* samtools-0.1.5-34 (r451)

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index 64867f10733f6889c1a0e0fa7a61e8e2802c2407..ec983dfdd183042ef67a019e215a6dff6724c71f 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -113,6 +113,10 @@ typedef struct {
 /*! @abstract optical or PCR duplicate */
 #define BAM_FDUP        1024
 
+#define BAM_OFDEC          0
+#define BAM_OFHEX          1
+#define BAM_OFSTR          2
+
 /*! @abstract defautl mask for pileup */
 #define BAM_DEF_MASK (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP)
 
@@ -431,6 +435,8 @@ 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 of);
+
        /*! @typedef
          @abstract Structure for one alignment covering the pileup position.
          @field  b      pointer to the alignment
@@ -604,8 +610,8 @@ 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()
 
        /*!