* samtools-0.1.7-12 (r589)

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index 86939b2e85d48edb0c55e0d3c2a2b35234f69a7b..21a7598d8e9ac81ac994dc13ea6adf4161279513 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -463,11 +463,15 @@ 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;
+       struct __bam_plp_t;
+       typedef struct __bam_plp_t *bam_plp_t;
 
-       void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask);
+       bam_plp_t bam_plp_init();
+       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);
+       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);
 
        /*! @typedef
          @abstract    Type of function to be called by bam_plbuf_push().
@@ -480,44 +484,16 @@ 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);