/*! @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
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()
/*!