-
Notifications
You must be signed in to change notification settings - Fork 1
/
filter.c
140 lines (108 loc) · 3.68 KB
/
filter.c
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
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
#include<stdio.h>
#include<pthread.h>
#include<stdlib.h>
#include<string.h>
#include"smith-waterman.h"
#include"dataset.h"
typedef struct {
unsigned int max_dist;
dataset* ds;
char* target;
size_t target_length;
size_t start;
size_t stride;
char* is_in_dataset;
} thread_handle_filter_SW;
dataset filter_ds_by_size(dataset in_set, size_t size,
size_t plus, size_t minus) {
int i,counter;
dataset out_set;
out_set.sequences = (char**)malloc(sizeof(char*)*in_set.n_values);
out_set.sequence_lengths = (size_t*)malloc(sizeof(size_t)*in_set.n_values);
counter = 0;
for(i=0;i<in_set.n_values;i++) {
if(in_set.sequence_lengths[i] <= size+plus &&
in_set.sequence_lengths[i] >= size-minus) {
out_set.sequences[counter] =
(char*)malloc(sizeof(char)*in_set.sequence_lengths[i]+1);
memcpy(out_set.sequences[counter],in_set.sequences[i],
sizeof(char)*in_set.sequence_lengths[i]);
out_set.sequences[counter][in_set.sequence_lengths[i]] = 0;
out_set.sequence_lengths[counter] = in_set.sequence_lengths[i];
counter++;
}
}
out_set.n_values = counter;
out_set.sequences =
(char**)realloc(out_set.sequences,sizeof(char*)*out_set.n_values);
out_set.sequence_lengths =
(size_t*)realloc(out_set.sequence_lengths,sizeof(size_t)*out_set.n_values);
return(out_set);
}
void* filter_by_SW_distance_thread(void* arg) {
thread_handle_filter_SW* th = (thread_handle_filter_SW*)arg;
int i;
int current_score;
for(i = th->start; i< th->start+th->stride; i++) {
current_score = score(th->ds->sequences[i],
th->target,
th->ds->sequence_lengths[i],
th->target_length,NULL);
if(th->max_dist >= current_score ) {
th->is_in_dataset[i] = 1;
}
}
}
dataset filter_by_SW_distance(dataset in_set,
char* target,
size_t target_length,
unsigned int max_distance,
int n_threads) {
int i,counter;
dataset out_set;
thread_handle_filter_SW* th =
(thread_handle_filter_SW*)malloc(sizeof(thread_handle_filter_SW)
*n_threads);
pthread_t* threads = (pthread_t*)malloc(sizeof(pthread_t)*n_threads);
size_t stride = in_set.n_values/n_threads;
size_t stride_rest = in_set.n_values%n_threads;
char* is_in_dataset = (char*)malloc(sizeof(char)*in_set.n_values);
memset(is_in_dataset,0,sizeof(char)*in_set.n_values);
for(i=0;i<n_threads;i++) {
th[i].ds = &in_set;
th[i].target = target;
th[i].target_length = target_length;
th[i].start = i*stride;
th[i].stride = stride;
if(i == n_threads-1) th[i].stride+=stride_rest;
th[i].is_in_dataset = is_in_dataset;
th[i].max_dist = max_distance;
pthread_create(threads+i, NULL, filter_by_SW_distance_thread, th+i);
}
for(i=0;i<n_threads;i++) {
pthread_join(threads[i],NULL);
}
out_set.sequences = (char**)malloc(sizeof(char*)*in_set.n_values);
out_set.sequence_lengths = (size_t*)malloc(sizeof(size_t)*in_set.n_values);
counter = 0;
for(i=0;i<in_set.n_values;i++) {
if(is_in_dataset[i] == 1) {
out_set.sequences[counter] =
(char*)malloc(sizeof(char)*in_set.sequence_lengths[i]+1);
memcpy(out_set.sequences[counter],in_set.sequences[i],
sizeof(char)*in_set.sequence_lengths[i]);
out_set.sequences[counter][in_set.sequence_lengths[i]] = 0;
out_set.sequence_lengths[counter] = in_set.sequence_lengths[i];
counter++;
}
}
out_set.n_values = counter;
out_set.sequences =
(char**)realloc(out_set.sequences,sizeof(char*)*out_set.n_values);
out_set.sequence_lengths =
(size_t*)realloc(out_set.sequence_lengths,sizeof(size_t)*out_set.n_values);
free(is_in_dataset);
free(threads);
free(th);
return(out_set);
}