public VcfWriterConfig(VariantCallingParameters callerOptions,
VcfWritingParameters outputOptions, BamFilterParameters bamFilterOptions, SampleAggregationParameters sampleAggregationParameters,
bool debugMode, bool outputBiasFiles, bool hasForcedGT = false)
{
DepthFilterThreshold = outputOptions.OutputGvcfFile ? callerOptions.MinimumCoverage : (callerOptions.LowDepthFilter > callerOptions.MinimumCoverage) ? callerOptions.LowDepthFilter : (int?)null;
IndelRepeatFilterThreshold = callerOptions.IndelRepeatFilter > 0 ? callerOptions.IndelRepeatFilter : (int?)null;
VariantQualityFilterThreshold = callerOptions.MinimumVariantQScoreFilter;
GenotypeQualityFilterThreshold = callerOptions.LowGenotypeQualityFilter.HasValue && callerOptions.MinimumVariantQScoreFilter > callerOptions.MinimumVariantQScore ? callerOptions.LowGenotypeQualityFilter : null;
StrandBiasFilterThreshold = callerOptions.StrandBiasAcceptanceCriteria < 1 ? callerOptions.StrandBiasAcceptanceCriteria : (float?)null;
AmpliconBiasFilterThreshold = callerOptions.AmpliconBiasFilterThreshold > 0 ? callerOptions.AmpliconBiasFilterThreshold : (float?)null;
FrequencyFilterThreshold = GetMinFreqFilterForVcfHeader(callerOptions);
MinFrequencyThreshold = callerOptions.MinimumFrequency;
ShouldOutputNoCallFraction = outputOptions.ReportNoCalls;
ShouldOutputStrandBiasAndNoiseLevel = ShouldOutputNoiseLevelAndStrandBias(debugMode, outputBiasFiles, callerOptions.StrandBiasAcceptanceCriteria);
ShouldFilterOnlyOneStrandCoverage = callerOptions.FilterOutVariantsPresentOnlyOneStrand;
EstimatedBaseCallQuality = callerOptions.NoiseLevelUsedForQScoring;
ShouldOutputRcCounts = outputOptions.ReportRcCounts;
ShouldOutputTsCounts = outputOptions.ReportTsCounts;
AllowMultipleVcfLinesPerLoci = outputOptions.AllowMultipleVcfLinesPerLoci;
PloidyModel = callerOptions.PloidyModel;
RMxNFilterMaxLengthRepeat = callerOptions.RMxNFilterMaxLengthRepeat;
RMxNFilterMinRepetitions = callerOptions.RMxNFilterMinRepetitions;
RMxNFilterFrequencyLimit = callerOptions.RMxNFilterFrequencyLimit;
NoiseModel = callerOptions.NoiseModel;
ShouldReportGp = outputOptions.ReportGp;
NoCallFilterThreshold = callerOptions.NoCallFilterThreshold;
ShouldOutputSuspiciousCoverageFraction = outputOptions.ReportSuspiciousCoverageFraction;
if (sampleAggregationParameters != null)
{
ShouldOutputProbeBias = true;
ProbePoolBiasFilterThreshold = sampleAggregationParameters.ProbePoolBiasThreshold;
}
HasForcedGt = hasForcedGT;
}
//if I was not in a hurry, we could refactor this into the Config class and let it be re-used by Scylla and VQR...
private static VcfWriterConfig GetWriterConfigToMatchInputVcf(string vcfIn)
{
List <string> vcfHeaderLines;
using (var reader = new VcfReader(vcfIn))
{
vcfHeaderLines = reader.HeaderLines;
}
PiscesOptionsParser piscesOptionsParser = VcfConsumerAppParsingUtils.GetPiscesOptionsFromVcfHeader(vcfHeaderLines);
if (piscesOptionsParser.ParsingFailed)
{
Logger.WriteToLog("Unable to parse the original Pisces commandline");
throw new ArgumentException("Unable to parse the input vcf header: " + vcfIn);
}
VariantCallingParameters variantCallingParams = piscesOptionsParser.PiscesOptions.VariantCallingParameters;
VcfWritingParameters vcfWritingParams = piscesOptionsParser.PiscesOptions.VcfWritingParameters;
BamFilterParameters bamFilterParams = piscesOptionsParser.PiscesOptions.BamFilterParameters;
var config = new VcfWriterConfig(variantCallingParams, vcfWritingParams, bamFilterParams, null, false, false);
return(config);
}
public static Dictionary <string, OptionSet> GetVcfWritingOptionsMethods(VcfWritingParameters options)
{
var vcfWriterOps = new OptionSet
{
{
"gvcf=",
OptionTypes.BOOL + " Output gVCF files, 'true' or 'false'",
value => options.OutputGvcfFile = bool.Parse(value)
},
{
"crushvcf=",
OptionTypes.BOOL + " To crush vcf output to one line per loci",
value => options.ForceCrush = bool.Parse(value)
},
{
"reportnocalls=",
OptionTypes.BOOL + " 'true' or 'false'. default, false",
value => options.ReportNoCalls = bool.Parse(value)
},
{
"reportrccounts=",
OptionTypes.BOOL + " Report collapsed read count, When BAM files contain X1 and X2 tags, output read counts for duplex-stitched, duplex-nonstitched, simplex-stitched, and simplex-nonstitched. 'true' or 'false'. default, false",
value => options.ReportRcCounts = bool.Parse(value)
},
{
"reporttscounts=",
OptionTypes.BOOL + " Report collapsed read count by different template strands, Conditional on ReportRcCounts, output read counts for duplex-stitched, duplex-nonstitched, simplex-forward-stitched, simplex-forward-nonstitched, simplex-reverse-stitched, simplex-reverse-nonstitched. 'true' or 'false'. default, false",
value => options.ReportTsCounts = bool.Parse(value)
},
{
"reportSuspiciousCoverageFraction=",
OptionTypes.BOOL + " Report fraction of total coverage (for spanning variants, this is start + end coverage, so up to double the reported coverage) that is 'suspicious' i.e. unanchored and bearing some resemblance to an insertion at that site. 'true' or 'false'. default, false",
value => options.ReportSuspiciousCoverageFraction = bool.Parse(value)
}
};
var optionDict = new Dictionary <string, OptionSet>
{
{ OptionSetNames.VcfWriting, vcfWriterOps },
};
return(optionDict);
}
public AdaptiveGtOptions()
{
// Set defaults
VariantCallingParams = new VariantCallingParameters
{
PloidyModel = Pisces.Domain.Types.PloidyModel.DiploidByAdaptiveGT,
IsMale = false
};
VcfWritingParams = new VcfWritingParameters
{
OutputGvcfFile = false,
ForceCrush = true,
ReportGp = true
};
SetDerivedValues();
}
public static void AddVcfWritingArgumentParsing(Dictionary <string, OptionSet> parsingMethods, VcfWritingParameters options)
{
var vcfWritingOptionDict = GetVcfWritingOptionsMethods(options);
foreach (var key in vcfWritingOptionDict.Keys)
{
foreach (var optSet in vcfWritingOptionDict[key])
{
if (!parsingMethods.ContainsKey(key))
{
parsingMethods.Add(key, new OptionSet());
}
parsingMethods[key].Add(optSet);
}
}
}
