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/**********************************************************************
* Skewer - a fast and accurate adapter trimming tool
* using the bit-masked k-difference matching algorithm
* Copyright (c) 2013-2014 by Hongshan Jiang
* hongshan.jiang@gmail.com
*
* If you use this program, please cite the paper:
* Jiang, H., Lei, R., Ding, S.W. and Zhu, S. (2014) Skewer: a fast and
* accurate adapter trimmer for next-generation sequencing paired-end reads.
* BMC Bioinformatics, 15, 182.
* http://www.biomedcentral.com/1471-2105/15/182
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
#ifndef _FASTQ_H
#define _FASTQ_H
// standard libs
#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <string.h>
#include <errno.h>
#include <getopt.h>
#include <assert.h>
#include <math.h>
#include <sys/stat.h>
#include <search.h>
#include <limits.h>
#include <time.h>
#ifdef __MACH__
#include <mach/mach_time.h>
#define ORWL_NANO (+1.0E-9)
#define ORWL_GIGA UINT64_C(1000000000)
#endif
#include "common.h"
typedef struct tag_LINE {
char *s;
int n;
size_t a;
}LINE;
typedef enum{
TAG_NORMAL = 0,
TAG_BLURRY = 1,
TAG_BADQUAL = 2,
TAG_EMPTY = 3,
TAG_SHORT = 4,
TAG_CONTAMINANT = 5,
TAG_UNDETERMINED = 6,
TAG_LONG = 7
}REC_TAG;
typedef struct tag_REC{
uint32 tag:7; // REC_TAG
uint32 bExchange:1;
uint32 nCnt:24;
INDEX idx;
LINE id;
LINE seq;
LINE com;
LINE qual;
}RECORD;
class cFQ
{
private:
// int size;
public:
char tag;
RECORD rec;
// RECORD *pBuffer;
// int cnt;
FILE * in;
int64 offset;
int64 next_pos;
int rno;
private:
inline int read_line(LINE &l);
public:
cFQ();
~cFQ();
// bool InitBuffer(int nBuffSize=256);
// void DestroyBuffer();
// void clearBuffer();
void associateFile(FILE * fp);
int readRecord(RECORD *pRecord=NULL);
// int readRecord2Buffer();
// RECORD * getLastRecord();
inline int64 tell(){ return offset; }
};
typedef struct tag_CFILE{
FILE * fp;
bool bGz;
}CFILE;
enum FASTQ_FORMAT{
SANGER_FASTQ = 0,
SOLEXA_FASTQ = 1,
UNKNOWN_FASTQ = 2,
CONTRADICT_FASTQ = 3,
FASTA = 4,
FASTQ_FORMAT_CNT = 5
};
extern const char * FASTQ_FORMAT_NAME[FASTQ_FORMAT_CNT];
// open a file, possibly gzipped, exit on failure
extern CFILE gzopen(const char * fileName, const char *mode);
extern int gzclose(CFILE *f);
extern int64 gzsize(const char * fileName);
extern enum FASTQ_FORMAT gzformat(char * fileNames[], int nFileCnt);
extern int gzreadlen(char * fileName);
extern void gzstrncpy (char * dest, const char * src, int n);
// time function
extern void versatile_gettime(struct timespec *tp);
#endif // _FASTQ_H
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