Unfinished modification. Please do not use this revision...

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index a33006d617093cc07a334de7cc74eeb37d880a63..b0fcd9c4c76354dde31a0e184720c74e42254634 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)
 
@@ -431,7 +435,7 @@ 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);
+       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.
@@ -628,13 +632,7 @@ extern "C" {
        */
        int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar);
 
-       typedef struct {
-               int32_t qbeg, qend;
-               int32_t tbeg, tend;
-               int32_t cbeg, cend;
-       } bam_segreg_t;
-
-       int bam_segreg(int32_t pos, const bam1_core_t *c, const uint32_t *cigar, bam_segreg_t *reg);
+       int bam_tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int32_t *_tpos);
 
 #ifdef __cplusplus
 }