FastqPuri
fq_read.h
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1 /****************************************************************************
2  * Copyright (C) 2017 by Paula Perez Rubio *
3  * *
4  * This file is part of FastqPuri. *
5  * *
6  * FastqPuri is free software: you can redistribute it and/or modify *
7  * it under the terms of the GNU General Public License as *
8  * published by the Free Software Foundation, either version 3 of the *
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13  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
14  * GNU General Public License for more details. *
15  * *
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17  * along with FastqPuri. *
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19  ****************************************************************************/
20 
29 #ifndef FQ_READ_H_
30 #define FQ_READ_H_
31 
32 #include "config.h"
33 
37 typedef struct _fq_read {
38  char line1[READ_MAXLEN];
39  char line2[READ_MAXLEN];
40  char line3[READ_MAXLEN];
41  char line4[READ_MAXLEN];
42  int L;
43  int start;
45  int Lhalf;
46  char extended[READ_MAXLEN];
47  unsigned char pack[(READ_MAXLEN+1)/2];
48  unsigned char packsh[(READ_MAXLEN+1)/2];
49  int L_ad;
50  int L_ext;
51  int L_pack;
52  int L_packsh;
53 } Fq_read;
54 
55 int get_fqread(Fq_read* seq, char* buffer, int pos1, int pos2,
56  int nline, int read_len, int filter);
57 
58 int string_seq(Fq_read *seq, char *char_seq);
59 
60 #endif // endif FQ_READ_H_
int L
Definition: fq_read.h:42
char line3[READ_MAXLEN]
Definition: fq_read.h:40
char line2[READ_MAXLEN]
Definition: fq_read.h:39
char line4[READ_MAXLEN]
Definition: fq_read.h:41
int L_ext
Definition: fq_read.h:50
int L_ad
Definition: fq_read.h:49
stores a fastq entry
Definition: fq_read.h:37
int start
Definition: fq_read.h:43
unsigned char packsh[(READ_MAXLEN+1)/2]
Definition: fq_read.h:48
int L_packsh
Definition: fq_read.h:52
int string_seq(Fq_read *seq, char *char_seq)
writes the fq entry in a string
Definition: fq_read.c:133
char extended[READ_MAXLEN]
Definition: fq_read.h:46
int Lhalf
Definition: fq_read.h:45
unsigned char pack[(READ_MAXLEN+1)/2]
Definition: fq_read.h:47
char line1[READ_MAXLEN]
Definition: fq_read.h:38
int L_pack
Definition: fq_read.h:51
int get_fqread(Fq_read *seq, char *buffer, int pos1, int pos2, int nline, int read_len, int filter)
reads fastq line from a buffer
Definition: fq_read.c:55
struct _fq_read Fq_read
stores a fastq entry