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Imported Upstream version 0.2.0
[tabix.git]
/
main.c
diff --git
a/main.c
b/main.c
index a05939dd96f306843d877859148246c30a44f90b..a2a456566fb9f9a68e3692827cc8fd99943f3f2c 100644
(file)
--- a/
main.c
+++ b/
main.c
@@
-84,9
+84,8
@@
int main(int argc, char *argv[])
return ti_index_build(argv[optind], &conf);
}
{ // retrieve
return ti_index_build(argv[optind], &conf);
}
{ // retrieve
- BGZF *fp;
- fp = bgzf_open(argv[optind], "r");
- if (fp == 0) {
+ tabix_t *t;
+ if ((t = ti_open(argv[optind], 0)) == 0) {
fprintf(stderr, "[main] fail to open the data file.\n");
return 1;
}
fprintf(stderr, "[main] fail to open the data file.\n");
return 1;
}
@@
-94,36
+93,29
@@
int main(int argc, char *argv[])
ti_iter_t iter;
const char *s;
int len;
ti_iter_t iter;
const char *s;
int len;
- iter = ti_
first(fp
);
- while ((s = ti_
iter_read(
iter, &len)) != 0) {
+ iter = ti_
query(t, 0, 0, 0
);
+ while ((s = ti_
read(t,
iter, &len)) != 0) {
fputs(s, stdout); fputc('\n', stdout);
}
ti_iter_destroy(iter);
} else { // retrieve from specified regions
fputs(s, stdout); fputc('\n', stdout);
}
ti_iter_destroy(iter);
} else { // retrieve from specified regions
- ti_index_t *idx;
int i;
int i;
- idx = ti_index_load(argv[optind]);
- if (idx == 0) {
- bgzf_close(fp);
- fprintf(stderr, "[main] fail to load the index.\n");
- return 1;
- }
+ ti_lazy_index_load(t);
for (i = optind + 1; i < argc; ++i) {
int tid, beg, end;
for (i = optind + 1; i < argc; ++i) {
int tid, beg, end;
- if (ti_parse_region(idx, argv[i], &tid, &beg, &end) == 0) {
+ if (ti_parse_region(
t->
idx, argv[i], &tid, &beg, &end) == 0) {
ti_iter_t iter;
const char *s;
int len;
ti_iter_t iter;
const char *s;
int len;
- iter = ti_query
(fp, idx
, tid, beg, end);
- while ((s = ti_
iter_read(
iter, &len)) != 0) {
+ iter = ti_query
i(t
, tid, beg, end);
+ while ((s = ti_
read(t,
iter, &len)) != 0) {
fputs(s, stdout); fputc('\n', stdout);
}
ti_iter_destroy(iter);
} else fprintf(stderr, "[main] invalid region: unknown target name or minus interval.\n");
}
fputs(s, stdout); fputc('\n', stdout);
}
ti_iter_destroy(iter);
} else fprintf(stderr, "[main] invalid region: unknown target name or minus interval.\n");
}
- ti_index_destroy(idx);
}
}
-
bgzf_close(fp
);
+
ti_close(t
);
}
return 0;
}
}
return 0;
}