int main(int argc, char **argv)
{
uint32_t num_chrms = 100;
if ((argc != 4)) {
errx(1,
"usage:\t%s <index dir> <region> <w|i>",
argv[0]);
}
char *index_dir = argv[1];
char *region_s = argv[2];
char *i_type = argv[3];
struct giggle_index *gi;
gi = giggle_load(index_dir,
uint32_t_ll_giggle_set_data_handler);
#if 0
char *chrm = region_s;
uint32_t start = 0, end = 0;
uint32_t i, len = strlen(region_s);
for (i = 0; i < len; ++i) {
if (region_s[i] == ':') {
region_s[i] = '\0';
start = atoi(region_s + i + 1);
} else if (region_s[i] == '-') {
region_s[i] = '\0';
end = atoi(region_s + i + 1);
break;
}
}
struct giggle_index *gi;
if (i_type[0] == 'i') {
gi = giggle_load(index_dir,
uint32_t_ll_giggle_set_data_handler);
struct uint32_t_ll *R =
(struct uint32_t_ll *)giggle_query_region(gi,
chrm,
start,
end);
if (R != NULL)
printf("Hits:%u\n", R->len);
else
printf("Hits:0\n");
} else {
gi = giggle_load(index_dir,
wah_giggle_set_data_handler);
uint32_t chr_id = giggle_get_chrm_id(gi, chrm);
//return giggle_search(chr_id, gi->root_ids[chr_id], start, end);
uint32_t domain = chr_id;
uint32_t root_id = gi->root_ids[chr_id];
uint32_t leaf_start_id;
int pos_start_id;
uint32_t nld_start_id = bpt_find(domain,
root_id,
&leaf_start_id,
&pos_start_id,
start);
fprintf(stderr,
"nld_start_id:%u\t"
"leaf_start_id:%u\t"
"pos_start_id:%u\n",
nld_start_id,
leaf_start_id,
pos_start_id);
struct bpt_node *leaf_start = cache.get(domain,
leaf_start_id - 1,
&bpt_node_cache_handler);
bpt_print_node(leaf_start);
struct wah_bpt_non_leading_data *nld =
cache.get(domain,
BPT_POINTERS(leaf_start)[0] - 1,
&wah_non_leading_cache_handler);
fprintf(stderr,
"WAH_LEN:%u\t"
"wah_get_ints_count:%u\t"
"\n",
WAH_LEN(nld->SA),
wah_get_ints_count(nld->SA));
uint32_t *R = NULL;
uint32_t R_len = wah_get_ints(nld->SA, &R);
uint32_t i;
for (i = 0; i < R_len; ++i) {
fprintf(stderr, "%u:%u\n", i, R[i]);
}
/*
uint8_t *R = (uint8_t *)giggle_query_region(gi,
chrm,
start,
end);
if (R != NULL)
printf("Hits:%u\n", wah_get_ints_count(R));
else
printf("Hits:0\n");
*/
}
#endif
giggle_index_destroy(&gi);
cache.destroy();
}
// NOTE: this function could easily be rewritten using the general funtions
//{{{ void wah_leading_repair(uint32_t domain,
void wah_leading_repair(uint32_t domain,
struct bpt_node *a,
struct bpt_node *b)
{
#if DEBUG
fprintf(stderr, "START leading_repair\n");
#endif
if ( (BPT_IS_LEAF(a) == 1) && (BPT_IS_LEAF(b) == 1) ) {
// make a new leading value for the new right node
struct wah_bpt_leading_data *d =
(struct wah_bpt_leading_data *)
malloc(sizeof(struct wah_bpt_leading_data));
d->B = NULL;
// if the left node had leading data, grab all of it
if (BPT_LEADING(a) != 0) {
// get it from cache
struct wah_bpt_leading_data *l =
cache.get(domain,
BPT_LEADING(a) - 1,
&wah_leading_cache_handler);
#if DEBUG
uint32_t *R = NULL, R_size;
uint32_t j;
fprintf(stderr, "LEADING\t");
if (l->B != NULL) {
R_size = wah_get_ints(l->B, &R);
fprintf(stderr, "R_size:%u\t", R_size);
for (j = 0; j < R_size; ++j)
fprintf(stderr, "R[%u]:%u\t", j, R[j]);
free(R);
R = NULL;
}
fprintf(stderr, "\n");
#endif
d->B = wah_copy(l->B);
}
uint32_t i;
for (i = 0 ; i < BPT_NUM_KEYS(a); ++i) {
struct wah_bpt_non_leading_data *nl =
cache.get(domain,
BPT_POINTERS(a)[i] - 1,
&wah_non_leading_cache_handler);
#if DEBUG
uint32_t *R = NULL, R_size;
uint32_t j;
fprintf(stderr, "%u\tSA\t",BPT_KEYS(a)[i]);
if (nl->SA != NULL) {
R_size = wah_get_ints(nl->SA, &R);
fprintf(stderr, "R_size:%u\t", R_size);
for (j = 0; j < R_size; ++j)
fprintf(stderr, "R[%u]:%u\t", j, R[j]);
free(R);
R = NULL;
}
fprintf(stderr, "\n");
fprintf(stderr, "SE\t");
if (nl->SE != NULL) {
R_size = wah_get_ints(nl->SE, &R);
fprintf(stderr, "R_size:%u\t", R_size);
for (j = 0; j < R_size; ++j)
fprintf(stderr, "R[%u]:%u\t", j, R[j]);
free(R);
R = NULL;
}
fprintf(stderr, "\n");
#endif
wah_non_leading_union_with_SA_subtract_SE(domain,
(void **)(&d->B),
nl);
}
if (d->B != NULL) {
uint32_t v_id = cache.seen(domain) + 1;
cache.add(domain, v_id - 1, d, &wah_leading_cache_handler);
BPT_LEADING(b) = v_id;
} else {
free(d);
}
}
#if DEBUG
fprintf(stderr, "END leading_repair\n");
#endif
}
