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/*++
Module Name:
PairedEndAligner.h
Abstract:
Superclass for implementations of paired end aligners
Authors:
Matei Zaharia, December, 2011
Environment:
User mode service.
Revision History:
--*/
#pragma once
#include "AlignmentResult.h"
#include "directions.h"
#include "LandauVishkin.h"
#include "AffineGap.h"
#include "AffineGapVectorized.h"
#include "Read.h"
/**
* Abstract interface for paired-end aligners.
*/
class PairedEndAligner
{
public:
virtual ~PairedEndAligner() {}
virtual bool align(
Read *read0,
Read *read1,
PairedAlignmentResult* result,
PairedAlignmentResult* firstALTResult,
int maxEditDistanceForSecondaryResults,
_int64 secondaryResultBufferSize,
_int64 *nSecondaryResults,
PairedAlignmentResult *secondaryResults, // The caller passes in a buffer of secondaryResultBufferSize and it's filled in by align()
_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
) = 0; // return value is false iff there wasn't enough space in the secondary buffers
virtual void setLandauVishkin(
LandauVishkin<1> *landauVishkin,
LandauVishkin<-1> *reverseLandauVishkin)
{
}
virtual void setAffineGap(
AffineGapVectorized<1> *affineGap,
AffineGapVectorized<-1> *reverseAffineGap)
// AffineGap<1> *affineGap,
// AffineGap<-1> *reverseAffineGap)
{
}
virtual _int64 getLocationsScoredWithLandauVishkin() const = 0;
virtual _int64 getLocationsScoredWithAffineGap() const = 0;
};
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