Merge commit 'upstream/0.1.7a.dfsg'

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index ec983dfdd183042ef67a019e215a6dff6724c71f..291b30314f75d3d882b1d5dc9960e7b709a50c02 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -73,6 +73,7 @@ typedef gzFile bamFile;
   @field n_targets   number of reference sequences
   @field target_name names of the reference sequences
   @field target_len  lengths of the referene sequences
+  @field dict        header dictionary
   @field hash        hash table for fast name lookup
   @field rg2lib      hash table for @RG-ID -> LB lookup
   @field l_text      length of the plain text in the header
@@ -85,7 +86,7 @@ typedef struct {
        int32_t n_targets;
        char **target_name;
        uint32_t *target_len;
-       void *hash, *rg2lib;
+       void *dict, *hash, *rg2lib;
        int l_text;
        char *text;
 } bam_header_t;
@@ -423,8 +424,8 @@ extern "C" {
          @abstract  Free the memory allocated for an alignment.
          @param  b  pointer to an alignment
         */
-#define bam_destroy1(b) do {           \
-               free((b)->data); free(b);       \
+#define bam_destroy1(b) do {                                   \
+               if (b) { free((b)->data); free(b); }    \
        } while (0)
 
        /*!
@@ -437,6 +438,8 @@ extern "C" {
 
        char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of);
 
+       const char *bam_get_library(bam_header_t *header, const bam1_t *b);
+
        /*! @typedef
          @abstract Structure for one alignment covering the pileup position.
          @field  b      pointer to the alignment
@@ -632,14 +635,6 @@ 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);
-
 #ifdef __cplusplus
 }
 #endif