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/*
* =============================================================================
*
* Filename: BWTAln.h
*
* Description:
*
* Revision: none
* Compiler: gcc 4.3.2 or above
*
* Author: Chang Yu (yc), yuchang@genomics.org.cn
* Company: BGI Shenzhen
* CopyRight: Copyright (c) 2009, BGI Shenzhen
*
* =============================================================================
*/
#ifndef _BWTALN_H__INC
#define _BWTALN_H__INC
#include "BWT.h"
#include "extratools.h"
#include "HSP.h"
unsigned int REVBWTForwardSearch(const unsigned char *convertedKey, const unsigned int keyLength, const BWT *rev_bwt,unsigned int *resultSaIndexLeft, unsigned int *resultSaIndexRight,unsigned int *rev_resultSaIndexLeft, unsigned int *rev_resultSaIndexRight);
unsigned int REVBWTContForwardSearch(const unsigned char *convertedKey, const unsigned int start, const unsigned int len,const BWT *rev_bwt,unsigned int *saL, unsigned int *saR,unsigned int *rev_saL, unsigned int *rev_saR);
unsigned int BWTContBackwardSearch(const unsigned char *convertedKey, const unsigned int start, const unsigned int len, const BWT *bwt, unsigned int *saL, unsigned int *saR);
unsigned int BWTBackward1Error(const unsigned char *querypattern, const BWTOPT *bo, BWT *bwt, unsigned int start, unsigned int len, unsigned int pl, unsigned int pr, unsigned int info, HITTABLE *hits);
unsigned int REVBWTForward1Error(const unsigned char *queryPattern,const BWTOPT *bo, BWT *bwt, BWT * rev_bwt, unsigned int start,unsigned int len, unsigned int pl,unsigned int pr, unsigned int rev_pl,unsigned int rev_pr, unsigned int info, HITTABLE *hits);
int BWTExactMatching(const unsigned char *convertedKey, const BWTOPT *bo, const int chain, BWT *bwt, LOOKUPTABLE *lookup, HITTABLE *hits);
int BWT1ErrorMatching(const unsigned char *convertedKey, const BWTOPT *bo, const int chain, BWT *bwt, BWT *rev_bwt, LOOKUPTABLE *lookup, LOOKUPTABLE *rev_lookup, HITTABLE *hits);
int BWT2ErrorMatching(const unsigned char *convertedKey, const BWTOPT *bo, const int chain, BWT *bwt, BWT *rev_bwt, LOOKUPTABLE *lookup, LOOKUPTABLE *rev_lookup, HITTABLE *hits);
int BWTGapMatching(const unsigned char *convertedKey, const BWTOPT *bo, const int chain, BWT *bwt, BWT *rev_bwt, LOOKUPTABLE *lookup, LOOKUPTABLE *rev_lookup, HITTABLE *hits);
#endif /* ----- #ifndef _BWTALN_H__INC ----- */
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