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/*++
Module Name:
AlignmentAdjuster.h
Abstract:
Header for code to adjust alignments to avoid indels at ends, or overhanging contig boundaries
Authors:
Bill Bolosky, May, 2016
Environment:
User mode service.
Revision History:
Pulled out of other places in SNAP
--*/
#pragma once
#include "GenomeIndex.h"
#include "LandauVishkin.h"
#include "Read.h"
class AlignmentAdjuster {
public:
AlignmentAdjuster(const Genome *genome);
void AdjustAlignment(Read *read, SingleAlignmentResult *result);
void AdjustAlignments(Read **reads, PairedAlignmentResult *result);
private:
LandauVishkinWithCigar lv;
const Genome *genome;
};
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