int32_t n_targets;
char **target_name;
uint32_t *target_len;
- void *hash;
+ void *hash, *rg2lib;
int l_text;
char *text;
} bam_header_t;
*/
bam_header_t *sam_header_read2(const char *fn_list);
+ bam_header_t *sam_header_read(tamFile fp);
+ int sam_header_parse(bam_header_t *h);
+ int sam_header_parse_rg(bam_header_t *h);
+
#define sam_write1(header, b) bam_view1(header, b)
+ int bam_strmap_put(void *strmap, const char *rg, const char *lib);
+ const char *bam_strmap_get(const void *strmap, const char *rg);
+ void *bam_strmap_dup(const void*);
+ void *bam_strmap_init();
+ void bam_strmap_destroy(void *strmap);
+
/*!
@abstract Initialize a header structure.
@return the pointer to the header structure
void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);
- uint8_t *bam_aux_get(bam1_t *b, const char tag[2]);
+ // uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2]); // an alias of bam_aux_get()
+ uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]);
int32_t bam_aux2i(const uint8_t *s);
float bam_aux2f(const uint8_t *s);
double bam_aux2d(const uint8_t *s);