outputFilePath, config, context, bufferLimit)
{
_originalHeader = originalHeader;
_originalFilterLines = VcfVariantUtilities.GetFilterStringsByType(originalHeader);
_formatter = new VcfFormatter(config);
AllowMultipleVcfLinesPerLoci = config.AllowMultipleVcfLinesPerLoci;
_vqrCommandLine = phasingCommandLine;
}
public PhasedVcfWriter(string outputFilePath, VcfWriterConfig config, VcfWriterInputContext context, List <string> originalHeader, string phasingCommandLine, int bufferLimit = 2000) : base(outputFilePath, config, context, bufferLimit)
{
_originalHeader = originalHeader;
_originalFilterLines = Extensions.GetFilterStringsByType(originalHeader);
if (_originalFilterLines.ContainsKey(FilterType.RMxN))
{
config = ExtractRMxNThresholds(config);
}
if (_originalFilterLines.ContainsKey(FilterType.IndelRepeatLength))
{
config = ExtractR8Threshold(config);
}
//-ReportNoCalls True
_formatter = new VcfFormatter(config);
AllowMultipleVcfLinesPerLoci = config.AllowMultipleVcfLinesPerLoci;
_phasingCommandLine = phasingCommandLine;
}
public static void UpdateVariant(int maxQscore, int filterQScore, Dictionary <MutationCategory, int> qCalibratedRates, VcfVariant originalVar, MutationCategory cat)
{
int depth;
int callCount;
bool canUpdateQ = HaveInfoToUpdateQ(originalVar, out depth, out callCount);
if (canUpdateQ)
{
int newQ = VariantQualityCalculator.AssignPoissonQScore(
callCount, depth, qCalibratedRates[cat], maxQscore);
InsertNewQ(qCalibratedRates, originalVar, cat, newQ);
//update filters if needed
if (newQ < filterQScore)
{
var vcfConfig = new VcfWriterConfig();
vcfConfig.VariantQualityFilterThreshold = filterQScore;
var formatter = new VcfFormatter(vcfConfig);
string lowQString = formatter.MapFilter(FilterType.LowVariantQscore);
string passString = VcfFormatter.PassFilter;
if (originalVar.Filters.Contains(lowQString))
{
return;
}
if (originalVar.Filters == passString)
{
originalVar.Filters = lowQString;
}
else
{
originalVar.Filters += VcfFormatter.FilterSeparator + lowQString;
}
}
}
}
public void Initialize()
{
VcfWriterConfig config = new VcfWriterConfig
{
DepthFilterThreshold = 500,
VariantQualityFilterThreshold = 20,
StrandBiasFilterThreshold = 0.5f,
FrequencyFilterThreshold = 0.007f,
MinFrequencyThreshold = 0.007f,
ShouldOutputNoCallFraction = true,
ShouldOutputStrandBiasAndNoiseLevel = true,
ShouldFilterOnlyOneStrandCoverage = true,
EstimatedBaseCallQuality = _estimatedBaseCallQuality,
//AllowMultipleVcfLinesPerLoci = true
};
_formatter = new VcfFormatter(config);
_v1 = TestHelper.CreatePassingVariant(false);
_v2 = TestHelper.CreatePassingVariant(false);
_v3 = TestHelper.CreatePassingVariant(false);
}
public void FilterMerge()
{
Initialize();
_v1.Filters = new List <FilterType> {
FilterType.LowDepth, FilterType.LowVariantQscore
};
_v2.Filters = new List <FilterType> {
FilterType.MultiAllelicSite
};
_v3.Filters = new List <FilterType> {
FilterType.LowDepth
};
var mergedFilters = VcfFormatter.MergeFilters(new List <CalledAllele> {
_v1, _v2, _v3
});
var expectedFilters = new List <FilterType> {
FilterType.LowDepth, FilterType.LowVariantQscore, FilterType.MultiAllelicSite
};
Assert.Equal(expectedFilters, mergedFilters);
}
public void GenoytyeOthersRepresentedCorrectly()
{
var vcfFormatter = new VcfFormatter();
Assert.Equal("2/2", vcfFormatter.MapGenotype(Genotype.Others));
}
public static List <FilterType> CombineFilters(CalledAllele VariantA, CalledAllele VariantB)
{
return(VcfFormatter.MergeFilters(new List <CalledAllele> {
VariantA, VariantB
}).ToList());
}
