fastq entries manipulations (read/write)
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#include "config.h"
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fastq entries manipulations (read/write)
- Author
- Paula Perez paula.nosp@m.pere.nosp@m.zrubi.nosp@m.o@gm.nosp@m.ail.c.nosp@m.om
- Date
- 03.08.2017
◆ get_fqread()
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.
- Parameters
-
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 |
◆ string_seq()
int string_seq |
( |
Fq_read * |
seq, |
|
|
char * |
char_seq |
|
) |
| |
writes the fq entry in a string
- Parameters
-
seq | pointer to Fq_read, where the info will be stored. |
char_seq | pointer to buffer, where the sequence will be stored |
- Warning
- change the call to sprintf to snprintf