X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam.h;h=8e26ea69d3b7c6b008aba6112052310a4072b08a;hp=291b30314f75d3d882b1d5dc9960e7b709a50c02;hb=049705238f6c2d4cdd79022e7bcf2cc7d83ba9c7;hpb=317f5e8dd22cc9e1e5e05fbcaeb3b9aca7447351 diff --git a/bam.h b/bam.h index 291b303..8e26ea6 100644 --- a/bam.h +++ b/bam.h @@ -87,7 +87,7 @@ typedef struct { char **target_name; uint32_t *target_len; void *dict, *hash, *rg2lib; - int l_text; + size_t l_text, n_text; char *text; } bam_header_t; @@ -190,6 +190,8 @@ typedef struct { uint8_t *data; } bam1_t; +typedef struct __bam_iter_t *bam_iter_t; + #define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0) #define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0) @@ -272,6 +274,10 @@ extern char bam_nt16_nt4_table[]; extern "C" { #endif + /********************* + * Low-level SAM I/O * + *********************/ + /*! @abstract TAM file handler */ typedef struct __tamFile_t *tamFile; @@ -323,6 +329,7 @@ extern "C" { be destroyed in the first place. */ int sam_header_parse(bam_header_t *h); + int32_t bam_get_tid(const bam_header_t *header, const char *seq_name); /*! @abstract Parse @RG lines a update a header struct @@ -336,12 +343,22 @@ extern "C" { #define sam_write1(header, b) bam_view1(header, b) + + /******************************** + * APIs for string dictionaries * + ********************************/ + 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); + + /********************* + * Low-level BAM I/O * + *********************/ + /*! @abstract Initialize a header structure. @return the pointer to the header structure @@ -440,6 +457,11 @@ extern "C" { const char *bam_get_library(bam_header_t *header, const bam1_t *b); + + /*************** + * pileup APIs * + ***************/ + /*! @typedef @abstract Structure for one alignment covering the pileup position. @field b pointer to the alignment @@ -461,11 +483,25 @@ extern "C" { uint32_t is_del:1, is_head:1, is_tail:1; } bam_pileup1_t; - struct __bam_plbuf_t; - /*! @abstract pileup buffer */ - typedef struct __bam_plbuf_t bam_plbuf_t; + typedef int (*bam_plp_auto_f)(void *data, bam1_t *b); - void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask); + struct __bam_plp_t; + typedef struct __bam_plp_t *bam_plp_t; + + bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data); + int bam_plp_push(bam_plp_t iter, const bam1_t *b); + const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp); + const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp); + void bam_plp_set_mask(bam_plp_t iter, int mask); + void bam_plp_reset(bam_plp_t iter); + void bam_plp_destroy(bam_plp_t iter); + + struct __bam_mplp_t; + typedef struct __bam_mplp_t *bam_mplp_t; + + bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data); + void bam_mplp_destroy(bam_mplp_t iter); + int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); /*! @typedef @abstract Type of function to be called by bam_plbuf_push(). @@ -478,44 +514,16 @@ extern "C" { */ typedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data); - /*! - @abstract Reset a pileup buffer for another pileup process - @param buf the pileup buffer to be reset - */ - void bam_plbuf_reset(bam_plbuf_t *buf); + typedef struct { + bam_plp_t iter; + bam_pileup_f func; + void *data; + } bam_plbuf_t; - /*! - @abstract Initialize a buffer for pileup. - @param func fucntion to be called by bam_pileup_core() - @param data user provided data - @return pointer to the pileup buffer - */ + void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask); + void bam_plbuf_reset(bam_plbuf_t *buf); bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data); - - /*! - @abstract Destroy a pileup buffer. - @param buf pointer to the pileup buffer - */ void bam_plbuf_destroy(bam_plbuf_t *buf); - - /*! - @abstract Push an alignment to the pileup buffer. - @param b alignment to be pushed - @param buf pileup buffer - @see bam_plbuf_init() - @return always 0 currently - - @discussion If all the alignments covering a particular site have - been collected, this function will call the user defined function - as is provided to bam_plbuf_init(). The coordinate of the site and - all the alignments will be transferred to the user defined - function as function parameters. - - When all the alignments are pushed to the buffer, this function - needs to be called with b equal to NULL. This will flush the - buffer. A pileup buffer can only be reused when bam_plbuf_reset() - is called. - */ 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); @@ -534,6 +542,11 @@ extern "C" { /*! @abstract bam_plbuf_push() equivalent with level calculated. */ int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf); + + /********************* + * BAM indexing APIs * + *********************/ + struct __bam_index_t; typedef struct __bam_index_t bam_index_t; @@ -582,6 +595,10 @@ extern "C" { */ int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func); + bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end); + int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b); + void bam_iter_destroy(bam_iter_t iter); + /*! @abstract Parse a region in the format: "chr2:100,000-200,000". @discussion bam_header_t::hash will be initialized if empty. @@ -594,6 +611,11 @@ extern "C" { */ int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end); + + /************************** + * APIs for optional tags * + **************************/ + /*! @abstract Retrieve data of a tag @param b pointer to an alignment struct @@ -617,6 +639,11 @@ extern "C" { 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() + + /***************** + * Miscellaneous * + *****************/ + /*! @abstract Calculate the rightmost coordinate of an alignment on the reference genome.