* samtools-0.1.5-12 (r415)

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index 124817e71f50db325abe220be8420eeb1442ed84..a33006d617093cc07a334de7cc74eeb37d880a63 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -431,6 +431,8 @@ extern "C" {
         */
        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 is_hex);
+
        /*! @typedef
          @abstract Structure for one alignment covering the pileup position.
          @field  b      pointer to the alignment
@@ -509,6 +511,8 @@ extern "C" {
         */
        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);
+
        struct __bam_lplbuf_t;
        typedef struct __bam_lplbuf_t bam_lplbuf_t;
 
@@ -523,9 +527,6 @@ extern "C" {
        /*! @abstract  bam_plbuf_push() equivalent with level calculated. */
        int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf);
 
-       /*! @abstract  bam_plbuf_file() equivalent with level calculated. */
-       int bam_lpileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
-
        struct __bam_index_t;
        typedef struct __bam_index_t bam_index_t;
 
@@ -605,8 +606,8 @@ extern "C" {
        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()
 
        /*!