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
-               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;
                }
@@ -94,36 +93,29 @@ int main(int argc, char *argv[])
                        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
-                       ti_index_t *idx;
                        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;
-                               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;
-                                       iter = ti_query(fp, idx, tid, beg, end);
-                                       while ((s = ti_iter_read(iter, &len)) != 0) {
+                                       iter = ti_queryi(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");
                        }
-                       ti_index_destroy(idx);
                }
-               bgzf_close(fp);
+               ti_close(t);
        }
        return 0;
 }