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
} while (0)
/*!
- @abstract Print an alignment to the standard output in TAM format.
+ @abstract Format a BAM record in the SAM format
@param header pointer to the header structure
@param b alignment to print
+ @return a pointer to the SAM string
*/
- void bam_view1(const bam_header_t *header, const bam1_t *b);
+ char *bam_format1(const bam_header_t *header, const bam1_t *b);
/*!
@abstract Merge multiple sorted BAM.
*/
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(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);
char bam_aux2A(const uint8_t *s);
char *bam_aux2Z(const uint8_t *s);
+ /*!
+ @abstract Get the color encoding the previous and current base
+ @param b pointer to an alignment
+ @param i The i-th position, 0-based
+ @return color
+
+ @discussion Returns 0 no color information is found.
+ */
+ char bam_aux_getCSi(bam1_t *b, int i);
+
+ /*!
+ @abstract Get the color quality of the color encoding the previous and current base
+ @param b pointer to an alignment
+ @param i The i-th position, 0-based
+ @return color quality
+
+ @discussion Returns 0 no color information is found.
+ */
+ char bam_aux_getCQi(bam1_t *b, int i);
+
+ /*!
+ @abstract Get the color error profile at the give position
+ @param b pointer to an alignment
+ @return the original color if the color was an error, '-' (dash) otherwise
+
+ @discussion Returns 0 no color information is found.
+ */
+ char bam_aux_getCEi(bam1_t *b, int i);
+
/*!
@abstract Calculate the rightmost coordinate of an alignment on the
reference genome.