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
|
#ifndef _FLASH_READ_QUEUE_H_
#define _FLASH_READ_QUEUE_H_
#include <stdbool.h>
struct read;
struct read_format_params;
struct input_stream;
struct output_stream;
/* BASE_READS_PER_READ_SET: The base number of reads per read set (i.e. per
* chunk processed by combiner threads). This number must be at least 1; it is
* a heuristic value that affects performance only. The faster the core
* algorithm runs, the higher it should be.
*
* PERTHREAD_READS_PER_READ_SET: Additional number of reads per read set per
* combiner thread.
*/
#if defined(__GNUC__) && defined(__SSE2__)
# define BASE_READS_PER_READ_SET 30
# define PERTHREAD_READS_PER_READ_SET 5
#else
# define BASE_READS_PER_READ_SET 24
# define PERTHREAD_READS_PER_READ_SET 4
#endif
/* NUmber of read sets to allocate per combiner thread. Must be at least 6. */
#define QUEUE_SIZE_PER_THREAD 8
struct read_io_handle;
struct read_set {
unsigned filled;
unsigned num_reads;
enum {
READS_UNCOMBINED,
READS_COMBINED,
READS_UNPAIRED,
} type;
struct read *reads[];
};
extern struct read_io_handle *
start_readers_and_writers(struct input_stream *in_1,
struct input_stream *in_2,
struct output_stream *out_combined,
struct output_stream *out_uncombined_1,
struct output_stream *out_uncombined_2,
const struct read_format_params *iparams,
const struct read_format_params *oparams,
unsigned num_combiner_threads,
bool verbose);
extern struct read_set *
get_avail_read_set(struct read_io_handle *handle);
extern bool
get_unprocessed_read_pairs(struct read_io_handle *handle,
struct read_set **s1_ret, struct read_set **s2_ret);
extern void
put_combined_reads(struct read_io_handle *handle, struct read_set *s);
extern void
put_uncombined_read_pairs(struct read_io_handle *handle,
struct read_set *s1, struct read_set *s2);
extern void
put_avail_read_pairs(struct read_io_handle *handle,
struct read_set *s1, struct read_set *s2);
extern void
notify_combiner_terminated(struct read_io_handle *h);
extern struct read_set *
new_empty_read_set(struct read_io_handle *h);
extern void
free_read_set(struct read_set *s);
extern void
stop_readers_and_writers(struct read_io_handle *h);
#endif /* _FLASH_READ_QUEUE_H_ */
|
