/usr/include/io_lib/sff.h is in libstaden-read-dev 1.12.4-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 | #ifndef _SFF_H_
#define _SFF_H_
#include "io_lib/Read.h"
#include "io_lib/os.h"
#include "io_lib/mFILE.h"
#ifdef __cplusplus
extern "C" {
#endif
/*
* This mirrors the order that the SFF header has on disc. We have one of
* these only.
*
* The flow and key are variable length fields as defined by flow_len
* and key_len.
* The on-disc structure is then also padded out with zeros to the 8-byte
* word boundary.
*/
typedef struct {
uint32_t magic;
char version[4];
uint64_t index_offset;
uint32_t index_len;
uint32_t nreads;
uint16_t header_len;
uint16_t key_len;
uint16_t flow_len;
uint8_t flowgram_format;
char *flow;
char *key;
} sff_common_header;
#define SFF_MAGIC 0x2e736666 /* ".sff" */
#define SFF_VERSION "\0\0\0\1"
/*
* We have one read_header per "reading" in the SFF archive.
* It too is padded to an 8-byte boundary.
*/
typedef struct {
uint16_t header_len;
uint16_t name_len;
uint32_t nbases;
uint16_t clip_qual_left;
uint16_t clip_qual_right;
uint16_t clip_adapter_left;
uint16_t clip_adapter_right;
char *name;
} sff_read_header;
/*
* We have one read_data section per reading, following the read_header.
* It is padded to an 8-byte boundary.
*/
typedef struct {
uint16_t *flowgram; /* x 100.0 */
uint8_t *flow_index; /* relative to last */
char *bases;
uint8_t *quality;
} sff_read_data;
/*
* Low level functions to decode SFF internals
*/
sff_common_header *decode_sff_common_header(unsigned char *buf);
sff_common_header *read_sff_common_header(mFILE *mf);
void free_sff_common_header(sff_common_header *h);
sff_read_header *decode_sff_read_header(unsigned char *buf);
void free_sff_read_header(sff_read_header *h);
sff_read_header *read_sff_read_header(mFILE *mf);
void free_sff_read_data(sff_read_data *d);
sff_read_data *read_sff_read_data(mFILE *mf, int nflows, int nbases);
/*
* Loads the first SFF sequence from an SFF container and returns as a Read.
*/
Read *mfread_sff(mFILE *mf);
#ifdef __cplusplus
}
#endif
#endif /* _SFF_H_ */
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