fixed a minor bug in idxstats

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index 21a7598d8e9ac81ac994dc13ea6adf4161279513..8e26ea69d3b7c6b008aba6112052310a4072b08a 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -190,7 +190,7 @@ typedef struct {
        uint8_t *data;
 } bam1_t;
 
-typedef struct __bam_iterf_t *bam_iterf_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)
@@ -274,6 +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;
 
@@ -325,6 +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
@@ -338,12 +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
@@ -442,6 +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
@@ -463,16 +483,26 @@ extern "C" {
                uint32_t is_del:1, is_head:1, is_tail:1;
        } bam_pileup1_t;
 
+       typedef int (*bam_plp_auto_f)(void *data, bam1_t *b);
+
        struct __bam_plp_t;
        typedef struct __bam_plp_t *bam_plp_t;
 
-       bam_plp_t bam_plp_init();
+       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 *_n_plp, int *_tid, int *_pos);
+       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().
          @param  tid  chromosome ID as is defined in the header
@@ -512,6 +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;
 
@@ -560,9 +595,9 @@ 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_iterf_t bam_iterf_query(const bam_index_t *idx, int tid, int beg, int end);
-       int bam_iterf_read(bamFile fp, bam_iterf_t iter, bam1_t *b);
-       void bam_iterf_destroy(bam_iterf_t iter);
+       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".
@@ -576,6 +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
@@ -599,6 +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.