#define __skip_tag(s) do { \
int type = toupper(*(s)); \
++(s); \
- if (type == 'C') ++(s); \
+ if (type == 'C' || type == 'A') ++(s); \
else if (type == 'S') (s) += 2; \
else if (type == 'I' || type == 'F') (s) += 4; \
else if (type == 'D') (s) += 8; \
*ref_id = kh_value(h, iter);
if (i == k) { /* dump the whole sequence */
*begin = 0; *end = 1<<29; free(s);
- return -1;
+ return 0;
}
for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
*begin = atoi(p);
if (type == 'Z' || type == 'H') return (char*)s;
else return 0;
}
-
-/******************
- * rg2lib related *
- ******************/
-
-int bam_strmap_put(void *rg2lib, const char *rg, const char *lib)
-{
- int ret;
- khint_t k;
- khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
- char *key;
- if (h == 0) return 1;
- key = strdup(rg);
- k = kh_put(r2l, h, key, &ret);
- if (ret) kh_val(h, k) = strdup(lib);
- else {
- fprintf(stderr, "[bam_rg2lib_put] duplicated @RG ID: %s\n", rg);
- free(key);
- }
- return 0;
-}
-
-const char *bam_strmap_get(const void *rg2lib, const char *rg)
-{
- const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
- khint_t k;
- if (h == 0) return 0;
- k = kh_get(r2l, h, rg);
- if (k != kh_end(h)) return (const char*)kh_val(h, k);
- else return 0;
-}
-
-void *bam_strmap_dup(const void *rg2lib)
-{
- const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
- khash_t(r2l) *g;
- khint_t k, l;
- int ret;
- if (h == 0) return 0;
- g = kh_init(r2l);
- for (k = kh_begin(h); k < kh_end(h); ++k) {
- if (kh_exist(h, k)) {
- char *key = strdup(kh_key(h, k));
- l = kh_put(r2l, g, key, &ret);
- kh_val(g, l) = strdup(kh_val(h, k));
- }
- }
- return g;
-}
-
-void *bam_strmap_init()
-{
- return (void*)kh_init(r2l);
-}
-
-void bam_strmap_destroy(void *rg2lib)
-{
- khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
- khint_t k;
- if (h == 0) return;
- for (k = kh_begin(h); k < kh_end(h); ++k) {
- if (kh_exist(h, k)) {
- free((char*)kh_key(h, k)); free(kh_val(h, k));
- }
- }
- kh_destroy(r2l, h);
-}