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/*
* =============================================================================
*
* Filename: Match.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 _MATCH_H_
#define _MATCH_H_
#include "SeqIO.h"
#include "BWTAln.h"
#include "BWT.h"
#include "extratools.h"
#include "soapio.h"
#include "stdaln.h"
#ifdef PTHREADS
#include <pthread.h>
#define NSEQ_PER_THREAD 0xF00
static pthread_mutex_t lock = PTHREAD_MUTEX_INITIALIZER;
#define SEQ_ALLOC() {\
if (opt->nthreads > 1) { \
pthread_mutex_lock(&lock); \
if (alnSeq->tid < 0) { \
int j; \
for (j = i; j < mseqs->n && j < i + NSEQ_PER_THREAD; ++j) \
alnSeq[j].tid = tid; \
} else if (alnSeq->tid != tid) { \
pthread_mutex_unlock(&lock); \
continue; \
} \
pthread_mutex_unlock(&lock); \
} \
}
#else
#define SEQ_ALLOC()
#endif
#define MULTI_SEQ 0x100000
#ifndef MAX_MISMATCH
#define MAX_MISMATCH 20
#endif
#ifndef MAX_GAP_LEN
#define MAX_GAP_LEN 10
#endif
#define MAX_SEQ_LEN 256
#define MAX_ALN 10000
#define FORWARD 0
#define REVERSE 1
#define ALN_MAT 0
#define ALN_MIS 0x11
#define ALN_INS 0x22
#define ALN_DEL 0x33
#include <assert.h>
#define HITCPY(dest, ori) { \
(dest)->info = (ori)->info; \
(dest)->strain = (ori)->strain; \
(dest)->chr = (ori)->chr; \
(dest)->occ_pos = (ori)->occ_pos; \
(dest)->pos = (ori)->pos; \
(dest)->n_mm = (ori)->n_mm; \
(dest)->n_gapo = (ori)->n_gapo; \
(dest)->n_gape = (ori)->n_gape; \
(dest)->gap_beg = (ori)->gap_beg; \
(dest)->n_diff = (ori)->n_diff; \
(dest)->n_cigar = (ori)->n_cigar; \
}
#define PacReadExt(fw, rc, start, len, seqPac, rcPac) {\
int j; \
for(j=0; j<len; ++j){ \
seqPac[j>>4] <<= 2; \
seqPac[j>>4] |= *(fw+j+start); \
rcPac[j>>4] <<= 2; \
rcPac[j>>4] |= *(rc+j); \
} \
}
typedef struct _SOAPOPT_{
int fast, o_format, chain;
int aln_len, ns, max_mm, gap_len, gap_fb;
int mode, cutoff;
int pe;
int zero_qual;
int min_ins, max_ins, FR;
int rr;
int unmapped;
int nthreads; //number of pthreads
int id;
int bisulfite;
int allErr;
int min_len;
int uniq;
}SOAPOPT;
typedef struct _FILEDS_{
int ifdA, ifdB;
int ofdAln, ofdSe, ofdUn;
}FILEDS;
typedef struct _MATCHAUX_TYPE_{
int max_mm;
int len, ext;
unsigned int *pac;
unsigned int dnaLen;
int allErr;
}MATCHAUX;
typedef struct _PEAUX_TYPE_{
int min_ins, max_ins;
int FR;
int cutoff, len;
int allErr;
}PEAUX;
inline int CheckIns(HITITEM *, HITITEM *, PEAUX *);
void MatchProcess (FILEDS *, BWT *, BWT *, LOOKUPTABLE *, LOOKUPTABLE *, HSP *, SOAPOPT * const );
inline void PickupHit(ALNSEQ *, const int ,int *, HITTABLE *,const unsigned int *, const unsigned int, unsigned short * );
void SEAlnCore(int , MULTISEQ *, BWT *, BWT *, LOOKUPTABLE *, LOOKUPTABLE *, HSP *, const SOAPOPT *);
void PEAlnCore(int , MULTISEQ *, BWT *, BWT *, LOOKUPTABLE *, LOOKUPTABLE *, HSP *, const SOAPOPT *);
int HITCMP(const void *a, const void *b);
#endif /* ----- #ifndef _MATCH_H_INC ----- */
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