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
));
}
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 void AlignmentScorer()
{
var scorer = new AlignmentScorer();
var perfect = new AlignmentSummary();
var oneIndel = new AlignmentSummary()
{
NumIndels = 1
};
var twoIndels = new AlignmentSummary()
{
NumIndels = 2,
};
var oneMismatch = new AlignmentSummary()
{
NumMismatches = 1
};
var twoMismatches = new AlignmentSummary()
{
NumMismatches = 2,
};
var oneIndelOneMismatch = new AlignmentSummary()
{
NumIndels = 1,
NumMismatches = 1
};
var everything = new AlignmentSummary()
{
NumIndels = 1,
NumMismatches = 1,
NumIndelBases = 1,
NumNonNSoftclips = 1,
AnchorLength = 1
};
// By default, everything is 0
Assert.Equal(0, scorer.GetAlignmentScore(perfect));
Assert.Equal(0, scorer.GetAlignmentScore(oneIndel));
Assert.Equal(0, scorer.GetAlignmentScore(twoIndels));
Assert.Equal(0, scorer.GetAlignmentScore(oneIndelOneMismatch));
// Count against mismatches: -1 score for each
scorer = new AlignmentScorer()
{
MismatchCoefficient = -1
};
Assert.Equal(-1, scorer.GetAlignmentScore(oneMismatch));
Assert.Equal(-1, scorer.GetAlignmentScore(oneIndelOneMismatch));
Assert.Equal(-2, scorer.GetAlignmentScore(twoMismatches));
Assert.Equal(0, scorer.GetAlignmentScore(oneIndel));
Assert.Equal(0, scorer.GetAlignmentScore(twoIndels));
// Count against indels: -1 score for each
scorer = new AlignmentScorer()
{
IndelCoefficient = -1
};
Assert.Equal(0, scorer.GetAlignmentScore(oneMismatch));
Assert.Equal(-1, scorer.GetAlignmentScore(oneIndelOneMismatch));
Assert.Equal(0, scorer.GetAlignmentScore(twoMismatches));
Assert.Equal(-1, scorer.GetAlignmentScore(oneIndel));
Assert.Equal(-2, scorer.GetAlignmentScore(twoIndels));
// Count against indels and mismatches
scorer = new AlignmentScorer()
{
IndelCoefficient = -3, MismatchCoefficient = -1
};
Assert.Equal(-1, scorer.GetAlignmentScore(oneMismatch));
Assert.Equal(-4, scorer.GetAlignmentScore(oneIndelOneMismatch));
Assert.Equal(-2, scorer.GetAlignmentScore(twoMismatches));
Assert.Equal(-3, scorer.GetAlignmentScore(oneIndel));
Assert.Equal(-6, scorer.GetAlignmentScore(twoIndels));
// Make sure the other stuff is working
scorer = new AlignmentScorer()
{
IndelLengthCoefficient = 1
};
Assert.Equal(1, scorer.GetAlignmentScore(everything));
scorer.IndelCoefficient = 1;
Assert.Equal(2, scorer.GetAlignmentScore(everything));
scorer.MismatchCoefficient = 1;
Assert.Equal(3, scorer.GetAlignmentScore(everything));
scorer.NonNSoftclipCoefficient = 1;
Assert.Equal(4, scorer.GetAlignmentScore(everything));
scorer.AnchorLengthCoefficient = 1;
Assert.Equal(5, scorer.GetAlignmentScore(everything));
}
