public static Tuple <Dictionary <int, List <LoadTestResult> >, List <Domain.Models.Alleles.CandidateAllele> > LoadReads
(List <BamAlignment> reads, PiscesApplicationOptions options, ChrReference chrRef,
bool expectedvariants, string expectedLoading, string expectedDirectionString)
{
RegionStateManager manager = new RegionStateManager(expectStitchedReads: true);
var variantFinder = new CandidateVariantFinder(options.BamFilterParameters.MinimumBaseCallQuality, options.MaxSizeMNV, options.MaxGapBetweenMNV, options.CallMNVs);
var candidateVariants = new List <Domain.Models.Alleles.CandidateAllele>();
try
{
foreach (var b in reads)
{
if (b == null)
{
continue;
}
var r = new Read(chrRef.Name, b);
// find candidate variants
candidateVariants = variantFinder.FindCandidates(r, chrRef.Sequence, chrRef.Name).ToList();
// track in state manager
manager.AddCandidates(candidateVariants);
manager.AddAlleleCounts(r);
}
Dictionary <int, List <LoadTestResult> > countResults = GetCountsFromManager(manager);
var loadingResults = Tuple.Create(countResults, candidateVariants);
return(loadingResults);
}
catch
{
return(null);
}
}
private ISomaticVariantCaller CreateMockVariantCaller(VcfFileWriter vcfWriter, ApplicationOptions options, ChrReference chrRef, MockAlignmentExtractor mae, IStrandBiasFileWriter biasFileWriter = null, string intervalFilePath = null)
{
var config = new AlignmentSourceConfig
{
MinimumMapQuality = options.MinimumMapQuality,
OnlyUseProperPairs = options.OnlyUseProperPairs,
};
IAlignmentStitcher stitcher = null;
if (options.StitchReads)
{
if (options.UseXCStitcher)
{
stitcher = new XCStitcher(options.MinimumBaseCallQuality);
}
else
{
stitcher = new BasicStitcher(options.MinimumBaseCallQuality);
}
}
var mateFinder = options.StitchReads ? new AlignmentMateFinder(MAX_FRAGMENT_SIZE) : null;
var RegionPadder = new RegionPadder(chrRef, null);
var alignmentSource = new AlignmentSource(mae, mateFinder, stitcher, config);
var variantFinder = new CandidateVariantFinder(options.MinimumBaseCallQuality, options.MaxSizeMNV, options.MaxGapBetweenMNV, options.CallMNVs);
var alleleCaller = new AlleleCaller(new VariantCallerConfig
{
IncludeReferenceCalls = options.OutputgVCFFiles,
MinVariantQscore = options.MinimumVariantQScore,
MaxVariantQscore = options.MaximumVariantQScore,
VariantQscoreFilterThreshold = options.FilteredVariantQScore > options.MinimumVariantQScore ? options.FilteredVariantQScore : (int?)null,
MinCoverage = options.MinimumCoverage,
MinFrequency = options.MinimumFrequency,
EstimatedBaseCallQuality = options.AppliedNoiseLevel == -1 ? options.MinimumBaseCallQuality : options.AppliedNoiseLevel,
StrandBiasModel = options.StrandBiasModel,
StrandBiasFilterThreshold = options.StrandBiasAcceptanceCriteria,
FilterSingleStrandVariants = options.FilterOutVariantsPresentOnlyOneStrand,
GenotypeModel = options.GTModel
});
var stateManager = new RegionStateManager();
return(new SomaticVariantCaller(
alignmentSource,
variantFinder,
alleleCaller,
vcfWriter,
stateManager,
chrRef,
RegionPadder,
biasFileWriter));
}
public static ISomaticVariantCaller CreateMockVariantCaller(VcfFileWriter vcfWriter, ApplicationOptions options, ChrReference chrRef, MockAlignmentExtractor mockAlignmentExtractor, IStrandBiasFileWriter biasFileWriter = null, string intervalFilePath = null)
{
var config = new AlignmentSourceConfig
{
MinimumMapQuality = options.MinimumMapQuality,
OnlyUseProperPairs = options.OnlyUseProperPairs,
};
//var mateFinder = options.StitchReads ? new AlignmentMateFinder() : null;
AlignmentMateFinder mateFinder = null;
var alignmentSource = new AlignmentSource(mockAlignmentExtractor, mateFinder, config);
var variantFinder = new CandidateVariantFinder(options.MinimumBaseCallQuality, options.MaxSizeMNV, options.MaxGapBetweenMNV, options.CallMNVs);
var coverageCalculator = new CoverageCalculator();
var alleleCaller = new AlleleCaller(new VariantCallerConfig
{
IncludeReferenceCalls = options.OutputgVCFFiles,
MinVariantQscore = options.MinimumVariantQScore,
MaxVariantQscore = options.MaximumVariantQScore,
VariantQscoreFilterThreshold = options.FilteredVariantQScore > options.MinimumVariantQScore ? options.FilteredVariantQScore : (int?)null,
MinCoverage = options.MinimumDepth,
MinFrequency = options.MinimumFrequency,
EstimatedBaseCallQuality = options.AppliedNoiseLevel == -1 ? options.MinimumBaseCallQuality : options.AppliedNoiseLevel,
StrandBiasModel = options.StrandBiasModel,
StrandBiasFilterThreshold = options.StrandBiasAcceptanceCriteria,
FilterSingleStrandVariants = options.FilterOutVariantsPresentOnlyOneStrand,
ChrReference = chrRef
},
coverageCalculator: coverageCalculator,
variantCollapser: options.Collapse ? new VariantCollapser(null, coverageCalculator) : null);
var stateManager = new RegionStateManager(
expectStitchedReads: mockAlignmentExtractor.SourceIsStitched,
trackOpenEnded: options.Collapse, trackReadSummaries: options.CoverageMethod == CoverageMethod.Approximate);
//statmanager is an allele source
Assert.Equal(0, stateManager.GetAlleleCount(1, AlleleType.A, DirectionType.Forward));
return(new SomaticVariantCaller(
alignmentSource,
variantFinder,
alleleCaller,
vcfWriter,
stateManager,
chrRef,
null,
biasFileWriter));
}
public void AddAlleleCounts(Read alignment)
{
if (!_readLength.HasValue)
{
_readLength = alignment.ReadLength;
}
var lastPosition = alignment.Position - 1;
var cigarData = alignment.CigarData;
var deletionLength = 0;
var lengthBeforeDeletion = alignment.ReadLength;
var endsInDeletion = cigarData.HasOperationAtOpIndex(0, 'D', true);
var endsInDeletionBeforeSoftclip = cigarData.HasOperationAtOpIndex(1, 'D', true) && cigarData.HasOperationAtOpIndex(0, 'S', true);
if (endsInDeletion || endsInDeletionBeforeSoftclip)
{
deletionLength = (int)(endsInDeletionBeforeSoftclip ? cigarData[cigarData.Count - 2].Length :
cigarData[cigarData.Count - 1].Length);
lengthBeforeDeletion = (int)(endsInDeletionBeforeSoftclip ? alignment.ReadLength - cigarData[cigarData.Count - 1].Length : alignment.ReadLength);
}
var positionMapLength = alignment.PositionMap.Length;
var alignmentEndPosition = alignment.EndPosition;
var alignmentStartPosition = alignment.Position;
for (var positionMapIndex = 0; positionMapIndex < positionMapLength; positionMapIndex++)
{
DirectionType directionType = alignment.SequencedBaseDirectionMap[positionMapIndex];
if ((endsInDeletionBeforeSoftclip) && positionMapIndex == lengthBeforeDeletion)
{
if (CandidateVariantFinder.CheckDeletionQuality(alignment, positionMapIndex, _minBasecallQuality))
{
for (var j = 1; j < deletionLength + 1; j++) // add any terminal deletion counts
{
var anchorIndex = NumAnchorIndexes - 1; // Last index
AddAlleleCount(j + lastPosition, AlleleType.Deletion, directionType, anchorIndex);
AddCollapsedReadCount(j + lastPosition, alignment, directionType);
}
}
}
var position = alignment.PositionMap.GetPositionAtIndex(positionMapIndex);
if (position == -1)
{
continue; // not mapped to reference
}
var anchorType = GetAnchorType(alignmentEndPosition, position, alignmentStartPosition);
//if the deletion is of decent quality, add it to the counts matix
if (CandidateVariantFinder.CheckDeletionQuality(alignment, positionMapIndex, _minBasecallQuality))
{
for (var j = lastPosition + 1; j < position; j++) // add any deletion counts
{
AddAlleleCount(j, AlleleType.Deletion, directionType, anchorType);
AddCollapsedReadCount(j, alignment, directionType);
}
}
var alleleType = AlleleHelper.GetAlleleType(alignment.Sequence[positionMapIndex]);
if (alignment.Qualities[positionMapIndex] < _minBasecallQuality)
{
alleleType = AlleleType.N; // record this event as a no call
}
AddAlleleCount(position, alleleType, directionType, anchorType);
if (alleleType != AlleleType.N)
{
AddCollapsedReadCount(position, alignment, directionType);
AddAmpliconCount(_trackAmpliconCounts, position, alignment.GetAmpliconNameIfExists());
}
AddAlleleBaseQuality(position, alleleType, directionType, Math.Pow(10, -1 * (int)alignment.Qualities[positionMapIndex] / 10f), anchorType);
lastPosition = position;
}
if (endsInDeletion)
{
if (CandidateVariantFinder.CheckDeletionQuality(alignment, alignment.SequencedBaseDirectionMap.Length - 1, _minBasecallQuality))
{
for (var j = 1; j < deletionLength + 1; j++) // add any terminal deletion counts
{
DirectionType directionType =
alignment.SequencedBaseDirectionMap[alignment.SequencedBaseDirectionMap.Length - 1];
var anchorIndex = NumAnchorIndexes - 1; // Last index
AddAlleleCount(j + lastPosition, AlleleType.Deletion, directionType, anchorIndex); // ends in deletion -> within 1
AddCollapsedReadCount(j + lastPosition, alignment, directionType);
}
}
}
// add coverage summary
if (_trackReadSummaries)
{
var coverageSummary = alignment.GetCoverageSummary();
var block = GetBlock(coverageSummary.ClipAdjustedEndPosition);
// store by end position so we can always be forward looking
block.AddReadSummary(coverageSummary.ClipAdjustedEndPosition, coverageSummary);
}
}
public DirectionType GetSupportDirection(CandidateAllele variant, Read read)
{
return(CandidateVariantFinder.GetSupportDirection(variant, read, VariantStartInRead));
}
public DirectionType GetDeletionDirectionForStitchedRead(CandidateAllele variant, Read read, int deletionLength)
{
int zeroBasedVariantStartInRead = VariantStartInRead - 1;
return(CandidateVariantFinder.GetDeletionDirectionForStitchedRead(read, zeroBasedVariantStartInRead, zeroBasedVariantStartInRead + 1));
}
