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DV-DPForBothUnalign.h
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DV-DPForBothUnalign.h
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/*
*
* DV-DPForBothUnalign.h
* Soap3(gpu)
*
* Copyright (C) 2011, HKU
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
*/
#ifndef _DP_FOR_BOTH_UNALIGN_H_
#define _DP_FOR_BOTH_UNALIGN_H_
#include "AlgnResult.h"
#include "definitions.h"
#include "IndexHandler.h"
//////////////////////////////////////////////////////////////////////////////////////
// The functions are for the DP designed for pairs of which both ends are unaligned //
//////////////////////////////////////////////////////////////////////////////////////
// To perform semi-global DP for both-unaligned pairs (i.e. both ends cannot be aligned)
void DPForUnalignPairs2 ( BothUnalignedPairsArrays * unalignedReads, int insert_high, int insert_low,
unsigned int * queries, unsigned int * readLengths, unsigned int * origReadIDs, char * upkdQueryNames, char * upkdQualities,
unsigned int maxReadLength,
int peStrandLeftLeg, int peStrandRightLeg,
Soap3Index * index,
unsigned int * _bwt, unsigned int * _revBwt,
unsigned int * _occ, unsigned int * _revOcc,
int alignmentType, DPParameters * dpParameters,
unsigned int & numDPAlignedRead, unsigned int & numDPAlignment,
unsigned int accumReadNum, int outputFormat,
FILE * outputFile, samfile_t * samOutputDPFilePtr );
// To perform semi-global DP for both-unaligned pairs (i.e. both ends cannot be aligned)
void DPForUnalignPairs ( BothUnalignedPairsArrays * unalignedReads, int insert_high, int insert_low,
unsigned char * upkdQueries, char * upkdQueryNames,
unsigned int * upkdReadLengths, unsigned int maxReadLength,
int peStrandLeftLeg, int peStrandRightLeg,
Soap3Index * index,
unsigned int * _bwt, unsigned int * _revBwt,
unsigned int * _occ, unsigned int * _revOcc,
int alignmentType, DPParameters * dpParameters,
unsigned int & numDPAlignedRead, unsigned int & numDPAlignment,
unsigned int accumReadNum, int outputFormat,
FILE * outputFile, samfile_t * samOutputDPFilePtr );
#endif