public VeadGroupSource(IAlignmentExtractor alignmentExtractor, BamFilterParameters options, bool debugMode, string logFolder)
{
_alignmentExtractor = alignmentExtractor;
_options = options;
_debugMode = debugMode;
_debugLogRoot = logFolder;
}
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 VeadGroupSource(IAlignmentExtractor alignmentExtractor, BamFilterParameters options, bool debugMode, string logFolder)
{
_alignmentExtractor = alignmentExtractor;
_options = options;
_debugMode = debugMode;
_debugLogRoot = logFolder;
_readfilter = new NeighborhoodReadFilter(_options);
}
public static Dictionary <string, OptionSet> GetBamFilterParsingMethods(BamFilterParameters options)
{
var bamFilterOps = new OptionSet
{
{
"minbq|minbasecallquality=",
OptionTypes.INT + " MinimumBaseCallQuality to use a base of the read",
value => options.MinimumBaseCallQuality = int.Parse(value)
},
{
"minmq|minmapquality=",
OptionTypes.INT + " MinimumMapQuality required to use a read",
value => options.MinimumMapQuality = int.Parse(value)
},
{
"filterduplicates|duplicatereadfilter=",
OptionTypes.BOOL + " To filter reads marked as duplicates",
value => options.RemoveDuplicates = bool.Parse(value)
},
{
"pp|onlyuseproperpairs=",
OptionTypes.BOOL + " Only use proper pairs, 'true' or 'false",
value => options.OnlyUseProperPairs = bool.Parse(value)
}
};
var optionDict = new Dictionary <string, OptionSet>
{
{ OptionSetNames.BamFiltering, bamFilterOps },
};
return(optionDict);
}
public VeadFinder(BamFilterParameters bamFilterParams)
{
_bamFilterParams = bamFilterParams;
}
public static void AddBamFilterArgumentParsing(Dictionary <string, OptionSet> parsingMethods, BamFilterParameters options)
{
var bamfilterOptionDict = GetBamFilterParsingMethods(options);
foreach (var key in bamfilterOptionDict.Keys)
{
foreach (var optSet in bamfilterOptionDict[key])
{
if (!parsingMethods.ContainsKey(key))
{
parsingMethods.Add(key, new OptionSet());
}
parsingMethods[key].Add(optSet);
}
}
}
public VariantCaller(VariantCallingParameters callerParams, BamFilterParameters bamParams)
{
_bamParams = bamParams;
_callerParams = callerParams;
}
public NeighborhoodReadFilter(BamFilterParameters options)
{
_options = options;
}