public override void Write(IEnumerable <CalledAllele> calledAlleles, IRegionMapper mapper = null)
{
var comparer = new AlleleCompareByLoci();
var sortedVariants = calledAlleles.OrderBy(a => a, comparer).ThenBy(a => a.ReferenceAllele).ThenBy(a => a.AlternateAllele);
base.Write(sortedVariants);
}
public override void Write(IEnumerable <CalledAllele> calledAlleles, IRegionMapper mapper = null)
{
var comparer = new AlleleCompareByLociAndAllele();
var sortedVariants = calledAlleles.OrderBy(a => a, comparer);
base.Write(sortedVariants, mapper);
}
public override void Write(IEnumerable <CalledAllele> calledAlleles, IRegionMapper mapper = null)
{
//this is a cheap hack, to be removed as soon as I merge another change.
var comparer = new AlleleComparer();
var sortedVariants = calledAlleles.OrderBy(a => a, comparer).ThenBy(a => a.Reference).ThenBy(a => a.Alternate);
base.Write(sortedVariants);
}
public virtual void Write(string msg, IRegionMapper mapper = null)
{
if (Writer == null)
{
throw new IOException("Stream already closed");
}
FlushBuffer(mapper);
Writer.WriteLine(msg);
FlushBuffer(mapper);
}
public SomaticVariantCaller(IAlignmentSource alignmentSource, ICandidateVariantFinder variantFinder, IAlleleCaller alleleCaller,
IVcfWriter <CalledAllele> vcfWriter, IStateManager stateManager, ChrReference chrReference, IRegionMapper regionMapper,
IStrandBiasFileWriter biasFileWriter, ChrIntervalSet intervalSet = null)
{
_alignmentSource = alignmentSource;
_variantFinder = variantFinder;
_alleleCaller = alleleCaller;
_vcfWriter = vcfWriter;
_stateManager = stateManager;
_chrReference = chrReference;
_regionMapper = regionMapper;
_biasFileWriter = biasFileWriter;
_intervalSet = intervalSet;
}
public virtual void Write(IEnumerable <T> BaseCalledAlleles, IRegionMapper mapper = null)
{
if (Writer == null)
{
throw new IOException("Stream already closed");
}
BufferList.AddRange(BaseCalledAlleles);
if (BufferList.Count >= BufferLimit)
{
FlushBuffer(mapper);
}
}
public SomaticVariantCaller(IAlignmentSource alignmentSource, ICandidateVariantFinder variantFinder, IAlleleCaller alleleCaller,
IVcfWriter <CalledAllele> vcfWriter, IStateManager stateManager, ChrReference chrReference, IRegionMapper regionMapper,
IStrandBiasFileWriter biasFileWriter, ChrIntervalSet intervalSet = null, HashSet <Tuple <string, int, string, string> > forcedGTAlleles = null)
{
_alignmentSource = alignmentSource;
_variantFinder = variantFinder;
_alleleCaller = alleleCaller;
_vcfWriter = vcfWriter;
_stateManager = stateManager;
_chrReference = chrReference;
_regionMapper = regionMapper;
_biasFileWriter = biasFileWriter;
_intervalSet = intervalSet;
_forcedGtAlleles = forcedGTAlleles;
_unProcessedForcedAllelesByPos = CreateForcedAllelePos(_forcedGtAlleles);
}
private void PadIfNeeded(StreamWriter writer, int position, IRegionMapper mapper)
{
// Pad any no calls that are in intervals between this allele and the last allele written.
// We should also enter this block on the first allele encountered (to pick up any intervals before coverage starts).
if (mapper != null &&
(_lastVariantPositionWritten == 0 || _lastVariantPositionWritten + 1 < position))
{
CalledAllele nocall;
var alleleList = new List <CalledAllele>(); // reuse the list
while ((nocall = mapper.GetNextEmptyCall(_lastVariantPositionWritten + 1, position - 1)) !=
null)
{
WriteNoCall(nocall, alleleList);
}
}
}
public virtual void Write(List <string> msgs, IRegionMapper mapper = null)
{
if (Writer == null)
{
throw new IOException("Stream already closed");
}
FlushBuffer(mapper);
foreach (var msg in msgs)
{
Writer.WriteLine(msg);
}
FlushBuffer(mapper);
}
public void FlushBuffer(IRegionMapper mapper = null)
{
if (AllowMultipleVcfLinesPerLoci)
{
//we dont crush
foreach (var variant in BufferList)
{
WriteSingleAllele(Writer, variant, mapper);
}
}
else //the VCF spec that makes parsers cry
{
GroupsAllelesThenWrite(Writer, BufferList, mapper);
}
BufferList.Clear();
}
public override void WriteRemaining(IRegionMapper mapper = null)
{
// Pad any nocalls in intervals after coverage ends.
// Unlike WriteSingleAllele which is called internally during buffer flushing this is called directly
// by external components, like the somatic variant caller.
if (mapper != null)
{
FlushBuffer(mapper); // flush real alleles that are hanging out
CalledAllele nocall;
var alleleList = new List <CalledAllele>(); // reuse list
while ((nocall = mapper.GetNextEmptyCall(_lastVariantPositionWritten + 1, null)) != null)
{
WriteNoCall(nocall, alleleList);
}
_lastVariantPositionWritten = 0; // reset in case writer is reused for the next chromosome
}
}
protected override void WriteSingleAllele(StreamWriter writer, CalledAllele variant, IRegionMapper mapper = null)
{
// Pad intervals if necessary
PadIfNeeded(writer, variant.ReferencePosition, mapper);
WriteListOfColocatedAlleles(writer, new List <CalledAllele> {
variant
});
}
protected abstract void WriteSingleAllele(StreamWriter writer, T variant, IRegionMapper mapper = null);
public VcfFileWriter CreateVcfWriter(string outputVcfPath, VcfWriterInputContext context, IRegionMapper mapper = null)
{
return(new VcfFileWriter(outputVcfPath,
new VcfWriterConfig
{
DepthFilterThreshold = _options.OutputgVCFFiles ? _options.MinimumDepth : (_options.LowDepthFilter > _options.MinimumDepth)? _options.LowDepthFilter : (int?)null,
IndelRepeatFilterThreshold = _options.IndelRepeatFilter > 0 ? _options.IndelRepeatFilter : (int?)null,
VariantQualityFilterThreshold = _options.FilteredVariantQScore,
GenotypeQualityFilterThreshold = _options.LowGenotypeQualityFilter.HasValue && _options.LowGenotypeQualityFilter > _options.MinimumVariantQScore ? _options.LowGenotypeQualityFilter : null,
StrandBiasFilterThreshold = _options.StrandBiasAcceptanceCriteria < 1 ? _options.StrandBiasAcceptanceCriteria : (float?)null,
FrequencyFilterThreshold = (_options.FilteredVariantFrequency > _options.MinimumFrequency) ? _options.FilteredVariantFrequency : (float?)null,
MinFrequencyThreshold = _options.MinimumFrequency,
ShouldOutputNoCallFraction = _options.ReportNoCalls,
ShouldOutputStrandBiasAndNoiseLevel = _options.OutputNoiseLevelAndStrandBias(),
ShouldFilterOnlyOneStrandCoverage = _options.FilterOutVariantsPresentOnlyOneStrand,
EstimatedBaseCallQuality = GetEstimatedBaseCallQuality(),
ShouldOutputRcCounts = _options.ReportRcCounts,
AllowMultipleVcfLinesPerLoci = _options.AllowMultipleVcfLinesPerLoci,
PloidyModel = _options.PloidyModel,
RMxNFilterMaxLengthRepeat = _options.RMxNFilterMaxLengthRepeat,
RMxNFilterMinRepetitions = _options.RMxNFilterMinRepetitions,
RMxNFilterFrequencyLimit = _options.RMxNFilterFrequencyLimit,
NoiseModel = _options.NoiseModel
}, context));
}
protected abstract void GroupsAllelesThenWrite(StreamWriter writer, List <T> variants, IRegionMapper mapper = null);
protected override void GroupsAllelesThenWrite(StreamWriter writer, List <CalledAllele> variants, IRegionMapper mapper = null)
{
// variant list is already sorted properly, group as we go.
var variantsAtSamePosition = new List <CalledAllele>();
foreach (var variant in variants)
{
if (!variantsAtSamePosition.Any() ||
((variant.ReferencePosition == variantsAtSamePosition[0].ReferencePosition) && (variant.Chromosome == variantsAtSamePosition[0].Chromosome)))
{
variantsAtSamePosition.Add(variant);
}
else
{
// flush
PadIfNeeded(writer, variantsAtSamePosition[0].ReferencePosition, mapper); // Pad intervals if necessary
WriteListOfColocatedAlleles(Writer, variantsAtSamePosition);
variantsAtSamePosition.Clear();
variantsAtSamePosition.Add(variant);
}
}
// final flush
if (variantsAtSamePosition.Any())
{
PadIfNeeded(writer, variantsAtSamePosition[0].ReferencePosition, mapper); // Pad intervals if necessary
WriteListOfColocatedAlleles(Writer, variantsAtSamePosition);
}
}
public VcfFileWriter CreateVcfWriter(string outputVcfPath, VcfWriterInputContext context, IRegionMapper mapper = null)
{
return(new VcfFileWriter(outputVcfPath,
new VcfWriterConfig(_options.VariantCallingParameters, _options.VcfWritingParameters,
_options.BamFilterParameters, null, _options.DebugMode, _options.OutputBiasFiles, _options.ForcedAllelesFileNames.Count > 0), context));
}
public RegionProcessor(IDataReader dataReader, IGraphParser graphParser, IRegionMapper regionMapper)
{
this._dataReader = dataReader;
this._graphParser = graphParser;
this._regionMapper = regionMapper;
}
public virtual void WriteRemaining(IRegionMapper mapper = null)
{
// do nothing by default
}
public StorefrontCountriesContentsResolver(IStorefrontContext storefrontContext, IRegionMapper mapper)
{
this.storefrontContext = storefrontContext;
this.mapper = mapper;
}