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/*
* =============================================================================
*
* Filename: soapio.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 _SOAPIO_H_
#define _SOAPIO_H_
#include <stdio.h>
#include <stdlib.h>
#include "extratools.h"
#include "SeqIO.h"
#define MAX_MULTI_READS 0x20000
typedef struct _ALNSEQ_TYPE_{
int tid;
int id, len, ns;
char *name, *seq, *rc, *qual, *rcqual;
unsigned int flag;
int nhits;
struct {
int H0;
int H1;
int H2;
}top;
int report;
HITITEM *itemList;
}ALNSEQ;
typedef struct _MULTISEQ_TYPE_{
int n, max;
ALNSEQ *seqList;
}MULTISEQ;
typedef struct _OUTAUX_TYPE_{
int id, un, chrNum;
char **chrName;
int allErr;
}OUTAUX;
typedef struct _INFILELIST_{
FILE *ifpA, *ifpB;
int id;
int lock;
}InFileList;
typedef struct _OUTFILELIST_{
FILE *ofpAln, *ofpSe, *ofpUn;
int id;
int lock;
}OutFileList;
void FreeMultiSeq(MULTISEQ *);
int GenMultiReads(const HSP *, MULTISEQ *, const int , const int , unsigned int *, int *);
int GetMultiSeq (InFileList *, MULTISEQ *, const int , int (*)(FILE *, seq_t *, const int));
void DumpAln(MULTISEQ *, OUTAUX *, OutFileList *,unsigned int *, unsigned int *);
#endif /* ----- #ifndef SOAPIO_INC ----- */
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