*/
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);
+
#define sam_write1(header, b) bam_view1(header, b)
/*!
*/
int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
- /*!
- @abstract A more convenient interface to bam_plbuf_push()
- @param fp BAM file handler
- @param func user defined function
- @param func_data user provided data
-
- @discussion The file position indicator must be placed right
- before the start of an alignment. See also bam_plbuf_push().
- */
- int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
-
struct __bam_lplbuf_t;
typedef struct __bam_lplbuf_t bam_lplbuf_t;
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_core(bam1_t *b, const char tag[2]); // an alias of bam_aux_get()
uint8_t *bam_aux_get(bam1_t *b, const char tag[2]);
int32_t bam_aux2i(const uint8_t *s);
float bam_aux2f(const uint8_t *s);