return bam_aux_get(b, tag);
}
+#define __skip_tag(s) do { \
+ int type = toupper(*(s)); \
+ ++(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; \
+ else if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \
+ } while (0)
+
uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
{
uint8_t *s;
int y = tag[0]<<8 | tag[1];
s = bam1_aux(b);
while (s < b->data + b->data_len) {
- int type, x = (int)s[0]<<8 | s[1];
+ int x = (int)s[0]<<8 | s[1];
s += 2;
if (x == y) return s;
- type = toupper(*s); ++s;
- if (type == 'C') ++s;
- else if (type == 'S') s += 2;
- else if (type == 'I' || type == 'F') s += 4;
- else if (type == 'D') s += 8;
- else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
+ __skip_tag(s);
}
return 0;
}
+// s MUST BE returned by bam_aux_get()
+int bam_aux_del(bam1_t *b, uint8_t *s)
+{
+ uint8_t *p, *aux;
+ aux = bam1_aux(b);
+ p = s - 2;
+ __skip_tag(s);
+ memmove(p, s, b->l_aux - (s - aux));
+ b->data_len -= s - p;
+ b->l_aux -= s - p;
+ return 0;
+}
void bam_init_header_hash(bam_header_t *header)
{
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);
-}