private void SetupMocksandExecute(IAlignmentExtractor extractorForRealign, IRealignmentWriter writer, bool skipDups, int maxShift, string chrReference = null, ITargetCaller targetCaller = null, IStateManager stateManager = null)
{
var extractorForCandidates = new Mock <IAlignmentExtractor>();
var ranker = new Mock <IIndelRanker>();
var indel = new CandidateIndel(new CandidateAllele("chr", 10, "C", "CTATATA", AlleleCategory.Insertion));
var indelFinder = new Mock <IIndelCandidateFinder>();
if (targetCaller == null)
{
var mocktargetCaller = new Mock <ITargetCaller>();
mocktargetCaller.Setup(x => x.Call(It.IsAny <List <CandidateIndel> >(), It.IsAny <IAlleleSource>()))
.Returns(new List <CandidateIndel>()
{
indel
});
targetCaller = mocktargetCaller.Object;
}
var realigner = new ChrRealigner(new ChrReference()
{
Sequence = chrReference ?? string.Join(string.Empty, Enumerable.Repeat("ACGT", 10))
}, extractorForCandidates.Object,
extractorForRealign, indelFinder.Object, ranker.Object, targetCaller,
new RealignStateManager(), writer, skipDuplicates: skipDups, maxRealignShift: maxShift);
realigner.Execute();
}
private void WriteChromosomeReads(string inputBamFile, string chrName, IRealignmentWriter writer)
{
using (var extractor = _factory.CreateAlignmentExtractor(inputBamFile, chrName))
{
var read = new Read();
while (extractor.GetNextAlignment(read))
{
var bamAlignment = read.BamAlignment;
writer.WriteRead(ref bamAlignment, false);
}
}
writer.FlushAllBufferedRecords();
}
public ChrRealigner(ChrReference chrReference, IAlignmentExtractor extractorForCandidates,
IAlignmentExtractor extractorForRealign, IIndelCandidateFinder indelFinder, IIndelRanker indelRanker,
ITargetCaller caller, RealignStateManager stateManager, IRealignmentWriter writer,
List <CandidateAllele> knownIndels = null, int maxIndelSize = 25, bool tryThree = false,
int anchorSizeThreshold = 10, bool skipDuplicates = false, bool skipAndRemoveDuplicates = false, bool remaskSoftclips = true, bool maskPartialInsertion = false, int minimumUnanchoredInsertionLength = 0,
bool tryRealignCleanSoftclippedReads = true, bool allowRescoringOrig0 = true, int maxRealignShift = 250, AlignmentScorer alignmentScorer = null, bool debug = false)
{
_chrReference = chrReference;
_extractorForCandidates = extractorForCandidates;
_extractorForRealign = extractorForRealign;
_indelFinder = indelFinder;
_indelRanker = indelRanker;
_caller = caller;
_stateManager = stateManager;
_writer = writer;
_knownIndels = knownIndels == null ? null : knownIndels.Select(i => new CandidateIndel(i)).ToList();
_maxIndelSize = maxIndelSize;
_anchorSizeThreshold = anchorSizeThreshold;
_skipDuplicates = skipDuplicates;
_skipAndRemoveDuplicates = skipAndRemoveDuplicates;
_allowRescoringOrig0 = allowRescoringOrig0;
_maxRealignShift = maxRealignShift;
_tryRealignCleanSoftclippedReads = tryRealignCleanSoftclippedReads;
_alignmentScorer = alignmentScorer;
_debug = debug;
if (alignmentScorer != null)
{
_alignmentComparer = new ScoredAlignmentComparer(alignmentScorer);
}
else
{
_alignmentComparer = new BasicAlignmentComparer();
}
_readRealigner = new ReadRealigner(_alignmentComparer, tryThree, remaskSoftclips, maskPartialInsertion, minimumUnanchoredInsertionLength);
}
public override IChrRealigner CreateRealigner(ChrReference chrReference, string bamFilePath, IRealignmentWriter writer)
{
return(MockChrRealigner != null ? MockChrRealigner.Object : base.CreateRealigner(chrReference, bamFilePath, writer));
}
public virtual IChrRealigner CreateRealigner(ChrReference chrReference, string bamFilePath, IRealignmentWriter writer)
{
var knownIndels = _knownVariants == null || !_knownVariants.ContainsKey(chrReference.Name) ?
null : _knownVariants[chrReference.Name];
AlignmentScorer alignmentScorer = null;
if (_options.UseAlignmentScorer)
{
alignmentScorer = new AlignmentScorer()
{
AnchorLengthCoefficient = _options.AnchorLengthCoefficient,
MismatchCoefficient = _options.MismatchCoefficient,
IndelCoefficient = _options.IndelCoefficient,
NonNSoftclipCoefficient = _options.SoftclipCoefficient,
IndelLengthCoefficient = _options.IndelLengthCoefficient
};
}
return(new ChrRealigner(chrReference,
CreateAlignmentExtractor(bamFilePath, chrReference.Name),
CreateAlignmentExtractor(bamFilePath, chrReference.Name),
CreateCandidateFinder(),
CreateRanker(),
CreateCaller(),
new RealignStateManager(_options.MinimumBaseCallQuality, _options.RealignWindowSize),
writer,
knownIndels,
_options.MaxIndelSize,
_options.TryThree,
skipDuplicates: _options.SkipDuplicates,
skipAndRemoveDuplicates: _options.SkipAndRemoveDuplicates,
remaskSoftclips: _options.RemaskSoftclips, maskPartialInsertion: _options.MaskPartialInsertion, minimumUnanchoredInsertionLength: _options.MinimumUnanchoredInsertionLength, allowRescoringOrig0: _options.AllowRescoringOrigZero,
maxRealignShift: _options.MaxRealignShift,
tryRealignCleanSoftclippedReads: _options.TryRealignSoftclippedReads,
alignmentScorer: alignmentScorer,
debug: _options.Debug
));
}
