static int recreate_nsec3_tree(const zone_contents_t *z, zone_contents_t *out)
{
out->nsec3_nodes = hattrie_dup(z->nsec3_nodes, NULL);
if (out->nsec3_nodes == NULL) {
return KNOT_ENOMEM;
}
hattrie_iter_t *itt = hattrie_iter_begin(z->nsec3_nodes, false);
if (itt == NULL) {
return KNOT_ENOMEM;
}
while (!hattrie_iter_finished(itt)) {
const zone_node_t *to_cpy = (zone_node_t *)*hattrie_iter_val(itt);
zone_node_t *to_add = node_shallow_copy(to_cpy, NULL);
if (to_add == NULL) {
hattrie_iter_free(itt);
return KNOT_ENOMEM;
}
int ret = zone_contents_add_nsec3_node(out, to_add);
if (ret != KNOT_EOK) {
hattrie_iter_free(itt);
node_free(&to_add, NULL);
return ret;
}
hattrie_iter_next(itt);
}
hattrie_iter_free(itt);
hattrie_build_index(out->nsec3_nodes);
return KNOT_EOK;
}
static int recreate_normal_tree(const zone_contents_t *z, zone_contents_t *out)
{
out->nodes = hattrie_dup(z->nodes, NULL);
if (out->nodes == NULL) {
return KNOT_ENOMEM;
}
// Insert APEX first.
zone_node_t *apex_cpy = node_shallow_copy(z->apex, NULL);
if (apex_cpy == NULL) {
return KNOT_ENOMEM;
}
// Normal additions need apex ... so we need to insert directly.
int ret = zone_tree_insert(out->nodes, apex_cpy);
if (ret != KNOT_EOK) {
node_free(&apex_cpy, NULL);
return ret;
}
out->apex = apex_cpy;
hattrie_iter_t *itt = hattrie_iter_begin(z->nodes, true);
if (itt == NULL) {
return KNOT_ENOMEM;
}
while (!hattrie_iter_finished(itt)) {
const zone_node_t *to_cpy = (zone_node_t *)*hattrie_iter_val(itt);
if (to_cpy == z->apex) {
// Inserted already.
hattrie_iter_next(itt);
continue;
}
zone_node_t *to_add = node_shallow_copy(to_cpy, NULL);
if (to_add == NULL) {
hattrie_iter_free(itt);
return KNOT_ENOMEM;
}
int ret = zone_contents_add_node(out, to_add, true);
if (ret != KNOT_EOK) {
node_free(&to_add, NULL);
hattrie_iter_free(itt);
return ret;
}
hattrie_iter_next(itt);
}
hattrie_iter_free(itt);
hattrie_build_index(out->nodes);
return KNOT_EOK;
}
int main()
{
hattrie_t* T = hattrie_create();
const size_t n = 1000000; // how many strings
const size_t m_low = 50; // minimum length of each string
const size_t m_high = 500; // maximum length of each string
char x[501];
size_t i, m;
for (i = 0; i < n; ++i) {
m = m_low + rand() % (m_high - m_low);
randstr(x, m);
*hattrie_get(T, x, m) = 1;
}
hattrie_iter_t* it;
clock_t t0, t;
const size_t repetitions = 100;
size_t r;
/* iterate in unsorted order */
fprintf(stderr, "iterating out of order ... ");
t0 = clock();
for (r = 0; r < repetitions; ++r) {
it = hattrie_iter_begin(T, false);
while (!hattrie_iter_finished(it)) {
hattrie_iter_next(it);
}
hattrie_iter_free(it);
}
t = clock();
fprintf(stderr, "finished. (%0.2f seconds)\n", (double) (t - t0) / (double) CLOCKS_PER_SEC);
/* iterate in sorted order */
fprintf(stderr, "iterating in order ... ");
t0 = clock();
for (r = 0; r < repetitions; ++r) {
it = hattrie_iter_begin(T, true);
while (!hattrie_iter_finished(it)) {
hattrie_iter_next(it);
}
hattrie_iter_free(it);
}
t = clock();
fprintf(stderr, "finished. (%0.2f seconds)\n", (double) (t - t0) / (double) CLOCKS_PER_SEC);
hattrie_free(T);
return 0;
}
int zone_tree_apply_inorder(zone_tree_t *tree,
zone_tree_apply_cb_t function,
void *data)
{
if (function == NULL) {
return KNOT_EINVAL;
}
if (zone_tree_is_empty(tree)) {
return KNOT_EOK;
}
int result = KNOT_EOK;
hattrie_iter_t *i = hattrie_iter_begin(tree, 1);
while(!hattrie_iter_finished(i)) {
result = function((zone_node_t **)hattrie_iter_val(i), data);
if (result != KNOT_EOK) {
break;
}
hattrie_iter_next(i);
}
hattrie_iter_free(i);
return result;
}
zone_node_t *zone_tree_get_next(zone_tree_t *tree,
const knot_dname_t *owner)
{
if (tree == NULL || owner == NULL) {
return NULL;
}
uint8_t lf[KNOT_DNAME_MAXLEN];
knot_dname_lf(lf, owner, NULL);
value_t *fval = NULL;
zone_node_t *n = NULL;
(void)hattrie_find_next(tree, (char*)lf + 1, *lf, &fval);
if (fval == NULL) {
/* Return first node. */
hattrie_iter_t *it = hattrie_iter_begin(tree, true);
if (it == NULL) {
return NULL;
}
fval = hattrie_iter_val(it);
hattrie_iter_free(it);
}
n = (zone_node_t *)*fval;
/* Next node must be non-empty and auth. */
if (n->rrset_count == 0 || n->flags & NODE_FLAGS_NONAUTH) {
return zone_tree_get_next(tree, n->owner);
} else {
return n;
}
}
static int axfr_process_node_tree(knot_pkt_t *pkt, const void *item,
struct xfr_proc *state)
{
assert(item != NULL);
struct axfr_proc *axfr = (struct axfr_proc*)state;
if (axfr->i == NULL) {
axfr->i = hattrie_iter_begin(item, true);
}
/* Put responses. */
int ret = KNOT_EOK;
zone_node_t *node = NULL;
while (!hattrie_iter_finished(axfr->i)) {
node = (zone_node_t *)*hattrie_iter_val(axfr->i);
ret = axfr_put_rrsets(pkt, node, axfr);
if (ret != KNOT_EOK) {
break;
}
hattrie_iter_next(axfr->i);
}
/* Finished all nodes. */
if (ret == KNOT_EOK) {
hattrie_iter_free(axfr->i);
axfr->i = NULL;
}
return ret;
}
/*!
* \brief Call a function for each piece of the chain formed by sorted nodes.
*/
int knot_nsec_chain_iterate_create(knot_zone_tree_t *nodes,
chain_iterate_create_cb callback,
nsec_chain_iterate_data_t *data)
{
assert(nodes);
assert(callback);
bool sorted = true;
hattrie_iter_t *it = hattrie_iter_begin(nodes, sorted);
if (!it) {
return KNOT_ENOMEM;
}
if (hattrie_iter_finished(it)) {
hattrie_iter_free(it);
return KNOT_EINVAL;
}
zone_node_t *first = (zone_node_t *)*hattrie_iter_val(it);
zone_node_t *previous = first;
zone_node_t *current = first;
hattrie_iter_next(it);
int result = KNOT_EOK;
while (!hattrie_iter_finished(it)) {
current = (zone_node_t *)*hattrie_iter_val(it);
result = callback(previous, current, data);
if (result == NSEC_NODE_SKIP) {
// No NSEC should be created for 'current' node, skip
;
} else if (result == KNOT_EOK) {
previous = current;
} else {
hattrie_iter_free(it);
return result;
}
hattrie_iter_next(it);
}
hattrie_iter_free(it);
return result == NSEC_NODE_SKIP ? callback(previous, first, data) :
callback(current, first, data);
}
static void axfr_query_cleanup(struct query_data *qdata)
{
struct axfr_proc *axfr = (struct axfr_proc *)qdata->ext;
hattrie_iter_free(axfr->i);
ptrlist_free(&axfr->proc.nodes, qdata->mm);
mm_free(qdata->mm, axfr);
/* Allow zone changes (finished). */
rcu_read_unlock();
}
int zone_tree_get_less_or_equal(zone_tree_t *tree,
const knot_dname_t *owner,
zone_node_t **found,
zone_node_t **previous)
{
if (owner == NULL || found == NULL || previous == NULL) {
return KNOT_EINVAL;
}
if (zone_tree_is_empty(tree)) {
return KNOT_ENONODE;
}
uint8_t lf[KNOT_DNAME_MAXLEN];
knot_dname_lf(lf, owner, NULL);
value_t *fval = NULL;
int ret = hattrie_find_leq(tree, (char*)lf+1, *lf, &fval);
if (fval) {
*found = (zone_node_t *)(*fval);
}
int exact_match = 0;
if (ret == 0) {
if (fval) {
*previous = (*found)->prev;
}
exact_match = 1;
} else if (ret < 0) {
*previous = *found;
*found = NULL;
} else if (ret > 0) {
/* Previous should be the rightmost node.
* For regular zone it is the node left of apex, but for some
* cases like NSEC3, there is no such sort of thing (name wise).
*/
/*! \todo We could store rightmost node in zonetree probably. */
hattrie_iter_t *i = hattrie_iter_begin(tree, 1);
*previous = *(zone_node_t **)hattrie_iter_val(i); /* leftmost */
*previous = (*previous)->prev; /* rightmost */
*found = NULL;
hattrie_iter_free(i);
}
/* Previous node for proof must be non-empty and authoritative. */
if (*previous &&
((*previous)->rrset_count == 0 || (*previous)->flags & NODE_FLAGS_NONAUTH)) {
*previous = (*previous)->prev;
}
return exact_match;
}
void test_hattrie_find_prev()
{
fprintf(stderr, "finding previous for %zu keys ... \n", k);
hattrie_build_index(T);
hattrie_iter_t* i = hattrie_iter_begin(T, true);
value_t* u;
const char *key = NULL;
char *dkey = NULL;
char *fkey = NULL;
size_t len = 0, flen = 0;
while (!hattrie_iter_finished(i)) {
u = hattrie_iter_val(i);
key = hattrie_iter_key(i, &len);
/* first key */
if (!fkey) {
fkey = malloc(len); memcpy(fkey, key, len);
--fkey[len-1];
flen = len;
}
/* check hattrie_find_leq functionality */
dkey = realloc(dkey, len); memcpy(dkey, key, len);
++dkey[len-1];
value_t *fp = NULL;
int r = hattrie_find_leq(T, dkey, len, &fp);
if (*fp != *u || r != -1) {
fprintf(stderr, "[error] hattrie_find_leq should find %lu, "
"but found prev=%lu, rval=%d\n",
*u, *fp, r);
}
hattrie_iter_next(i);
}
hattrie_iter_free(i);
/* check before first key */
value_t *fp = NULL;
int r = hattrie_find_leq(T, fkey, flen, &fp);
if (r != 1 || fp != NULL) {
fprintf(stderr, "[error] hattrie_find_leq should return 1 and NULL for "
"string < first string, returned %d (%p)\n",
r, (void*)fp);
}
free(fkey);
free(dkey);
fprintf(stderr, "done.\n");
}
void test_hattrie_iteration()
{
fprintf(stderr, "iterating through %zu keys ... \n", k);
hattrie_iter_t* i = hattrie_iter_begin(T, false);
size_t count = 0;
value_t* u;
value_t v;
size_t len;
const char* key;
while (!hattrie_iter_finished(i)) {
++count;
key = hattrie_iter_key(i, &len);
u = hattrie_iter_val(i);
v = str_map_get(M, key, len);
if (*u != v) {
if (v == 0) {
fprintf(stderr, "[error] incorrect iteration (%lu, %lu)\n", *u, v);
}
else {
fprintf(stderr, "[error] incorrect iteration tally (%lu, %lu)\n", *u, v);
}
}
// this way we will see an error if the same key is iterated through
// twice
str_map_set(M, key, len, 0);
hattrie_iter_next(i);
}
if (count != M->m) {
fprintf(stderr, "[error] iterated through %zu element, expected %zu\n",
count, M->m);
}
hattrie_iter_free(i);
fprintf(stderr, "done.\n");
}
hattrie_t* hattrie_dup(const hattrie_t* T, value_t (*nval)(value_t))
{
hattrie_t *N = hattrie_create_n(T->bsize, &T->mm);
/* assignment */
if (!nval) nval = hattrie_setval;
/*! \todo could be probably implemented faster */
size_t l = 0;
const char *k = 0;
hattrie_iter_t *i = hattrie_iter_begin(T, false);
while (!hattrie_iter_finished(i)) {
k = hattrie_iter_key(i, &l);
*hattrie_get(N, k, l) = nval(*hattrie_iter_val(i));
hattrie_iter_next(i);
}
hattrie_iter_free(i);
return N;
}
void test_hattrie_sorted_iteration()
{
fprintf(stderr, "iterating in order through %zu keys ... \n", k);
hattrie_iter_t* i = hattrie_iter_begin(T, true);
size_t count = 0;
value_t* u;
value_t v;
char* key_copy = malloc(m_high + 1);
char* prev_key = malloc(m_high + 1);
memset(prev_key, 0, m_high + 1);
size_t prev_len = 0;
const char *key = NULL;
size_t len = 0;
while (!hattrie_iter_finished(i)) {
memcpy(prev_key, key_copy, len);
prev_key[len] = '\0';
prev_len = len;
++count;
key = hattrie_iter_key(i, &len);
/* memory for key may be changed on iter, copy it */
strncpy(key_copy, key, len);
if (prev_key != NULL && cmpkey(prev_key, prev_len, key, len) > 0) {
fprintf(stderr, "[error] iteration is not correctly ordered.\n");
}
u = hattrie_iter_val(i);
v = str_map_get(M, key, len);
if (*u != v) {
if (v == 0) {
fprintf(stderr, "[error] incorrect iteration (%lu, %lu)\n", *u, v);
}
else {
fprintf(stderr, "[error] incorrect iteration tally (%lu, %lu)\n", *u, v);
}
}
// this way we will see an error if the same key is iterated through
// twice
str_map_set(M, key, len, 0);
hattrie_iter_next(i);
}
if (count != M->m) {
fprintf(stderr, "[error] iterated through %zu element, expected %zu\n",
count, M->m);
}
hattrie_iter_free(i);
free(prev_key);
free(key_copy);
fprintf(stderr, "done.\n");
}
int main(int argc, char *argv[])
{
plan_lazy();
/* Random keys. */
srand(time(NULL));
unsigned key_count = 100000;
char **keys = malloc(sizeof(char*) * key_count);
for (unsigned i = 0; i < key_count; ++i) {
keys[i] = str_key_rand(KEY_MAXLEN);
}
/* Sort random keys. */
str_key_sort(keys, key_count);
/* Create trie */
value_t *val = NULL;
hattrie_t *trie = hattrie_create();
ok(trie != NULL, "hattrie: create");
/* Insert keys */
bool passed = true;
size_t inserted = 0;
for (unsigned i = 0; i < key_count; ++i) {
val = hattrie_get(trie, keys[i], strlen(keys[i]) + 1);
if (!val) {
passed = false;
break;
}
if (*val == NULL) {
*val = keys[i];
++inserted;
}
}
ok(passed, "hattrie: insert");
/* Check total insertions against trie weight. */
is_int(hattrie_weight(trie), inserted, "hattrie: trie weight matches insertions");
/* Build order-index. */
hattrie_build_index(trie);
/* Lookup all keys */
passed = true;
for (unsigned i = 0; i < key_count; ++i) {
val = hattrie_tryget(trie, keys[i], strlen(keys[i]) + 1);
if (val && (*val == keys[i] || strcmp(*val, keys[i]) == 0)) {
continue;
} else {
diag("hattrie: mismatch on element '%u'", i);
passed = false;
break;
}
}
ok(passed, "hattrie: lookup all keys");
/* Lesser or equal lookup. */
passed = true;
for (unsigned i = 0; i < key_count; ++i) {
if (!str_key_find_leq(trie, keys, i, key_count)) {
passed = false;
for (int off = -10; off < 10; ++off) {
int k = (int)i + off;
if (k < 0 || k >= key_count) {
continue;
}
diag("[%u/%d]: %s%s", i, off, off == 0?">":"",keys[k]);
}
break;
}
}
ok(passed, "hattrie: find lesser or equal for all keys");
/* Next lookup. */
passed = true;
for (unsigned i = 0; i < key_count - 1 && passed; ++i) {
value_t *val;
hattrie_find_next(trie, keys[i], strlen(keys[i]), &val);
passed = val && *val == (void *)keys[(i + 1)];
}
ok(passed, "hattrie: find next for all keys");
/* Unsorted iteration */
size_t iterated = 0;
hattrie_iter_t *it = hattrie_iter_begin(trie, false);
while (!hattrie_iter_finished(it)) {
++iterated;
hattrie_iter_next(it);
}
is_int(inserted, iterated, "hattrie: unsorted iteration");
hattrie_iter_free(it);
/* Sorted iteration. */
char key_buf[KEY_MAXLEN] = {'\0'};
iterated = 0;
it = hattrie_iter_begin(trie, true);
while (!hattrie_iter_finished(it)) {
size_t cur_key_len = 0;
const char *cur_key = hattrie_iter_key(it, &cur_key_len);
if (iterated > 0) { /* Only if previous exists. */
if (strcmp(key_buf, cur_key) > 0) {
diag("'%s' <= '%s' FAIL\n", key_buf, cur_key);
break;
}
}
++iterated;
memcpy(key_buf, cur_key, cur_key_len);
hattrie_iter_next(it);
}
is_int(inserted, iterated, "hattrie: sorted iteration");
hattrie_iter_free(it);
/* Cleanup */
for (unsigned i = 0; i < key_count; ++i) {
free(keys[i]);
}
free(keys);
hattrie_free(trie);
return 0;
}
int proc_update_privileges(int uid, int gid)
{
#ifdef HAVE_SETGROUPS
/* Drop supplementary groups. */
if ((uid_t)uid != getuid() || (gid_t)gid != getgid()) {
if (setgroups(0, NULL) < 0) {
log_server_warning("Failed to drop supplementary groups"
" for uid '%d' (%s).\n",
getuid(), strerror(errno));
}
# ifdef HAVE_INITGROUPS
struct passwd *pw;
if ((pw = getpwuid(uid)) == NULL) {
log_server_warning("Failed to get passwd entry"
" for uid '%d' (%s).\n",
uid, strerror(errno));
} else {
if (initgroups(pw->pw_name, gid) < 0) {
log_server_warning("Failed to set supplementary groups"
" for uid '%d' (%s).\n",
uid, strerror(errno));
}
}
# endif /* HAVE_INITGROUPS */
}
#endif /* HAVE_SETGROUPS */
/* Watch uid/gid. */
if ((gid_t)gid != getgid()) {
log_server_info("Changing group id to '%d'.\n", gid);
if (setregid(gid, gid) < 0) {
log_server_error("Failed to change gid to '%d'.\n",
gid);
}
}
if ((uid_t)uid != getuid()) {
log_server_info("Changing user id to '%d'.\n", uid);
if (setreuid(uid, uid) < 0) {
log_server_error("Failed to change uid to '%d'.\n",
uid);
}
}
/* Check storage writeability. */
int ret = KNOT_EOK;
const bool sorted = false;
hattrie_iter_t *z_iter = hattrie_iter_begin(conf()->zones, sorted);
if (z_iter == NULL) {
return KNOT_ERROR;
}
for (; !hattrie_iter_finished(z_iter); hattrie_iter_next(z_iter)) {
conf_zone_t *zone = (conf_zone_t *)*hattrie_iter_val(z_iter);
char *lfile = strcdup(zone->storage, "/knot.lock");
assert(lfile != NULL);
FILE* fp = fopen(lfile, "w");
if (fp == NULL) {
log_server_warning("Storage directory '%s' is not "
"writeable.\n", zone->storage);
ret = KNOT_EACCES;
} else {
fclose(fp);
unlink(lfile);
}
free(lfile);
if (ret != KNOT_EOK) {
break;
}
}
hattrie_iter_free(z_iter);
return ret;
}
int main(int argc, char* argv[])
{
if (argc < 2) {
fprintf(stderr, "Usage: bam-summarize reads.bam\n");
exit(EXIT_FAILURE);
}
samfile_t* f = samopen(argv[1], "rb", NULL);
if (f == NULL) {
fprintf(stderr, "can't open bam file %s\n", argv[1]);
exit(1);
}
bam1_t* b = bam_init1();
hattrie_t* T = hattrie_create();
char* qname = NULL;
size_t qname_size = 0;
size_t j, n = 0;
uint32_t* cigar;
uint32_t cigar_op, cigar_len;
read_stat_t** val;
while (samread(f, b) >= 0) {
if (++n % 1000000 == 0) {
fprintf(stderr, "\t%zu alignments\n", n);
}
bool perfect = true;
bool spliced = false;
bool gapped = false;
cigar = bam1_cigar(b);
for (j = 0; j < b->core.n_cigar; ++j) {
cigar_op = cigar[j] & BAM_CIGAR_MASK;
cigar_len = cigar[j] >> BAM_CIGAR_SHIFT;
if (cigar_op == BAM_CREF_SKIP) {
if (cigar_len < min_splice_length) gapped = true;
else spliced = true;
}
else if (cigar_op != BAM_CMATCH) perfect = false;
if (cigar_op == BAM_CSOFT_CLIP || cigar_op == BAM_CHARD_CLIP) break;
}
/* Skip any clipped alignments. We don't want your kind! */
if (cigar_op == BAM_CSOFT_CLIP || cigar_op == BAM_CHARD_CLIP) continue;
/* Hack the read to include mate information. */
if (b->core.flag & BAM_FPAIRED) {
if (qname_size < b->core.l_qname + 3) {
qname_size = b->core.l_qname + 3;
qname = realloc(qname, qname_size);
}
memcpy(qname, bam1_qname(b), b->core.l_qname);
if (b->core.flag & BAM_FREAD1) {
qname[b->core.l_qname] = '/';
qname[b->core.l_qname + 1] = '2';
qname[b->core.l_qname + 2] = '\0';
}
else {
qname[b->core.l_qname] = '/';
qname[b->core.l_qname + 1] = '1';
qname[b->core.l_qname + 2] = '\0';
}
val = (read_stat_t**) hattrie_get(T, qname, b->core.l_qname + 2);
}
else {
val = (read_stat_t**) hattrie_get(T, bam1_qname(b), b->core.l_qname);
}
if (*val == NULL) {
*val = malloc(sizeof(read_stat_t));
memset(*val, 0, sizeof(read_stat_t));
}
(*val)->aln_count++;
if (perfect) {
if (spliced) (*val)->spliced_perfect_cnt++;
else (*val)->unspliced_perfect_cnt++;
}
if (spliced) (*val)->spliced_cnt++;
if (gapped) (*val)->gapped_cnt++;
}
printf("alignment_count\t%zu\n", n);
printf("read_count\t%zu\n", hattrie_size(T));
/* print stats from the table */
uint32_t multi_count = 0;
uint32_t unspliced_perfect_cnt = 0;
uint32_t spliced_perfect_cnt = 0;
uint32_t spliced_cnt = 0;
uint32_t gapped_cnt = 0;
/* excluding multireads */
uint32_t unique_unspliced_perfect_cnt = 0;
uint32_t unique_spliced_perfect_cnt = 0;
uint32_t unique_spliced_cnt = 0;
uint32_t unique_gapped_cnt = 0;
hattrie_iter_t* i;
for (i = hattrie_iter_begin(T);
!hattrie_iter_finished(i);
hattrie_iter_next(i))
{
val = (read_stat_t**) hattrie_iter_val(i);
if ((*val)->aln_count == 1) {
unique_unspliced_perfect_cnt += (*val)->unspliced_perfect_cnt;
unique_spliced_perfect_cnt += (*val)->spliced_perfect_cnt;
unique_spliced_cnt += (*val)->spliced_cnt;
unique_gapped_cnt += (*val)->gapped_cnt;
}
else multi_count++;
unspliced_perfect_cnt += (*val)->unspliced_perfect_cnt;
spliced_perfect_cnt += (*val)->spliced_perfect_cnt;
spliced_cnt += (*val)->spliced_cnt;
gapped_cnt += (*val)->gapped_cnt;
}
hattrie_iter_free(i);
printf("multi_count\t%u\n", multi_count);
printf("unspliced_perfect_cnt\t%u\n", unspliced_perfect_cnt);
printf("spliced_perfect_cnt\t%u\n", spliced_perfect_cnt);
printf("spliced_cnt\t%u\n", spliced_cnt);
printf("gapped_cnt\t%u\n", gapped_cnt);
printf("unique_unspliced_perfect_cnt\t%u\n", unique_unspliced_perfect_cnt);
printf("unique_spliced_perfect_cnt\t%u\n", unique_spliced_perfect_cnt);
printf("unique_spliced_cnt\t%u\n", unique_spliced_cnt);
printf("unique_gapped_cnt\t%u\n", unique_gapped_cnt);
/* free the table */
for (i = hattrie_iter_begin(T);
!hattrie_iter_finished(i);
hattrie_iter_next(i))
{
free(* (read_stat_t**) hattrie_iter_val(i));
}
hattrie_iter_free(i);
hattrie_free(T);
free(qname);
bam_destroy1(b);
return 0;
}