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 GeminiReadRealigner(AlignmentComparer comparer, bool remaskSoftclips = true, bool maskPartialInsertion = true,
bool keepProbeSoftclips = false, bool keepBothSideSoftclips = false, bool trackActualMismatches = false,
bool checkSoftclipsForMismatches = false, bool debug = false, bool maskNsOnly = true,
int minInsertionSizeToAllowMismatchingBases = 5, double maxProportionInsertSequenceMismatch = 0.2,
int minimumUnanchoredInsertionLength = 0)
{
_maskPartialInsertion = maskPartialInsertion;
_keepProbeSoftclips = keepProbeSoftclips;
_keepBothSideSoftclips = keepBothSideSoftclips;
_trackActualMismatches = trackActualMismatches;
_checkSoftclipsForMismatches = checkSoftclipsForMismatches;
_comparer = comparer;
_minInsertionSizeToAllowMismatchingBases = minInsertionSizeToAllowMismatchingBases;
_maxProportionInsertSequenceMismatch = maxProportionInsertSequenceMismatch;
_minimumUnanchoredInsertionLength = minimumUnanchoredInsertionLength;
if (_keepProbeSoftclips || _keepBothSideSoftclips)
{
_checkSoftclipsForMismatches = false;
maskNsOnly = false;
}
_softclipReapplier = new SoftclipReapplier(remaskSoftclips, maskNsOnly, keepProbeSoftclips, keepBothSideSoftclips, trackActualMismatches, checkSoftclipsForMismatches);
_debug = debug;
}
public RealignmentJudger(AlignmentComparer alignmentComparer)
{
_alignmentComparer = alignmentComparer;
}
