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/*++
Module Name:
ChimericPairedEndAligner.h
Abstract:
A paired-end aligner calls into a different paired-end aligner, and if
it fails to find an alignment, aligns each of the reads singly. This handles
chimeric reads that would otherwise be unalignable.
Authors:
Bill Bolosky, June, 2013
Environment:
User mode service.
Revision History:
--*/
#pragma once
#include "PairedEndAligner.h"
#include "BaseAligner.h"
#include "BigAlloc.h"
class ChimericPairedEndAligner : public PairedEndAligner {
public:
ChimericPairedEndAligner(
GenomeIndex *index_,
unsigned maxReadSize,
unsigned maxHits,
unsigned maxK,
unsigned maxSeedsFromCommandLine,
double seedCoverage,
unsigned minWeightToCheck,
bool forceSpacing_,
unsigned extraSearchDepth_,
DisabledOptimizations disabledOptimizations_,
bool useAffineGap,
bool ignoreAlignmentAdjustmentsForOm,
bool altAwareness,
bool emitALTAlignments,
PairedEndAligner *underlyingPairedEndAligner_,
unsigned minReadLength_,
int maxSecondaryAlignmentsPerContig,
int maxScoreGapToPreferNonAltAlignment,
int flattenMAPQAtOrBelow_,
bool useSoftClipping_,
unsigned matchReward = 1,
unsigned subPenalty = 4,
unsigned gapOpenPenalty = 6,
unsigned gapExtendPenalty = 1,
unsigned fivePrimeEndBonus = 10,
unsigned threePrimeEndBonus = 5,
int minScoreRealignment_ = 3,
int minScoreGapRealignmentALT_ = 3,
int minAGScoreImprovement_ = 24,
bool enableHammingScoringBaseAligner = false,
BigAllocator *allocator = NULL);
virtual ~ChimericPairedEndAligner();
static size_t getBigAllocatorReservation(GenomeIndex * index, unsigned maxReadSize, unsigned maxHits, unsigned seedLen, unsigned maxSeedsFromCommandLine,
double seedCoverage, unsigned maxEditDistanceToConsider, unsigned maxExtraSearchDepth, unsigned maxCandidatePoolSize,
int maxSecondaryAlignmentsPerContig);
void *operator new(size_t size, BigAllocator *allocator) {_ASSERT(size == sizeof(ChimericPairedEndAligner)); return allocator->allocate(size);}
void operator delete(void *ptr, BigAllocator *allocator) {/* do nothing. Memory gets cleaned up when the allocator is deleted.*/}
virtual bool align(
Read *read0,
Read *read1,
PairedAlignmentResult *result,
PairedAlignmentResult *firatALTResult,
int maxEditDistanceForSecondaryResults,
_int64 secondaryResultBufferSize,
_int64 *nSecondaryResults,
PairedAlignmentResult *secondaryResults, // The caller passes in a buffer of secondaryResultBufferSize and it's filled in by AlignRead()
_int64 singleSecondaryBufferSize,
_int64 maxSecondaryAlignmentsToReturn,
_int64 *nSingleEndSecondaryResultsForFirstRead,
_int64 *nSingleEndSecondaryResultsForSecondRead,
SingleAlignmentResult *singleEndSecondaryResults, // Single-end secondary alignments for when the paired-end alignment didn't work properly
_int64 maxPairedCandidatesForAffineGapBufferSize,
_int64 *nPairedCandidatesForAffineGap,
PairedAlignmentResult *pairedCandidatesForAffineGap,
_int64 maxSingleCandidatesForAffineGapBufferSize,
_int64 *nSingleCandidatesForAffineGapFirstRead,
_int64 *nSingleCandidatesForAffineGapSecondRead,
SingleAlignmentResult *singleCandidatesForAffineGap,
int maxK
);
void *operator new(size_t size) {return BigAlloc(size);}
void operator delete(void *ptr) {BigDealloc(ptr);}
virtual _int64 getLocationsScoredWithLandauVishkin() const {
return underlyingPairedEndAligner->getLocationsScoredWithLandauVishkin() + singleAligner->getLocationsScoredWithLandauVishkin();
}
virtual _int64 getLocationsScoredWithAffineGap() const {
return underlyingPairedEndAligner->getLocationsScoredWithAffineGap() + singleAligner->getLocationsScoredWithAffineGap();
}
private:
bool forceSpacing;
BaseAligner *singleAligner;
PairedEndAligner *underlyingPairedEndAligner;
// avoid allocation in aligner calls
IdPairVector* singleSecondary[2];
LandauVishkin<1> lv;
LandauVishkin<-1> reverseLV;
// AffineGap<1> ag;
// AffineGap<-1> reverseAG;
AffineGapVectorized<1> ag;
AffineGapVectorized<-1> reverseAG;
GenomeIndex *index;
unsigned minReadLength;
bool emitALTAlignments;
bool useSoftClipping;
unsigned maxKSingleEnd;
unsigned maxKPairedEnd;
int extraSearchDepth;
int minScoreRealignment;
int minScoreGapRealignmentALT;
int minAGScoreImprovement;
int flattenMAPQAtOrBelow;
bool enableHammingScoringBaseAligner;
bool useAffineGap;
};
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