FastqPuri
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fastq entries manipulations (read/write) More...
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include "fq_read.h"
#include "str_manip.h"
Functions | |
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 More... | |
int | string_seq (Fq_read *seq, char *char_seq) |
writes the fq entry in a string More... | |
fastq entries manipulations (read/write)
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
a fastq line is read from a buffer and the relevant information is stored in a structure Fq_read. Depending on the value of filter, information about whether the read was trimmed is stored.
seq | pointer to Fq_read, where the info will be stored. |
buffer | variable where the file being read is stored. |
pos1 | buffer start position of the line. |
pos2 | buffer end position of the line. |
nline | file line number being read. |
read_len | predefined read length |
filter | 0 original file, 1 file filtered with filter_trim, 2 file filtered with another tool |
int string_seq | ( | Fq_read * | seq, |
char * | char_seq | ||
) |
writes the fq entry in a string
seq | pointer to Fq_read, where the info will be stored. |
char_seq | pointer to buffer, where the sequence will be stored |