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
|
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include "util/util.h"
#include "qidx.h"
void qidx_die_err(qidx_err_t err) {
char const * errstr = qidx_strerr(err);
if(qidx_errno(err)) {
die_errno("err: %s", errstr);
} else {
die("err: %s", errstr);
}
}
void die_usage(char const * prog) {
err("%s {create,search}", prog);
err(" create [bamfile] [indexfile]");
die(" search [index] [bamfile] [read]");
}
int main(int argc, char ** argv) {
if(!argc) return 1;
if(argc < 3) die_usage(argv[0]);
char const * type = argv[1];
qidx_err_t err;
char const * prog = argv[0];
if(strcmp(type, "create") == 0) {
int option;
uint32_t n_buckets = 0;
uint32_t max_bucket_size = 1 << 18;
while((option = getopt(argc, argv, ":b:s:")) != -1) {
switch(option) {
case 'b':
if(1 != sscanf(optarg, "%u", &n_buckets)) {
die("could not parse -b");
}
break;
case 's':
if(1 != sscanf(optarg, "%u", &max_bucket_size)) {
die("could not parse -s");
}
break;
case ':':
die("option needs a value");
case '?':
die("Unknown option %c", optopt);
break;
}
}
if(argc - optind != 3) die_usage(prog);
char const * bamfile = argv[optind + 1];
char const * indexfile = argv[optind + 2];
if((err = qidx_create_index1(bamfile,
indexfile, n_buckets, max_bucket_size))) {
qidx_die_err(err);
}
} else if (strcmp(type, "search") == 0) {
if(argc != 5) die_usage(prog);
char const * indexfile = argv[2];
char const * bamfile = argv[3];
char const * qname = argv[4];
if((err = qidx_search_index(indexfile, bamfile, qname))) {
qidx_die_err(err);
}
} else {
die_usage(argv[0]);
}
}
|
