/*! @abstract optical or PCR duplicate */
#define BAM_FDUP 1024
+#define BAM_OFDEC 0
+#define BAM_OFHEX 1
+#define BAM_OFSTR 2
+
/*! @abstract defautl mask for pileup */
#define BAM_DEF_MASK (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP)
*/
char *bam_format1(const bam_header_t *header, const bam1_t *b);
+ char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of);
+
/*! @typedef
@abstract Structure for one alignment covering the pileup position.
@field b pointer to the alignment
*/
int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
+ 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;
/*! @abstract bam_plbuf_push() equivalent with level calculated. */
int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf);
- /*! @abstract bam_plbuf_file() equivalent with level calculated. */
- int bam_lpileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
-
struct __bam_index_t;
typedef struct __bam_index_t bam_index_t;
char bam_aux2A(const uint8_t *s);
char *bam_aux2Z(const uint8_t *s);
+ int bam_aux_del(bam1_t *b, uint8_t *s);
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()
/*!
*/
int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar);
- typedef struct {
- int32_t qbeg, qend;
- int32_t tbeg, tend;
- int32_t cbeg, cend;
- } bam_segreg_t;
-
- int bam_segreg(int32_t pos, const bam1_core_t *c, const uint32_t *cigar, bam_segreg_t *reg);
-
#ifdef __cplusplus
}
#endif