X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam.h;h=c635e72767e31852ddf8b2759a3d9493d13e58bc;hb=78de989ec56e7c17e1fa854cb8c1c4f9ae08856c;hp=4045684230a7cba886a0ed0fa390db3340866f91;hpb=41586185b43962c1ffb3f82e93066a480254aa17;p=samtools.git

diff --git a/bam.h b/bam.h
index 4045684..c635e72 100644
--- a/bam.h
+++ b/bam.h
@@ -100,7 +100,7 @@ typedef struct {
 	int32_t n_targets;
 	char **target_name;
 	uint32_t *target_len;
-	void *hash;
+	void *hash, *rg2lib;
 	int l_text;
 	char *text;
 } bam_header_t;
@@ -315,8 +315,18 @@ extern "C" {
 	 */
 	bam_header_t *sam_header_read2(const char *fn_list);
 
+	bam_header_t *sam_header_read(tamFile fp);
+	int sam_header_parse(bam_header_t *h);
+	int sam_header_parse_rg(bam_header_t *h);
+
 #define sam_write1(header, b) bam_view1(header, b)
 
+	int bam_strmap_put(void *strmap, const char *rg, const char *lib);
+	const char *bam_strmap_get(const void *strmap, const char *rg);
+	void *bam_strmap_dup(const void*);
+	void *bam_strmap_init();
+	void bam_strmap_destroy(void *strmap);
+
 	/*!
 	  @abstract Initialize a header structure.
 	  @return   the pointer to the header structure
@@ -404,11 +414,12 @@ extern "C" {
 	} while (0)
 
 	/*!
-	  @abstract       Print an alignment to the standard output in TAM format.
+	  @abstract       Format a BAM record in the SAM format
 	  @param  header  pointer to the header structure
 	  @param  b       alignment to print
+	  @return         a pointer to the SAM string
 	 */
-	void bam_view1(const bam_header_t *header, const bam1_t *b);
+	char *bam_format1(const bam_header_t *header, const bam1_t *b);
 
 	/*!
 	  @abstract    Merge multiple sorted BAM.
@@ -511,17 +522,6 @@ extern "C" {
 	 */
 	int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
 
-	/*!
-	  @abstract         A more convenient interface to bam_plbuf_push()
-	  @param  fp        BAM file handler
-	  @param  func      user defined function
-	  @param  func_data user provided data
-
-	  @discussion The file position indicator must be placed right
-	  before the start of an alignment. See also bam_plbuf_push().
-	 */
-	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;
 
@@ -599,7 +599,8 @@ extern "C" {
 	void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
 
 	void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);
-	uint8_t *bam_aux_get(bam1_t *b, const char tag[2]);
+	// uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2]); // an alias of bam_aux_get()
+	uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]);
 	int32_t bam_aux2i(const uint8_t *s);
 	float bam_aux2f(const uint8_t *s);
 	double bam_aux2d(const uint8_t *s);